/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/find_in_repositories.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env Warning: $CNS_SOLVE not defined. Some tests skipped. /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/find_in_repositories.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env libtbx.exec python -V Python 2.5b1 libtbx.env_run LIBTBX_BUILD bin/python -V /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/env_run.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env Python 2.5b1 libtbx.show_host_and_user libtbx.show_host_and_user: Command not found. libtbx.show_build_path /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/py25b1/build libtbx.show_bin_path /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_bin_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/py25b1/build/bin libtbx.show_lib_path /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_lib_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/py25b1/build/lib libtbx.show_dist_paths libtbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/dist/libtbx libtbx.show_repository_paths /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_repository_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/dist libtbx.show_build_options grep Build.mode /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_options.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env Build mode: release libtbx.show_commands grep refresh head -1 libtbx.assert_stdin libtbx.refresh /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_commands.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env libtbx.show_all_on_path /net/rosie/scratch1/rwgk/py25b1/build/bin phenix.show_build_path /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/py25b1/build phenix.show_dist_paths phenix /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/dist/phenix phenix.python -V Python 2.5b1 libtbx.show_dist_paths libtbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/run_tests.py libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/introspection.py /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/introspection.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.str_utils import size_as_string_with_commas Virtual memory size: 10,649,600 Resident set size: 3,284,992 Stack size: 90,112 Memory total: 16,744,742,912 Memory free: 1,979,035,648 OK libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/tst_utils.py /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/tst_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import utils OK libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/str_utils.py /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/str_utils.py:85: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import show_diff OK libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/table_utils.py /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/table_utils.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility # for sum /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/table_utils.py:99: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/table_utils.py:99: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math OK libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/tst_tokenizer.py /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/tst_tokenizer.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.phil import tokenizer /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math OK libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/tst.py /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/tst.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import phil /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math OK libtbx.show_dist_paths boost_adaptbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/run_tests.py /net/rosie/scratch1/rwgk/dist/boost_adaptbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils libtbx.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/tst_rational.py /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/tst_rational_truediv.py /net/rosie/scratch1/rwgk/dist/boost_adaptbx/tst_rational_truediv.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env OK libtbx.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/tst_optional.py /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.show_dist_paths scitbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/run_tests.py /net/rosie/scratch1/rwgk/dist/scitbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_1 Total OK: 435 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_2 Total OK: 268 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_3 Total OK: 164 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_4 Total OK: 1420 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_5 Total OK: 22 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_vec3 Total OK: 59 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_mat3 Total OK: 82 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_sym_mat3 Total OK: 71 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_mat_ref Total OK: 60 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_accessors Total OK: 1721 /net/rosie/scratch1/rwgk/py25b1/build/scitbx/serialization/tst_base_256 OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_map.py /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_map.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.stl import map /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/boost_python/slice.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_set.py /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_set.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.stl import set /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/stl/set.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_vector.py /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_vector.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.stl import vector /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/boost_python/slice.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/regression_test.py /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/regression_test.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_flex.py /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_shared.py /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_shared.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import shared /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/boost_python/slice.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional data_size = 1000 n_repeats = 30000 use_pointers = False use_iterators = 0 time = 0.09 s overhead = 0.00 s (d[p[i]] -6.82118e-09) use_iterators = 1 time = 0.09 s overhead = 0.00 s (d[*p++] -6.82118e-09) use_pointers = True use_iterators = 0 time = 0.09 s overhead = 0.00 s (*dp[i] -6.82118e-09) use_iterators = 1 time = 0.09 s overhead = 0.00 s (**dpi++ -6.82118e-09) use_iterators = 2 time = 0.09 s overhead = 0.00 s (**dpp++ -6.82118e-09) data_size = 10000 n_repeats = 3000 use_pointers = False use_iterators = 0 time = 0.17 s overhead = 0.00 s (d[p[i]] -6.54835e-08) use_iterators = 1 time = 0.17 s overhead = 0.00 s (d[*p++] -6.54835e-08) use_pointers = True use_iterators = 0 time = 0.17 s overhead = 0.00 s (*dp[i] -6.54835e-08) use_iterators = 1 time = 0.17 s overhead = 0.00 s (**dpi++ -6.54835e-08) use_iterators = 2 time = 0.17 s overhead = 0.00 s (**dpp++ -6.54835e-08) data_size = 100000 n_repeats = 300 use_pointers = False use_iterators = 0 time = 0.50 s overhead = 0.00 s (d[p[i]] 1.39698e-07) use_iterators = 1 time = 0.45 s overhead = 0.00 s (d[*p++] 1.39698e-07) use_pointers = True use_iterators = 0 time = 0.52 s overhead = 0.00 s (*dp[i] 1.39698e-07) use_iterators = 1 time = 0.46 s overhead = 0.00 s (**dpi++ 1.39698e-07) use_iterators = 2 time = 0.46 s overhead = 0.00 s (**dpp++ 1.39698e-07) data_size = 1000000 n_repeats = 30 use_pointers = False use_iterators = 0 time = 1.23 s overhead = 0.01 s (d[p[i]] 1.67619e-07) use_iterators = 1 time = 1.16 s overhead = 0.01 s (d[*p++] 1.67619e-07) use_pointers = True use_iterators = 0 time = 1.23 s overhead = 0.01 s (*dp[i] 1.67619e-07) use_iterators = 1 time = 1.16 s overhead = 0.01 s (**dpi++ 1.67619e-07) use_iterators = 2 time = 1.16 s overhead = 0.01 s (**dpp++ 1.67619e-07) data_size = 10000000 n_repeats = 3 use_pointers = False use_iterators = 0 time = 1.48 s overhead = 0.14 s (d[p[i]] -2.44615e-06) use_iterators = 1 time = 1.40 s overhead = 0.14 s (d[*p++] -2.44615e-06) use_pointers = True use_iterators = 0 time = 1.49 s overhead = 0.14 s (*dp[i] -2.44615e-06) use_iterators = 1 time = 1.40 s overhead = 0.14 s (**dpi++ -2.44615e-06) use_iterators = 2 time = 1.40 s overhead = 0.14 s (**dpp++ -2.44615e-06) OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/matrix.py /net/rosie/scratch1/rwgk/dist/libtbx/stdlib.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/matrix.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py class rec(object): /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/matrix.py:282: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/misc.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/misc.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import adopt_init_args # XXX backward compatibility 2005_07_29 OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/math_utils.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/math_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/math_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_random_transform.py /net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/random.py:43: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py from math import log as _log, exp as _exp, pi as _pi, e as _e, ceil as _ceil /net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/random.py:43: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py from math import log as _log, exp as _exp, pi as _pi, e as _e, ceil as _ceil /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_random_transform.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import approx_equal /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_random_transform.py:6: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_graph.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_graph.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.python_utils import graph_tools as gt /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_math.py /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_math.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python time_eigensystem_real_symmetric: 2.052 micro seconds Testing compatibility of cmath_lgamma and slatec_dlngam... OK OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_r3_rotation.py /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_r3_rotation.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python u+s,u,s: 2.18 2.14 0.04 libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_resample.py /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_resample.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_line_search.py /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_line_search.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_gaussian.py /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_gaussian.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.examples import immoptibox_ports /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python u+s,u,s: 17.97 17.90 0.07 libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_quadrature.py /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_quadrature.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/tst_superpose.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/tst_superpose.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.math.superpose import kabsch_rotation, least_squares_fit /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/sieve_of_eratosthenes.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/sieve_of_eratosthenes.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/sieve_of_eratosthenes.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/minpack/tst.py /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/minpack/tst.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx import minpack /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/lbfgs/boost_python/tst_lbfgs.py /net/rosie/scratch1/rwgk/dist/scitbx/lbfgs/boost_python/tst_lbfgs.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/scitbx/lbfgs/boost_python/tst_lbfgs.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/scitbx/lbfgs/boost_python/tst_lbfgs.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/lbfgsb/boost_python/tst_lbfgsb.py /net/rosie/scratch1/rwgk/dist/scitbx/lbfgsb/boost_python/tst_lbfgsb.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx import lbfgsb /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/fftpack/boost_python/tst_fftpack.py /net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/random.py:43: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py from math import log as _log, exp as _exp, pi as _pi, e as _e, ceil as _ceil /net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/random.py:43: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py from math import log as _log, exp as _exp, pi as _pi, e as _e, ceil as _ceil /net/rosie/scratch1/rwgk/dist/scitbx/fftpack/boost_python/tst_fftpack.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional u+s,u,s: 1.53 1.50 0.03 libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/flex_array_loops.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/flex_array_loops.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional 10.0 11.0 12.0 10.0 11.0 12.0 0 10.0 1 11.0 2 12.0 100.0 110.0 120.0 200.0 210.0 220.0 OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_recipe.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_recipe.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.lbfgs /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional refinery compute_functional_and_gradients callback_after_step OK libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_linear_least_squares_fit.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_linear_least_squares_fit.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.lbfgs /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_linear_least_squares_fit.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_linear_least_squares_fit.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math fit.slope: -3.1494292235 fit.y_intercept: 1.83564357154 x_obs y_obs y_calc diff 1.00 -1.31 -1.31 0.00 2.00 -4.46 -4.46 0.00 3.00 -7.61 -7.61 0.00 4.00 -10.77 -10.76 -0.01 5.00 -13.94 -13.91 -0.03 6.00 -17.03 -17.06 0.03 7.00 -20.23 -20.21 -0.02 8.00 -23.31 -23.36 0.05 9.00 -26.51 -26.51 -0.00 10.00 -29.68 -29.66 -0.02 libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/chebyshev_lsq_example.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/chebyshev_lsq_example.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/chebyshev_lsq_example.py:56: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import data_plots /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/data_plots.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex Trying to determine the best number of terms via cross validation techniques Fitting with 14 terms Least Squares residual: 1.596703 R2-value : 0.004557 Maximum deviation between fitted and error free data: 0.235 Mean deviation between fitted and error free data: 0.038 Maximum deviation between fitted and observed data: 0.254 Mean deviation between fitted and observed data: 0.109 Showing 10 points x y_obs y_ideal y_fit 0.010 1.165 1.195 1.189 0.099 1.870 2.061 2.064 0.188 0.791 0.814 0.837 0.277 0.655 0.448 0.458 0.366 1.948 2.025 1.918 0.455 2.212 2.322 2.327 0.545 1.050 0.980 0.990 0.634 1.106 1.301 1.286 0.723 2.703 2.931 2.957 0.812 2.425 2.646 2.663 Preparing output for loggraph in a file called chebyshev.loggraph libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/immoptibox_ports.py /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/immoptibox_ports.py:6: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python Skipping: exercise_lbfgsb() with meyer_function u+s,u,s: 7.78 7.72 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/regression/scitbx/tst_math_erf.py /net/rosie/scratch1/rwgk/dist/regression/scitbx/tst_math_erf.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.math import erf_verification, erf, erfc, erfcx /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.show_dist_paths cctbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/run_tests.py --Quick /net/rosie/scratch1/rwgk/dist/cctbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/math/boost_python/tst_math.py /net/rosie/scratch1/rwgk/dist/cctbx/math/boost_python/tst_math.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import math_module /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/math_module.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/array_family/boost_python/tst_flex.py /net/rosie/scratch1/rwgk/dist/cctbx/array_family/boost_python/tst_flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import approx_equal /net/rosie/scratch1/rwgk/dist/cctbx/array_family/boost_python/tst_flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/uctbx/boost_python/tst_uctbx.py /net/rosie/scratch1/rwgk/dist/cctbx/uctbx/boost_python/tst_uctbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py from math import pi, cos, asin, sqrt /net/rosie/scratch1/rwgk/dist/cctbx/uctbx/boost_python/tst_uctbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py from math import pi, cos, asin, sqrt /net/rosie/scratch1/rwgk/dist/cctbx/uctbx/boost_python/tst_uctbx.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_sgtbx.py /net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_sgtbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_sgtbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_sgtbx.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_N_fold_rot.py /net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_N_fold_rot.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx import matrix /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_N_fold_rot.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/crystal/tst_ext.py /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/crystal/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/adptbx/boost_python/tst_adptbx.py /net/rosie/scratch1/rwgk/dist/cctbx/adptbx/boost_python/tst_adptbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/miller/boost_python/tst_miller.py /net/rosie/scratch1/rwgk/dist/cctbx/miller/boost_python/tst_miller.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/miller/boost_python/tst_miller.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/miller/boost_python/tst_miller.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_xray_scattering.py /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.eltbx import xray_scattering /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math.gaussian # base class for gaussian /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_henke.py /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_henke.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.eltbx import henke /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/fp_fdp.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_icsd_radii.py /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_icsd_radii.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.eltbx import icsd_radii /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/icsd_radii.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_neutron.py /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_neutron.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.eltbx import neutron /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/neutron.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_sasaki.py /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_sasaki.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.eltbx import sasaki /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/fp_fdp.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_tiny_pse.py /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_tiny_pse.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.eltbx import tiny_pse /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/tiny_pse.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_wavelengths.py /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_wavelengths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.eltbx import wavelengths /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/wavelengths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/xray/boost_python/tst_xray.py /net/rosie/scratch1/rwgk/dist/cctbx/xray/boost_python/tst_xray.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/maptbx/boost_python/tst_maptbx.py /net/rosie/scratch1/rwgk/dist/cctbx/maptbx/boost_python/tst_maptbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import maptbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/dmtbx/boost_python/tst_dmtbx.py /net/rosie/scratch1/rwgk/dist/cctbx/dmtbx/boost_python/tst_dmtbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import dmtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/translation_search/boost_python/tst_translation_search.py /net/rosie/scratch1/rwgk/dist/cctbx/translation_search/boost_python/tst_translation_search.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import translation_search /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/geometry_restraints/tst_ext.py /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/geometry_restraints/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/adp_restraints/tst_ext.py /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/adp_restraints/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import approx_equal /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/adp_restraints/tst_ext.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.shelx import from_ins /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/shelx/from_ins.py:6: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_krivy_gruber.py --Quick /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_krivy_gruber.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.uctbx import reduction_base /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_denominators.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_denominators.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 0.23 0.18 0.05 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_subgroups.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_subgroups.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.sgtbx import subgroups /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_lattice_symmetry.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_lattice_symmetry.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional bravais type: P 1 bravais type: P 1 2 1 bravais type: C 1 2 1 bravais type: P 2 2 2 bravais type: C 2 2 2 bravais type: F 2 2 2 bravais type: I 2 2 2 bravais type: P 4 2 2 bravais type: I 4 2 2 bravais type: P 6 2 2 bravais type: R 3 2 :H bravais type: P 4 3 2 bravais type: I 4 3 2 bravais type: F 4 3 2 u+s,u,s: 8.69 8.66 0.03 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_adp_constraints.py P3 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_adp_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 3 u+s,u,s: 0.39 0.33 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_site_constraints.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_site_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reflection_statistics.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.development import debug_utils /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_harker.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_harker.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.sgtbx import harker /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/symbol_confidence.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/symbol_confidence.py:56: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/bravais_types.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/bravais_types.py:36: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_lookup_utils.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_lookup_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal.py I41/acd /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional I 41/a c d :2 u+s,u,s: 0.33 0.27 0.06 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_direct_space_asu.py I41/acd /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_direct_space_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional I 41/a c d :2 u+s,u,s: 2.78 2.70 0.08 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_pair_asu_table.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_pair_asu_table.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex u+s,u,s: 3.56 3.46 0.10 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_asu_clusters.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_asu_clusters.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_coordination_sequences.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_coordination_sequences.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py R-3mr /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.crystal import close_packing /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.pdb time groel_sampling: 0.55 seconds R -3 m :R u+s,u,s: 1.39 1.32 0.07 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray.py I41/acd /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.development import random_structure /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional I 41/a c d :2 u+s,u,s: 5.66 5.57 0.09 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 1.19 1.12 0.07 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reciprocal_space_asu.py P312 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reciprocal_space_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 3 1 2 u+s,u,s: 0.40 0.36 0.04 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py P41 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import approx_equal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import dmtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 41 u+s,u,s: 0.43 0.37 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_emma.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import euclidean_model_matching as emma /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 1.12 1.05 0.07 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_centre_of_inversion.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_centre_of_inversion.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import find_centre_of_inversion /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 0.46 0.37 0.09 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_expand_to_p1.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_expand_to_p1.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 0.42 0.36 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_change_basis.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_change_basis.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.xray import minimization /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 31 u+s,u,s: 0.48 0.39 0.09 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_wilson_plot.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_wilson_plot.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import statistics /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math.gaussian # base class for gaussian /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python P 31 u+s,u,s: 0.55 0.49 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_derivatives.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 31 u+s,u,s: 2.32 2.26 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_fast_gradients.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_fast_gradients.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 1.98 1.87 0.11 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_minimization.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_minimization.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 31 u+s,u,s: 7.96 7.88 0.08 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/maptbx/tst_real_space_refinement.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/maptbx/tst_real_space_refinement.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional u+s,u,s: 2.18 2.12 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_maptbx_structure_factors.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_maptbx_structure_factors.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import maptbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 0.49 0.40 0.09 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_merge_equivalents.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_merge_equivalents.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 0.45 0.38 0.07 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_fft_map.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_fft_map.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 0.81 0.75 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sampled_model_density.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sampled_model_density.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 31 u+s,u,s: 1.58 1.50 0.08 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_fast_nv1995.py F222 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_fast_nv1995.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import translation_search /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional F 2 2 2 u+s,u,s: 0.60 0.49 0.11 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import geometry_restraints /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.pymol import pml_stick, pml_write OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_lbfgs.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_lbfgs.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_2.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_2.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.geometry_restraints.distance_least_squares \ /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_2.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_2.py:348: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py try: from mmtbx.monomer_library import pdb_interpretation u+s,u,s: 1.40 1.30 0.10 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/make_cns_input.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/make_cns_input.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.eltbx.xray_scattering /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math.gaussian # base class for gaussian /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python P 31 u+s,u,s: 0.44 0.35 0.09 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.cns import reflection_reader CNS not available. libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.cns import reflection_reader CNS not available. libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import adptbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.shelx.write_ins import LATT_SYMM sh: shelxl: command not found SHELX not available. libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_pointgroup_tools.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_pointgroup_tools.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/sub_lattice_tools.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/sub_lattice_tools.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional u+s,u,s: 0.47 0.41 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_best_cell.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_best_cell.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.crystal.find_best_cell import alternative_find_best_cell as fbc /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK grep max_penalty tail -1 libtbx.show_dist_paths cctbx libtbx.assert_stdin 44: aP triclinic, matrix (1, 0, 0, 0, 1, 0, 0, 0, 1) max_penalty=0.00% /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/crystal/burzlaff_zimmermann_dewolff.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/crystal/burzlaff_zimmermann_dewolff.py:16: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/crystal/burzlaff_zimmermann_dewolff.py:19: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.command_line.lattice_symmetry import metric_subgroups if ( `libtbx.show_dist_paths PyCifRW` == None ) then libtbx.show_dist_paths PyCifRW /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env libtbx.show_dist_paths PyCifRW /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env libtbx.python /net/rosie/scratch1/rwgk/dist/PyCifRW/example_quartz.py /net/rosie/scratch1/rwgk/dist/PyCifRW/example_quartz.py:28: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx, sgtbx, crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Quartz Unit cell: (4.9965, 4.9965, 5.457, 90, 90, 120) Space group: P 62 2 2 (No. 180) Number of scatterers: 2 At special positions: 2 Unit cell: (4.9965, 4.9965, 5.457, 90, 90, 120) Space group: P 62 2 2 (No. 180) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Si Si 3 ( 0.5000 0.0000 0.0000) 1.00 0.0000 O O 6 ( 0.4152 0.2076 0.1667) 1.00 0.0000 Miller array info: None Observation type: None Type of data: double, size=7 Type of sigmas: None Number of Miller indices: 7 Anomalous flag: False Unit cell: (4.9965, 4.9965, 5.457, 90, 90, 120) Space group: P 62 2 2 (No. 180) (1, 0, 0) 15.6039104868 (1, 0, 1) 36.377014613 (1, 0, 2) 7.92275811058 (1, 1, 0) 15.0429918303 (1, 1, 1) 0.822934329217 (2, 0, 0) 15.6804655415 (2, 0, 1) 13.3231807159 OK endif libtbx.show_dist_paths phenix /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env phenix.python /net/rosie/scratch1/rwgk/dist/phenix/run_tests.py --Quick /net/rosie/scratch1/rwgk/dist/phenix/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils libtbx.python /net/rosie/scratch1/rwgk/dist/phenix/phenix/regression/tst_heavy_search.py C2 /net/rosie/scratch1/rwgk/dist/phenix/phenix/regression/tst_heavy_search.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex C 1 2 1 u+s,u,s: 0.98 0.90 0.08 libtbx.show_dist_paths cctbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/run_examples.py --Quick /net/rosie/scratch1/rwgk/dist/cctbx/run_examples.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils /net/rosie/scratch1/rwgk/py25b1/build/exe_dev/cctbx.getting_started unit cell: (11,12,13,90,100,90) space group: C 1 2 1 symmetry operations: x,y,z -x,y,-z x+1/2,y+1/2,z -x+1/2,y+1/2,-z /net/rosie/scratch1/rwgk/py25b1/build/exe_dev/cctbx.sym_equiv_sites unit cell: (11,12,13,90,100,90) space group: C 1 2 1 symmetry operations: x,y,z -x,y,-z x+1/2,y+1/2,z -x+1/2,y+1/2,-z original_site:(0,0.13,0.51) special_op: 0,y,1/2 is_special_position: 1 coordinates[0] = (0,0.13,0.5) coordinates[1] = (0.5,0.63,0.5) original_site:(0,0.13,0.53) special_op: x,y,z is_special_position: 0 coordinates[0] = (0,0.13,0.53) coordinates[1] = (0,0.13,-0.53) coordinates[2] = (0.5,0.63,0.53) coordinates[3] = (0.5,0.63,-0.53) libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/getting_started.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/getting_started.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Unit cell: (11, 12, 13, 90, 100, 90) Space group: C 1 2 1 (No. 5) x,y,z -x,y,-z x+1/2,y+1/2,z -x+1/2,y+1/2,-z libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/analyze_adp.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/analyze_adp.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Input Ucif: (0.17000000000000001, 0.17000000000000001, 0.19, 0.089999999999999997, 0, 0) Warning: ADP tensor is incompatible with site symmetry. Averaged Ucif: (0.16666666666666666, 0.16666666666666666, 0.19, 0.083333333333333329, 0.0, 0.0) Eigenvectors and values: v=(0.00000 0.00000 1.00000) lambda=0.1900 v=(0.90954 -0.41561 0.00000) lambda=0.1667 v=(0.41561 0.90954 -0.00000) lambda=0.1667 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/g_exp_i_partial_derivatives.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/g_exp_i_partial_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import approx_equal OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_exp_i_alpha_derivatives.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_exp_i_alpha_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.examples.exp_i_alpha_derivatives \ /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_exp_i_alpha_derivatives.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import approx_equal OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_g_exp_i_alpha_derivatives.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_g_exp_i_alpha_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.examples.g_exp_i_alpha_derivatives \ /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_g_exp_i_alpha_derivatives.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import approx_equal OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.examples.structure_factor_derivatives \ /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx import matrix /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_2.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_2.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_3.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_3.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 31 u+s,u,s: 7.36 7.26 0.10 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_4.py --tag=internal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_4.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_4.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat P 1 strudat tag: EDI u+s,u,s: 5.34 5.23 0.11 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/site_derivatives.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/site_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx import matrix /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/u_star_derivatives.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/u_star_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx import matrix /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_derivatives.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx import matrix /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_least_squares_derivatives.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_least_squares_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.examples.exp_i_alpha_derivatives import least_squares /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_least_squares_derivatives.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx import matrix /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/all_axes.py P31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/all_axes.py:13: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Space group: P 31 (No. 144) Rotation type, Axis direction, Intrinsic part, Origin shift ('1', '-', '-', '-') ('3', '[0,0,1]', '(0,0,1/3)', '(0,0,0)') ('3', '[0,0,1]', '(0,0,1/3)', '(1/3,2/3,0)') ('3', '[0,0,1]', '(0,0,1/3)', '(2/3,1/3,0)') ('3', '[0,0,1]', '(0,0,2/3)', '(0,0,0)') ('3', '[0,0,1]', '(0,0,2/3)', '(1/3,2/3,0)') ('3', '[0,0,1]', '(0,0,2/3)', '(2/3,1/3,0)') libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_phase_o_phrenia.py P2 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_phase_o_phrenia.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.examples import phase_o_phrenia /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 1 2 1 Number of scatterers: 1 At special positions: 0 Unit cell: (7.82191, 10.1685, 13.2972, 90, 109, 90) Space group: P 1 2 1 (No. 3) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Hg1 Hg 2 ( 0.8444 0.7580 0.4206) 1.00 0.0000 1.01997 0.00000 0.51804 0.00000 0.0579313 0.50000 0.51989 0.00000 0.0458863 0.00000 0.01467 0.00000 0.0423267 0.43849 0.73176 0.30706 0.0417496 0.43522 0.29739 0.31214 0.0285953 0.50000 0.01661 0.50000 0.0275397 0.00000 0.38158 0.50000 0.0236526 -0.00462 0.01598 0.30704 0.0109534 0.50000 0.03812 1.00000 u+s,u,s: 0.44 0.38 0.06 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/map_skewness.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/map_skewness.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Number of scatterers: 20 At special positions: 0 Unit cell: (13.5341, 17.5943, 23.0079, 83, 109, 129) Space group: P 1 (No. 1) Miller array info: None Observation type: None Type of data: complex_double, size=312 Type of sigmas: None Number of Miller indices: 312 Anomalous flag: False Unit cell: (13.5341, 17.5943, 23.0079, 83, 109, 129) Space group: P 1 (No. 1) fudge factor, phase difference, map skewness: 0.00, 0.00, 2.427 fudge factor, phase difference, map skewness: 0.10, 9.11, 2.319 fudge factor, phase difference, map skewness: 0.20, 18.38, 1.923 fudge factor, phase difference, map skewness: 0.30, 26.84, 1.6 fudge factor, phase difference, map skewness: 0.40, 37.42, 0.9556 fudge factor, phase difference, map skewness: 0.50, 41.88, 0.7947 fudge factor, phase difference, map skewness: 0.60, 54.57, 0.2354 fudge factor, phase difference, map skewness: 0.70, 61.09, 0.2007 fudge factor, phase difference, map skewness: 0.80, 78.31, -0.01075 fudge factor, phase difference, map skewness: 0.90, 82.85, 0.007508 fudge factor, phase difference, map skewness: 1.00, 88.95, -0.06533 Number of scatterers: 20 At special positions: 0 Unit cell: (19.71, 25.623, 33.5069, 90, 109, 90) Space group: C 1 2 1 (No. 5) Miller array info: None Observation type: None Type of data: complex_double, size=338 Type of sigmas: None Number of Miller indices: 338 Anomalous flag: False Unit cell: (19.71, 25.623, 33.5069, 90, 109, 90) Space group: C 1 2 1 (No. 5) fudge factor, phase difference, map skewness: 0.00, 0.00, 2.586 fudge factor, phase difference, map skewness: 0.10, 8.16, 2.447 fudge factor, phase difference, map skewness: 0.20, 18.14, 2.074 fudge factor, phase difference, map skewness: 0.30, 26.13, 1.483 fudge factor, phase difference, map skewness: 0.40, 40.42, 0.8995 fudge factor, phase difference, map skewness: 0.50, 44.18, 0.666 fudge factor, phase difference, map skewness: 0.60, 54.97, 0.2334 fudge factor, phase difference, map skewness: 0.70, 63.68, 0.08674 fudge factor, phase difference, map skewness: 0.80, 73.35, 0.0479 fudge factor, phase difference, map skewness: 0.90, 79.38, -0.1527 fudge factor, phase difference, map skewness: 1.00, 88.45, 0.09656 Number of scatterers: 20 At special positions: 0 Unit cell: (19.3453, 25.1489, 32.887, 90, 90, 90) Space group: P 21 21 21 (No. 19) Miller array info: None Observation type: None Type of data: complex_double, size=390 Type of sigmas: None Number of Miller indices: 390 Anomalous flag: False Unit cell: (19.3453, 25.1489, 32.887, 90, 90, 90) Space group: P 21 21 21 (No. 19) fudge factor, phase difference, map skewness: 0.00, 0.00, 2.67 fudge factor, phase difference, map skewness: 0.10, 8.48, 2.435 fudge factor, phase difference, map skewness: 0.20, 19.81, 1.894 fudge factor, phase difference, map skewness: 0.30, 30.42, 1.315 fudge factor, phase difference, map skewness: 0.40, 36.22, 0.8785 fudge factor, phase difference, map skewness: 0.50, 48.27, 0.349 fudge factor, phase difference, map skewness: 0.60, 55.81, 0.3359 fudge factor, phase difference, map skewness: 0.70, 61.67, 0.1178 fudge factor, phase difference, map skewness: 0.80, 75.70, -0.05378 fudge factor, phase difference, map skewness: 0.90, 84.76, 0.06294 fudge factor, phase difference, map skewness: 1.00, 83.79, -0.06893 Number of scatterers: 20 At special positions: 0 Unit cell: (36.5694, 36.5694, 62.168, 90, 90, 120) Space group: R 3 2 :H (No. 155) Miller array info: None Observation type: None Type of data: complex_double, size=371 Type of sigmas: None Number of Miller indices: 371 Anomalous flag: False Unit cell: (36.5694, 36.5694, 62.168, 90, 90, 120) Space group: R 3 2 :H (No. 155) fudge factor, phase difference, map skewness: 0.00, 0.00, 2.682 fudge factor, phase difference, map skewness: 0.10, 9.31, 2.094 fudge factor, phase difference, map skewness: 0.20, 20.39, 1.909 fudge factor, phase difference, map skewness: 0.30, 23.40, 1.752 fudge factor, phase difference, map skewness: 0.40, 35.97, 1.037 fudge factor, phase difference, map skewness: 0.50, 44.23, 0.6243 fudge factor, phase difference, map skewness: 0.60, 55.96, 0.1541 fudge factor, phase difference, map skewness: 0.70, 62.99, 0.1125 fudge factor, phase difference, map skewness: 0.80, 76.50, 0.0861 fudge factor, phase difference, map skewness: 0.90, 83.30, 0.1264 fudge factor, phase difference, map skewness: 1.00, 96.67, -0.08465 Number of scatterers: 20 At special positions: 0 Unit cell: (72.6848, 72.6848, 72.6848, 90, 90, 90) Space group: F 4 3 2 (No. 209) Miller array info: None Observation type: None Type of data: complex_double, size=434 Type of sigmas: None Number of Miller indices: 434 Anomalous flag: False Unit cell: (72.6848, 72.6848, 72.6848, 90, 90, 90) Space group: F 4 3 2 (No. 209) fudge factor, phase difference, map skewness: 0.00, 0.00, 3.156 fudge factor, phase difference, map skewness: 0.10, 7.14, 2.937 fudge factor, phase difference, map skewness: 0.20, 14.46, 2.499 fudge factor, phase difference, map skewness: 0.30, 27.93, 1.453 fudge factor, phase difference, map skewness: 0.40, 34.75, 0.9865 fudge factor, phase difference, map skewness: 0.50, 49.06, 0.2723 fudge factor, phase difference, map skewness: 0.60, 54.71, 0.2318 fudge factor, phase difference, map skewness: 0.70, 64.03, 0.07332 fudge factor, phase difference, map skewness: 0.80, 71.43, 0.02207 fudge factor, phase difference, map skewness: 0.90, 83.93, 0.178 fudge factor, phase difference, map skewness: 1.00, 89.03, -0.06762 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/site_symmetry_table.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/site_symmetry_table.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional 0,0,0 1/2,1/2,1/2 x,y,z OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/site_symmetry_constraints.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/site_symmetry_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Unit cell: (12, 12, 15, 90, 90, 120) Space group: P 6 (No. 168) special position operator: 1/3,2/3,z exact location of special position: (0.33333333333333331, 0.66666666666666663, 0.0) n_indep: 1 site_shifted: (0.33333333333333331, 0.66666666666666663, 0.10000000000000001) independent_gradients: (0.02,) independent_curvatures: (6.0,) OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/adp_symmetry_constraints.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/adp_symmetry_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/unit_cell_refinement.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/unit_cell_refinement.py:44: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional ( 0, 1, 1) 8.81 - 12.52 = -3.71 ( 0, 0, 2) 12.23 - 17.74 = -5.51 ( 0, 2, 0) 12.71 - 17.74 = -5.03 ( 1, 1, 0) 12.97 - 12.52 = 0.45 ( 0, 1, 2) 13.79 - 19.85 = -6.06 ( 0, 2, 1) 14.11 - 19.85 = -5.74 ( 1, 1, 1) 14.35 - 15.35 = -1.00 ( 1, 0, 2) 16.68 - 19.85 = -3.17 ( 1, 2, 0) 17.03 - 19.85 = -2.82 ( 0, 2, 2) 17.67 - 25.19 = -7.52 ( 1, 1, 2) 17.86 - 21.77 = -3.91 ( 0, 1, 3) 19.47 - 28.22 = -8.75 ( 1, 2, 2) 21.03 - 26.74 = -5.71 ( 1, 3, 0) 22.26 - 28.22 = -5.96 ( 0, 2, 3) 22.41 - 32.28 = -9.87 ( 1, 1, 3) 22.56 - 29.63 = -7.07 ( 2, 0, 0) 22.72 - 17.74 = 4.98 ( 1, 3, 1) 23.10 - 29.63 = -6.53 ( 2, 1, 1) 24.40 - 21.77 = 2.63 ( 0, 0, 4) 24.60 - 35.92 = -11.32 ( 1, 2, 3) 25.17 - 33.53 = -8.36 ( 0, 1, 4) 25.43 - 37.07 = -11.64 ( 2, 0, 2) 25.87 - 25.19 = 0.68 ( 2, 2, 0) 26.11 - 25.19 = 0.92 ( 0, 4, 1) 26.32 - 37.07 = -10.75 ( 2, 1, 2) 26.66 - 26.74 = -0.08 ( 2, 2, 1) 26.84 - 26.74 = 0.10 ( 1, 0, 4) 27.15 - 37.07 = -9.92 ( 0, 2, 4) 27.78 - 40.33 = -12.55 ( 1, 1, 4) 27.90 - 38.18 = -10.28 ( 0, 4, 2) 28.44 - 40.33 = -11.89 ( 1, 4, 1) 28.72 - 38.18 = -9.46 ( 2, 2, 2) 28.92 - 30.98 = -2.06 ( 1, 3, 3) 29.02 - 39.27 = -10.25 ( 2, 1, 3) 30.08 - 33.53 = -3.45 ( 2, 3, 1) 30.49 - 33.53 = -3.04 ( 1, 4, 2) 30.69 - 41.38 = -10.69 ( 0, 3, 4) 31.34 - 45.34 = -14.00 ( 0, 1, 5) 31.56 - 46.29 = -14.73 ( 2, 2, 3) 32.12 - 37.07 = -4.95 functional: 2321.58 gradient norm: 1207.44 functional: 1351.63 gradient norm: 763.055 LBFGS step functional: 460.578 gradient norm: 305.314 LBFGS step functional: 193.168 gradient norm: 143.672 LBFGS step functional: 47.9382 gradient norm: 71.6896 LBFGS step functional: 19.9431 gradient norm: 89.0333 functional: 5.22162 gradient norm: 23.2996 LBFGS step functional: 0.773471 gradient norm: 15.0906 LBFGS step functional: 0.0424125 gradient norm: 0.859899 LBFGS step functional: 0.0347316 gradient norm: 0.305121 LBFGS step functional: 0.0335577 gradient norm: 0.152589 LBFGS step functional: 0.0328786 gradient norm: 0.127443 LBFGS step functional: 0.0318193 gradient norm: 0.219987 LBFGS step functional: 0.0289939 gradient norm: 0.427834 LBFGS step functional: 0.0231493 gradient norm: 0.637841 LBFGS step functional: 0.0265728 gradient norm: 2.44424 functional: 0.0197091 gradient norm: 1.24135 LBFGS step functional: 0.0103005 gradient norm: 0.846735 LBFGS step functional: 0.00286258 gradient norm: 0.33518 LBFGS step functional: 0.00135783 gradient norm: 0.0748069 LBFGS step functional: 0.00126888 gradient norm: 0.0240333 LBFGS step functional: 0.00125005 gradient norm: 0.0241467 LBFGS step functional: 0.00115246 gradient norm: 0.0586707 LBFGS step functional: 0.000998979 gradient norm: 0.066586 LBFGS step functional: 0.00289854 gradient norm: 0.873259 functional: 0.000926904 gradient norm: 0.164675 LBFGS step functional: 0.000721104 gradient norm: 0.10673 LBFGS step functional: 0.000496383 gradient norm: 0.0156637 LBFGS step functional: 0.000436098 gradient norm: 0.0187089 LBFGS step functional: 0.000405012 gradient norm: 0.0141628 LBFGS step functional: 0.000437224 gradient norm: 0.0606772 functional: 0.00040312 gradient norm: 0.0132963 LBFGS step functional: 0.000400413 gradient norm: 0.00486466 LBFGS step functional: 0.000400027 gradient norm: 0.00909801 LBFGS step functional: 0.000399624 gradient norm: 0.00699387 LBFGS step functional: 0.000398287 gradient norm: 0.00462518 LBFGS step functional: 0.000395683 gradient norm: 0.00493142 LBFGS step functional: 0.000391549 gradient norm: 0.00839497 LBFGS step functional: 0.000397074 gradient norm: 0.0313135 functional: 0.000389325 gradient norm: 0.00955157 LBFGS step functional: 0.000387577 gradient norm: 0.029918 LBFGS step functional: 0.000384514 gradient norm: 0.00250443 LBFGS step functional: 0.000384214 gradient norm: 0.00179238 LBFGS step functional: 0.000384067 gradient norm: 0.00168088 LBFGS step functional: 0.000383912 gradient norm: 0.00139472 LBFGS step ( 0, 1, 1) 8.81 - 8.81 = 0.00 ( 0, 0, 2) 12.23 - 12.23 = 0.00 ( 0, 2, 0) 12.71 - 12.71 = 0.00 ( 1, 1, 0) 12.97 - 12.97 = 0.00 ( 0, 1, 2) 13.79 - 13.79 = 0.00 ( 0, 2, 1) 14.11 - 14.11 = -0.00 ( 1, 1, 1) 14.35 - 14.34 = 0.01 ( 1, 0, 2) 16.68 - 16.68 = 0.00 ( 1, 2, 0) 17.03 - 17.04 = -0.01 ( 0, 2, 2) 17.67 - 17.67 = -0.00 ( 1, 1, 2) 17.86 - 17.86 = 0.00 ( 0, 1, 3) 19.47 - 19.47 = 0.00 ( 1, 2, 2) 21.03 - 21.02 = 0.01 ( 1, 3, 0) 22.26 - 22.26 = 0.00 ( 0, 2, 3) 22.41 - 22.41 = -0.00 ( 1, 1, 3) 22.56 - 22.56 = -0.00 ( 2, 0, 0) 22.72 - 22.71 = 0.01 ( 1, 3, 1) 23.10 - 23.10 = 0.00 ( 2, 1, 1) 24.40 - 24.40 = -0.00 ( 0, 0, 4) 24.60 - 24.60 = -0.00 ( 1, 2, 3) 25.17 - 25.17 = 0.00 ( 0, 1, 4) 25.43 - 25.43 = 0.00 ( 2, 0, 2) 25.87 - 25.87 = -0.00 ( 2, 2, 0) 26.11 - 26.11 = 0.00 ( 0, 4, 1) 26.32 - 26.32 = -0.00 ( 2, 1, 2) 26.66 - 26.66 = -0.00 ( 2, 2, 1) 26.84 - 26.84 = 0.00 ( 1, 0, 4) 27.15 - 27.14 = 0.01 ( 0, 2, 4) 27.78 - 27.78 = -0.00 ( 1, 1, 4) 27.90 - 27.90 = -0.00 ( 0, 4, 2) 28.44 - 28.44 = -0.00 ( 1, 4, 1) 28.72 - 28.72 = -0.00 ( 2, 2, 2) 28.92 - 28.92 = -0.00 ( 1, 3, 3) 29.02 - 29.02 = 0.00 ( 2, 1, 3) 30.08 - 30.08 = -0.00 ( 2, 3, 1) 30.49 - 30.49 = -0.00 ( 1, 4, 2) 30.69 - 30.69 = 0.00 ( 0, 3, 4) 31.34 - 31.34 = 0.00 ( 0, 1, 5) 31.56 - 31.56 = -0.00 ( 2, 2, 3) 32.12 - 32.12 = 0.00 (7.82934, 13.9295, 14.4747, 89.9925, 89.9881, 89.9857) u+s,u,s: 0.15 0.11 0.04 libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/miller_common_sets.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/miller_common_sets.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional asu a: (0, 1, 2) asu a: (1, 2, 3) asu a: (2, 3, 4) asu a: (3, 4, 5) asu a: (4, 5, 6) asu b: (5, 6, 7) asu b: (0, 1, 2) asu b: (3, 4, 5) asu b: (1, 2, 3) asu b: (4, 5, 6) common a: (0, 1, 2) common a: (3, 4, 5) common a: (1, 2, 3) common a: (4, 5, 6) common b: (0, 1, 2) common b: (3, 4, 5) common b: (1, 2, 3) common b: (4, 5, 6) lone a: (2, 3, 4) lone b: (5, 6, 7) asu a: (0, 1, 2) 0.0307678046942 asu a: (1, 2, 3) 0.33752477667 asu a: (2, 3, 4) 0.940635716831 asu a: (3, 4, 5) 0.0700093884992 asu a: (4, 5, 6) 0.278603566608 asu b: (5, 6, 7) 0.851550812603 asu b: (0, 1, 2) 0.928183997514 asu b: (3, 4, 5) 0.0733799609814 asu b: (1, 2, 3) 0.0801495396935 asu b: (4, 5, 6) 0.803735972149 common a: (0, 1, 2) 0.0307678046942 common a: (3, 4, 5) 0.0700093884992 common a: (1, 2, 3) 0.33752477667 common a: (4, 5, 6) 0.278603566608 common b: (0, 1, 2) 0.928183997514 common b: (3, 4, 5) 0.0733799609814 common b: (1, 2, 3) 0.0801495396935 common b: (4, 5, 6) 0.803735972149 lone a: (2, 3, 4) 0.940635716831 lone b: (5, 6, 7) 0.851550812603 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/steve_collins.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/steve_collins.py:47: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional x,y,z {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}} {{0, 0, 0}} -y+1/4,x+3/4,z+1/4 {{0, -1, 0}, {1, 0, 0}, {0, 0, 1}} {{1/4, 3/4, 1/4}} y+1/4,-x+1/4,z+3/4 {{0, 1, 0}, {-1, 0, 0}, {0, 0, 1}} {{1/4, 1/4, 3/4}} x,-y,-z {{1, 0, 0}, {0, -1, 0}, {0, 0, -1}} {{0, 0, 0}} -x,y+1/2,-z {{-1, 0, 0}, {0, 1, 0}, {0, 0, -1}} {{0, 1/2, 0}} -x,-y+1/2,z {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}} {{0, 1/2, 0}} y+1/4,x+3/4,-z+1/4 {{0, 1, 0}, {1, 0, 0}, {0, 0, -1}} {{1/4, 3/4, 1/4}} -y+1/4,-x+1/4,-z+3/4 {{0, -1, 0}, {-1, 0, 0}, {0, 0, -1}} {{1/4, 1/4, 3/4}} -x,-y,-z {{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}} {{0, 0, 0}} y-1/4,-x-3/4,-z-1/4 {{0, 1, 0}, {-1, 0, 0}, {0, 0, -1}} {{-1/4, -3/4, -1/4}} -y-1/4,x-1/4,-z-3/4 {{0, -1, 0}, {1, 0, 0}, {0, 0, -1}} {{-1/4, -1/4, -3/4}} -x,y,z {{-1, 0, 0}, {0, 1, 0}, {0, 0, 1}} {{0, 0, 0}} x,-y-1/2,z {{1, 0, 0}, {0, -1, 0}, {0, 0, 1}} {{0, -1/2, 0}} x,y-1/2,-z {{1, 0, 0}, {0, 1, 0}, {0, 0, -1}} {{0, -1/2, 0}} -y-1/4,-x-3/4,z-1/4 {{0, -1, 0}, {-1, 0, 0}, {0, 0, 1}} {{-1/4, -3/4, -1/4}} y-1/4,x-1/4,z-3/4 {{0, 1, 0}, {1, 0, 0}, {0, 0, 1}} {{-1/4, -1/4, -3/4}} x+1/2,y+1/2,z+1/2 {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}} {{1/2, 1/2, 1/2}} -y+3/4,x+5/4,z+3/4 {{0, -1, 0}, {1, 0, 0}, {0, 0, 1}} {{3/4, 5/4, 3/4}} y+3/4,-x+3/4,z+5/4 {{0, 1, 0}, {-1, 0, 0}, {0, 0, 1}} {{3/4, 3/4, 5/4}} x+1/2,-y+1/2,-z+1/2 {{1, 0, 0}, {0, -1, 0}, {0, 0, -1}} {{1/2, 1/2, 1/2}} -x+1/2,y+1,-z+1/2 {{-1, 0, 0}, {0, 1, 0}, {0, 0, -1}} {{1/2, 1, 1/2}} -x+1/2,-y+1,z+1/2 {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}} {{1/2, 1, 1/2}} y+3/4,x+5/4,-z+3/4 {{0, 1, 0}, {1, 0, 0}, {0, 0, -1}} {{3/4, 5/4, 3/4}} -y+3/4,-x+3/4,-z+5/4 {{0, -1, 0}, {-1, 0, 0}, {0, 0, -1}} {{3/4, 3/4, 5/4}} -x+1/2,-y+1/2,-z+1/2 {{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}} {{1/2, 1/2, 1/2}} y+1/4,-x-1/4,-z+1/4 {{0, 1, 0}, {-1, 0, 0}, {0, 0, -1}} {{1/4, -1/4, 1/4}} -y+1/4,x+1/4,-z-1/4 {{0, -1, 0}, {1, 0, 0}, {0, 0, -1}} {{1/4, 1/4, -1/4}} -x+1/2,y+1/2,z+1/2 {{-1, 0, 0}, {0, 1, 0}, {0, 0, 1}} {{1/2, 1/2, 1/2}} x+1/2,-y,z+1/2 {{1, 0, 0}, {0, -1, 0}, {0, 0, 1}} {{1/2, 0, 1/2}} x+1/2,y,-z+1/2 {{1, 0, 0}, {0, 1, 0}, {0, 0, -1}} {{1/2, 0, 1/2}} -y+1/4,-x-1/4,z+1/4 {{0, -1, 0}, {-1, 0, 0}, {0, 0, 1}} {{1/4, -1/4, 1/4}} y+1/4,x+1/4,z-1/4 {{0, 1, 0}, {1, 0, 0}, {0, 0, 1}} {{1/4, 1/4, -1/4}} Space group: P 4/m m m (No. 123) (0, 0, 1) True (0, 0, 2) True (0, 0, 3) True (1, 0, 0) True (1, 0, 1) False (1, 0, 2) True (1, 1, 0) True (1, 1, 1) True (1, 1, 2) False (2, 0, 0) False (2, 0, 1) True (2, 1, 0) True (2, 1, 1) False Space group: P 4/m m m (No. 123) x,y,z -y,x,z y,-x,z x,-y,-z -x,y,-z -x,-y,z y,x,-z -y,-x,-z -x,-y,-z y,-x,-z -y,x,-z -x,y,z x,-y,z x,y,-z -y,-x,z y,x,z special position operator: 0,1/2,0 distance to original site: 0.2 point group of the special position: x,y,z x,-y+1,-z -x,-y+1,-z -x,y,z 0 13.9976000786 0.01 13.9735949492 0.02 13.902379971 0.5 6.24008847468 0.5 0.0307999998331 0.034200001508 0.8 0.0900999978185 0.0899000018835 0.9 0.111299999058 0.114200003445 0.5 0.0416212081909 0.0341104492545 0.8 0.100048065186 0.0897070690989 0.9 0.12097454071 0.113592810929 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/cr2o3_primitive_cell.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/cr2o3_primitive_cell.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex Number of scatterers: 2 At special positions: 2 Unit cell: (4.96195, 4.96195, 13.5974, 90, 90, 120) Space group: R -3 c :H (No. 167) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Cr1 Cr 12 ( 0.0000 0.0000 0.3476) 1.00 0.0000 O1 O 18 ( 0.3058 0.0000 0.2500) 1.00 0.0000 Cr1 pair count: 6 << 0.0000, 0.0000, 0.3476>> O1: 1.9654 ( 0.0275, -0.3333, 0.4167) O1: 1.9654 sym. equiv. ( 0.3333, 0.3608, 0.4167) O1: 1.9654 sym. equiv. ( -0.3608, -0.0275, 0.4167) O1: 2.0157 ( 0.3058, 0.0000, 0.2500) O1: 2.0157 sym. equiv. ( 0.0000, 0.3058, 0.2500) O1: 2.0157 sym. equiv. ( -0.3058, -0.3058, 0.2500) O1 pair count: 4 << 0.3058, 0.0000, 0.2500>> Cr1: 1.9654 ( 0.3333, -0.3333, 0.3191) Cr1: 1.9654 sym. equiv. ( 0.6667, 0.3333, 0.1809) Cr1: 2.0157 ( 0.0000, 0.0000, 0.3476) Cr1: 2.0157 sym. equiv. ( 0.0000, 0.0000, 0.1524) Number of scatterers: 2 At special positions: 2 Unit cell: (5.36192, 5.36192, 5.36192, 55.1232, 55.1232, 55.1232) Space group: R -3 c :R (No. 167) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Cr1 Cr 4 ( 0.3476 0.3476 0.3476) 1.00 0.0000 O1 O 6 ( 0.5558 -0.0558 0.2500) 1.00 0.0000 Number of scatterers: 10 At special positions: 0 Unit cell: (5.36192, 5.36192, 5.36192, 55.1232, 55.1232, 55.1232) Space group: P 1 (No. 1) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Cr1 Cr 1 ( 0.3476 0.3476 0.3476) 1.00 0.0000 Cr1 Cr 1 ( 0.1524 0.1524 0.1524) 1.00 0.0000 Cr1 Cr 1 (-0.3476 -0.3476 -0.3476) 1.00 0.0000 Cr1 Cr 1 (-0.1524 -0.1524 -0.1524) 1.00 0.0000 O1 O 1 ( 0.5558 -0.0558 0.2500) 1.00 0.0000 O1 O 1 ( 0.2500 0.5558 -0.0558) 1.00 0.0000 O1 O 1 (-0.0558 0.2500 0.5558) 1.00 0.0000 O1 O 1 (-0.5558 0.0558 -0.2500) 1.00 0.0000 O1 O 1 (-0.2500 -0.5558 0.0558) 1.00 0.0000 O1 O 1 ( 0.0558 -0.2500 -0.5558) 1.00 0.0000 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/cr2o3_consistency_checks.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/cr2o3_consistency_checks.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex Number of scatterers: 2 At special positions: 2 Unit cell: (4.96195, 4.96195, 13.5974, 90, 90, 120) Space group: R -3 c :H (No. 167) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Cr1 Cr 12 ( 0.0000 0.0000 0.3476) 1.00 0.0000 O1 O 18 ( 0.3058 0.0000 0.2500) 1.00 0.0000 Cr1 pair count: 6 << 0.0000, 0.0000, 0.3476>> O1: 1.9654 ( 0.0275, -0.3333, 0.4167) O1: 1.9654 sym. equiv. ( 0.3333, 0.3608, 0.4167) O1: 1.9654 sym. equiv. ( -0.3608, -0.0275, 0.4167) O1: 2.0157 ( 0.3058, 0.0000, 0.2500) O1: 2.0157 sym. equiv. ( 0.0000, 0.3058, 0.2500) O1: 2.0157 sym. equiv. ( -0.3058, -0.3058, 0.2500) O1 pair count: 4 << 0.3058, 0.0000, 0.2500>> Cr1: 1.9654 ( 0.3333, -0.3333, 0.3191) Cr1: 1.9654 sym. equiv. ( 0.6667, 0.3333, 0.1809) Cr1: 2.0157 ( 0.0000, 0.0000, 0.3476) Cr1: 2.0157 sym. equiv. ( 0.0000, 0.0000, 0.1524) Number of scatterers: 2 At special positions: 2 Unit cell: (5.36192, 5.36192, 5.36192, 55.1232, 55.1232, 55.1232) Space group: R -3 c :R (No. 167) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Cr1 Cr 4 ( 0.3476 0.3476 0.3476) 1.00 0.0000 O1 O 6 ( 0.5558 -0.0558 0.2500) 1.00 0.0000 Number of scatterers: 10 At special positions: 0 Unit cell: (5.36192, 5.36192, 5.36192, 55.1232, 55.1232, 55.1232) Space group: P 1 (No. 1) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso Cr1 Cr 1 ( 0.3476 0.3476 0.3476) 1.00 0.0000 Cr1 Cr 1 ( 0.1524 0.1524 0.1524) 1.00 0.0000 Cr1 Cr 1 (-0.3476 -0.3476 -0.3476) 1.00 0.0000 Cr1 Cr 1 (-0.1524 -0.1524 -0.1524) 1.00 0.0000 O1 O 1 ( 0.5558 -0.0558 0.2500) 1.00 0.0000 O1 O 1 ( 0.2500 0.5558 -0.0558) 1.00 0.0000 O1 O 1 (-0.0558 0.2500 0.5558) 1.00 0.0000 O1 O 1 (-0.5558 0.0558 -0.2500) 1.00 0.0000 O1 O 1 (-0.2500 -0.5558 0.0558) 1.00 0.0000 O1 O 1 ( 0.0558 -0.2500 -0.5558) 1.00 0.0000 Cr1 pair count: 6 << 0.3476, 0.3476, 0.3476>> O1: 1.9654 ( 0.4442, 0.0558, 0.7500) O1: 1.9654 ( 0.7500, 0.4442, 0.0558) O1: 1.9654 ( 0.0558, 0.7500, 0.4442) O1: 2.0157 ( 0.2500, 0.5558, -0.0558) O1: 2.0157 ( -0.0558, 0.2500, 0.5558) O1: 2.0157 ( 0.5558, -0.0558, 0.2500) Cr1 pair count: 6 << 0.1524, 0.1524, 0.1524>> O1: 1.9654 ( 0.0558, -0.2500, 0.4442) O1: 1.9654 ( 0.4442, 0.0558, -0.2500) O1: 1.9654 ( -0.2500, 0.4442, 0.0558) O1: 2.0157 ( 0.2500, 0.5558, -0.0558) O1: 2.0157 ( -0.0558, 0.2500, 0.5558) O1: 2.0157 ( 0.5558, -0.0558, 0.2500) Cr1 pair count: 6 << -0.3476, -0.3476, -0.3476>> O1: 1.9654 ( -0.4442, -0.0558, -0.7500) O1: 1.9654 ( -0.7500, -0.4442, -0.0558) O1: 1.9654 ( -0.0558, -0.7500, -0.4442) O1: 2.0157 ( -0.2500, -0.5558, 0.0558) O1: 2.0157 ( 0.0558, -0.2500, -0.5558) O1: 2.0157 ( -0.5558, 0.0558, -0.2500) Cr1 pair count: 6 << -0.1524, -0.1524, -0.1524>> O1: 1.9654 ( -0.0558, 0.2500, -0.4442) O1: 1.9654 ( -0.4442, -0.0558, 0.2500) O1: 1.9654 ( 0.2500, -0.4442, -0.0558) O1: 2.0157 ( -0.2500, -0.5558, 0.0558) O1: 2.0157 ( 0.0558, -0.2500, -0.5558) O1: 2.0157 ( -0.5558, 0.0558, -0.2500) O1 pair count: 4 << 0.5558, -0.0558, 0.2500>> Cr1: 1.9654 ( 0.6524, -0.3476, 0.6524) Cr1: 1.9654 ( 0.8476, -0.1524, -0.1524) Cr1: 2.0157 ( 0.3476, 0.3476, 0.3476) Cr1: 2.0157 ( 0.1524, 0.1524, 0.1524) O1 pair count: 4 << 0.2500, 0.5558, -0.0558>> Cr1: 1.9654 ( 0.6524, 0.6524, -0.3476) Cr1: 1.9654 ( -0.1524, 0.8476, -0.1524) Cr1: 2.0157 ( 0.3476, 0.3476, 0.3476) Cr1: 2.0157 ( 0.1524, 0.1524, 0.1524) O1 pair count: 4 << -0.0558, 0.2500, 0.5558>> Cr1: 1.9654 ( -0.1524, -0.1524, 0.8476) Cr1: 1.9654 ( -0.3476, 0.6524, 0.6524) Cr1: 2.0157 ( 0.3476, 0.3476, 0.3476) Cr1: 2.0157 ( 0.1524, 0.1524, 0.1524) O1 pair count: 4 << -0.5558, 0.0558, -0.2500>> Cr1: 1.9654 ( -0.6524, 0.3476, -0.6524) Cr1: 1.9654 ( -0.8476, 0.1524, 0.1524) Cr1: 2.0157 ( -0.3476, -0.3476, -0.3476) Cr1: 2.0157 ( -0.1524, -0.1524, -0.1524) O1 pair count: 4 << -0.2500, -0.5558, 0.0558>> Cr1: 1.9654 ( -0.6524, -0.6524, 0.3476) Cr1: 1.9654 ( 0.1524, -0.8476, 0.1524) Cr1: 2.0157 ( -0.3476, -0.3476, -0.3476) Cr1: 2.0157 ( -0.1524, -0.1524, -0.1524) O1 pair count: 4 << 0.0558, -0.2500, -0.5558>> Cr1: 1.9654 ( 0.1524, 0.1524, -0.8476) Cr1: 1.9654 ( 0.3476, -0.6524, -0.6524) Cr1: 2.0157 ( -0.3476, -0.3476, -0.3476) Cr1: 2.0157 ( -0.1524, -0.1524, -0.1524) Coordination sequences for ICSD structure Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277] O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414] TD10: 1345.00 Coordination sequences for P1 structure Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277] Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277] Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277] Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277] O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414] O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414] O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414] O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414] O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414] O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414] TD10: 1345.00 (2, 2, 2) 86.0508424883 86.0508424883 (4, 4, 4) 113.047557719 113.047557719 (3, 2, 3) 40.4154044721 40.4154044721 (3, 3, 2) 40.4154044721 40.4154044721 (2, 3, 3) 40.4154044721 40.4154044721 (1, 0, 1) 95.4889181855 95.4889181855 (1, 1, 0) 95.4889181855 95.4889181855 (0, 1, 1) 95.4889181855 95.4889181855 (2, 1, 1) 162.211900743 162.211900743 (1, 1, 2) 162.211900743 162.211900743 (1, 2, 1) 162.211900743 162.211900743 (4, 3, 3) 155.00906081 155.00906081 (3, 3, 4) 155.00906081 155.00906081 (3, 4, 3) 155.00906081 155.00906081 (0, -1, 1) 169.838481281 169.838481281 (-1, 0, 1) 169.838481281 169.838481281 (1, -1, 0) 169.838481281 169.838481281 (2, 1, 0) 77.6623864446 77.6623864446 (1, 0, 2) 77.6623864446 77.6623864446 (0, 2, 1) 77.6623864446 77.6623864446 (1, 2, 0) 77.6623864446 77.6623864446 (0, 1, 2) 77.6623864446 77.6623864446 (2, 0, 1) 77.6623864446 77.6623864446 (3, 2, 1) 190.423823139 190.423823139 (2, 1, 3) 190.423823139 190.423823139 (1, 3, 2) 190.423823139 190.423823139 (2, 3, 1) 190.423823139 190.423823139 (1, 2, 3) 190.423823139 190.423823139 (3, 1, 2) 190.423823139 190.423823139 (4, 3, 2) 47.1902503064 47.1902503064 (3, 2, 4) 47.1902503064 47.1902503064 (2, 4, 3) 47.1902503064 47.1902503064 (3, 4, 2) 47.1902503064 47.1902503064 (2, 3, 4) 47.1902503064 47.1902503064 (4, 2, 3) 47.1902503064 47.1902503064 (5, 4, 3) 38.7011643914 38.7011643914 (4, 3, 5) 38.7011643914 38.7011643914 (3, 5, 4) 38.7011643914 38.7011643914 (4, 5, 3) 38.7011643914 38.7011643914 (3, 4, 5) 38.7011643914 38.7011643914 (5, 3, 4) 38.7011643914 38.7011643914 (4, 2, 4) 126.854496289 126.854496289 (4, 4, 2) 126.854496289 126.854496289 (2, 4, 4) 126.854496289 126.854496289 (2, 0, 2) 159.758114444 159.758114444 (2, 2, 0) 159.758114444 159.758114444 (0, 2, 2) 159.758114444 159.758114444 (2, 0, 0) 52.4585599646 52.4585599646 (0, 0, 2) 52.4585599646 52.4585599646 (0, 2, 0) 52.4585599646 52.4585599646 (4, 2, 2) 19.175305094 19.175305094 (2, 2, 4) 19.175305094 19.175305094 (2, 4, 2) 19.175305094 19.175305094 (3, 1, 4) 22.6189348657 22.6189348657 (4, 3, 1) 22.6189348657 22.6189348657 (1, 4, 3) 22.6189348657 22.6189348657 (1, 3, 4) 22.6189348657 22.6189348657 (3, 4, 1) 22.6189348657 22.6189348657 (4, 1, 3) 22.6189348657 22.6189348657 (2, 0, 3) 16.0896242359 16.0896242359 (3, 2, 0) 16.0896242359 16.0896242359 (0, 3, 2) 16.0896242359 16.0896242359 (0, 2, 3) 16.0896242359 16.0896242359 (2, 3, 0) 16.0896242359 16.0896242359 (3, 0, 2) 16.0896242359 16.0896242359 (-1, -2, 1) 53.0970522234 53.0970522234 (1, -1, 2) 53.0970522234 53.0970522234 (-1, 2, 1) 53.0970522234 53.0970522234 (-1, 1, 2) 53.0970522234 53.0970522234 (2, -1, 1) 53.0970522234 53.0970522234 (-2, -1, 1) 53.0970522234 53.0970522234 (0, -1, 2) 18.7461313511 18.7461313511 (0, -2, 1) 18.7461313511 18.7461313511 (-2, 0, 1) 18.7461313511 18.7461313511 (1, -2, 0) 18.7461313511 18.7461313511 (-1, 0, 2) 18.7461313511 18.7461313511 (2, -1, 0) 18.7461313511 18.7461313511 (3, 1, 0) 132.488142531 132.488142531 (1, 0, 3) 132.488142531 132.488142531 (0, 3, 1) 132.488142531 132.488142531 (1, 3, 0) 132.488142531 132.488142531 (0, 1, 3) 132.488142531 132.488142531 (3, 0, 1) 132.488142531 132.488142531 (4, 2, 1) 14.1831500279 14.1831500279 (2, 1, 4) 14.1831500279 14.1831500279 (1, 4, 2) 14.1831500279 14.1831500279 (2, 4, 1) 14.1831500279 14.1831500279 (1, 2, 4) 14.1831500279 14.1831500279 (4, 1, 2) 14.1831500279 14.1831500279 (5, 3, 2) 121.452908825 121.452908825 (3, 2, 5) 121.452908825 121.452908825 (2, 5, 3) 121.452908825 121.452908825 (3, 5, 2) 121.452908825 121.452908825 (2, 3, 5) 121.452908825 121.452908825 (5, 2, 3) 121.452908825 121.452908825 (0, -2, 2) 121.476041154 121.476041154 (-2, 0, 2) 121.476041154 121.476041154 (2, -2, 0) 121.476041154 121.476041154 (1, -1, 3) 39.0693132248 39.0693132248 (-1, 3, 1) 39.0693132248 39.0693132248 (-1, -3, 1) 39.0693132248 39.0693132248 (-3, -1, 1) 39.0693132248 39.0693132248 (-1, 1, 3) 39.0693132248 39.0693132248 (3, -1, 1) 39.0693132248 39.0693132248 (4, 2, 0) 133.588352208 133.588352208 (2, 0, 4) 133.588352208 133.588352208 (0, 4, 2) 133.588352208 133.588352208 (2, 4, 0) 133.588352208 133.588352208 (0, 2, 4) 133.588352208 133.588352208 (4, 0, 2) 133.588352208 133.588352208 (3, 0, 3) 75.3123159831 75.3123159831 (3, 3, 0) 75.3123159831 75.3123159831 (0, 3, 3) 75.3123159831 75.3123159831 (-1, -1, 2) 219.874202958 219.874202958 (1, -2, 1) 219.874202958 219.874202958 (-2, 1, 1) 219.874202958 219.874202958 (4, 1, 1) 75.3123159831 75.3123159831 (1, 1, 4) 75.3123159831 75.3123159831 (1, 4, 1) 75.3123159831 75.3123159831 (3, 0, 4) 7.74006832091 7.74006832091 (4, 3, 0) 7.74006832091 7.74006832091 (0, 4, 3) 7.74006832091 7.74006832091 (0, 3, 4) 7.74006832091 7.74006832091 (3, 4, 0) 7.74006832091 7.74006832091 (4, 0, 3) 7.74006832091 7.74006832091 (-2, -3, 1) 92.880272839 92.880272839 (2, -1, 3) 92.880272839 92.880272839 (-1, 3, 2) 92.880272839 92.880272839 (-1, 2, 3) 92.880272839 92.880272839 (3, -1, 2) 92.880272839 92.880272839 (-3, -2, 1) 92.880272839 92.880272839 (-1, -2, 2) 9.22539071273 9.22539071273 (1, -2, 2) 9.22539071273 9.22539071273 (-2, 2, 1) 9.22539071273 9.22539071273 (-2, 1, 2) 9.22539071273 9.22539071273 (2, -2, 1) 9.22539071273 9.22539071273 (-2, -1, 2) 9.22539071273 9.22539071273 (0, -1, 3) 58.7597521751 58.7597521751 (0, -3, 1) 58.7597521751 58.7597521751 (-3, 0, 1) 58.7597521751 58.7597521751 (1, -3, 0) 58.7597521751 58.7597521751 (-1, 0, 3) 58.7597521751 58.7597521751 (3, -1, 0) 58.7597521751 58.7597521751 (4, 1, 0) 8.38469863314 8.38469863314 (1, 0, 4) 8.38469863314 8.38469863314 (0, 4, 1) 8.38469863314 8.38469863314 (1, 4, 0) 8.38469863314 8.38469863314 (0, 1, 4) 8.38469863314 8.38469863314 (4, 0, 1) 8.38469863314 8.38469863314 (-2, -2, 2) 63.3334064079 63.3334064079 (2, -2, 2) 63.3334064079 63.3334064079 (-2, 2, 2) 63.3334064079 63.3334064079 (4, 0, 0) 76.9075882126 76.9075882126 (0, 0, 4) 76.9075882126 76.9075882126 (0, 4, 0) 76.9075882126 76.9075882126 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/reduced_cell_two_folds.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/reduced_cell_two_folds.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional (-1, -1, -1, 0, 0, 1, 0, 1, 0) (-1, 1, 1) (0, 1, 1) (-1, -1, 0, 0, 1, 0, 0, -1, -1) (1, -2, 1) (0, 1, 0) (-1, -1, 0, 0, 1, 0, 0, 0, -1) (-1, 2, 0) (0, 1, 0) (-1, -1, 0, 0, 1, 0, 0, 1, -1) (-1, 2, 1) (0, 1, 0) (-1, -1, 1, 0, 0, -1, 0, -1, 0) (1, -1, 1) (0, -1, 1) (-1, 0, -1, 0, -1, -1, 0, 0, 1) (-1, -1, 2) (0, 0, 1) (-1, 0, -1, 0, -1, 0, 0, 0, 1) (-1, 0, 2) (0, 0, 1) (-1, 0, -1, 0, -1, 1, 0, 0, 1) (-1, 1, 2) (0, 0, 1) (-1, 0, 0, -1, 0, -1, 1, -1, 0) (0, -1, 1) (1, -1, 1) (-1, 0, 0, -1, 0, 1, -1, 1, 0) (0, 1, 1) (-1, 1, 1) (-1, 0, 0, -1, 1, -1, 0, 0, -1) (0, 1, 0) (1, -2, 1) (-1, 0, 0, -1, 1, 0, 0, 0, -1) (0, 1, 0) (-1, 2, 0) (-1, 0, 0, -1, 1, 1, 0, 0, -1) (0, 1, 0) (-1, 2, 1) (-1, 0, 0, 0, -1, -1, 0, 0, 1) (0, -1, 2) (0, 0, 1) (-1, 0, 0, 0, -1, 0, -1, -1, 1) (0, 0, 1) (-1, -1, 2) (-1, 0, 0, 0, -1, 0, -1, 0, 1) (0, 0, 1) (-1, 0, 2) (-1, 0, 0, 0, -1, 0, -1, 1, 1) (0, 0, 1) (-1, 1, 2) (-1, 0, 0, 0, -1, 0, 0, -1, 1) (0, 0, 1) (0, -1, 2) (-1, 0, 0, 0, -1, 0, 0, 0, 1) (0, 0, 1) (0, 0, 1) (-1, 0, 0, 0, -1, 0, 0, 1, 1) (0, 0, 1) (0, 1, 2) (-1, 0, 0, 0, -1, 0, 1, -1, 1) (0, 0, 1) (1, -1, 2) (-1, 0, 0, 0, -1, 0, 1, 0, 1) (0, 0, 1) (1, 0, 2) (-1, 0, 0, 0, -1, 0, 1, 1, 1) (0, 0, 1) (1, 1, 2) (-1, 0, 0, 0, -1, 1, 0, 0, 1) (0, 1, 2) (0, 0, 1) (-1, 0, 0, 0, 0, -1, 0, -1, 0) (0, -1, 1) (0, -1, 1) (-1, 0, 0, 0, 0, 1, 0, 1, 0) (0, 1, 1) (0, 1, 1) (-1, 0, 0, 0, 1, -1, 0, 0, -1) (0, 1, 0) (0, -2, 1) (-1, 0, 0, 0, 1, 0, 0, -1, -1) (0, -2, 1) (0, 1, 0) (-1, 0, 0, 0, 1, 0, 0, 0, -1) (0, 1, 0) (0, 1, 0) (-1, 0, 0, 0, 1, 0, 0, 1, -1) (0, 2, 1) (0, 1, 0) (-1, 0, 0, 0, 1, 1, 0, 0, -1) (0, 1, 0) (0, 2, 1) (-1, 0, 0, 1, 0, -1, -1, -1, 0) (0, -1, 1) (-1, -1, 1) (-1, 0, 0, 1, 0, 1, 1, 1, 0) (0, 1, 1) (1, 1, 1) (-1, 0, 0, 1, 1, -1, 0, 0, -1) (0, 1, 0) (-1, -2, 1) (-1, 0, 0, 1, 1, 0, 0, 0, -1) (0, 1, 0) (1, 2, 0) (-1, 0, 0, 1, 1, 1, 0, 0, -1) (0, 1, 0) (1, 2, 1) (-1, 0, 1, 0, -1, -1, 0, 0, 1) (1, -1, 2) (0, 0, 1) (-1, 0, 1, 0, -1, 0, 0, 0, 1) (1, 0, 2) (0, 0, 1) (-1, 0, 1, 0, -1, 1, 0, 0, 1) (1, 1, 2) (0, 0, 1) (-1, 1, -1, 0, 0, -1, 0, -1, 0) (-1, -1, 1) (0, -1, 1) (-1, 1, 0, 0, 1, 0, 0, -1, -1) (-1, -2, 1) (0, 1, 0) (-1, 1, 0, 0, 1, 0, 0, 0, -1) (1, 2, 0) (0, 1, 0) (-1, 1, 0, 0, 1, 0, 0, 1, -1) (1, 2, 1) (0, 1, 0) (-1, 1, 1, 0, 0, 1, 0, 1, 0) (1, 1, 1) (0, 1, 1) (0, -1, -1, -1, 0, 1, 0, 0, -1) (-1, 1, 0) (-1, 1, 1) (0, -1, -1, 0, -1, 0, -1, 1, 0) (-1, 0, 1) (-1, 1, 1) (0, -1, 0, -1, 0, 0, -1, 1, -1) (-1, 1, 1) (-1, 1, 0) (0, -1, 0, -1, 0, 0, 0, 0, -1) (-1, 1, 0) (-1, 1, 0) (0, -1, 0, -1, 0, 0, 1, -1, -1) (1, -1, 1) (-1, 1, 0) (0, -1, 1, -1, 0, -1, 0, 0, -1) (-1, 1, 0) (1, -1, 1) (0, -1, 1, 0, -1, 0, 1, -1, 0) (1, 0, 1) (1, -1, 1) (0, 0, -1, -1, -1, 1, -1, 0, 0) (-1, 1, 1) (-1, 0, 1) (0, 0, -1, 0, -1, 0, -1, 0, 0) (-1, 0, 1) (-1, 0, 1) (0, 0, -1, 1, -1, -1, -1, 0, 0) (-1, -1, 1) (-1, 0, 1) (0, 0, 1, -1, -1, -1, 1, 0, 0) (1, -1, 1) (1, 0, 1) (0, 0, 1, 0, -1, 0, 1, 0, 0) (1, 0, 1) (1, 0, 1) (0, 0, 1, 1, -1, 1, 1, 0, 0) (1, 1, 1) (1, 0, 1) (0, 1, -1, 0, -1, 0, -1, -1, 0) (-1, 0, 1) (-1, -1, 1) (0, 1, -1, 1, 0, -1, 0, 0, -1) (1, 1, 0) (-1, -1, 1) (0, 1, 0, 1, 0, 0, -1, -1, -1) (-1, -1, 1) (1, 1, 0) (0, 1, 0, 1, 0, 0, 0, 0, -1) (1, 1, 0) (1, 1, 0) (0, 1, 0, 1, 0, 0, 1, 1, -1) (1, 1, 1) (1, 1, 0) (0, 1, 1, 0, -1, 0, 1, 1, 0) (1, 0, 1) (1, 1, 1) (0, 1, 1, 1, 0, 1, 0, 0, -1) (1, 1, 0) (1, 1, 1) (1, -1, -1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (-2, 1, 1) (1, -1, 0, 0, -1, 0, 0, 0, -1) (1, 0, 0) (-2, 1, 0) (1, -1, 1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (2, -1, 1) (1, 0, -1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (-2, 0, 1) (1, 0, 0, -1, -1, 0, -1, 0, -1) (-2, 1, 1) (1, 0, 0) (1, 0, 0, -1, -1, 0, 0, 0, -1) (-2, 1, 0) (1, 0, 0) (1, 0, 0, -1, -1, 0, 1, 0, -1) (2, -1, 1) (1, 0, 0) (1, 0, 0, 0, -1, 0, -1, 0, -1) (-2, 0, 1) (1, 0, 0) (1, 0, 0, 0, -1, 0, 0, 0, -1) (1, 0, 0) (1, 0, 0) (1, 0, 0, 0, -1, 0, 1, 0, -1) (2, 0, 1) (1, 0, 0) (1, 0, 0, 1, -1, 0, -1, 0, -1) (-2, -1, 1) (1, 0, 0) (1, 0, 0, 1, -1, 0, 0, 0, -1) (2, 1, 0) (1, 0, 0) (1, 0, 0, 1, -1, 0, 1, 0, -1) (2, 1, 1) (1, 0, 0) (1, 0, 1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (2, 0, 1) (1, 1, -1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (-2, -1, 1) (1, 1, 0, 0, -1, 0, 0, 0, -1) (1, 0, 0) (2, 1, 0) (1, 1, 1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (2, 1, 1) OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/lebedev_2005_perturbation.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/lebedev_2005_perturbation.py:14: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional s={{6732.6948, -1414.631, -2529.5033}, {-1414.631, 4437.1585, -884.7347}, {-2529.5033, -884.7347, 7208.6892}} m={{0, 0, -1}, {0, -1, 0}, {-1, 0, 0}} rotation type: 2 axis direction: (-1, 0, 1) score given: 0.06996537 score reproduced: 0.0699653749294 Le Page delta: 0.0848717968347 s={{6176.9399, 260.7664, 128.5781}, {260.7664, 1340.4385, -14.6349}, {128.5781, -14.6349, 524.5932}} m={{-1, 0, 0}, {0, -1, 0}, {1, 0, 1}} rotation type: 2 axis direction: (0, 0, 1) score given: 0.06177181 score reproduced: 0.0617717889751 Le Page delta: 0.0750886664342 s={{7578.2248, -1951.4527, -1447.0019}, {-1951.4527, 7501.6385, -256.6406}, {-1447.0019, -256.6406, 7208.6892}} m={{-1, 0, 0}, {0, 0, -1}, {0, -1, 0}} rotation type: 2 axis direction: (0, -1, 1) score given: 0.03867617 score reproduced: 0.0386761646506 Le Page delta: 0.0472278316943 s={{7930.4368, -2942.6005, -1480.2461}, {-2942.6005, 9333.8785, -429.2985}, {-1480.2461, -429.2985, 7208.6892}} m={{0, -1, 0}, {-1, 0, 0}, {0, 0, -1}} rotation type: 2 axis direction: (-1, 1, 0) score given: 0.11207609 score reproduced: 0.112076089497 Le Page delta: 0.134026806814 s={{8473.7548, -1587.0355, -175.9529}, {-1587.0355, 4437.1585, -394.5165}, {-175.9529, -394.5165, 7208.6892}} m={{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}} rotation type: 2 axis direction: (0, 0, 1) score given: 0.06714734 score reproduced: 0.0671473468463 Le Page delta: 0.0815139175486 s={{10414.8148, -414.5907, 2452.0864}, {-414.5907, 2172.6785, -304.2978}, {2452.0864, -304.2978, 5610.6092}} m={{1, 0, 0}, {0, -1, 0}, {-1, 0, -1}} rotation type: 2 axis direction: (-2, 0, 1) score given: 0.06543032 score reproduced: 0.0654303257975 Le Page delta: 0.0794643933624 s={{9817.4017, -451.9168, 1807.5581}, {-451.9168, 4437.1585, -451.9168}, {1807.5581, -451.9168, 4212.5292}} m={{1, 0, 0}, {0, -1, 0}, {-1, 0, -1}} rotation type: 2 axis direction: (-2, 0, 1) score given: 0.05202084 score reproduced: 0.0520208375975 Le Page delta: 0.063372263802 s={{2814.6208, 446.7217, -65.5759}, {446.7217, 9333.8785, -646.4419}, {-65.5759, -646.4419, 3014.4492}} m={{0, 0, 1}, {0, -1, 0}, {1, 0, 0}} rotation type: 2 axis direction: (1, 0, 1) score given: 0.03361885 score reproduced: 0.0336188434566 Le Page delta: 0.0410819848677 s={{9103.413, 420.0088, 352.4837}, {420.0088, 1340.4385, -228.8041}, {352.4837, -228.8041, 2016.3692}} m={{1, 0, 0}, {-1, -1, 0}, {0, 0, -1}} rotation type: 2 axis direction: (-2, 1, 0) score given: 0.10323493 score reproduced: 0.103234924615 Le Page delta: 0.12388279713 s={{9046.4187, 1355.7037, -75.0535}, {1355.7037, 4437.1585, -403.7364}, {-75.0535, -403.7364, 1218.2892}} m={{-1, 0, 0}, {0, -1, 0}, {0, -1, 1}} rotation type: 2 axis direction: (0, 0, 1) score given: 0.0819319 score reproduced: 0.0819319050724 Le Page delta: 0.0990441384163 OK libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/le_page_1982_vs_lebedev_2005.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/le_page_1982_vs_lebedev_2005.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK set ccp4_symop_lib=`libtbx.show_dist_paths ccp4io`/lib/data/symop.lib libtbx.show_dist_paths ccp4io /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env libtbx.show_dist_paths cctbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/convert_ccp4_symop_lib.py /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/convert_ccp4_symop_lib.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional grep Fd-3m convert_ccp4_symop_py_out libtbx.assert_stdin 227 192 48 Fd-3m PGm3barm CUBIC 'F 41/d -3 2/m' 'F d -3 m' cctbx.convert_ccp4_symop_lib diff convert_ccp4_symop_py_out convert_ccp4_symop_cpp_out libtbx.assert_stdin if ( 0 ) then cctbx.structure_factor_timings /net/rosie/scratch1/rwgk/dist/regression/cctbx/1ab1.ent 4 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.pdb Number of scatterers: 684 At special positions: 0 Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) Number of Miller indices: 320 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) d_min: 4.0 direct simple: 0.14 seconds wing_cutoff for following fft calculations: 1.0e-03 S:1*6 O:1*69 N:1*58 C:1*222 H:1*329 direct cos+sin function: 0.08 seconds, r-factor: 0.000020 direct cos+sin table: 0.03 seconds, r-factor: 0.000055 fft exp function: 0.01 seconds, r-factor: 0.000122 fft exp table: 0.01 seconds, r-factor: 0.000124 S:5+c*6 O:5+c*69 N:5+c*58 C:5+c*222 H:5+c*329 direct cos+sin function: 0.08 seconds, r-factor: 0.000000 direct cos+sin table: 0.03 seconds, r-factor: 0.000044 fft exp function: 0.02 seconds, r-factor: 0.000097 fft exp table: 0.01 seconds, r-factor: 0.000097 S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 direct cos+sin function: 0.08 seconds, r-factor: 0.000000 direct cos+sin table: 0.03 seconds, r-factor: 0.000044 fft exp function: 0.02 seconds, r-factor: 0.000095 fft exp table: 0.01 seconds, r-factor: 0.000095 S:2*6 O:2*69 N:2*58 C:2*222 H:2*329 direct cos+sin function: 0.08 seconds, r-factor: 0.000003 direct cos+sin table: 0.03 seconds, r-factor: 0.000040 fft exp function: 0.01 seconds, r-factor: 0.000116 fft exp table: 0.01 seconds, r-factor: 0.000116 S:1*6 O:1*69 N:1*58 C:1*222 H:2*329 direct cos+sin function: 0.08 seconds, r-factor: 0.013726 direct cos+sin table: 0.03 seconds, r-factor: 0.013798 fft exp function: 0.01 seconds, r-factor: 0.014112 fft exp table: 0.00 seconds, r-factor: 0.014131 cctbx.structure_factor_timings /net/rosie/scratch1/rwgk/dist/regression/cctbx/1ab1.ent --fft_only 3 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.pdb Number of scatterers: 684 At special positions: 0 Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) Number of Miller indices: 728 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) d_min: 3.0 fft exp function wing_cutoff=1.0e-06: 0.11 seconds wing_cutoff for following fft calculations: 1.0e-03 S:2*6 O:1*69 N:1*58 C:2*222 H:1*329 fft exp function: 0.01 seconds, r-factor: 0.000086 fft exp table: 0.01 seconds, r-factor: 0.000087 S:5+c*6 O:5+c*69 N:5+c*58 C:5+c*222 H:5+c*329 fft exp function: 0.02 seconds, r-factor: 0.000041 fft exp table: 0.02 seconds, r-factor: 0.000041 S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 fft exp function: 0.02 seconds, r-factor: 0.000042 fft exp table: 0.01 seconds, r-factor: 0.000042 S:2*6 O:2*69 N:2*58 C:2*222 H:2*329 fft exp function: 0.01 seconds, r-factor: 0.000050 fft exp table: 0.01 seconds, r-factor: 0.000051 S:1*6 O:1*69 N:1*58 C:1*222 H:2*329 fft exp function: 0.01 seconds, r-factor: 0.040792 fft exp table: 0.00 seconds, r-factor: 0.040847 libtbx.show_dist_paths cctbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/electron_density_sampling.py /net/rosie/scratch1/rwgk/dist/regression/cctbx/1ab1.ent /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/electron_density_sampling.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.pdb Number of scatterers: 684 At special positions: 0 Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) wing_cutoff for following fft calculations: 1.0e-03 exp function: Number of Miller indices: 320 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) S:1*6 O:1*69 N:1*58 C:1*222 H:1*329 0.00 seconds, S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 0.01 seconds, d_min=4: 0.00 s / 0.01 s = 0.00 Number of Miller indices: 728 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) S:2*6 O:1*69 N:1*58 C:2*222 H:1*329 0.01 seconds, S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 0.02 seconds, d_min=3: 0.01 s / 0.02 s = 0.50 Number of Miller indices: 2370 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) S:2*6 O:2*69 N:2*58 C:2*222 H:2*329 0.01 seconds, S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 0.03 seconds, d_min=2: 0.01 s / 0.03 s = 0.33 Number of Miller indices: 18204 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) S:2*6 O:2*69 N:2*58 C:2*222 H:3*329 0.07 seconds, S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 0.12 seconds, d_min=1: 0.07 s / 0.12 s = 0.58 exp table: Number of Miller indices: 320 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) S:1*6 O:1*69 N:1*58 C:1*222 H:1*329 0.01 seconds, S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 0.01 seconds, d_min=4: 0.01 s / 0.01 s = 1.00 Number of Miller indices: 728 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) S:2*6 O:1*69 N:1*58 C:2*222 H:1*329 0.00 seconds, S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 0.01 seconds, d_min=3: 0.00 s / 0.01 s = 0.00 Number of Miller indices: 2370 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) S:2*6 O:2*69 N:2*58 C:2*222 H:2*329 0.00 seconds, S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 0.01 seconds, d_min=2: 0.00 s / 0.01 s = 0.00 Number of Miller indices: 18204 Anomalous flag: False Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90) Space group: P 1 21 1 (No. 4) S:2*6 O:2*69 N:2*58 C:2*222 H:3*329 0.03 seconds, S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329 0.06 seconds, d_min=1: 0.03 s / 0.06 s = 0.50 libtbx.show_dist_paths cctbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/web/asu_gallery/jv_asu.py 213 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/web/asu_gallery/jv_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.web.asu_gallery import jvx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Space group number: 213 libtbx.show_dist_paths cctbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/direct_space_asu/check_redundancies.py 12 181 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/direct_space_asu/check_redundancies.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.sgtbx.direct_space_asu import reference_table /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Writing asu_gallery files Space group: P 64 2 2 (No. 181) Gridding: (12, 12, 12) number of redundancies: 0+0, Space group: P 64 2 2 (No. 181) grep -i error libtbx.show_dist_paths cctbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/web/replay.py /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/all_axes_2002_11_22_16_57_14 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/browse_settings_2002_11_22_16_35_50 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/browse_settings_2002_11_22_16_35_58 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/change_hand_2002_11_22_16_55_27 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/change_hand_2002_11_22_16_56_35 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/change_setting_2002_11_22_16_53_15 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/change_setting_2002_11_22_16_54_28 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2002_11_22_16_45_58 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2002_11_22_17_03_15 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2004_05_25_10_02_10 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2004_05_25_10_03_53 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2004_05_25_10_05_21 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/explore_symmetry_2002_11_22_16_34_28 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/explore_symmetry_2002_11_22_16_35_25 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/frac_cart_2002_11_22_16_50_33 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/frac_cart_2002_11_22_16_52_04 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/lattice_symmetry_2003_08_28_06_17_15 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/libtbx_help_2005_08_14_02_41_20 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_05_12_26 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_07_09_15 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_07_16_53 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_08_52_08 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_08_53_42 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_08_55_55 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_08_57_00 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/shelx_2002_11_22_16_46_31 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/shelx_2002_11_22_16_46_38 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_2005_11_10_21_32_10 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_2005_11_10_21_33_32 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_2005_11_10_21_34_02 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_2005_11_10_22_27_47 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_pdb_2004_12_17_15_25_48 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_pdb_2004_12_17_15_26_06 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_pdb_2004_12_17_15_26_25 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/wyckoff_2002_11_22_16_47_49 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/wyckoff_2002_11_22_16_48_33 /net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/pickle.py:1124: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py __import__(module) /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/web/io_utils.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb cctbx Error: Brick is not available for the given space group representation. libtbx.show_dist_paths mmtbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env mmtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/run_tests.py /net/rosie/scratch1/rwgk/dist/mmtbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/refinement/tst_rigid_body.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/refinement/tst_rigid_body.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/refinement/tst_rigid_body.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/refinement/tst_rigid_body.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py import mmtbx.f_model |-----------------------------------------------------------------------------| | | | all data [41.9-2.00] high resolution [6.0-2.00] low resolution [41.9-6.00] | | r_work = 0.0000 r_work = 0.0000 r_work = 0.0152 | | r_free = 0.0000 r_free = 0.0000 r_free = 0.0131 | | | | scale (work) = 1.0000 scale (free) = 1.0000 ksol = 0.00 Bsol = 0.00 | | | | overall anisotropic scale matrix (Cartesian basis): | | (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00) | | (B11+B22+B33)/3 = 0.00 | | | | Target ls_wunit_k1: work = 0.000000E+00 free = 0.000000E+00 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 41.9535 - 2.8845 1.00 2301 254 0.0000 0.0000 0.0000E+00 0.0000E+00| | 2: 2.8845 - 2.2896 1.00 2197 237 0.0000 0.0000 0.0000E+00 0.0000E+00| | 3: 2.2896 - 2.0001 1.00 2153 247 0.0000 0.0000 0.0000E+00 0.0000E+00| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase error Alpha Beta | | # range work test work test | | 1: 41.9535 - 2.8845 2301 254 1.000 0.000 0.000 1.000 0.000 | | 2: 2.8845 - 2.2896 2197 237 1.000 0.000 0.000 1.000 0.000 | | 3: 2.2896 - 2.0001 2153 247 1.000 0.000 0.000 1.000 0.000 | |alpha: min = 1.0000 max = 1.0000 mean = 1.0000 | |beta: min = 0.0000 max = 0.0000 mean = 0.0000 | |figures of merit: min = 1.0000 max = 1.0000 mean = 1.0000 | |phase err.(work): min = 0.0000 max = 0.0000 mean = 0.0000 | |phase err.(test): min = 0.0000 max = 0.0000 mean = 0.0000 | |-----------------------------------------------------------------------------| test 1: High resolution cutoffs for mz-protocol: ['3.854', '2.000'] ----------Refinement at resolution: 41.9 - 3.9---------- |-rigid body refinement: Euler angles xyz (macro cycle = 1; iterations = 17)--| | resolution range: 41.944 - 3.855 (1010 reflections) convergence test = on | | r_work = 0.010563 r_free = 0.009630 target = 0.000112 | | rotation (deg.) translation (A) | | group 1: 0.0000 0.0000 0.0000 -2.4990 -2.5001 -2.5004 | |-----------------------------------------------------------------------------| |-rigid body refinement: Euler angles xyz (macro cycle = 2; iterations = 7)---| | resolution range: 41.944 - 3.855 (1010 reflections) convergence test = on | | r_work = 0.010556 r_free = 0.009638 target = 0.000112 | | rotation (deg.) translation (A) | | group 1: 0.0000 0.0000 0.0000 -2.4990 -2.5001 -2.5004 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.9 - 2.0---------- |-rigid body refinement: Euler angles xyz (macro cycle = 1; iterations = 5)---| | resolution range: 41.944 - 2.000 (6651 reflections) convergence test = on | | r_work = 0.000238 r_free = 0.000243 target = 0.000000 | | rotation (deg.) translation (A) | | group 1: 0.0000 0.0000 0.0000 -2.5000 -2.5000 -2.5000 | |-----------------------------------------------------------------------------| |-rigid body refinement: Euler angles xyz (macro cycle = 2; iterations = 4)---| | resolution range: 41.944 - 2.000 (6651 reflections) convergence test = on | | r_work = 0.000217 r_free = 0.000222 target = 0.000000 | | rotation (deg.) translation (A) | | group 1: 0.0000 0.0000 0.0000 -2.5000 -2.5000 -2.5000 | |-----------------------------------------------------------------------------| finite_differences_test: |-----------------------------------------------------------------------------| | | | all data [11.1-1.00] high resolution [6.0-1.00] low resolution [11.1-6.00] | | r_work = 0.1137 r_work = 0.1192 r_work = 0.0451 | | r_free = 0.1137 r_free = 0.1192 r_free = 0.0451 | | | | scale (work) = 0.9924 scale (free) = 0.9924 ksol = 0.00 Bsol = 0.00 | | | | overall anisotropic scale matrix (Cartesian basis): | | (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00) | | (B11+B22+B33)/3 = 0.00 | | | | Target ls_wunit_k1: work = 7.568666E-03 free = 7.568666E-03 | |-----------------------------------------------------------------------------| u+s,u,s: 11.33 11.03 0.30 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math, time, sys, os /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math, time, sys, os /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py import mmtbx.model /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/model.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb |-----------------------------------------------------------------------------| |Type| Deviation from ideal | Targets ||Target (sum)|| Deviation of start | | | mean max min | || || model from current | |bond| 0.001 0.002 0.000| 0.039|| || mean max min | |angl| 0.113 0.948 0.004| 0.269|| || | |chir| 0.001 0.003 0.001| 0.000|| 3.295|| undefined | |plan| 0.001 0.001 0.000| 0.031|| || | |dihe| 4.206 23.983 0.067| 1.925|| || | |repu| 4.229 4.899 2.642| 1.032|| || | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |Type| Deviation from ideal | Targets ||Target (sum)|| Deviation of start | | | mean max min | || || model from current | |bond| 0.001 0.002 0.000| 0.039|| || mean max min | |angl| 0.113 0.948 0.004| 0.269|| || | |chir| 0.001 0.003 0.001| 0.000|| 3.295|| 0.000 0.000 0.000| |plan| 0.001 0.001 0.000| 0.031|| || | |dihe| 4.206 23.983 0.067| 1.925|| || | |repu| 4.229 4.899 2.642| 1.032|| || | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |Type| Deviation from ideal | Targets ||Target (sum)|| Deviation of start | | | mean max min | || || model from current | |bond| 0.012 0.412 0.000| 429.074|| || mean max min | |angl| 1.321 35.828 0.004| 195.506|| || | |chir| 0.001 0.003 0.001| 0.000|| 1770.938|| 0.000 0.000 0.000| |plan| 0.020 0.138 0.000| 190.298|| || | |dihe| 10.168 69.790 0.067| 7.337|| || | |repu| 4.052 4.899 0.478| 948.724|| || | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |Type| Deviation from ideal | Targets ||Target (sum)|| Deviation of start | | | mean max min | || || model from current | |bond| 0.001 0.002 0.000| 0.039|| || mean max min | |angl| 0.113 0.948 0.004| 0.269|| || | |chir| 0.001 0.003 0.001| 0.000|| 3.295|| undefined | |plan| 0.001 0.001 0.000| 0.031|| || | |dihe| 4.206 23.983 0.067| 1.925|| || | |repu| 4.229 4.899 2.642| 1.032|| || | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Wilson B = None | | | | Reference model: | Current model: | | min max mean | min max mean | | 0.760 2.240 1.221 | 0.850 1.880 1.187 | | number of B < 1.0: 12 | number of B < 1.0: 10 | | number of B < 100.0: 0 | number of B < 100.0: 0 | | | | Number of anisotropically refinable ADP = 0 out of 33 total | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Wilson B = None | | | | Reference model: | Current model: | | min max mean | min max mean | | 0.850 1.880 1.187 | 0.850 1.880 1.187 | | number of B < 1.0: 10 | number of B < 1.0: 10 | | number of B < 100.0: 0 | number of B < 100.0: 0 | | | | Number of anisotropically refinable ADP = 0 out of 33 total | |-----------------------------------------------------------------------------| libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py import mmtbx.f_model /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/f_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math, time /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/f_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math, time /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:11: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.xplor.map P 1 P 4 C 1 2/c 1 u+s,u,s: 24.88 24.59 0.29 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel_fd.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel_fd.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel_fd.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py import mmtbx.f_model /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/f_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math, time /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/f_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math, time /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:11: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.xplor.map P 1 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P -1 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 1 2 1 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml C 1 2/c 1 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 2 2 2 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml I m m a ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 4 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 41 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml I 41/a c d :2 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 3 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 31 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 3 1 m ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml R -3 c :H ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 6 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 63/m m c ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml P 2 3 ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml I a -3 d ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml Hall: -I 4 2c (1/2*x+1/2*y+1/12,-1/2*x+1/2*y-1/12,z-1/4) ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_k1 lsm_k2 lsm_kunit lsm_k1_fixed lsm_k1ask3_fixed ml u+s,u,s: 270.94 268.38 2.56 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/ncs/tst_restraints.py /net/rosie/scratch1/rwgk/dist/mmtbx/ncs/tst_restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import ncs /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/restraints.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/restraints.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import adptbx u+s,u,s: 0.50 0.46 0.04 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/tst_restraints.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/tst_restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import ncs /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/restraints.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/restraints.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import adptbx /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb u+s,u,s: 2.02 1.91 0.11 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/regression/tst_adp_restraints.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/regression/tst_adp_restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import monomer_library /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import geometry_restraints /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb u+s,u,s: 1.00 0.90 0.10 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/tst_scaling.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/tst_scaling.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/tst_scaling.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import scaling /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/twin_analyses.py:22: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import data_plots very_quick_erf*15000000 optimized=False: 4.34 s very_quick_erf*15000000 optimized=True: 0.24 s quick_ei0*5000000 optimized=False: 1.28 s quick_ei0*5000000 optimized=True: 0.35 s OK libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_cif_types.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.monomer_library import cif_types /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import geometry_restraints /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_motif.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_motif.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.monomer_library import server /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import geometry_restraints /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_selection.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_selection.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import monomer_library /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_tyr_from_gly_and_bnz.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_tyr_from_gly_and_bnz.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import monomer_library /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 12 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 12 Number of chains: 1 Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Time building chain proxies: 0.00, per 1000 atoms: 0.00 Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 12 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 12 Number of chains: 1 Number of residues, atoms: 2, 12 Unusual residues: {'BNZ%bnz_to_tyr_sidechain': 1} Unexpected atoms: {'GLY,CB': 1} Classifications: {'undetermined': 1, 'peptide': 1} Modifications used: {'bnz_to_tyr_sidechain': 1} Link IDs: {'gly_bnz_to_tyr': 1} Number of atoms with unknown nonbonded energy type symbols: 1 " CB GLY 1 " Time building chain proxies: 0.01, per 1000 atoms: 0.83 geo_tyr Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 1.23 - 1.29: 1 1.29 - 1.35: 0 1.35 - 1.41: 7 1.41 - 1.47: 1 1.47 - 1.53: 3 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CD1 TYR 1 " - " CE1 TYR 1 " 1.382 1.394 -0.012 1.11e+03 1.67e-01 " CD2 TYR 1 " - " CE2 TYR 1 " 1.382 1.393 -0.011 1.11e+03 1.31e-01 " CE2 TYR 1 " - " CZ TYR 1 " 1.378 1.386 -0.008 1.74e+03 1.09e-01 " N TYR 1 " - " CA TYR 1 " 1.458 1.453 0.005 2.77e+03 6.34e-02 " CG TYR 1 " - " CD1 TYR 1 " 1.389 1.394 -0.005 2.27e+03 4.84e-02 ... (remaining 7 not shown) Histogram of nonbonded interaction distances: 2.77 - 3.15: 4 3.15 - 3.53: 6 3.53 - 3.90: 8 3.90 - 4.28: 2 4.28 - 4.66: 9 Nonbonded interactions sorted by model distance: atom i - atom j model vdw " CD2 TYR 1 " - " CE1 TYR 1 " 2.772 2.533 " CD1 TYR 1 " - " CE2 TYR 1 " 2.773 2.533 " CG TYR 1 " - " CZ TYR 1 " 2.797 2.267 " C TYR 1 " - " CG TYR 1 " 2.865 2.267 " O TYR 1 " - " CG TYR 1 " 3.226 3.220 ... (remaining 24 not shown) Histogram of dihedral angle deviations from ideal: 9.88 - 10.28: 1 10.28 - 10.68: 0 10.68 - 11.09: 0 11.09 - 11.49: 0 11.49 - 11.89: 1 Dihedral angle restraints sorted by residual: " N TYR 1 " " CA TYR 1 " " CB TYR 1 " " CG TYR 1 " ideal model delta periodicty weight residual 180.00 170.12 9.88 3 4.44e-03 4.34e-01 " CA TYR 1 " " CB TYR 1 " " CG TYR 1 " " CD1 TYR 1 " ideal model delta periodicty weight residual 90.00 78.11 11.89 2 2.50e-03 3.53e-01 target: 4.15715 bond_residual_sum (n=12): 0.630997 nonbonded_residual_sum (n=29): 0.587045 angle_residual_sum (n=15): 0.662897 dihedral_residual_sum (n=2): 0.787227 chirality_residual_sum (n=1): 0.00143684 planarity_residual_sum (n=1): 1.48755 Time first energy calculation (mainly nonbonded setup): 0.00 geo_gly_bnz Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 1.23 - 1.29: 1 1.29 - 1.35: 0 1.35 - 1.41: 7 1.41 - 1.47: 1 1.47 - 1.53: 2 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA GLY 1 " - " C GLY 1 " 1.516 1.527 -0.011 3.09e+03 3.98e-01 " CD1 BNZ 2 " - " CE1 BNZ 2 " 1.382 1.394 -0.012 1.11e+03 1.67e-01 " CD2 BNZ 2 " - " CE2 BNZ 2 " 1.382 1.393 -0.011 1.11e+03 1.31e-01 " CE2 BNZ 2 " - " CZ BNZ 2 " 1.378 1.386 -0.008 1.74e+03 1.09e-01 " CG BNZ 2 " - " CD1 BNZ 2 " 1.389 1.394 -0.005 2.27e+03 4.84e-02 ... (remaining 6 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1 2.15 - 2.78: 5 2.78 - 3.41: 6 3.41 - 4.03: 10 4.03 - 4.66: 11 Nonbonded interactions sorted by model distance: atom i - atom j model vdw " CA GLY 1 " - " CB GLY 1 " 1.529 1.000 " N GLY 1 " - " CB GLY 1 " 2.455 1.000 " C GLY 1 " - " CB GLY 1 " 2.498 1.000 " CA GLY 1 " - " CG BNZ 2 " 2.534 3.400 " CD2 BNZ 2 " - " CE1 BNZ 2 " 2.772 2.533 ... (remaining 28 not shown) Histogram of dihedral angle deviations from ideal: 9.88 - 10.28: 1 10.28 - 10.68: 0 10.68 - 11.09: 0 11.09 - 11.49: 0 11.49 - 11.89: 1 Dihedral angle restraints sorted by residual: " N GLY 1 " " CA GLY 1 " " CB GLY 1 " " CG BNZ 2 " ideal model delta periodicty weight residual 180.00 170.12 9.88 3 4.44e-03 4.34e-01 " CA GLY 1 " " CB GLY 1 " " CG BNZ 2 " " CD1 BNZ 2 " ideal model delta periodicty weight residual 90.00 78.11 11.89 2 2.50e-03 3.53e-01 target: 15.6457 bond_residual_sum (n=11): 0.970446 nonbonded_residual_sum (n=33): 12.4201 angle_residual_sum (n=13): 0.797076 dihedral_residual_sum (n=2): 0.787227 chirality_residual_sum (n=0): 0 planarity_residual_sum (n=1): 0.670882 Time first energy calculation (mainly nonbonded setup): 0.00 TODO: compare geometry restraints OK libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/hydrogens/build_hydrogens.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/hydrogens/build_hydrogens.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import monomer_library /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import geometry_restraints /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/arg.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 12 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 12 Number of chains: 1 Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.03, per 1000 atoms: 2.50 Residue name: ARG%COO ARG Missing hydrogen atoms: ['HE', 'HD2', 'HD1', 'H', 'HG2', 'HG1', 'HH22', 'HH21', 'HH12', 'HH11', 'HA', 'HB1', 'HB2'] missing HE: bond: NE HE bond distance = 0.970 HE: angle: HE NE CZ = 117.900 HE: angle: CD NE HE = 117.900 Building: HE ... missing HD2: bond: CD HD2 bond distance = 0.970 HD2: angle: HD1 CD HD2 = 110.000 HD2: angle: HD2 CD NE = 108.000 HD2: angle: CG CD HD2 = 109.000 Building: HD2 and HD1 missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HG2: bond: CG HG2 bond distance = 0.970 HG2: angle: HG1 CG HG2 = 110.000 HG2: angle: HG2 CG CD = 108.000 HG2: angle: CB CG HG2 = 109.000 Building: HG2 and HG1 missing HH22: bond: NH2 HH22 bond distance = 0.860 HH22: angle: HH21 NH2 HH22 = 120.000 HH22: angle: CZ NH2 HH22 = 120.000 Building: HH22 ... missing HH12: bond: NH1 HH12 bond distance = 0.860 HH12: angle: HH11 NH1 HH12 = 120.000 HH12: angle: CZ NH1 HH12 = 120.000 Building: HH12 ... missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.970 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB CG = 108.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Still missing: ARG ['H'] Build 12 from 13 % = 92.3076923077 ('ARG', ['H']) arg.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 24 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 24 Number of chains: 1 Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 0.42 Number of scatterers: 24 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 2 8.00 N 4 7.00 C 6 6.00 H 12 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 0.86 - 1.00: 10 1.00 - 1.14: 2 1.14 - 1.28: 2 1.28 - 1.42: 3 1.42 - 1.56: 6 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA ARG 1 " - "HA ARG 1 " 0.980 1.062 -0.082 2.50e+03 1.69e+01 " NE ARG 1 " - " CZ ARG 1 " 1.329 1.367 -0.038 5.10e+03 7.42e+00 " CA ARG 1 " - " N ARG 1 " 1.458 1.507 -0.049 2.77e+03 6.52e+00 " NE ARG 1 " - "HE ARG 1 " 0.970 1.010 -0.040 2.50e+03 4.09e+00 " CB ARG 1 " - " CA ARG 1 " 1.530 1.559 -0.029 2.50e+03 2.14e+00 ... (remaining 18 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.68: 27 2.68 - 3.20: 30 3.20 - 3.72: 34 3.72 - 4.24: 26 4.24 - 4.76: 31 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HD2 ARG 1 " - "HH12 ARG 1 " 2.158 2.400 "HE ARG 1 " - "HH21 ARG 1 " 2.266 2.400 "HD1 ARG 1 " - "HG2 ARG 1 " 2.275 1.600 "HE ARG 1 " - "HD1 ARG 1 " 2.285 1.600 "HH22 ARG 1 " - "HH11 ARG 1 " 2.294 2.400 ... (remaining 143 not shown) Histogram of dihedral angle deviations from ideal: 0.15 - 5.55: 6 5.55 - 10.96: 0 10.96 - 16.37: 1 16.37 - 21.78: 0 21.78 - 27.18: 1 Dihedral angle restraints sorted by residual: " OXT ARG 1 " " C ARG 1 " " CA ARG 1 " " N ARG 1 " ideal model delta periodicty weight residual 160.00 132.82 27.18 2 1.11e-03 8.21e-01 " CB ARG 1 " " CG ARG 1 " " CD ARG 1 " " NE ARG 1 " ideal model delta periodicty weight residual 180.00 71.06 -11.06 3 4.44e-03 5.44e-01 " CG ARG 1 " " CB ARG 1 " " CA ARG 1 " " N ARG 1 " ideal model delta periodicty weight residual 60.00 58.02 1.98 3 4.44e-03 1.74e-02 ... (remaining 5 not shown) target: 59.5404 bond_residual_sum (n=23): 43.5818 nonbonded_residual_sum (n=148): 0.401844 angle_residual_sum (n=39): 13.8295 dihedral_residual_sum (n=8): 1.39834 chirality_residual_sum (n=1): 0.245561 planarity_residual_sum (n=2): 0.0833694 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 59.5404 bond_residual_sum (n=23): 43.5818 nonbonded_residual_sum (n=148): 0.401844 angle_residual_sum (n=39): 13.8295 dihedral_residual_sum (n=8): 1.39834 chirality_residual_sum (n=1): 0.245561 planarity_residual_sum (n=2): 0.0833694 norm of gradients: 782.779 Energies after minimization: target: 2.16128 bond_residual_sum (n=23): 0.0230452 nonbonded_residual_sum (n=148): 1.44523 angle_residual_sum (n=39): 0.534692 dihedral_residual_sum (n=8): 0.13943 chirality_residual_sum (n=1): 0.017907 planarity_residual_sum (n=2): 0.00097234 norm of gradients: 9.26042e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/lys.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 10 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 10 Number of chains: 1 Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 2.00 Residue name: LYS%COO LYS Missing hydrogen atoms: ['HE2', 'HD2', 'HD1', 'H', 'HG2', 'HG1', 'HZ1', 'HZ3', 'HZ2', 'HE1', 'HA', 'HB1', 'HB2'] missing HE2: bond: CE HE2 bond distance = 0.970 HE2: angle: HE1 CE HE2 = 110.000 HE2: angle: HE2 CE NZ = 108.000 HE2: angle: CD CE HE2 = 109.000 Building: HE2 and HE1 missing HD2: bond: CD HD2 bond distance = 0.970 HD2: angle: HD1 CD HD2 = 110.000 HD2: angle: HD2 CD CE = 108.000 HD2: angle: CG CD HD2 = 109.000 Building: HD2 and HD1 Building: HD2 and HD1 missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HG2: bond: CG HG2 bond distance = 0.970 HG2: angle: HG1 CG HG2 = 110.000 HG2: angle: HG2 CG CD = 108.000 HG2: angle: CB CG HG2 = 109.000 Building: HG2 and HG1 missing HZ1: bond: NZ HZ1 bond distance = 0.960 HZ1: angle: HZ1 NZ HZ2 = 109.000 HZ1: angle: HZ1 NZ HZ3 = 109.000 HZ1: angle: CE NZ HZ1 = 110.000 Building: HZ1 ... missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.970 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB CG = 108.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Building: HB1 ... Still missing: LYS ['H'] Build 12 from 13 % = 92.3076923077 ('LYS', ['H']) lys.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 25 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 25 Number of chains: 1 Number of residues, atoms: 1, 23 Unexpected atoms: {'LYS%COO,HB3': 1} Duplicate atoms: {'LYS%COO,HB2': 1, 'LYS%COO,HB1': 1} Classifications: {'peptide': 1} Modifications used: {'COO': 1} Number of atoms with unknown scattering type symbols: 3 "HB1 LYS 1 " "HB2 LYS 1 " "HB3 LYS 1 " Number of atoms with unknown nonbonded energy type symbols: 3 "HB1 LYS 1 " "HB2 LYS 1 " "HB3 LYS 1 " Time building chain proxies: 0.01, per 1000 atoms: 0.40 Number of scatterers: 25 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) O 2 8.00 N 2 7.00 C 6 6.00 H 12 1.00 ? 3 0.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.00 seconds Histogram of bond lengths: 0.96 - 1.08: 12 1.08 - 1.20: 0 1.20 - 1.32: 2 1.32 - 1.44: 0 1.44 - 1.55: 7 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA LYS 1 " - " N LYS 1 " 1.458 1.506 -0.048 2.77e+03 6.37e+00 " CA LYS 1 " - "HA LYS 1 " 0.980 1.020 -0.040 2.50e+03 4.08e+00 " CB LYS 1 " - " CA LYS 1 " 1.530 1.555 -0.025 2.50e+03 1.52e+00 " C LYS 1 " - " OXT LYS 1 " 1.231 1.250 -0.019 2.50e+03 8.82e-01 " C LYS 1 " - " O LYS 1 " 1.231 1.249 -0.018 2.50e+03 8.33e-01 ... (remaining 16 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.56: 9 1.56 - 2.36: 25 2.36 - 3.17: 59 3.17 - 3.97: 48 3.97 - 4.78: 41 Warning: very small nonbonded interaction distances. Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HB1 LYS 1 " - "HB2 LYS 1 " 0.754 1.000 "HB2 LYS 1 " - "HB1 LYS 1 " 0.795 1.000 " CB LYS 1 " - "HB1 LYS 1 " 0.970 1.000 " CB LYS 1 " - "HB2 LYS 1 " 0.970 1.000 " CB LYS 1 " - "HB3 LYS 1 " 0.971 1.000 ... (remaining 177 not shown) Histogram of dihedral angle deviations from ideal: 0.22 - 7.96: 1 7.96 - 15.70: 3 15.70 - 23.45: 0 23.45 - 31.19: 1 31.19 - 38.93: 1 Dihedral angle restraints sorted by residual: " CD LYS 1 " " CE LYS 1 " " NZ LYS 1 " "HZ3 LYS 1 " ideal model delta periodicty weight residual 60.00 141.07 38.93 3 1.11e-03 1.68e+00 " OXT LYS 1 " " C LYS 1 " " CA LYS 1 " " N LYS 1 " ideal model delta periodicty weight residual 160.00 -49.77 29.77 2 1.11e-03 9.85e-01 " CA LYS 1 " " CB LYS 1 " " CG LYS 1 " " CD LYS 1 " ideal model delta periodicty weight residual 180.00 -73.50 13.50 3 4.44e-03 8.10e-01 ... (remaining 3 not shown) target: 27.5582 bond_residual_sum (n=21): 14.692 nonbonded_residual_sum (n=182): 0.0935827 angle_residual_sum (n=39): 7.55969 dihedral_residual_sum (n=6): 4.52202 chirality_residual_sum (n=1): 0.690449 planarity_residual_sum (n=1): 0.000506488 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 27.5582 bond_residual_sum (n=21): 14.692 nonbonded_residual_sum (n=182): 0.0935827 angle_residual_sum (n=39): 7.55969 dihedral_residual_sum (n=6): 4.52202 chirality_residual_sum (n=1): 0.690449 planarity_residual_sum (n=1): 0.000506488 norm of gradients: 484.198 Energies after minimization: target: 0.606765 bond_residual_sum (n=21): 0.00276302 nonbonded_residual_sum (n=182): 0.14388 angle_residual_sum (n=39): 0.377241 dihedral_residual_sum (n=6): 0.0617973 chirality_residual_sum (n=1): 0.0210834 planarity_residual_sum (n=1): 7.2611e-15 norm of gradients: 1.56354e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/ala.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 6 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 6 Number of chains: 1 Number of residues, atoms: 1, 6 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 1.67 Residue name: ALA%COO ALA Missing hydrogen atoms: ['H', 'HA', 'HB1', 'HB3', 'HB2'] missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.960 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB HB3 = 110.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Building: HB1 and HB2 Building: HB1 and HB2 Building: HB1 ... Still missing: ALA ['H'] Build 4 from 5 % = 80.0 ('ALA', ['H']) ala.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 10 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 10 Number of chains: 1 Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.00, per 1000 atoms: 0.00 Number of scatterers: 10 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 2 8.00 N 1 7.00 C 3 6.00 H 4 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 0.96 - 1.07: 4 1.07 - 1.19: 0 1.19 - 1.30: 2 1.30 - 1.42: 0 1.42 - 1.53: 3 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA ALA 1 " - "HA ALA 1 " 0.980 1.050 -0.070 2.50e+03 1.23e+01 " CA ALA 1 " - " N ALA 1 " 1.458 1.503 -0.045 2.77e+03 5.55e+00 " C ALA 1 " - " OXT ALA 1 " 1.231 1.250 -0.019 2.50e+03 9.41e-01 " C ALA 1 " - " O ALA 1 " 1.231 1.249 -0.018 2.50e+03 7.81e-01 " C ALA 1 " - " CA ALA 1 " 1.525 1.534 -0.009 2.27e+03 1.75e-01 ... (remaining 4 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.68: 5 2.68 - 3.05: 5 3.05 - 3.43: 6 3.43 - 3.81: 3 3.81 - 4.19: 2 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HA ALA 1 " - "HB3 ALA 1 " 2.298 1.600 " OXT ALA 1 " - "HA ALA 1 " 2.457 1.813 "HA ALA 1 " - "HB1 ALA 1 " 2.473 1.600 " N ALA 1 " - "HB1 ALA 1 " 2.586 1.833 " C ALA 1 " - "HB2 ALA 1 " 2.615 1.933 ... (remaining 16 not shown) Histogram of dihedral angle deviations from ideal: 16.71 - 19.19: 1 19.19 - 21.67: 0 21.67 - 24.15: 0 24.15 - 26.63: 0 26.63 - 29.11: 1 Dihedral angle restraints sorted by residual: " N ALA 1 " " CB ALA 1 " " CA ALA 1 " "HB3 ALA 1 " ideal model delta periodicty weight residual -60.00 163.29 16.71 3 4.44e-03 1.24e+00 " OXT ALA 1 " " C ALA 1 " " CA ALA 1 " " N ALA 1 " ideal model delta periodicty weight residual 160.00 130.89 29.11 2 1.11e-03 9.42e-01 target: 28.6918 bond_residual_sum (n=9): 19.9062 nonbonded_residual_sum (n=21): 0 angle_residual_sum (n=15): 6.41999 dihedral_residual_sum (n=2): 2.18223 chirality_residual_sum (n=1): 0.183373 planarity_residual_sum (n=1): 1.80044e-05 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 28.6918 bond_residual_sum (n=9): 19.9062 nonbonded_residual_sum (n=21): 0 angle_residual_sum (n=15): 6.41999 dihedral_residual_sum (n=2): 2.18223 chirality_residual_sum (n=1): 0.183373 planarity_residual_sum (n=1): 1.80044e-05 norm of gradients: 591.226 Energies after minimization: target: 0.306869 bond_residual_sum (n=9): 0.00245699 nonbonded_residual_sum (n=21): 0 angle_residual_sum (n=15): 0.285572 dihedral_residual_sum (n=2): 7.20081e-13 chirality_residual_sum (n=1): 0.0188403 planarity_residual_sum (n=1): 3.60129e-17 norm of gradients: 8.87014e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/gly.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 5 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 5 Number of chains: 1 Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.00, per 1000 atoms: 0.00 Residue name: GLY%COO GLY Missing hydrogen atoms: ['H', 'HA2', 'HA1'] missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HA2: bond: CA HA2 bond distance = 0.970 HA2: angle: HA1 CA HA2 = 109.000 HA2: angle: HA2 CA C = 109.000 HA2: angle: N CA HA2 = 110.000 Building: HA1 and HA2 Still missing: GLY ['H'] Build 2 from 3 % = 66.6666666667 ('GLY', ['H']) gly.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 7 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 7 Number of chains: 1 Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Number of resolved scattering type symbol conflicts: 2 Time building chain proxies: 0.01, per 1000 atoms: 1.43 Number of scatterers: 7 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 2 8.00 N 1 7.00 C 2 6.00 H 2 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.00 seconds Histogram of bond lengths: 0.97 - 1.08: 2 1.08 - 1.19: 0 1.19 - 1.30: 2 1.30 - 1.41: 0 1.41 - 1.52: 2 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA GLY 1 " - " N GLY 1 " 1.451 1.491 -0.040 3.91e+03 6.31e+00 " C GLY 1 " - " O GLY 1 " 1.231 1.250 -0.019 2.50e+03 8.56e-01 " OXT GLY 1 " - " C GLY 1 " 1.231 1.249 -0.018 2.50e+03 7.95e-01 " C GLY 1 " - " CA GLY 1 " 1.516 1.524 -0.008 3.09e+03 2.10e-01 " CA GLY 1 " - "HA2 GLY 1 " 0.970 0.970 0.000 2.50e+03 4.41e-04 " CA GLY 1 " - "HA1 GLY 1 " 0.970 0.970 -0.000 2.50e+03 3.54e-05 Histogram of nonbonded interaction distances: 2.43 - 2.63: 1 2.63 - 2.83: 1 2.83 - 3.03: 2 3.03 - 3.22: 1 3.22 - 3.42: 1 Nonbonded interactions sorted by model distance: atom i - atom j model vdw " OXT GLY 1 " - "HA2 GLY 1 " 2.435 1.813 " O GLY 1 " - "HA1 GLY 1 " 2.646 1.813 " O GLY 1 " - " N GLY 1 " 2.924 2.167 " OXT GLY 1 " - "HA1 GLY 1 " 2.983 1.813 " O GLY 1 " - "HA2 GLY 1 " 3.158 1.813 " OXT GLY 1 " - " N GLY 1 " 3.421 2.167 Histogram of dihedral angle deviations from ideal: 39.17 - 39.17: 1 39.17 - 39.17: 0 39.17 - 39.17: 0 39.17 - 39.17: 0 39.17 - 39.17: 0 Dihedral angle restraints sorted by residual: " OXT GLY 1 " " C GLY 1 " " CA GLY 1 " " N GLY 1 " ideal model delta periodicty weight residual 160.00 120.83 39.17 2 1.11e-03 1.70e+00 target: 16.1071 bond_residual_sum (n=6): 8.17073 nonbonded_residual_sum (n=6): 0 angle_residual_sum (n=9): 6.23143 dihedral_residual_sum (n=1): 1.7049 chirality_residual_sum (n=0): 0 planarity_residual_sum (n=1): 2.26356e-05 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 16.1071 bond_residual_sum (n=6): 8.17073 nonbonded_residual_sum (n=6): 0 angle_residual_sum (n=9): 6.23143 dihedral_residual_sum (n=1): 1.7049 chirality_residual_sum (n=0): 0 planarity_residual_sum (n=1): 2.26356e-05 norm of gradients: 488.772 Energies after minimization: target: 0.13971 bond_residual_sum (n=6): 2.73651e-15 nonbonded_residual_sum (n=6): 0 angle_residual_sum (n=9): 0.13971 dihedral_residual_sum (n=1): 1.01096e-14 chirality_residual_sum (n=0): 0 planarity_residual_sum (n=1): 5.29595e-16 norm of gradients: 8.47466e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/his.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 11 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 11 Number of chains: 1 Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 1.82 Residue name: HIS%COO HIS Missing hydrogen atoms: ['HE2', 'HE1', 'HD1', 'H', 'HD2', 'HA', 'HB1', 'HB2'] missing HE2: bond: NE2 HE2 bond distance = 0.860 HE2: angle: HE2 NE2 CD2 = 125.500 HE2: angle: CE1 NE2 HE2 = 125.500 Building: HE2 ... missing HE1: bond: CE1 HE1 bond distance = 0.930 HE1: angle: HE1 CE1 NE2 = 125.800 HE1: angle: ND1 CE1 HE1 = 125.800 Building: HE1 ... missing HD1: bond: ND1 HD1 bond distance = 0.860 HD1: angle: HD1 ND1 CE1 = 125.350 HD1: angle: CG ND1 HD1 = 125.350 Building: HD1 ... missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HD2: bond: CD2 HD2 bond distance = 0.930 HD2: angle: NE2 CD2 HD2 = 126.400 HD2: angle: CG CD2 HD2 = 126.400 Building: HD2 ... missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.970 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB CG = 108.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Still missing: HIS ['H'] Build 7 from 8 % = 87.5 ('HIS', ['H']) his.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 18 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 18 Number of chains: 1 Number of residues, atoms: 1, 18 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 1.11 Number of scatterers: 18 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 2 8.00 N 3 7.00 C 6 6.00 H 7 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.00 seconds Histogram of bond lengths: 0.86 - 1.00: 6 1.00 - 1.14: 1 1.14 - 1.28: 2 1.28 - 1.42: 5 1.42 - 1.56: 4 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA HIS 1 " - " N HIS 1 " 1.458 1.505 -0.047 2.77e+03 6.20e+00 " CA HIS 1 " - "HA HIS 1 " 0.980 1.028 -0.048 2.50e+03 5.66e+00 " CB HIS 1 " - " CA HIS 1 " 1.530 1.557 -0.027 2.50e+03 1.76e+00 " C HIS 1 " - " OXT HIS 1 " 1.231 1.250 -0.019 2.50e+03 9.07e-01 " C HIS 1 " - " O HIS 1 " 1.231 1.249 -0.018 2.50e+03 7.83e-01 ... (remaining 13 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.85: 14 2.85 - 3.33: 19 3.33 - 3.82: 21 3.82 - 4.30: 13 4.30 - 4.79: 15 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HE1 HIS 1 " - "HD1 HIS 1 " 2.363 1.600 "HE2 HIS 1 " - "HE1 HIS 1 " 2.364 1.600 "HE2 HIS 1 " - "HD2 HIS 1 " 2.426 1.600 " OXT HIS 1 " - "HA HIS 1 " 2.462 1.813 "HD1 HIS 1 " - "HB1 HIS 1 " 2.486 2.400 ... (remaining 77 not shown) Histogram of dihedral angle deviations from ideal: 19.37 - 21.37: 2 21.37 - 23.36: 0 23.36 - 25.35: 0 25.35 - 27.35: 0 27.35 - 29.34: 1 Dihedral angle restraints sorted by residual: " CG HIS 1 " " CB HIS 1 " " CA HIS 1 " " N HIS 1 " ideal model delta periodicty weight residual 180.00 -160.63 -19.37 3 4.44e-03 1.67e+00 " CA HIS 1 " " CB HIS 1 " " CG HIS 1 " " ND1 HIS 1 " ideal model delta periodicty weight residual 90.00 110.09 -20.09 2 2.50e-03 1.01e+00 " OXT HIS 1 " " C HIS 1 " " CA HIS 1 " " N HIS 1 " ideal model delta periodicty weight residual 160.00 130.66 29.34 2 1.11e-03 9.57e-01 target: 27.8228 bond_residual_sum (n=18): 16.2986 nonbonded_residual_sum (n=82): 0 angle_residual_sum (n=30): 7.23089 dihedral_residual_sum (n=3): 3.63384 chirality_residual_sum (n=1): 0.646547 planarity_residual_sum (n=2): 0.0129392 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 27.8228 bond_residual_sum (n=18): 16.2986 nonbonded_residual_sum (n=82): 0 angle_residual_sum (n=30): 7.23089 dihedral_residual_sum (n=3): 3.63384 chirality_residual_sum (n=1): 0.646547 planarity_residual_sum (n=2): 0.0129392 norm of gradients: 494.121 Energies after minimization: target: 0.310556 bond_residual_sum (n=18): 0.00295388 nonbonded_residual_sum (n=82): 0.0216123 angle_residual_sum (n=30): 0.253279 dihedral_residual_sum (n=3): 0.0122131 chirality_residual_sum (n=1): 0.0204814 planarity_residual_sum (n=2): 1.70664e-05 norm of gradients: 1.564e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/ile.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 9 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 9 Number of chains: 1 Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 2.22 Residue name: ILE%COO ILE Missing hydrogen atoms: ['HG22', 'H', 'HG21', 'HG11', 'HG12', 'HD13', 'HB', 'HD12', 'HD11', 'HA', 'HG23'] missing HG22: bond: CG2 HG22 bond distance = 0.960 HG22: angle: HG21 CG2 HG22 = 110.000 HG22: angle: HG22 CG2 HG23 = 110.000 HG22: angle: CB CG2 HG22 = 109.000 Building: HG22 ... missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HG11: bond: CG1 HG11 bond distance = 0.970 HG11: angle: HG11 CG1 HG12 = 110.000 HG11: angle: HG11 CG1 CD1 = 108.000 HG11: angle: CB CG1 HG11 = 109.000 Building: HG11 ... missing HD13: bond: CD1 HD13 bond distance = 0.960 HD13: angle: HD12 CD1 HD13 = 110.000 HD13: angle: HD11 CD1 HD13 = 110.000 HD13: angle: CG1 CD1 HD13 = 109.000 Building: HD13 ... missing HB: bond: CB HB bond distance = 0.970 HB: angle: HB CB CG1 = 109.000 HB: angle: HB CB CG2 = 109.000 HB: angle: CA CB HB = 109.000 Building: HB missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA Still missing: ILE ['H'] Build 10 from 11 % = 90.9090909091 ('ILE', ['H']) ile.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 20 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 20 Number of chains: 1 Number of residues, atoms: 1, 20 Unexpected atoms: {'ILE%COO,HG13': 1} Classifications: {'peptide': 1} Modifications used: {'COO': 1} Number of atoms with unknown scattering type symbols: 1 "HG13 ILE 1 " Number of atoms with unknown nonbonded energy type symbols: 1 "HG13 ILE 1 " Time building chain proxies: 0.01, per 1000 atoms: 0.50 Number of scatterers: 20 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) O 2 8.00 N 1 7.00 C 6 6.00 H 10 1.00 ? 1 0.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 0.96 - 1.09: 9 1.09 - 1.21: 1 1.21 - 1.34: 2 1.34 - 1.46: 0 1.46 - 1.59: 6 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA ILE 1 " - "HA ILE 1 " 0.980 1.117 -0.137 2.50e+03 4.71e+01 " CB ILE 1 " - "HB ILE 1 " 0.970 1.035 -0.065 2.50e+03 1.07e+01 " CA ILE 1 " - " N ILE 1 " 1.458 1.506 -0.048 2.77e+03 6.33e+00 " CB ILE 1 " - " CA ILE 1 " 1.540 1.588 -0.048 1.37e+03 3.18e+00 " CB ILE 1 " - " CG1 ILE 1 " 1.530 1.565 -0.035 2.50e+03 3.08e+00 ... (remaining 13 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.74: 6 1.74 - 2.50: 8 2.50 - 3.27: 44 3.27 - 4.04: 42 4.04 - 4.80: 31 Warning: very small nonbonded interaction distances. Nonbonded interactions sorted by model distance: atom i - atom j model vdw " CG1 ILE 1 " - "HG13 ILE 1 " 0.970 1.000 "HG12 ILE 1 " - "HD11 ILE 1 " 1.196 1.600 "HG12 ILE 1 " - "HD12 ILE 1 " 1.284 1.600 "HG12 ILE 1 " - "HD13 ILE 1 " 1.320 1.600 "HG12 ILE 1 " - "HG13 ILE 1 " 1.577 1.000 ... (remaining 126 not shown) Histogram of dihedral angle deviations from ideal: 1.23 - 9.85: 1 9.85 - 18.48: 2 18.48 - 27.10: 1 27.10 - 35.72: 0 35.72 - 44.34: 1 Dihedral angle restraints sorted by residual: " CB ILE 1 " " CD1 ILE 1 " " CG1 ILE 1 " "HD13 ILE 1 " ideal model delta periodicty weight residual -60.00 104.34 -44.34 3 1.11e-03 2.18e+00 " CA ILE 1 " " CB ILE 1 " " CG1 ILE 1 " " CD1 ILE 1 " ideal model delta periodicty weight residual 180.00 74.80 -14.80 3 4.44e-03 9.73e-01 " N ILE 1 " " CB ILE 1 " " CA ILE 1 " " CG2 ILE 1 " ideal model delta periodicty weight residual -180.00 73.35 -13.35 3 4.44e-03 7.92e-01 ... (remaining 2 not shown) target: 1250.78 bond_residual_sum (n=18): 73.4561 nonbonded_residual_sum (n=131): 1.78373 angle_residual_sum (n=33): 1170.92 dihedral_residual_sum (n=5): 4.36609 chirality_residual_sum (n=2): 0.254482 planarity_residual_sum (n=1): 6.19818e-05 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 1250.78 bond_residual_sum (n=18): 73.4561 nonbonded_residual_sum (n=131): 1.78373 angle_residual_sum (n=33): 1170.92 dihedral_residual_sum (n=5): 4.36609 chirality_residual_sum (n=2): 0.254482 planarity_residual_sum (n=1): 6.19818e-05 norm of gradients: 1975.1 Energies after minimization: target: 468.73 bond_residual_sum (n=18): 0.100701 nonbonded_residual_sum (n=131): 3.04479 angle_residual_sum (n=33): 463.605 dihedral_residual_sum (n=5): 1.96075 chirality_residual_sum (n=2): 0.0181844 planarity_residual_sum (n=1): 0.000934329 norm of gradients: 3.32362e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/leu.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 9 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 9 Number of chains: 1 Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 2.22 Residue name: LEU%COO LEU Missing hydrogen atoms: ['HD22', 'HD23', 'HD21', 'H', 'HD13', 'HD12', 'HD11', 'HA', 'HB1', 'HG', 'HB2'] missing HD22: bond: CD2 HD22 bond distance = 0.960 HD22: angle: HD21 CD2 HD22 = 110.000 HD22: angle: HD22 CD2 HD23 = 110.000 HD22: angle: CG CD2 HD22 = 109.000 Building: HD22 ... missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HD13: bond: CD1 HD13 bond distance = 0.960 HD13: angle: HD12 CD1 HD13 = 110.000 HD13: angle: HD11 CD1 HD13 = 110.000 HD13: angle: CG CD1 HD13 = 109.000 Building: HD13 ... missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.970 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB CG = 108.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Building: HB1 ... missing HG: bond: CG HG bond distance = 0.970 HG: angle: HG CG CD1 = 108.000 HG: angle: HG CG CD2 = 108.000 HG: angle: CB CG HG = 109.000 Building: HG Still missing: LEU ['H'] Build 10 from 11 % = 90.9090909091 ('LEU', ['H']) leu.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 22 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 22 Number of chains: 1 Number of residues, atoms: 1, 20 Unexpected atoms: {'LEU%COO,HB3': 1} Duplicate atoms: {'LEU%COO,HB1': 1, 'LEU%COO,HB2': 1} Classifications: {'peptide': 1} Modifications used: {'COO': 1} Number of resolved scattering type symbol conflicts: 10 Number of atoms with unknown nonbonded energy type symbols: 3 "HB1 LEU 1 " "HB2 LEU 1 " "HB3 LEU 1 " Time building chain proxies: 0.01, per 1000 atoms: 0.45 Number of scatterers: 22 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 2 8.00 N 1 7.00 C 9 6.00 H 10 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 0.96 - 1.08: 10 1.08 - 1.20: 0 1.20 - 1.32: 2 1.32 - 1.44: 0 1.44 - 1.56: 6 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CG LEU 1 " - "HG LEU 1 " 0.970 1.055 -0.085 2.50e+03 1.81e+01 " CA LEU 1 " - "HA LEU 1 " 0.980 1.032 -0.052 2.50e+03 6.72e+00 " CA LEU 1 " - " N LEU 1 " 1.458 1.503 -0.045 2.77e+03 5.52e+00 " CB LEU 1 " - " CG LEU 1 " 1.530 1.565 -0.035 2.50e+03 2.99e+00 " CB LEU 1 " - " CA LEU 1 " 1.530 1.563 -0.033 2.50e+03 2.68e+00 ... (remaining 13 not shown) Histogram of nonbonded interaction distances: 0.02 - 0.98: 6 0.98 - 1.94: 10 1.94 - 2.91: 57 2.91 - 3.87: 63 3.87 - 4.83: 30 Warning: very small nonbonded interaction distances. Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HB1 LEU 1 " - "HB2 LEU 1 " 0.021 1.000 "HB2 LEU 1 " - "HB3 LEU 1 " 0.143 1.000 " CG LEU 1 " - "HB1 LEU 1 " 0.630 1.000 " CB LEU 1 " - "HB2 LEU 1 " 0.970 1.000 " CB LEU 1 " - "HB3 LEU 1 " 0.970 1.000 ... (remaining 161 not shown) Histogram of dihedral angle deviations from ideal: 1.70 - 7.51: 1 7.51 - 13.31: 0 13.31 - 19.11: 1 19.11 - 24.92: 1 24.92 - 30.72: 2 Dihedral angle restraints sorted by residual: " CA LEU 1 " " CB LEU 1 " " CG LEU 1 " " CD2 LEU 1 " ideal model delta periodicty weight residual 180.00 82.11 -22.11 3 4.44e-03 2.17e+00 " CB LEU 1 " " CG LEU 1 " " CD2 LEU 1 " "HD23 LEU 1 " ideal model delta periodicty weight residual 60.00 149.28 30.72 3 1.11e-03 1.05e+00 " OXT LEU 1 " " C LEU 1 " " CA LEU 1 " " N LEU 1 " ideal model delta periodicty weight residual 160.00 130.57 29.43 2 1.11e-03 9.62e-01 ... (remaining 2 not shown) target: 81.9297 bond_residual_sum (n=18): 38.4452 nonbonded_residual_sum (n=166): 24.0123 angle_residual_sum (n=33): 14.3639 dihedral_residual_sum (n=5): 4.4702 chirality_residual_sum (n=2): 0.637222 planarity_residual_sum (n=1): 0.000879497 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 81.9297 bond_residual_sum (n=18): 38.4452 nonbonded_residual_sum (n=166): 24.0123 angle_residual_sum (n=33): 14.3639 dihedral_residual_sum (n=5): 4.4702 chirality_residual_sum (n=2): 0.637222 planarity_residual_sum (n=1): 0.000879497 norm of gradients: 807.361 Energies after minimization: target: 3.70968 bond_residual_sum (n=18): 0.026014 nonbonded_residual_sum (n=166): 1.47424 angle_residual_sum (n=33): 0.873991 dihedral_residual_sum (n=5): 1.31309 chirality_residual_sum (n=2): 0.0223345 planarity_residual_sum (n=1): 1.58556e-15 norm of gradients: 1.76535e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/phe.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 12 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 12 Number of chains: 1 Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 1.67 Residue name: PHE%COO PHE Missing hydrogen atoms: ['HZ', 'HE2', 'HE1', 'HD1', 'H', 'HD2', 'HA', 'HB1', 'HB2'] missing HZ: bond: CZ HZ bond distance = 0.930 HZ: angle: HZ CZ CE2 = 120.000 HZ: angle: CE1 CZ HZ = 120.000 Building: HZ ... missing HE2: bond: CE2 HE2 bond distance = 0.930 HE2: angle: HE2 CE2 CD2 = 120.000 HE2: angle: CZ CE2 HE2 = 120.000 Building: HE2 ... missing HE1: bond: CE1 HE1 bond distance = 0.930 HE1: angle: HE1 CE1 CZ = 120.000 HE1: angle: CD1 CE1 HE1 = 120.000 Building: HE1 ... missing HD1: bond: CD1 HD1 bond distance = 0.930 HD1: angle: HD1 CD1 CE1 = 119.650 HD1: angle: CG CD1 HD1 = 119.650 Building: HD1 ... missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HD2: bond: CD2 HD2 bond distance = 0.930 HD2: angle: CG CD2 HD2 = 119.650 HD2: angle: CE2 CD2 HD2 = 119.650 Building: HD2 ... missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.970 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB CG = 108.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Still missing: PHE ['H'] Build 8 from 9 % = 88.8888888889 ('PHE', ['H']) phe.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 20 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 20 Number of chains: 1 Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 0.50 Number of scatterers: 20 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 2 8.00 N 1 7.00 C 9 6.00 H 8 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 0.92 - 1.05: 8 1.05 - 1.17: 0 1.17 - 1.29: 2 1.29 - 1.41: 1 1.41 - 1.53: 9 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA PHE 1 " - " N PHE 1 " 1.458 1.491 -0.033 2.77e+03 3.05e+00 " CD2 PHE 1 " - " CE2 PHE 1 " 1.382 1.430 -0.048 1.11e+03 2.53e+00 " CD1 PHE 1 " - " CE1 PHE 1 " 1.382 1.430 -0.048 1.11e+03 2.51e+00 " CG PHE 1 " - " CD1 PHE 1 " 1.384 1.414 -0.030 2.27e+03 2.04e+00 " CA PHE 1 " - "HA PHE 1 " 0.980 1.008 -0.028 2.50e+03 1.92e+00 ... (remaining 15 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.83: 19 2.83 - 3.32: 25 3.32 - 3.81: 16 3.81 - 4.31: 11 4.31 - 4.80: 25 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HD2 PHE 1 " - "HB2 PHE 1 " 2.341 2.400 "HZ PHE 1 " - "HE1 PHE 1 " 2.353 1.600 "HZ PHE 1 " - "HE2 PHE 1 " 2.353 1.600 "HE1 PHE 1 " - "HD1 PHE 1 " 2.354 1.600 "HE2 PHE 1 " - "HD2 PHE 1 " 2.354 1.600 ... (remaining 91 not shown) Histogram of dihedral angle deviations from ideal: 1.50 - 9.03: 1 9.03 - 16.57: 0 16.57 - 24.10: 1 24.10 - 31.64: 0 31.64 - 39.17: 1 Dihedral angle restraints sorted by residual: " OXT PHE 1 " " C PHE 1 " " CA PHE 1 " " N PHE 1 " ideal model delta periodicty weight residual 160.00 120.83 39.17 2 1.11e-03 1.70e+00 " CA PHE 1 " " CB PHE 1 " " CG PHE 1 " " CD1 PHE 1 " ideal model delta periodicty weight residual 90.00 70.30 19.70 2 2.50e-03 9.71e-01 " CG PHE 1 " " CB PHE 1 " " CA PHE 1 " " N PHE 1 " ideal model delta periodicty weight residual 180.00 -61.50 1.50 3 4.44e-03 9.94e-03 target: 30.4027 bond_residual_sum (n=20): 19.3992 nonbonded_residual_sum (n=96): 1.39216 angle_residual_sum (n=33): 6.61389 dihedral_residual_sum (n=3): 2.68534 chirality_residual_sum (n=1): 0.311507 planarity_residual_sum (n=2): 0.000673786 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 30.4027 bond_residual_sum (n=20): 19.3992 nonbonded_residual_sum (n=96): 1.39216 angle_residual_sum (n=33): 6.61389 dihedral_residual_sum (n=3): 2.68534 chirality_residual_sum (n=1): 0.311507 planarity_residual_sum (n=2): 0.000673786 norm of gradients: 455.299 Energies after minimization: target: 0.424633 bond_residual_sum (n=20): 0.0121589 nonbonded_residual_sum (n=95): 0.0862652 angle_residual_sum (n=33): 0.269303 dihedral_residual_sum (n=3): 0.0381779 chirality_residual_sum (n=1): 0.0187277 planarity_residual_sum (n=2): 3.11324e-14 norm of gradients: 1.42258e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/tyr.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 13 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 13 Number of chains: 1 Number of residues, atoms: 1, 13 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 1.54 Residue name: TYR%COO TYR Missing hydrogen atoms: ['HE2', 'HE1', 'HD1', 'H', 'HH', 'HD2', 'HA', 'HB1', 'HB2'] missing HE2: bond: CE2 HE2 bond distance = 0.930 HE2: angle: HE2 CE2 CD2 = 120.200 HE2: angle: CZ CE2 HE2 = 120.200 Building: HE2 ... missing HE1: bond: CE1 HE1 bond distance = 0.930 HE1: angle: HE1 CE1 CZ = 120.200 HE1: angle: CD1 CE1 HE1 = 120.200 Building: HE1 ... missing HD1: bond: CD1 HD1 bond distance = 0.930 HD1: angle: HD1 CD1 CE1 = 119.400 HD1: angle: CG CD1 HD1 = 119.400 Building: HD1 ... missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HH: bond: OH HH bond distance = 0.820 HH: angle: CZ OH HH = 110.000 Building: HH ... missing HD2: bond: CD2 HD2 bond distance = 0.930 HD2: angle: HD2 CD2 CE2 = 119.400 HD2: angle: CG CD2 HD2 = 119.400 Building: HD2 ... missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.970 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB CG = 108.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Still missing: TYR ['H'] Build 8 from 9 % = 88.8888888889 ('TYR', ['H']) tyr.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 21 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 21 Number of chains: 1 Number of residues, atoms: 1, 21 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 0.95 Number of scatterers: 21 At special positions: 0 Unit cell: (72.24, 72.01, 86.99, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 3 8.00 N 1 7.00 C 9 6.00 H 8 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 0.82 - 0.97: 5 0.97 - 1.11: 3 1.11 - 1.26: 2 1.26 - 1.40: 1 1.40 - 1.55: 10 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA TYR 1 " - " N TYR 1 " 1.458 1.507 -0.049 2.77e+03 6.73e+00 " CA TYR 1 " - "HA TYR 1 " 0.980 1.021 -0.041 2.50e+03 4.14e+00 " CD2 TYR 1 " - " CG TYR 1 " 1.389 1.429 -0.040 2.27e+03 3.69e+00 " CG TYR 1 " - " CD1 TYR 1 " 1.389 1.429 -0.040 2.27e+03 3.65e+00 " CZ TYR 1 " - " CE2 TYR 1 " 1.378 1.414 -0.036 1.74e+03 2.22e+00 ... (remaining 16 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.77: 17 2.77 - 3.28: 16 3.28 - 3.78: 28 3.78 - 4.28: 13 4.28 - 4.78: 25 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HE2 TYR 1 " - "HH TYR 1 " 2.274 2.400 "HE1 TYR 1 " - "HD1 TYR 1 " 2.340 1.600 "HE2 TYR 1 " - "HD2 TYR 1 " 2.341 1.600 " CE2 TYR 1 " - "HH TYR 1 " 2.402 1.933 "HA TYR 1 " - "HB2 TYR 1 " 2.442 1.600 ... (remaining 94 not shown) Histogram of dihedral angle deviations from ideal: 4.49 - 15.60: 2 15.60 - 26.70: 0 26.70 - 37.81: 1 37.81 - 48.92: 0 48.92 - 60.03: 1 Dihedral angle restraints sorted by residual: " CE1 TYR 1 " " OH TYR 1 " " CZ TYR 1 " "HH TYR 1 " ideal model delta periodicty weight residual -60.00 -179.97 -60.03 2 1.11e-03 4.00e+00 " OXT TYR 1 " " C TYR 1 " " CA TYR 1 " " N TYR 1 " ideal model delta periodicty weight residual 160.00 -49.67 29.67 2 1.11e-03 9.78e-01 " CG TYR 1 " " CB TYR 1 " " CA TYR 1 " " N TYR 1 " ideal model delta periodicty weight residual 180.00 -68.78 8.78 3 4.44e-03 3.42e-01 " CA TYR 1 " " CB TYR 1 " " CG TYR 1 " " CD1 TYR 1 " ideal model delta periodicty weight residual 90.00 -85.51 -4.49 2 2.50e-03 5.04e-02 target: 40.7025 bond_residual_sum (n=21): 28.8817 nonbonded_residual_sum (n=99): 0.00767341 angle_residual_sum (n=34): 5.73976 dihedral_residual_sum (n=4): 5.37431 chirality_residual_sum (n=1): 0.660392 planarity_residual_sum (n=2): 0.0386784 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 40.7025 bond_residual_sum (n=21): 28.8817 nonbonded_residual_sum (n=99): 0.00767341 angle_residual_sum (n=34): 5.73976 dihedral_residual_sum (n=4): 5.37431 chirality_residual_sum (n=1): 0.660392 planarity_residual_sum (n=2): 0.0386784 norm of gradients: 573.519 Energies after minimization: target: 0.403008 bond_residual_sum (n=21): 0.00376556 nonbonded_residual_sum (n=99): 0.0746504 angle_residual_sum (n=34): 0.274608 dihedral_residual_sum (n=4): 0.0305242 chirality_residual_sum (n=1): 0.0187801 planarity_residual_sum (n=2): 0.000680611 norm of gradients: 1.15053e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/trp.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 15 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 15 Number of chains: 1 Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 1.33 Residue name: TRP%COO TRP Missing hydrogen atoms: ['HH2', 'HE1', 'HD1', 'HE3', 'H', 'HZ3', 'HZ2', 'HA', 'HB1', 'HB2'] missing HH2: bond: CH2 HH2 bond distance = 0.930 HH2: angle: HH2 CH2 CZ2 = 119.250 HH2: angle: CZ3 CH2 HH2 = 119.250 Building: HH2 ... missing HE1: bond: NE1 HE1 bond distance = 0.860 HE1: angle: HE1 NE1 CE2 = 125.550 HE1: angle: CD1 NE1 HE1 = 125.550 Building: HE1 ... missing HD1: bond: CD1 HD1 bond distance = 0.930 HD1: angle: HD1 CD1 NE1 = 124.900 HD1: angle: CG CD1 HD1 = 124.900 Building: HD1 ... missing HE3: bond: CE3 HE3 bond distance = 0.930 HE3: angle: HE3 CE3 CZ3 = 120.700 HE3: angle: CD2 CE3 HE3 = 120.700 Building: HE3 ... missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HZ3: bond: CZ3 HZ3 bond distance = 0.930 HZ3: angle: HZ3 CZ3 CH2 = 119.450 HZ3: angle: CE3 CZ3 HZ3 = 119.450 Building: HZ3 ... missing HZ2: bond: CZ2 HZ2 bond distance = 0.930 HZ2: angle: CH2 CZ2 HZ2 = 121.250 HZ2: angle: CE2 CZ2 HZ2 = 121.250 Building: HZ2 ... missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.970 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB CG = 108.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Still missing: TRP ['H'] Build 9 from 10 % = 90.0 ('TRP', ['H']) trp.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 24 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 24 Number of chains: 1 Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 0.42 Number of scatterers: 24 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 2 8.00 N 2 7.00 C 11 6.00 H 9 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 0.86 - 1.00: 8 1.00 - 1.14: 1 1.14 - 1.27: 2 1.27 - 1.41: 4 1.41 - 1.55: 10 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA TRP 1 " - " N TRP 1 " 1.458 1.507 -0.049 2.77e+03 6.78e+00 " CE3 TRP 1 " - " CD2 TRP 1 " 1.398 1.433 -0.035 3.91e+03 4.74e+00 " CA TRP 1 " - "HA TRP 1 " 0.980 1.020 -0.040 2.50e+03 4.09e+00 " CZ2 TRP 1 " - " CH2 TRP 1 " 1.368 1.403 -0.035 2.77e+03 3.34e+00 " CZ2 TRP 1 " - " CE2 TRP 1 " 1.394 1.427 -0.033 2.27e+03 2.47e+00 ... (remaining 20 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.83: 18 2.83 - 3.32: 30 3.32 - 3.81: 26 3.81 - 4.30: 24 4.30 - 4.79: 31 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HH2 TRP 1 " - "HZ2 TRP 1 " 2.339 1.600 "HH2 TRP 1 " - "HZ3 TRP 1 " 2.347 1.600 "HE3 TRP 1 " - "HZ3 TRP 1 " 2.349 1.600 "HE1 TRP 1 " - "HD1 TRP 1 " 2.411 1.600 "HA TRP 1 " - "HB2 TRP 1 " 2.445 1.600 ... (remaining 124 not shown) Histogram of dihedral angle deviations from ideal: 0.23 - 6.06: 1 6.06 - 11.89: 1 11.89 - 17.72: 0 17.72 - 23.55: 0 23.55 - 29.38: 1 Dihedral angle restraints sorted by residual: " N TRP 1 " " C TRP 1 " " CA TRP 1 " " OXT TRP 1 " ideal model delta periodicty weight residual -160.00 -130.62 -29.38 2 1.11e-03 9.59e-01 " CG TRP 1 " " CB TRP 1 " " CA TRP 1 " " N TRP 1 " ideal model delta periodicty weight residual 180.00 -69.24 9.24 3 4.44e-03 3.79e-01 " CA TRP 1 " " CB TRP 1 " " CG TRP 1 " " CD1 TRP 1 " ideal model delta periodicty weight residual 90.00 90.23 -0.23 2 2.50e-03 1.27e-04 target: 38.5693 bond_residual_sum (n=25): 30.5434 nonbonded_residual_sum (n=129): 0 angle_residual_sum (n=42): 5.981 dihedral_residual_sum (n=3): 1.33836 chirality_residual_sum (n=1): 0.679262 planarity_residual_sum (n=2): 0.0272789 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 38.5693 bond_residual_sum (n=25): 30.5434 nonbonded_residual_sum (n=129): 0 angle_residual_sum (n=42): 5.981 dihedral_residual_sum (n=3): 1.33836 chirality_residual_sum (n=1): 0.679262 planarity_residual_sum (n=2): 0.0272789 norm of gradients: 676.859 Energies after minimization: target: 0.278592 bond_residual_sum (n=25): 0.00650554 nonbonded_residual_sum (n=129): 0 angle_residual_sum (n=42): 0.252833 dihedral_residual_sum (n=3): 5.14472e-13 chirality_residual_sum (n=1): 0.0192529 planarity_residual_sum (n=2): 3.90508e-15 norm of gradients: 1.01642e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/thr.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 8 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 8 Number of chains: 1 Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 1.25 Residue name: THR%COO THR Missing hydrogen atoms: ['HA', 'H', 'HG1', 'HG21', 'HB', 'HG23', 'HG22'] missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HG1: bond: OG1 HG1 bond distance = 0.820 HG1: angle: CB OG1 HG1 = 110.000 Building: HG1 Unknown hydrogen type: HG1 missing HG21: bond: CG2 HG21 bond distance = 0.960 HG21: angle: HG21 CG2 HG22 = 109.000 HG21: angle: HG21 CG2 HG23 = 109.000 HG21: angle: CB CG2 HG21 = 110.000 Building: HG21 ... missing HB: bond: CB HB bond distance = 0.970 HB: angle: HB CB OG1 = 109.000 HB: angle: HB CB CG2 = 108.000 HB: angle: CA CB HB = 109.000 Building: HB Building: HB Still missing: THR ['H', 'HG1'] Build 5 from 7 % = 71.4285714286 ('THR', ['H', 'HG1']) thr.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 13 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 13 Number of chains: 1 Number of residues, atoms: 1, 13 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 0.77 Number of scatterers: 13 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 3 8.00 N 1 7.00 C 4 6.00 H 5 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.00 seconds Histogram of bond lengths: 0.96 - 1.08: 5 1.08 - 1.20: 0 1.20 - 1.32: 2 1.32 - 1.44: 1 1.44 - 1.56: 4 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CB THR 1 " - "HB THR 1 " 0.970 1.029 -0.059 2.50e+03 8.81e+00 " CA THR 1 " - " N THR 1 " 1.458 1.508 -0.050 2.77e+03 6.87e+00 " CA THR 1 " - "HA THR 1 " 0.980 1.031 -0.051 2.50e+03 6.60e+00 " C THR 1 " - " OXT THR 1 " 1.231 1.250 -0.019 2.50e+03 8.89e-01 " C THR 1 " - " O THR 1 " 1.231 1.250 -0.019 2.50e+03 8.66e-01 ... (remaining 7 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 8 2.70 - 3.24: 15 3.24 - 3.78: 8 3.78 - 4.32: 4 4.32 - 4.85: 9 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HG21 THR 1 " - "HB THR 1 " 2.165 1.600 "HA THR 1 " - "HG22 THR 1 " 2.360 2.400 " OG1 THR 1 " - "HG23 THR 1 " 2.377 1.813 "HA THR 1 " - "HB THR 1 " 2.451 1.600 " O THR 1 " - "HA THR 1 " 2.459 1.813 ... (remaining 39 not shown) Histogram of dihedral angle deviations from ideal: 8.60 - 15.06: 1 15.06 - 21.53: 0 21.53 - 28.00: 0 28.00 - 34.47: 1 34.47 - 40.94: 1 Dihedral angle restraints sorted by residual: " CA THR 1 " " CB THR 1 " " CG2 THR 1 " "HG23 THR 1 " ideal model delta periodicty weight residual 60.00 100.94 -40.94 3 1.11e-03 1.86e+00 " OXT THR 1 " " C THR 1 " " CA THR 1 " " N THR 1 " ideal model delta periodicty weight residual 160.00 -49.57 29.57 2 1.11e-03 9.72e-01 " N THR 1 " " CB THR 1 " " CA THR 1 " " CG2 THR 1 " ideal model delta periodicty weight residual -180.00 68.60 -8.60 3 4.44e-03 3.28e-01 target: 41.9888 bond_residual_sum (n=12): 24.73 nonbonded_residual_sum (n=44): 0.0634987 angle_residual_sum (n=21): 13.1355 dihedral_residual_sum (n=3): 3.16212 chirality_residual_sum (n=2): 0.896754 planarity_residual_sum (n=1): 0.000866164 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 41.9888 bond_residual_sum (n=12): 24.73 nonbonded_residual_sum (n=44): 0.0634987 angle_residual_sum (n=21): 13.1355 dihedral_residual_sum (n=3): 3.16212 chirality_residual_sum (n=2): 0.896754 planarity_residual_sum (n=1): 0.000866164 norm of gradients: 845.041 Energies after minimization: target: 0.307825 bond_residual_sum (n=12): 0.00188959 nonbonded_residual_sum (n=44): 0.00310892 angle_residual_sum (n=21): 0.279099 dihedral_residual_sum (n=3): 0.000232147 chirality_residual_sum (n=2): 0.0234957 planarity_residual_sum (n=1): 4.01819e-16 norm of gradients: 9.01203e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/val.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 8 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 8 Number of chains: 1 Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 1.25 Residue name: VAL%COO VAL Missing hydrogen atoms: ['HG22', 'H', 'HG21', 'HG11', 'HG12', 'HG13', 'HB', 'HG23', 'HA'] missing HG22: bond: CG2 HG22 bond distance = 0.960 HG22: angle: HG21 CG2 HG22 = 110.000 HG22: angle: HG22 CG2 HG23 = 110.000 HG22: angle: CB CG2 HG22 = 109.000 Building: HG22 ... missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HG11: bond: CG1 HG11 bond distance = 0.960 HG11: angle: HG11 CG1 HG12 = 110.000 HG11: angle: HG11 CG1 HG13 = 110.000 HG11: angle: CB CG1 HG11 = 109.000 Building: HG11 ... missing HB: bond: CB HB bond distance = 0.980 HB: angle: HB CB CG1 = 108.000 HB: angle: HB CB CG2 = 108.000 HB: angle: CA CB HB = 109.000 Building: HB missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA Still missing: VAL ['H'] Build 8 from 9 % = 88.8888888889 ('VAL', ['H']) val.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 16 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 16 Number of chains: 1 Number of residues, atoms: 1, 16 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 1.25 Number of scatterers: 16 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 2 8.00 N 1 7.00 C 5 6.00 H 8 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.00 seconds Histogram of bond lengths: 0.96 - 1.08: 7 1.08 - 1.21: 1 1.21 - 1.33: 2 1.33 - 1.46: 0 1.46 - 1.58: 5 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA VAL 1 " - "HA VAL 1 " 0.980 1.091 -0.111 2.50e+03 3.07e+01 " CA VAL 1 " - " N VAL 1 " 1.458 1.505 -0.047 2.77e+03 6.17e+00 " CB VAL 1 " - "HB VAL 1 " 0.980 1.026 -0.046 2.50e+03 5.22e+00 " CB VAL 1 " - " CA VAL 1 " 1.540 1.581 -0.041 1.37e+03 2.30e+00 " C VAL 1 " - " O VAL 1 " 1.231 1.250 -0.019 2.50e+03 9.13e-01 ... (remaining 10 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.60: 10 2.60 - 3.15: 20 3.15 - 3.71: 24 3.71 - 4.26: 13 4.26 - 4.81: 7 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HG23 VAL 1 " - "HG13 VAL 1 " 2.050 2.400 "HG12 VAL 1 " - "HB VAL 1 " 2.164 1.600 "HG21 VAL 1 " - "HB VAL 1 " 2.186 1.600 "HG11 VAL 1 " - "HA VAL 1 " 2.372 2.400 " CG2 VAL 1 " - "HG13 VAL 1 " 2.458 1.933 ... (remaining 69 not shown) Histogram of dihedral angle deviations from ideal: 4.61 - 16.45: 2 16.45 - 28.29: 1 28.29 - 40.13: 0 40.13 - 51.97: 0 51.97 - 63.81: 1 Dihedral angle restraints sorted by residual: " CA VAL 1 " " CB VAL 1 " " CG1 VAL 1 " "HG13 VAL 1 " ideal model delta periodicty weight residual 60.00 123.81 -63.81 2 1.11e-03 4.52e+00 " OXT VAL 1 " " C VAL 1 " " CA VAL 1 " " N VAL 1 " ideal model delta periodicty weight residual 160.00 135.14 24.86 2 1.11e-03 6.87e-01 " CA VAL 1 " " CB VAL 1 " " CG2 VAL 1 " "HG23 VAL 1 " ideal model delta periodicty weight residual 60.00 -135.02 15.02 2 1.11e-03 2.51e-01 " N VAL 1 " " CB VAL 1 " " CA VAL 1 " " CG2 VAL 1 " ideal model delta periodicty weight residual -180.00 -55.39 -4.61 3 4.44e-03 9.44e-02 target: 64.4875 bond_residual_sum (n=15): 47.3506 nonbonded_residual_sum (n=74): 0.526769 angle_residual_sum (n=27): 10.9254 dihedral_residual_sum (n=4): 5.55583 chirality_residual_sum (n=2): 0.128855 planarity_residual_sum (n=1): 5.12181e-05 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 64.4875 bond_residual_sum (n=15): 47.3506 nonbonded_residual_sum (n=74): 0.526769 angle_residual_sum (n=27): 10.9254 dihedral_residual_sum (n=4): 5.55583 chirality_residual_sum (n=2): 0.128855 planarity_residual_sum (n=1): 5.12181e-05 norm of gradients: 882.216 Energies after minimization: target: 0.396236 bond_residual_sum (n=15): 0.00109572 nonbonded_residual_sum (n=74): 0.112962 angle_residual_sum (n=27): 0.23705 dihedral_residual_sum (n=4): 0.0290599 chirality_residual_sum (n=2): 0.015864 planarity_residual_sum (n=1): 0.000204325 norm of gradients: 1.71926e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/cys.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 7 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 7 Number of chains: 1 Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 1.43 Residue name: CYS%COO CYS Missing hydrogen atoms: ['H', 'HA', 'HB1', 'HG', 'HB2'] missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.970 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB SG = 108.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Building: HB1 and HB2 Building: HB1 and HB2 missing HG: bond: HG SG bond distance = 1.340 HG: angle: CB SG HG = 109.000 Building: HG Building: HG ... Still missing: CYS ['H'] Build 4 from 5 % = 80.0 ('CYS', ['H']) cys.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 11 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 11 Number of chains: 1 Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 0.91 Number of scatterers: 11 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 1 16.00 O 2 8.00 N 1 7.00 C 3 6.00 H 4 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 0.97 - 1.14: 3 1.14 - 1.31: 2 1.31 - 1.48: 1 1.48 - 1.65: 3 1.65 - 1.82: 1 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA CYS 1 " - "HA CYS 1 " 0.980 1.072 -0.092 2.50e+03 2.12e+01 " CA CYS 1 " - " N CYS 1 " 1.458 1.506 -0.048 2.77e+03 6.44e+00 " CB CYS 1 " - " CA CYS 1 " 1.530 1.561 -0.031 2.50e+03 2.47e+00 " C CYS 1 " - " OXT CYS 1 " 1.231 1.250 -0.019 2.50e+03 9.05e-01 " C CYS 1 " - " O CYS 1 " 1.231 1.249 -0.018 2.50e+03 8.46e-01 ... (remaining 5 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.78: 6 2.78 - 3.19: 5 3.19 - 3.60: 12 3.60 - 4.01: 1 4.01 - 4.42: 5 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HA CYS 1 " - "HB1 CYS 1 " 2.369 1.600 "HA CYS 1 " - "HB2 CYS 1 " 2.402 1.600 " OXT CYS 1 " - "HA CYS 1 " 2.467 1.813 " O CYS 1 " - "HG CYS 1 " 2.593 2.720 " C CYS 1 " - "HB2 CYS 1 " 2.721 1.933 ... (remaining 24 not shown) Histogram of dihedral angle deviations from ideal: 0.69 - 12.55: 1 12.55 - 24.41: 0 24.41 - 36.27: 1 36.27 - 48.13: 0 48.13 - 59.99: 1 Dihedral angle restraints sorted by residual: " CA CYS 1 " " CB CYS 1 " " SG CYS 1 " "HG CYS 1 " ideal model delta periodicty weight residual 180.00 -0.01 -59.99 3 4.44e-03 1.60e+01 " OXT CYS 1 " " C CYS 1 " " CA CYS 1 " " N CYS 1 " ideal model delta periodicty weight residual 160.00 133.17 26.83 2 1.11e-03 8.00e-01 " N CYS 1 " " CB CYS 1 " " CA CYS 1 " " SG CYS 1 " ideal model delta periodicty weight residual -180.00 -59.31 -0.69 3 4.44e-03 2.14e-03 target: 60.0107 bond_residual_sum (n=10): 32.5394 nonbonded_residual_sum (n=29): 0.0383642 angle_residual_sum (n=16): 10.4642 dihedral_residual_sum (n=3): 16.7978 chirality_residual_sum (n=1): 0.170388 planarity_residual_sum (n=1): 0.000445961 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 60.0107 bond_residual_sum (n=10): 32.5394 nonbonded_residual_sum (n=29): 0.0383642 angle_residual_sum (n=16): 10.4642 dihedral_residual_sum (n=3): 16.7978 chirality_residual_sum (n=1): 0.170388 planarity_residual_sum (n=1): 0.000445961 norm of gradients: 705.66 Energies after minimization: target: 0.298138 bond_residual_sum (n=10): 0.00162971 nonbonded_residual_sum (n=29): 6.56403e-05 angle_residual_sum (n=16): 0.277211 dihedral_residual_sum (n=3): 1.73645e-06 chirality_residual_sum (n=1): 0.0192296 planarity_residual_sum (n=1): 2.14662e-08 norm of gradients: 1.25602e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/rosie/scratch1/rwgk/dist/regression/hydrogens/ser.pdb Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 7 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 7 Number of chains: 1 Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 1.43 Residue name: SER%COO SER Missing hydrogen atoms: ['H', 'HA', 'HB1', 'HG', 'HB2'] missing H: bond: N H bond distance = 0.860 H: angle: H N CA = 114.000 Unknown hydrogen type: H missing HA: bond: CA HA bond distance = 0.980 HA: angle: HA CA CB = 109.000 HA: angle: HA CA C = 109.000 HA: angle: N CA HA = 110.000 Building: HA missing HB1: bond: CB HB1 bond distance = 0.970 HB1: angle: HB1 CB HB2 = 110.000 HB1: angle: HB1 CB OG = 109.000 HB1: angle: CA CB HB1 = 109.000 Building: HB1 and HB2 Building: HB1 and HB2 missing HG: bond: OG HG bond distance = 0.820 HG: angle: CB OG HG = 110.000 Building: HG Building: HG ... Still missing: SER ['H'] Build 4 from 5 % = 80.0 ('SER', ['H']) ser.pdb_h Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 11 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 11 Number of chains: 1 Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 0.91 Number of scatterers: 11 At special positions: 0 Unit cell: (10, 10, 10, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 3 8.00 N 1 7.00 C 3 6.00 H 4 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.01 seconds Histogram of bond lengths: 0.82 - 0.96: 1 0.96 - 1.11: 3 1.11 - 1.26: 2 1.26 - 1.40: 0 1.40 - 1.55: 4 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " CA SER 1 " - " N SER 1 " 1.458 1.504 -0.046 2.77e+03 5.86e+00 " CA SER 1 " - "HA SER 1 " 0.980 1.027 -0.047 2.50e+03 5.50e+00 " C SER 1 " - " OXT SER 1 " 1.231 1.249 -0.018 2.50e+03 8.06e-01 " C SER 1 " - " O SER 1 " 1.231 1.249 -0.018 2.50e+03 7.75e-01 " CB SER 1 " - " CA SER 1 " 1.530 1.545 -0.015 2.50e+03 5.78e-01 ... (remaining 5 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.71: 11 2.71 - 3.07: 4 3.07 - 3.42: 9 3.42 - 3.78: 1 3.78 - 4.14: 4 Nonbonded interactions sorted by model distance: atom i - atom j model vdw "HA SER 1 " - "HB1 SER 1 " 2.352 1.600 " CA SER 1 " - "HG SER 1 " 2.363 1.933 "HA SER 1 " - "HB2 SER 1 " 2.400 1.600 " O SER 1 " - "HG SER 1 " 2.419 2.720 " OXT SER 1 " - "HA SER 1 " 2.458 1.813 ... (remaining 24 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 5.75: 2 5.75 - 11.46: 0 11.46 - 17.17: 0 17.17 - 22.88: 0 22.88 - 28.59: 1 Dihedral angle restraints sorted by residual: " N SER 1 " " C SER 1 " " CA SER 1 " " OXT SER 1 " ideal model delta periodicty weight residual -160.00 -131.41 -28.59 2 1.11e-03 9.08e-01 " OG SER 1 " " CB SER 1 " " CA SER 1 " " N SER 1 " ideal model delta periodicty weight residual 180.00 57.04 2.96 3 4.44e-03 3.89e-02 " CA SER 1 " " OG SER 1 " " CB SER 1 " "HG SER 1 " ideal model delta periodicty weight residual -180.00 -0.03 0.03 2 1.11e-03 1.32e-06 target: 21.3981 bond_residual_sum (n=10): 13.8342 nonbonded_residual_sum (n=29): 0.29357 angle_residual_sum (n=16): 5.87119 dihedral_residual_sum (n=3): 0.947303 chirality_residual_sum (n=1): 0.451758 planarity_residual_sum (n=1): 5.48188e-05 Time first energy calculation (mainly nonbonded setup): 0.00 Energies at start of minimization: target: 21.3981 bond_residual_sum (n=10): 13.8342 nonbonded_residual_sum (n=29): 0.29357 angle_residual_sum (n=16): 5.87119 dihedral_residual_sum (n=3): 0.947303 chirality_residual_sum (n=1): 0.451758 planarity_residual_sum (n=1): 5.48188e-05 norm of gradients: 480.26 Energies after minimization: target: 0.36904 bond_residual_sum (n=10): 0.000845077 nonbonded_residual_sum (n=29): 0.110287 angle_residual_sum (n=16): 0.235222 dihedral_residual_sum (n=3): 0.00655037 chirality_residual_sum (n=1): 0.0161358 planarity_residual_sum (n=1): 9.05847e-12 norm of gradients: 7.63484e-06 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/max_lik/tst_maxlik.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/max_lik/tst_maxlik.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/max_lik/tst_maxlik.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/max_lik/tst_maxlik.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import max_lik u+s,u,s: 22.24 22.16 0.08 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/masks/tst_masks.py /net/rosie/scratch1/rwgk/dist/mmtbx/masks/tst_masks.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import masks /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import maptbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:11: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.xplor.map P 1 P -1 P 1 2 1 C 1 2/c 1 P 2 2 2 I m m a P 4 P 41 I 41/a c d :2 P 3 P 31 P 3 1 m R -3 c :H P 6 P 63/m m c P 2 3 I a -3 d Hall: -I 4 2c (1/2*x+1/2*y+1/12,-1/2*x+1/2*y-1/12,z-1/4) u+s,u,s: 2.95 2.62 0.33 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/max_lik/tst_max_lik.py /net/rosie/scratch1/rwgk/dist/mmtbx/max_lik/tst_max_lik.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/max_lik/tst_max_lik.py:14: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.max_lik import max_like_non_uniform P 1 P -1 P 1 2 1 C 1 2/c 1 P 2 2 2 I m m a P 4 P 41 I 41/a c d :2 P 3 P 31 P 3 1 m R -3 c :H P 6 P 63/m m c P 2 3 I a -3 d Hall: -I 4 2c (1/2*x+1/2*y+1/12,-1/2*x+1/2*y-1/12,z-1/4) u+s,u,s: 10.63 10.43 0.20 P 1 P -1 P 1 2 1 C 1 2/c 1 P 2 2 2 I m m a P 4 P 41 I 41/a c d :2 P 3 P 31 P 3 1 m R -3 c :H P 6 P 63/m m c P 2 3 I a -3 d Hall: -I 4 2c (1/2*x+1/2*y+1/12,-1/2*x+1/2*y-1/12,z-1/4) u+s,u,s: 34.39 32.79 1.60 OK libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/dynamics/tst_cartesian_dynamics.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/dynamics/tst_cartesian_dynamics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py import mmtbx.restraints /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.adp_restraints /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/dynamics/cartesian_dynamics.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb u+s,u,s: 1.88 1.78 0.10 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import monomer_library |-----------------------------------------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 40.4770 20.8090 77.3260 | |T11= 0.1100 T22= 0.2200 T33= 0.3300 T12= 0.1200 T13= 0.1300 T23= 0.2300| |L11= 1.1100 L22= 1.2200 L33= 1.3300 L12= 1.1200 L13= 1.1300 L23= 1.2300| |S11= 0.1100 S22= 0.2200 S33= -0.3300 S12= 0.1200 S13= 0.1300 S21= 0.2100| |S23= 0.2300 S31= 0.3100 S32= 0.3200 | |TLS group number 2: | | Origin (x,y,z) = 16.2750 -1.2230 59.5040 | |T11= 0.2200 T22= 0.4400 T33= 0.6600 T12= 0.2400 T13= 0.2600 T23= 0.4600| |L11= 2.1100 L22= 2.2200 L33= 2.3300 L12= 2.1200 L13= 2.1300 L23= 2.2300| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |-----------------------------------------------------------------------------| TLS from Uaniso: |-----------------------------------------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 40.4765 20.8088 77.3262 | |T11= 0.1100 T22= 0.2200 T33= 0.3300 T12= 0.1200 T13= 0.1300 T23= 0.2300| |L11= 1.1100 L22= 1.2200 L33= 1.3300 L12= 1.1200 L13= 1.1300 L23= 1.2300| |S11= 0.1100 S22= 0.2200 S33= -0.3300 S12= 0.1200 S13= 0.1300 S21= 0.2100| |S23= 0.2300 S31= 0.3100 S32= 0.3200 | |TLS group number 2: | | Origin (x,y,z) = 16.2748 -1.2233 59.5036 | |T11= 0.2200 T22= 0.4400 T33= 0.6600 T12= 0.2400 T13= 0.2600 T23= 0.4600| |L11= 2.1100 L22= 2.2200 L33= 2.3300 L12= 2.1200 L13= 2.1300 L23= 2.2300| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |-----------------------------------------------------------------------------| u+s,u,s: 12.54 12.22 0.32 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls_refinement_fft.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls_refinement_fft.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls_refinement_fft.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import monomer_library random_seed: 461690984 |-----------------------------------------------------------------------------| | iso = 0 aniso = 36 pos. def. = 36 non-pos. def. = 0 | | Total B(isotropic equivalent): min = 17.09 max = 53.74 mean = 35.10 | | Isotropic B only: min = -78.96 max = -78.96 mean = -78.96 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | -78.957 - -78.957: 36 | 17.095 - 20.759: 12 | | -78.957 - -78.957: 0 | 20.759 - 24.423: 0 | | -78.957 - -78.957: 0 | 24.423 - 28.088: 0 | | -78.957 - -78.957: 0 | 28.088 - 31.752: 0 | | -78.957 - -78.957: 0 | 31.752 - 35.416: 8 | | -78.957 - -78.957: 0 | 35.416 - 39.080: 4 | | -78.957 - -78.957: 0 | 39.080 - 42.744: 0 | | -78.957 - -78.957: 0 | 42.744 - 46.409: 0 | | -78.957 - -78.957: 0 | 46.409 - 50.073: 0 | | -78.957 - -78.957: 0 | 50.073 - 53.737: 12 | |-----------------------------------------------------------------------------| |-ANSWER----------------------------------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.1100 T22= 0.2200 T33= 0.3300 T12= 0.1200 T13= 0.1300 T23= 0.2300| |L11= 1.1100 L22= 1.2200 L33= 1.3300 L12= 1.1200 L13= 1.1300 L23= 1.2300| |S11= 0.1100 S22= 0.2200 S33= -0.3300 S12= 0.1200 S13= 0.1300 S21= 0.2100| |S23= 0.2300 S31= 0.3100 S32= 0.3200 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.2200 T22= 0.4400 T33= 0.6600 T12= 0.2400 T13= 0.2600 T23= 0.4600| |L11= 2.2200 L22= 2.4400 L33= 2.6600 L12= 2.2400 L13= 2.2600 L23= 2.4600| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.3300 T22= 0.6600 T33= 0.9900 T12= 0.3600 T13= 0.3900 T23= 0.6900| |L11= 2.3300 L22= 2.6600 L33= 2.9900 L12= 2.3600 L13= 2.3900 L23= 2.6900| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | | | all data [11.8-1.50] high resolution [6.0-1.50] low resolution [11.8-6.00] | | r_work = 0.0000 r_work = 0.0000 r_work = 0.0000 | | r_free = 0.0000 r_free = 0.0000 r_free = 0.0000 | | | | scale (work) = 1.0000 scale (free) = 1.0000 ksol = 0.00 Bsol = 0.00 | | | | overall anisotropic scale matrix (Cartesian basis): | | (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00) | | (B11+B22+B33)/3 = 0.00 | | | | Target ls_wunit_k1: work = 0.000000E+00 free = 0.000000E+00 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 11.8227 - 1.5003 1.00 909 48 0.0000 0.0000 0.0000E+00 0.0000E+00| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase error Alpha Beta | | # range work test work test | | 1: 11.8227 - 1.5003 909 48 1.000 0.000 0.000 1.000 0.000 | |alpha: min = 1.0000 max = 1.0000 mean = 1.0000 | |beta: min = 0.0000 max = 0.0000 mean = 0.0000 | |figures of merit: min = 1.0000 max = 1.0000 mean = 1.0000 | |phase err.(work): min = 0.0000 max = 0.0000 mean = 0.0000 | |phase err.(test): min = 0.0000 max = 0.0000 mean = 0.0000 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | | | all data [11.8-1.50] high resolution [6.0-1.50] low resolution [11.8-6.00] | | r_work = 0.4848 r_work = 0.5116 r_work = 0.0741 | | r_free = 0.4934 r_free = 0.5628 r_free = 0.0000 | | | | scale (work) = 1.0714 scale (free) = 0.9195 ksol = 0.00 Bsol = 0.00 | | | | overall anisotropic scale matrix (Cartesian basis): | | (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00) | | (B11+B22+B33)/3 = 0.00 | | | | Target ls_wunit_k1: work = 1.615700E-01 free = 2.171270E-01 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 11.8227 - 1.5003 1.00 909 48 0.4848 0.4934 1.6157E-01 2.1713E-01| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase error Alpha Beta | | # range work test work test | | 1: 11.8227 - 1.5003 909 48 0.356 62.347 64.114 0.863 30.521 | |alpha: min = 0.8633 max = 0.8633 mean = 0.8633 | |beta: min = 30.5215 max = 30.5215 mean = 30.5215 | |figures of merit: min = 0.0003 max = 0.9992 mean = 0.3564 | |phase err.(work): min = 0.0000 max = 89.9818 mean = 62.3466 | |phase err.(test): min = 0.0000 max = 89.9620 mean = 64.1145 | |-----------------------------------------------------------------------------| ******************************************************************************** 0.0 |-TLS refinement: start model-------------------------------------------------| | target_work(ls_wunit_k1) = 1.615700e-01 r_work = 0.4848 r_free = 0.4934 | |-----------------------------------------------------------------------------| |-TLS refinement: start model-------------------------------------------------| | iso = 0 aniso = 36 pos. def. = 36 non-pos. def. = 0 | | Total B(isotropic equivalent): min = 25.00 max = 25.00 mean = 25.00 | | Isotropic B only: min = -78.96 max = -78.96 mean = -78.96 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | -78.957 - -78.957: 36 | 25.000 - 25.000: 36 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | |-----------------------------------------------------------------------------| |-TLS refinement: start parameters--------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.0000 T22= 0.0000 T33= 0.0000 T12= 0.0000 T13= 0.0000 T23= 0.0000| |L11= 0.0000 L22= 0.0000 L33= 0.0000 L12= 0.0000 L13= 0.0000 L23= 0.0000| |S11= 0.0000 S22= 0.0000 S33= 0.0000 S12= 0.0000 S13= 0.0000 S21= 0.0000| |S23= 0.0000 S31= 0.0000 S32= 0.0000 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.0000 T22= 0.0000 T33= 0.0000 T12= 0.0000 T13= 0.0000 T23= 0.0000| |L11= 0.0000 L22= 0.0000 L33= 0.0000 L12= 0.0000 L13= 0.0000 L23= 0.0000| |S11= 0.0000 S22= 0.0000 S33= 0.0000 S12= 0.0000 S13= 0.0000 S21= 0.0000| |S23= 0.0000 S31= 0.0000 S32= 0.0000 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.0000 T22= 0.0000 T33= 0.0000 T12= 0.0000 T13= 0.0000 T23= 0.0000| |L11= 0.0000 L22= 0.0000 L33= 0.0000 L12= 0.0000 L13= 0.0000 L23= 0.0000| |S11= 0.0000 S22= 0.0000 S33= 0.0000 S12= 0.0000 S13= 0.0000 S21= 0.0000| |S23= 0.0000 S31= 0.0000 S32= 0.0000 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| | iso = 0 aniso = 36 pos. def. = 36 non-pos. def. = 0 | | Total B(isotropic equivalent): min = 16.96 max = 31.03 mean = 24.35 | | Isotropic B only: min = -78.96 max = -78.96 mean = -78.96 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | -78.957 - -78.957: 36 | 16.961 - 18.368: 12 | | -78.957 - -78.957: 0 | 18.368 - 19.775: 0 | | -78.957 - -78.957: 0 | 19.775 - 21.183: 0 | | -78.957 - -78.957: 0 | 21.183 - 22.590: 0 | | -78.957 - -78.957: 0 | 22.590 - 23.997: 0 | | -78.957 - -78.957: 0 | 23.997 - 25.404: 12 | | -78.957 - -78.957: 0 | 25.404 - 26.811: 0 | | -78.957 - -78.957: 0 | 26.811 - 28.218: 0 | | -78.957 - -78.957: 0 | 28.218 - 29.625: 0 | | -78.957 - -78.957: 0 | 29.625 - 31.032: 12 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.0707 T22= 0.2304 T33= 0.3306 T12= 0.1272 T13= 0.1685 T23= 0.2761| |L11= 0.0010 L22= 0.0002 L33= 0.0000 L12= -0.0006 L13= -0.0001 L23= 0.0001| |S11= 0.0032 S22= -0.0022 S33= -0.0010 S12= 0.0087 S13= 0.0100 S21= 0.0046| |S23= -0.0027 S31= 0.0068 S32= 0.0014 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.1903 T22= 0.3382 T33= 0.4254 T12= 0.1696 T13= 0.1536 T23= 0.2781| |L11= 0.0010 L22= 0.0006 L33= 0.0002 L12= -0.0010 L13= 0.0002 L23= 0.0001| |S11= 0.0061 S22= -0.0005 S33= -0.0056 S12= 0.0102 S13= 0.0090 S21= -0.0040| |S23= -0.0090 S31= -0.0006 S32= 0.0047 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.2950 T22= 0.4147 T33= 0.4667 T12= 0.1318 T13= 0.1894 T23= 0.2388| |L11= 0.0010 L22= 0.0008 L33= 0.0003 L12= -0.0010 L13= 0.0003 L23= 0.0002| |S11= 0.0036 S22= -0.0028 S33= -0.0007 S12= 0.0115 S13= 0.0084 S21= -0.0056| |S23= -0.0076 S31= -0.0007 S32= 0.0043 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| | target_work(ls_wunit_k1) = 1.381012e-02 r_work = 0.1294 r_free = 0.1581 | |-----------------------------------------------------------------------------| |-TLS refinement: final values------------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.0707 T22= 0.2304 T33= 0.3306 T12= 0.1272 T13= 0.1685 T23= 0.2761| |L11= 0.0010 L22= 0.0002 L33= 0.0000 L12= -0.0006 L13= -0.0001 L23= 0.0001| |S11= 0.0032 S22= -0.0022 S33= -0.0010 S12= 0.0087 S13= 0.0100 S21= 0.0046| |S23= -0.0027 S31= 0.0068 S32= 0.0014 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.1903 T22= 0.3382 T33= 0.4254 T12= 0.1696 T13= 0.1536 T23= 0.2781| |L11= 0.0010 L22= 0.0006 L33= 0.0002 L12= -0.0010 L13= 0.0002 L23= 0.0001| |S11= 0.0061 S22= -0.0005 S33= -0.0056 S12= 0.0102 S13= 0.0090 S21= -0.0040| |S23= -0.0090 S31= -0.0006 S32= 0.0047 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.2950 T22= 0.4147 T33= 0.4667 T12= 0.1318 T13= 0.1894 T23= 0.2388| |L11= 0.0010 L22= 0.0008 L33= 0.0003 L12= -0.0010 L13= 0.0003 L23= 0.0002| |S11= 0.0036 S22= -0.0028 S33= -0.0007 S12= 0.0115 S13= 0.0084 S21= -0.0056| |S23= -0.0076 S31= -0.0007 S32= 0.0043 | |-----------------------------------------------------------------------------| [, , ] |-TLS refinement: start model-------------------------------------------------| | target_work(ls_wunit_k1) = 1.615700e-01 r_work = 0.4848 r_free = 0.4934 | |-----------------------------------------------------------------------------| |-TLS refinement: start model-------------------------------------------------| | iso = 0 aniso = 36 pos. def. = 36 non-pos. def. = 0 | | Total B(isotropic equivalent): min = 25.00 max = 25.00 mean = 25.00 | | Isotropic B only: min = -78.96 max = -78.96 mean = -78.96 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | -78.957 - -78.957: 36 | 25.000 - 25.000: 36 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | |-----------------------------------------------------------------------------| |-TLS refinement: start parameters--------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.1100 T22= 0.2200 T33= 0.3300 T12= 0.1200 T13= 0.1300 T23= 0.2300| |L11= 1.1100 L22= 1.2200 L33= 1.3300 L12= 1.1200 L13= 1.1300 L23= 1.2300| |S11= 0.1100 S22= 0.2200 S33= -0.3300 S12= 0.1200 S13= 0.1300 S21= 0.2100| |S23= 0.2300 S31= 0.3100 S32= 0.3200 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.2200 T22= 0.4400 T33= 0.6600 T12= 0.2400 T13= 0.2600 T23= 0.4600| |L11= 2.2200 L22= 2.4400 L33= 2.6600 L12= 2.2400 L13= 2.2600 L23= 2.4600| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.3300 T22= 0.6600 T33= 0.9900 T12= 0.3600 T13= 0.3900 T23= 0.6900| |L11= 2.3300 L22= 2.6600 L33= 2.9900 L12= 2.3600 L13= 2.3900 L23= 2.6900| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| | iso = 0 aniso = 36 pos. def. = 36 non-pos. def. = 0 | | Total B(isotropic equivalent): min = 17.09 max = 53.74 mean = 35.10 | | Isotropic B only: min = -78.96 max = -78.96 mean = -78.96 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | -78.957 - -78.957: 36 | 17.095 - 20.759: 12 | | -78.957 - -78.957: 0 | 20.759 - 24.423: 0 | | -78.957 - -78.957: 0 | 24.423 - 28.088: 0 | | -78.957 - -78.957: 0 | 28.088 - 31.752: 0 | | -78.957 - -78.957: 0 | 31.752 - 35.416: 8 | | -78.957 - -78.957: 0 | 35.416 - 39.080: 4 | | -78.957 - -78.957: 0 | 39.080 - 42.744: 0 | | -78.957 - -78.957: 0 | 42.744 - 46.409: 0 | | -78.957 - -78.957: 0 | 46.409 - 50.073: 0 | | -78.957 - -78.957: 0 | 50.073 - 53.737: 12 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.1100 T22= 0.2200 T33= 0.3300 T12= 0.1200 T13= 0.1300 T23= 0.2300| |L11= 1.1100 L22= 1.2200 L33= 1.3300 L12= 1.1200 L13= 1.1300 L23= 1.2300| |S11= 0.1100 S22= 0.2200 S33= -0.3300 S12= 0.1200 S13= 0.1300 S21= 0.2100| |S23= 0.2300 S31= 0.3100 S32= 0.3200 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.2200 T22= 0.4400 T33= 0.6600 T12= 0.2400 T13= 0.2600 T23= 0.4600| |L11= 2.2200 L22= 2.4400 L33= 2.6600 L12= 2.2400 L13= 2.2600 L23= 2.4600| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.3300 T22= 0.6600 T33= 0.9900 T12= 0.3600 T13= 0.3900 T23= 0.6900| |L11= 2.3300 L22= 2.6600 L33= 2.9900 L12= 2.3600 L13= 2.3900 L23= 2.6900| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| | target_work(ls_wunit_k1) = 2.277375e-23 r_work = 0.0000 r_free = 0.0000 | |-----------------------------------------------------------------------------| |-TLS refinement: final values------------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.1100 T22= 0.2200 T33= 0.3300 T12= 0.1200 T13= 0.1300 T23= 0.2300| |L11= 1.1100 L22= 1.2200 L33= 1.3300 L12= 1.1200 L13= 1.1300 L23= 1.2300| |S11= 0.1100 S22= 0.2200 S33= -0.3300 S12= 0.1200 S13= 0.1300 S21= 0.2100| |S23= 0.2300 S31= 0.3100 S32= 0.3200 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.2200 T22= 0.4400 T33= 0.6600 T12= 0.2400 T13= 0.2600 T23= 0.4600| |L11= 2.2200 L22= 2.4400 L33= 2.6600 L12= 2.2400 L13= 2.2600 L23= 2.4600| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.3300 T22= 0.6600 T33= 0.9900 T12= 0.3600 T13= 0.3900 T23= 0.6900| |L11= 2.3300 L22= 2.6600 L33= 2.9900 L12= 2.3600 L13= 2.3900 L23= 2.6900| |S11= 0.2200 S22= 0.4400 S33= -0.6600 S12= 0.2400 S13= 0.2600 S21= 0.4200| |S23= 0.4600 S31= 0.6200 S32= 0.6400 | |-----------------------------------------------------------------------------| None |-TLS refinement: start model-------------------------------------------------| | target_work(ls_wunit_k1) = 1.615700e-01 r_work = 0.4848 r_free = 0.4934 | |-----------------------------------------------------------------------------| |-TLS refinement: start model-------------------------------------------------| | iso = 0 aniso = 36 pos. def. = 36 non-pos. def. = 0 | | Total B(isotropic equivalent): min = 25.00 max = 25.00 mean = 25.00 | | Isotropic B only: min = -78.96 max = -78.96 mean = -78.96 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | -78.957 - -78.957: 36 | 25.000 - 25.000: 36 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | | -78.957 - -78.957: 0 | 25.000 - 25.000: 0 | |-----------------------------------------------------------------------------| |-TLS refinement: start parameters--------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.3162 T22= 0.3165 T33= 0.3165 T12= 0.0002 T13= 0.0001 T23= -0.0001| |L11= 0.1757 L22= 0.6063 L33= 0.4083 L12= 0.3586 L13= -0.1743 L23= -0.4231| |S11= 0.0002 S22= -0.0006 S33= 0.0004 S12= -0.0004 S13= 0.0001 S21= -0.0006| |S23= -0.0008 S31= -0.0000 S32= 0.0012 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.3160 T22= 0.3162 T33= 0.3166 T12= 0.0005 T13= 0.0001 T23= -0.0000| |L11= 0.3007 L22= 0.5603 L33= 0.9046 L12= 0.4413 L13= -0.2863 L23= -0.4669| |S11= -0.0022 S22= -0.0007 S33= 0.0029 S12= -0.0004 S13= -0.0024 S21= -0.0022| |S23= -0.0033 S31= 0.0014 S32= 0.0004 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.3158 T22= 0.3163 T33= 0.3168 T12= 0.0008 T13= 0.0001 T23= 0.0002| |L11= 0.1960 L22= 0.6095 L33= 0.9342 L12= 0.5735 L13= -0.2105 L23= -0.3654| |S11= -0.0034 S22= -0.0005 S33= 0.0039 S12= 0.0002 S13= -0.0041 S21= -0.0021| |S23= -0.0046 S31= 0.0011 S32= -0.0013 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| | iso = 0 aniso = 36 pos. def. = 36 non-pos. def. = 0 | | Total B(isotropic equivalent): min = 17.53 max = 23.17 mean = 20.48 | | Isotropic B only: min = -78.96 max = -78.96 mean = -78.96 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | -78.957 - -78.957: 36 | 17.533 - 18.096: 12 | | -78.957 - -78.957: 0 | 18.096 - 18.660: 0 | | -78.957 - -78.957: 0 | 18.660 - 19.223: 0 | | -78.957 - -78.957: 0 | 19.223 - 19.787: 0 | | -78.957 - -78.957: 0 | 19.787 - 20.350: 0 | | -78.957 - -78.957: 0 | 20.350 - 20.914: 12 | | -78.957 - -78.957: 0 | 20.914 - 21.477: 0 | | -78.957 - -78.957: 0 | 21.477 - 22.041: 0 | | -78.957 - -78.957: 0 | 22.041 - 22.605: 0 | | -78.957 - -78.957: 0 | 22.605 - 23.168: 12 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.1597 T22= 0.2327 T33= 0.2741 T12= 0.0929 T13= 0.0747 T23= 0.1712| |L11= 0.1757 L22= 0.6061 L33= 0.4081 L12= 0.3584 L13= -0.1744 L23= -0.4234| |S11= 0.0020 S22= -0.0018 S33= -0.0002 S12= -0.0012 S13= 0.0005 S21= 0.0048| |S23= -0.0013 S31= 0.0059 S32= 0.0002 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.2146 T22= 0.2645 T33= 0.3075 T12= 0.1196 T13= 0.0507 T23= 0.1842| |L11= 0.3008 L22= 0.5602 L33= 0.9045 L12= 0.4409 L13= -0.2864 L23= -0.4673| |S11= -0.0009 S22= -0.0011 S33= 0.0020 S12= -0.0009 S13= -0.0012 S21= -0.0005| |S23= -0.0046 S31= 0.0034 S32= -0.0002 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.2567 T22= 0.2922 T33= 0.3294 T12= 0.1004 T13= 0.0492 T23= 0.1729| |L11= 0.1961 L22= 0.6094 L33= 0.9340 L12= 0.5732 L13= -0.2106 L23= -0.3656| |S11= -0.0031 S22= -0.0015 S33= 0.0046 S12= -0.0000 S13= -0.0029 S21= -0.0005| |S23= -0.0054 S31= 0.0027 S32= -0.0018 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| | target_work(ls_wunit_k1) = 3.598349e-02 r_work = 0.2268 r_free = 0.3000 | |-----------------------------------------------------------------------------| |-TLS refinement: final values------------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.1597 T22= 0.2327 T33= 0.2741 T12= 0.0929 T13= 0.0747 T23= 0.1712| |L11= 0.1757 L22= 0.6061 L33= 0.4081 L12= 0.3584 L13= -0.1744 L23= -0.4234| |S11= 0.0020 S22= -0.0018 S33= -0.0002 S12= -0.0012 S13= 0.0005 S21= 0.0048| |S23= -0.0013 S31= 0.0059 S32= 0.0002 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.2146 T22= 0.2645 T33= 0.3075 T12= 0.1196 T13= 0.0507 T23= 0.1842| |L11= 0.3008 L22= 0.5602 L33= 0.9045 L12= 0.4409 L13= -0.2864 L23= -0.4673| |S11= -0.0009 S22= -0.0011 S33= 0.0020 S12= -0.0009 S13= -0.0012 S21= -0.0005| |S23= -0.0046 S31= 0.0034 S32= -0.0002 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.2567 T22= 0.2922 T33= 0.3294 T12= 0.1004 T13= 0.0492 T23= 0.1729| |L11= 0.1961 L22= 0.6094 L33= 0.9340 L12= 0.5732 L13= -0.2106 L23= -0.3656| |S11= -0.0031 S22= -0.0015 S33= 0.0046 S12= -0.0000 S13= -0.0029 S21= -0.0005| |S23= -0.0054 S31= 0.0027 S32= -0.0018 | |-----------------------------------------------------------------------------| u+s,u,s: 8.46 8.34 0.12 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/examples/f_model_manager.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/examples/f_model_manager.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.development import random_structure /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/examples/f_model_manager.py:46: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py import mmtbx.f_model /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:11: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.xplor.map f_calc = f_obs = f_mask = r_free_flags = b_cart = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] k_sol = 0.0 b_sol = 0.0 sf_algorithm = fft target_name = None 0.276185393827 0.286931074917 Bin Resolution No. Refl. R-factors number range work test work test 1: 36.8046 - 3.8248 974 130 0.2596 0.3110 2: 3.8248 - 3.0363 918 122 0.2678 0.2499 3: 3.0363 - 2.6526 912 108 0.2726 0.2858 4: 2.6526 - 2.4101 909 95 0.2820 0.2624 5: 2.4101 - 2.2374 924 78 0.2917 0.2728 6: 2.2374 - 2.1055 907 100 0.2866 0.3145 7: 2.1055 - 2.0001 907 84 0.2945 0.3079 |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase error Alpha Beta | | # range work test work test | | 1: 36.8046 - 3.8248 974 130 0.820 22.852 22.017 0.948 7166.714 | | 2: 3.8248 - 3.0363 918 122 0.775 27.795 27.712 0.944 6402.645 | | 3: 3.0363 - 2.6526 912 108 0.797 26.300 25.441 0.935 4110.440 | | 4: 2.6526 - 2.4101 909 95 0.789 27.739 22.867 0.940 3546.703 | | 5: 2.4101 - 2.2374 924 78 0.802 26.508 23.350 0.944 2982.966 | | 6: 2.2374 - 2.1055 907 100 0.784 28.145 25.305 0.969 2583.097 | | 7: 2.1055 - 2.0001 907 84 0.760 29.998 29.866 0.977 2446.075 | |alpha: min = 0.9351 max = 0.9772 mean = 0.9509 | |beta: min = 2446.0747 max = 7166.7138 mean = 4232.4934 | |figures of merit: min = 0.0000 max = 1.0000 mean = 0.7899 | |phase err.(work): min = 0.0000 max = 89.9980 mean = 27.0040 | |phase err.(test): min = 0.0000 max = 89.7514 mean = 25.1376 | |-----------------------------------------------------------------------------| OK libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ls.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ls.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ls.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import max_lik |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.076152 r_work= 0.2097 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9623 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.35 b_sol= 65.00 target_w = 0.000075 r_work= 0.0044 | | B(11,22,33,12,13,23)= 5.0718 10.0454 -14.9289 0.0000 6.9997 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.063 | | mean alpha: 1.0018 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.35 b_sol= 65.00 target_w = 0.000075 r_work= 0.0044 | | B(11,22,33,12,13,23)= 5.0718 10.0454 -14.9289 0.0000 6.9997 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.063 | | mean alpha: 1.0018 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0002 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0001 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: LS min.&grid s.: u+s,u,s: 1.78 1.64 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.076152 r_work= 0.2097 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9623 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 4: k & b: minimization; T= ls_wunit_k1-------------------------| | k_sol= 0.35 b_sol= 65.20 target_w = 0.047005 r_work= 0.1866 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0013 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 4: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.35 b_sol= 65.20 target_w = 0.000050 r_work= 0.0044 | | B(11,22,33,12,13,23)= 5.0227 9.9880 -14.9766 0.0000 6.9958 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.011 | | mean alpha: 1.0002 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0006 10.0006 -15.0003 0.0000 7.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0002 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: LS minimization: u+s,u,s: 2.48 2.34 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.076152 r_work= 0.2097 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9623 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0001 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: LS fix_ksolbsol: u+s,u,s: 2.62 2.48 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.047067 r_work= 0.1864 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0013 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0001 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: LS fix_ksolbsol: u+s,u,s: 2.76 2.62 0.14 OK: LS fix_all 1: u+s,u,s: 2.80 2.66 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.076152 r_work= 0.2097 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9623 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: LS fix_all 2: u+s,u,s: 2.86 2.72 0.14 OK: LS fix_all 3: u+s,u,s: 2.91 2.77 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0000 10.0000 -15.0000 0.0000 7.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0001 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0001 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0001 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0001 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: LS fix_all 4: u+s,u,s: 3.51 3.37 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.047067 r_work= 0.1864 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0013 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0003 10.0001 -15.0005 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: exercise_7: u+s,u,s: 3.62 3.48 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.042954 r_work= 0.1808 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0008 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0002 10.0000 -15.0006 0.0000 7.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: exercise_8: u+s,u,s: 3.72 3.58 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.026255 r_work= 0.0847 | | B(11,22,33,12,13,23)= 5.0000 10.0000 -15.0000 0.0000 7.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9676 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000007 r_work= 0.0011 | | B(11,22,33,12,13,23)= 5.0000 10.0000 -15.0000 0.0000 7.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9997 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 5.0000 10.0000 -15.0000 0.0000 7.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: exercise_9: u+s,u,s: 4.12 3.98 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.028906 r_work= 0.0895 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9634 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.35 b_sol= 65.00 target_w = 0.000083 r_work= 0.0043 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0002 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: exercise_10: u+s,u,s: 4.37 4.23 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.028917 r_work= 0.1189 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9693 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.25 b_sol= 10.00 target_w = 0.000003 r_work= 0.0017 | | B(11,22,33,12,13,23)= 1.8969 3.8342 -6.0896 0.0000 2.9813 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.119 | | mean alpha: 0.9971 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.25 b_sol= 10.00 target_w = 0.000000 r_work= 0.0006 | | B(11,22,33,12,13,23)= 2.0101 4.0156 -5.9923 0.0000 3.0020 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.011 | | mean alpha: 1.0002 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.25 b_sol= 10.40 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0001 -6.0006 0.0000 3.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.25 b_sol= 10.40 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0001 -6.0006 0.0000 3.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.075532 r_work= 0.1729 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9395 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.50 b_sol= 20.00 target_w = 0.000120 r_work= 0.0044 | | B(11,22,33,12,13,23)= 1.9302 3.8424 -6.0407 0.0000 2.9732 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.089 | | mean alpha: 0.9986 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.50 b_sol= 20.00 target_w = 0.000115 r_work= 0.0036 | | B(11,22,33,12,13,23)= 2.0600 4.0817 -5.9341 0.0000 3.0036 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.069 | | mean alpha: 1.0024 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.48 b_sol= 18.90 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0000 -6.0006 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.48 b_sol= 18.90 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0000 -6.0006 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.074578 r_work= 0.1771 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9215 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.80 b_sol= 45.00 target_w = 0.000000 r_work= 0.0004 | | B(11,22,33,12,13,23)= 2.0011 4.0045 -6.0007 0.0000 3.0009 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.002 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.80 b_sol= 45.00 target_w = 0.000000 r_work= 0.0004 | | B(11,22,33,12,13,23)= 2.0011 4.0045 -6.0007 0.0000 3.0009 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.002 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.80 b_sol= 45.20 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0001 -6.0006 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.80 b_sol= 45.20 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0001 -6.0006 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.067056 r_work= 0.1505 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9256 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.70 b_sol= 70.00 target_w = 0.000080 r_work= 0.0049 | | B(11,22,33,12,13,23)= 2.0790 4.0845 -5.9175 0.0000 3.0073 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.082 | | mean alpha: 1.0026 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.70 b_sol= 70.00 target_w = 0.000079 r_work= 0.0051 | | B(11,22,33,12,13,23)= 2.1231 4.1720 -5.8722 0.0000 3.0153 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.141 | | mean alpha: 1.0040 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.72 b_sol= 77.10 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0001 -6.0006 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.72 b_sol= 77.10 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0001 -6.0006 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.039174 r_work= 0.1302 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9617 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.30 b_sol= 15.00 target_w = 0.000031 r_work= 0.0034 | | B(11,22,33,12,13,23)= 1.7725 3.6882 -6.2223 0.0000 2.9736 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.254 | | mean alpha: 0.9932 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.30 b_sol= 15.00 target_w = 0.000028 r_work= 0.0022 | | B(11,22,33,12,13,23)= 1.8900 3.8770 -6.1205 0.0000 2.9947 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.118 | | mean alpha: 0.9964 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.31 b_sol= 16.01 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0003 3.9998 -6.0007 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.31 b_sol= 16.01 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0003 3.9998 -6.0007 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.070098 r_work= 0.1495 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9340 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.65 b_sol= 75.00 target_w = 0.000073 r_work= 0.0035 | | B(11,22,33,12,13,23)= 1.8823 3.8243 -6.1240 0.0000 2.9849 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.139 | | mean alpha: 0.9964 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.65 b_sol= 75.00 target_w = 0.000072 r_work= 0.0031 | | B(11,22,33,12,13,23)= 1.9332 3.9112 -6.0703 0.0000 2.9915 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.075 | | mean alpha: 0.9980 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.63 b_sol= 70.45 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0001 -6.0007 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.63 b_sol= 70.45 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0001 -6.0007 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: closest to real: u+s,u,s: 10.58 10.43 0.15 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.013796 r_work= 0.1211 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8413 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.8876 7.7038 7.1928 -0.1093 0.2703 0.3535 | | trace(B) = (B11 + B22 + B33)/3 = 7.595 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.8876 7.7038 7.1928 -0.1093 0.2703 0.3535 | | trace(B) = (B11 + B22 + B33)/3 = 7.595 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.8876 7.7038 7.1928 -0.1093 0.2703 0.3535 | | trace(B) = (B11 + B22 + B33)/3 = 7.595 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.013796 r_work= 0.1211 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8413 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.8876 7.7038 7.1928 -0.1093 0.2703 0.3535 | | trace(B) = (B11 + B22 + B33)/3 = 7.595 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.8876 7.7038 7.1928 -0.1093 0.2703 0.3535 | | trace(B) = (B11 + B22 + B33)/3 = 7.595 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.8876 7.7038 7.1928 -0.1093 0.2703 0.3535 | | trace(B) = (B11 + B22 + B33)/3 = 7.595 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.012946 r_work= 0.1161 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8242 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000018 r_work= 0.0039 | | B(11,22,33,12,13,23)= 9.5846 8.6554 5.6714 0.0000 -0.3820 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.970 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000018 r_work= 0.0039 | | B(11,22,33,12,13,23)= 9.5846 8.6554 5.6714 0.0000 -0.3820 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.970 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 9.5519 9.0844 5.9949 -0.1109 -0.3483 -0.5996 | | trace(B) = (B11 + B22 + B33)/3 = 8.210 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.013514 r_work= 0.1193 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8193 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 9.5519 9.0844 5.9949 0.0000 -0.3483 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.210 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 9.5519 9.0844 5.9949 0.0000 -0.3483 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.210 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 9.5519 9.0844 5.9949 0.0000 -0.3483 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.210 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.010237 r_work= 0.1052 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8640 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000127 r_work= 0.0106 | | B(11,22,33,12,13,23)= 7.1491 7.2739 5.5949 0.0000 -1.0254 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.673 | | mean alpha: 0.9994 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000127 r_work= 0.0106 | | B(11,22,33,12,13,23)= 7.1491 7.2739 5.5949 0.0000 -1.0254 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.673 | | mean alpha: 0.9994 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.8469 6.8954 5.5875 -1.2783 -0.3653 0.3518 | | trace(B) = (B11 + B22 + B33)/3 = 6.443 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.009349 r_work= 0.1007 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8691 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.8469 6.8954 5.5875 0.0000 -0.3653 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.443 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.8469 6.8954 5.5875 0.0000 -0.3653 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.443 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.8469 6.8954 5.5875 0.0000 -0.3653 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.443 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.012438 r_work= 0.1155 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7996 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000020 r_work= 0.0040 | | B(11,22,33,12,13,23)= 6.9758 7.0023 8.2485 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.409 | | mean alpha: 0.9999 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000020 r_work= 0.0040 | | B(11,22,33,12,13,23)= 6.9758 7.0023 8.2485 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.409 | | mean alpha: 0.9999 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.3538 6.7230 8.2391 -0.1385 -0.5272 0.6033 | | trace(B) = (B11 + B22 + B33)/3 = 7.439 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.012525 r_work= 0.1158 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7988 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.3538 6.7230 8.2391 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.439 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.3538 6.7230 8.2391 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.439 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.3538 6.7230 8.2391 -0.0000 -0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.439 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.006040 r_work= 0.0816 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8396 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000010 r_work= 0.0031 | | B(11,22,33,12,13,23)= 5.5741 5.5431 5.1311 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.416 | | mean alpha: 0.9999 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000010 r_work= 0.0031 | | B(11,22,33,12,13,23)= 5.5741 5.5431 5.1311 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.416 | | mean alpha: 0.9999 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.4620 5.5699 5.3731 0.3988 -0.2103 -0.3390 | | trace(B) = (B11 + B22 + B33)/3 = 5.468 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.006186 r_work= 0.0827 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8382 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.4620 5.5699 5.3731 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.468 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.4620 5.5699 5.3731 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.468 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.4620 5.5699 5.3731 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.468 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.010109 r_work= 0.1046 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8055 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000031 r_work= 0.0051 | | B(11,22,33,12,13,23)= 7.1289 6.5922 6.5176 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.746 | | mean alpha: 1.0001 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000031 r_work= 0.0051 | | B(11,22,33,12,13,23)= 7.1289 6.5922 6.5176 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.746 | | mean alpha: 1.0001 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.5773 6.7188 6.1764 -0.8598 0.0200 0.6227 | | trace(B) = (B11 + B22 + B33)/3 = 6.824 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.010344 r_work= 0.1056 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8037 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.5773 6.7188 6.1764 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.824 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.5773 6.7188 6.1764 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.824 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.5773 6.7188 6.1764 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.824 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.009562 r_work= 0.0980 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8083 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000026 r_work= 0.0048 | | B(11,22,33,12,13,23)= 8.4657 5.7985 5.4881 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.584 | | mean alpha: 1.0012 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000026 r_work= 0.0048 | | B(11,22,33,12,13,23)= 8.4657 5.7985 5.4881 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.584 | | mean alpha: 1.0012 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 9.1210 5.9846 5.6871 -0.4486 -0.6196 0.1577 | | trace(B) = (B11 + B22 + B33)/3 = 6.931 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.010579 r_work= 0.1036 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7986 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 9.1210 5.9846 5.6871 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.931 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 9.1210 5.9846 5.6871 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.931 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 9.1210 5.9846 5.6871 0.0000 0.0000 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.931 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.009107 r_work= 0.1033 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8127 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000112 r_work= 0.0105 | | B(11,22,33,12,13,23)= 6.1075 6.1075 7.7428 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.653 | | mean alpha: 0.9971 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000112 r_work= 0.0105 | | B(11,22,33,12,13,23)= 6.1075 6.1075 7.7428 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.653 | | mean alpha: 0.9971 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.1727 7.2458 7.2068 0.3352 0.5118 0.7445 | | trace(B) = (B11 + B22 + B33)/3 = 6.542 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.008647 r_work= 0.1013 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8175 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.2093 6.2093 7.2068 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.542 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.2093 6.2093 7.2068 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.542 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.2093 6.2093 7.2068 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.542 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.016877 r_work= 0.1410 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7767 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0006 | | B(11,22,33,12,13,23)= 8.4545 8.4545 8.3400 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.416 | | mean alpha: 1.0002 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0006 | | B(11,22,33,12,13,23)= 8.4545 8.4545 8.3400 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.416 | | mean alpha: 1.0002 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.5600 8.5670 8.3593 -0.1351 -0.0554 0.0333 | | trace(B) = (B11 + B22 + B33)/3 = 8.495 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.017150 r_work= 0.1423 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7748 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.5635 8.5635 8.3593 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.495 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.5635 8.5635 8.3593 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.495 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.5635 8.5635 8.3593 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.495 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.008726 r_work= 0.1020 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8023 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000086 r_work= 0.0093 | | B(11,22,33,12,13,23)= 6.6775 6.6775 7.4541 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.936 | | mean alpha: 0.9973 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000086 r_work= 0.0093 | | B(11,22,33,12,13,23)= 6.6775 6.6775 7.4541 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.936 | | mean alpha: 0.9973 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.9267 8.5394 7.1572 -0.9879 -0.0395 1.1474 | | trace(B) = (B11 + B22 + B33)/3 = 7.208 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.009182 r_work= 0.1047 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7970 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.2331 7.2331 7.1572 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.208 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.2331 7.2331 7.1572 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.208 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.2331 7.2331 7.1572 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.208 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.014291 r_work= 0.1270 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7664 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000009 r_work= 0.0030 | | B(11,22,33,12,13,23)= 8.4841 8.4841 8.0971 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.355 | | mean alpha: 0.9998 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000009 r_work= 0.0030 | | B(11,22,33,12,13,23)= 8.4841 8.4841 8.0971 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.355 | | mean alpha: 0.9998 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.1645 8.3733 8.0462 0.2081 -0.2029 0.4660 | | trace(B) = (B11 + B22 + B33)/3 = 8.195 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.013789 r_work= 0.1246 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7703 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.2689 8.2689 8.0462 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.195 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.2689 8.2689 8.0462 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.195 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.2689 8.2689 8.0462 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.195 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.005417 r_work= 0.0814 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8553 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000001 r_work= 0.0009 | | B(11,22,33,12,13,23)= 5.1653 5.1653 5.1653 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.165 | | mean alpha: 1.0001 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000001 r_work= 0.0009 | | B(11,22,33,12,13,23)= 5.1653 5.1653 5.1653 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.165 | | mean alpha: 1.0001 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.2701 5.2409 5.9655 0.0543 -0.1968 -0.3110 | | trace(B) = (B11 + B22 + B33)/3 = 5.492 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.006089 r_work= 0.0866 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8470 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.4922 5.4922 5.4922 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.492 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.4922 5.4922 5.4922 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.492 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.4922 5.4922 5.4922 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.492 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.013699 r_work= 0.1293 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7834 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000014 r_work= 0.0036 | | B(11,22,33,12,13,23)= 8.0887 8.0887 8.0887 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.089 | | mean alpha: 1.0007 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000014 r_work= 0.0036 | | B(11,22,33,12,13,23)= 8.0887 8.0887 8.0887 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.089 | | mean alpha: 1.0007 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.9523 8.1336 9.5178 -0.0406 0.3017 -0.6763 | | trace(B) = (B11 + B22 + B33)/3 = 8.868 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.016250 r_work= 0.1422 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7654 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8679 8.8679 8.8679 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.868 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8679 8.8679 8.8679 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.868 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8679 8.8679 8.8679 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.868 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.011457 r_work= 0.1170 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8094 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000169 r_work= 0.0126 | | B(11,22,33,12,13,23)= 6.9874 6.9874 6.9874 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.987 | | mean alpha: 0.9978 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000169 r_work= 0.0126 | | B(11,22,33,12,13,23)= 6.9874 6.9874 6.9874 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.987 | | mean alpha: 0.9978 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.5330 8.3048 7.9826 -0.9643 -1.1388 -0.7708 | | trace(B) = (B11 + B22 + B33)/3 = 7.940 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.014344 r_work= 0.1318 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7893 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.9402 7.9402 7.9402 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.940 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.9402 7.9402 7.9402 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.940 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.9402 7.9402 7.9402 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.940 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.013957 r_work= 0.1191 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7587 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.2343 8.8299 7.0174 -0.8081 -1.5322 -1.4553 | | trace(B) = (B11 + B22 + B33)/3 = 8.027 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.2343 8.8299 7.0174 -0.8081 -1.5322 -1.4553 | | trace(B) = (B11 + B22 + B33)/3 = 8.027 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.2343 8.8299 7.0174 -0.8081 -1.5322 -1.4553 | | trace(B) = (B11 + B22 + B33)/3 = 8.027 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.013957 r_work= 0.1191 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7587 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.2343 8.8299 7.0174 -0.8081 -1.5322 -1.4553 | | trace(B) = (B11 + B22 + B33)/3 = 8.027 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.2343 8.8299 7.0174 -0.8081 -1.5322 -1.4553 | | trace(B) = (B11 + B22 + B33)/3 = 8.027 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.2343 8.8299 7.0174 -0.8081 -1.5322 -1.4553 | | trace(B) = (B11 + B22 + B33)/3 = 8.027 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.006746 r_work= 0.0859 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8202 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000016 r_work= 0.0039 | | B(11,22,33,12,13,23)= 6.1458 6.2690 5.1110 0.0000 -0.2329 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.842 | | mean alpha: 0.9996 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000016 r_work= 0.0039 | | B(11,22,33,12,13,23)= 6.1458 6.2690 5.1110 0.0000 -0.2329 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.842 | | mean alpha: 0.9996 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.0569 6.1086 5.1268 -0.4919 -0.0477 0.1139 | | trace(B) = (B11 + B22 + B33)/3 = 5.764 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.006572 r_work= 0.0846 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8223 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.0569 6.1086 5.1268 0.0000 -0.0477 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.764 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.0569 6.1086 5.1268 0.0000 -0.0477 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.764 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.0569 6.1086 5.1268 -0.0000 -0.0477 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.764 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.008106 r_work= 0.0959 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8122 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0006 | | B(11,22,33,12,13,23)= 6.3164 5.8219 6.2481 0.0000 0.0750 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.129 | | mean alpha: 1.0001 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0006 | | B(11,22,33,12,13,23)= 6.3164 5.8219 6.2481 0.0000 0.0750 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.129 | | mean alpha: 1.0001 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.3042 5.8650 6.2902 -0.0485 0.0967 -0.0741 | | trace(B) = (B11 + B22 + B33)/3 = 6.153 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.008160 r_work= 0.0962 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8116 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.3042 5.8650 6.2902 0.0000 0.0967 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.153 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.3042 5.8650 6.2902 0.0000 0.0967 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.153 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.3042 5.8650 6.2902 0.0000 0.0967 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.153 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.011804 r_work= 0.1271 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7735 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000058 r_work= 0.0079 | | B(11,22,33,12,13,23)= 8.6139 8.6818 6.4113 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.902 | | mean alpha: 1.0006 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000058 r_work= 0.0079 | | B(11,22,33,12,13,23)= 8.6139 8.6818 6.4113 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.902 | | mean alpha: 1.0006 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8145 8.6359 6.8993 0.8687 -1.0731 -0.4080 | | trace(B) = (B11 + B22 + B33)/3 = 8.117 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.012323 r_work= 0.1307 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7679 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8145 8.6359 6.8993 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.117 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8145 8.6359 6.8993 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.117 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8145 8.6359 6.8993 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.117 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.008852 r_work= 0.1076 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8005 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000022 r_work= 0.0050 | | B(11,22,33,12,13,23)= 5.2979 6.5849 8.2008 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.695 | | mean alpha: 0.9985 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000022 r_work= 0.0050 | | B(11,22,33,12,13,23)= 5.2979 6.5849 8.2008 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.695 | | mean alpha: 0.9985 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.0790 6.0597 7.6333 0.2289 0.2566 0.7610 | | trace(B) = (B11 + B22 + B33)/3 = 6.257 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.007755 r_work= 0.0995 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8128 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.0790 6.0597 7.6333 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.257 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.0790 6.0597 7.6333 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.257 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.0790 6.0597 7.6333 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.257 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.015933 r_work= 0.1318 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7467 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000014 r_work= 0.0036 | | B(11,22,33,12,13,23)= 8.9958 8.4030 9.3134 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.904 | | mean alpha: 0.9989 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000014 r_work= 0.0036 | | B(11,22,33,12,13,23)= 8.9958 8.4030 9.3134 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.904 | | mean alpha: 0.9989 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8352 8.0349 9.0082 0.1639 0.1234 0.5310 | | trace(B) = (B11 + B22 + B33)/3 = 8.626 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.015015 r_work= 0.1272 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7539 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8352 8.0349 9.0082 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.626 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8352 8.0349 9.0082 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.626 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.8352 8.0349 9.0082 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.626 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.009962 r_work= 0.1050 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7884 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000026 r_work= 0.0046 | | B(11,22,33,12,13,23)= 5.9067 6.2200 8.6700 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.932 | | mean alpha: 0.9999 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000026 r_work= 0.0046 | | B(11,22,33,12,13,23)= 5.9067 6.2200 8.6700 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.932 | | mean alpha: 0.9999 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.1226 6.0781 8.2641 -0.5259 0.1813 0.6015 | | trace(B) = (B11 + B22 + B33)/3 = 6.822 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.009533 r_work= 0.1029 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7913 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.1226 6.0781 8.2641 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.822 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.1226 6.0781 8.2641 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.822 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.1226 6.0781 8.2641 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.822 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.009387 r_work= 0.0992 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8170 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000041 r_work= 0.0063 | | B(11,22,33,12,13,23)= 5.6597 5.6597 7.2900 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.203 | | mean alpha: 1.0012 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000041 r_work= 0.0063 | | B(11,22,33,12,13,23)= 5.6597 5.6597 7.2900 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.203 | | mean alpha: 1.0012 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.9391 7.6049 7.1274 -1.4817 0.4860 -0.2503 | | trace(B) = (B11 + B22 + B33)/3 = 6.890 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.010866 r_work= 0.1104 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7985 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.7720 6.7720 7.1274 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.890 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.7720 6.7720 7.1274 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.890 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.7720 6.7720 7.1274 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.890 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.015043 r_work= 0.1365 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7599 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000009 r_work= 0.0029 | | B(11,22,33,12,13,23)= 8.4648 8.4648 8.5600 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.497 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000009 r_work= 0.0029 | | B(11,22,33,12,13,23)= 8.4648 8.4648 8.5600 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.497 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.4788 8.4142 8.7917 0.2418 0.0353 -0.8204 | | trace(B) = (B11 + B22 + B33)/3 = 8.562 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.015253 r_work= 0.1375 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7584 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.4465 8.4465 8.7917 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.562 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.4465 8.4465 8.7917 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.562 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.4465 8.4465 8.7917 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.562 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.010938 r_work= 0.1192 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7783 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000078 r_work= 0.0089 | | B(11,22,33,12,13,23)= 8.1105 8.1105 6.6422 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.621 | | mean alpha: 0.9982 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000078 r_work= 0.0089 | | B(11,22,33,12,13,23)= 8.1105 8.1105 6.6422 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.621 | | mean alpha: 0.9982 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.4034 9.0210 6.6581 1.0701 0.0484 0.0416 | | trace(B) = (B11 + B22 + B33)/3 = 7.028 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.009413 r_work= 0.1092 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7935 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.2122 7.2122 6.6581 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.028 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.2122 7.2122 6.6581 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.028 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.2122 7.2122 6.6581 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.028 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.010448 r_work= 0.1072 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7938 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000115 r_work= 0.0113 | | B(11,22,33,12,13,23)= 5.9975 5.9975 8.8174 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.937 | | mean alpha: 0.9994 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000115 r_work= 0.0113 | | B(11,22,33,12,13,23)= 5.9975 5.9975 8.8174 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.937 | | mean alpha: 0.9994 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.8529 7.6654 8.8904 -1.3320 -0.7881 -0.1526 | | trace(B) = (B11 + B22 + B33)/3 = 7.803 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.012447 r_work= 0.1194 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7723 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.2592 7.2592 8.8904 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.803 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.2592 7.2592 8.8904 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.803 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 7.2592 7.2592 8.8904 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 7.803 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.010826 r_work= 0.1128 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7988 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0004 | | B(11,22,33,12,13,23)= 6.9484 6.9484 6.9484 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.948 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0004 | | B(11,22,33,12,13,23)= 6.9484 6.9484 6.9484 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.948 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.9244 6.9246 6.9212 -0.1257 0.1063 0.0601 | | trace(B) = (B11 + B22 + B33)/3 = 6.923 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.010754 r_work= 0.1124 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7994 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.9234 6.9234 6.9234 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.923 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.9234 6.9234 6.9234 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.923 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.9234 6.9234 6.9234 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 6.923 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.006565 r_work= 0.0900 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8334 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000001 r_work= 0.0010 | | B(11,22,33,12,13,23)= 5.4785 5.4785 5.4785 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.479 | | mean alpha: 1.0001 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000001 r_work= 0.0010 | | B(11,22,33,12,13,23)= 5.4785 5.4785 5.4785 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.479 | | mean alpha: 1.0001 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 6.0054 5.5042 5.3567 0.0212 0.0060 -0.0449 | | trace(B) = (B11 + B22 + B33)/3 = 5.622 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.006895 r_work= 0.0924 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.8294 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.6221 5.6221 5.6221 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.622 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.6221 5.6221 5.6221 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.622 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 5.6221 5.6221 5.6221 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 5.622 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.015921 r_work= 0.1357 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7533 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000006 r_work= 0.0020 | | B(11,22,33,12,13,23)= 8.6640 8.6640 8.6640 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.664 | | mean alpha: 0.9995 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000006 r_work= 0.0020 | | B(11,22,33,12,13,23)= 8.6640 8.6640 8.6640 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.664 | | mean alpha: 0.9995 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 9.0761 8.3930 7.8696 -0.3029 0.2675 0.5716 | | trace(B) = (B11 + B22 + B33)/3 = 8.446 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.015183 r_work= 0.1320 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.7589 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.4463 8.4463 8.4463 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.446 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.4463 8.4463 8.4463 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.446 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0000 | | B(11,22,33,12,13,23)= 8.4463 8.4463 8.4463 -0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 8.446 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: uaniso constr.: u+s,u,s: 33.15 32.79 0.36 OK: scale_from_ls(): u+s,u,s: 33.15 32.79 0.36 libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ml.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ml.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ml.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import max_lik |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.076303 r_work= 0.2074 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9722 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.35 b_sol= 65.00 target_w = 0.000075 r_work= 0.0044 | | B(11,22,33,12,13,23)= 4.0695 5.0422 -8.9193 0.0000 12.0058 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.064 | | mean alpha: 1.0018 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.35 b_sol= 65.00 target_w = 0.000075 r_work= 0.0044 | | B(11,22,33,12,13,23)= 4.0695 5.0422 -8.9193 0.0000 12.0058 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.064 | | mean alpha: 1.0018 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 20: k_sol & b_sol min.; T= ls_wunit_k1-------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0003 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 20: anisotropic scale; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0003 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 20: k_sol & b_sol min.; T= ml----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0003 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: ML min.&grid s.: u+s,u,s: 7.17 7.04 0.13 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.076303 r_work= 0.2074 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9722 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: k & b: minimization; T= ls_wunit_k1-------------------------| | k_sol= 0.34 b_sol= 62.19 target_w = 0.046887 r_work= 0.1827 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0113 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.34 b_sol= 62.19 target_w = 0.000041 r_work= 0.0032 | | B(11,22,33,12,13,23)= 4.0551 5.0355 -8.9365 0.0000 12.0047 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.051 | | mean alpha: 1.0014 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 4: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0004 5.0003 -9.0004 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 4: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0003 5.0002 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 4: k_sol & b_sol min.; T= ml-----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0003 5.0002 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: ML minimization: u+s,u,s: 7.83 7.70 0.13 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.076303 r_work= 0.2074 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9722 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0002 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: ML fix_ksolbsol: u+s,u,s: 8.24 8.10 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.046935 r_work= 0.1827 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0111 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0002 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: ML fix_ksolbsol: u+s,u,s: 8.64 8.50 0.14 OK: ML fix_all 1: u+s,u,s: 8.69 8.55 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.076303 r_work= 0.2074 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9722 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: ML fix_all 2: u+s,u,s: 8.74 8.60 0.14 OK: ML fix_all 3: u+s,u,s: 8.79 8.65 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0000 5.0000 -9.0000 0.0000 12.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0002 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0002 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0003 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0003 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 3: k_sol & b_sol min.; T= ml-----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0003 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: ML fix_all 4: u+s,u,s: 9.42 9.28 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.046935 r_work= 0.1827 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0111 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0002 5.0001 -9.0005 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: exercise_7: u+s,u,s: 9.82 9.68 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.042917 r_work= 0.1773 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0108 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0002 5.0001 -9.0006 0.0000 12.0002 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: exercise_8: u+s,u,s: 9.93 9.79 0.14 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.026148 r_work= 0.0844 | | B(11,22,33,12,13,23)= 4.0000 5.0000 -9.0000 0.0000 12.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9668 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000007 r_work= 0.0011 | | B(11,22,33,12,13,23)= 4.0000 5.0000 -9.0000 0.0000 12.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9997 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0000 5.0000 -9.0000 0.0000 12.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ml-----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 4.0000 5.0000 -9.0000 0.0000 12.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: exercise_9: u+s,u,s: 10.43 10.28 0.15 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.028906 r_work= 0.0895 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9634 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 1: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.35 b_sol= 65.00 target_w = 0.000083 r_work= 0.0043 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0002 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k_sol & b_sol min.; T= ml-----------------------------------| | k_sol= 0.33 b_sol= 55.00 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: exercise_10: u+s,u,s: 10.77 10.62 0.15 |-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------| | k_sol= 0.00 b_sol= 0.00 target_w = 0.075532 r_work= 0.1729 | | B(11,22,33,12,13,23)= 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.000 | | mean alpha: 0.9395 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: k & b: grid search; T= ls_wunit_k1--------------------------| | k_sol= 0.50 b_sol= 20.00 target_w = 0.000115 r_work= 0.0036 | | B(11,22,33,12,13,23)= 2.0600 4.0817 -5.9341 0.0000 3.0036 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.069 | | mean alpha: 1.0024 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------| | k_sol= 0.50 b_sol= 20.00 target_w = 0.000115 r_work= 0.0036 | | B(11,22,33,12,13,23)= 2.0600 4.0817 -5.9341 0.0000 3.0036 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = 0.069 | | mean alpha: 1.0024 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 10: k_sol & b_sol min.; T= ls_wunit_k1-------------------------| | k_sol= 0.48 b_sol= 18.90 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0000 -6.0006 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 10: anisotropic scale; T= ls_wunit_k1--------------------------| | k_sol= 0.48 b_sol= 18.90 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0000 -6.0006 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| |-macro_cycle= 10: k_sol & b_sol min.; T= ml----------------------------------| | k_sol= 0.48 b_sol= 18.90 target_w = 0.000000 r_work= 0.0001 | | B(11,22,33,12,13,23)= 2.0004 4.0000 -6.0006 0.0000 3.0001 -0.0000 | | trace(B) = (B11 + B22 + B33)/3 = -0.000 | | mean alpha: 1.0000 number of alpha <= 0.0: 0 | |-----------------------------------------------------------------------------| OK: closest to real: u+s,u,s: 13.87 13.72 0.15 OK: scale_from_ml(): u+s,u,s: 13.87 13.72 0.15 libtbx.show_dist_paths mmtbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env mmtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_all_cif_files.py /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_all_cif_files.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.monomer_library import server /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import geometry_restraints /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional srv.root_path: /net/rosie/scratch1/rwgk/dist/mon_lib Mixed case: i/Ir.cif number of cif files read successfully: 2452 writing file table_of_contents mmtbx.monomer_library.comp_as_motif GLU grep description libtbx.assert_stdin description = "GLUTAMIC-ACID" /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/monomer_library.comp_as_motif.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.monomer_library import server /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import geometry_restraints /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional libtbx.show_dist_paths mmtbx grep ^ Number of atoms libtbx.assert_stdin Number of atoms with unknown nonbonded energy type symbols: 8 /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env mmtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py /net/rosie/scratch1/rwgk/dist/regression/pdb/pdb139l.ent /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:6: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.monomer_library import server mmtbx.pdb_interpretation /net/rosie/scratch1/rwgk/dist/regression/pdb/pdb103l.ent /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/pdb_interpretation.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.monomer_library import pdb_interpretation /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/regression/pdb/pdb103l.ent Monomer Library directory: "/net/rosie/scratch1/rwgk/dist/mon_lib" Total number of atoms: 1404 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 1404 Number of chains: 2 Number of residues, atoms: 159, 1270 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 155} Chain breaks: 1 Number of residues, atoms: 131, 134 Unusual residues: {'SEO': 1, ' CL': 2} Classifications: {'undetermined': 3, 'water': 128} Link IDs: {None: 130} Number of atoms with unknown nonbonded energy type symbols: 4 " OB1 SEO 900 " " CB1 SEO 900 " " CB SEO 900 " " SG SEO 900 " Time building chain proxies: 0.85, per 1000 atoms: 0.61 Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.07 seconds Histogram of bond lengths: 1.18 - 1.31: 246 1.31 - 1.44: 347 1.44 - 1.57: 683 1.57 - 1.70: 2 1.70 - 1.83: 10 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " C TYR 161 " - " N LYS 162 " 1.329 1.259 0.070 5.10e+03 2.49e+01 " CG ASP 159 " - " OD1 ASP 159 " 1.249 1.324 -0.075 2.77e+03 1.57e+01 " C TYR 24 " - " N TYR 25 " 1.329 1.275 0.054 5.10e+03 1.51e+01 " CD GLU 108 " - " OE1 GLU 108 " 1.249 1.320 -0.071 2.77e+03 1.40e+01 " CA TYR 24 " - " C TYR 24 " 1.525 1.448 0.077 2.27e+03 1.36e+01 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.10: 5 2.10 - 2.80: 471 2.80 - 3.50: 2282 3.50 - 4.20: 4362 4.20 - 4.90: 6791 Nonbonded interactions sorted by model distance: atom i - atom j model vdw sym.op. j " OB1 SEO 900 " - " CB1 SEO 900 " 1.394 1.000 " CB1 SEO 900 " - " CB SEO 900 " 1.525 1.000 "CL CL 173 " - " O HOH 291 " 1.682 3.270 y+1,x,-z " SG SEO 900 " - " SG SEO 900 " 1.755 1.000 x-y,-y,-z+1/3 " CB SEO 900 " - " SG SEO 900 " 1.829 1.000 ... (remaining 13906 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.74: 369 17.74 - 35.48: 69 35.48 - 53.22: 25 53.22 - 70.95: 12 70.95 - 88.69: 4 Dihedral angle restraints sorted by residual: " CB LYS 19 " " CG LYS 19 " " CD LYS 19 " " CE LYS 19 " ideal model delta periodicty weight residual 180.00 -119.76 59.76 3 4.44e-03 1.59e+01 " CA GLU 22 " " CB GLU 22 " " CG GLU 22 " " CD GLU 22 " ideal model delta periodicty weight residual 180.00 -120.27 -59.73 3 4.44e-03 1.59e+01 " CB LYS 16 " " CG LYS 16 " " CD LYS 16 " " CE LYS 16 " ideal model delta periodicty weight residual 180.00 -120.48 -59.52 3 4.44e-03 1.57e+01 ... (remaining 476 not shown) target: 7776.5 bond_residual_sum (n=1288): 1150.69 nonbonded_residual_sum (n=13911): 1379.45 angle_residual_sum (n=1736): 4266.02 dihedral_residual_sum (n=479): 608.911 chirality_residual_sum (n=194): 207.005 planarity_residual_sum (n=222): 164.43 Time first energy calculation (mainly nonbonded setup): 0.00 Number of scatterers: 1404 At special positions: 0 Unit cell: (60.9, 60.9, 95.6, 90, 90, 120) Space group: P 32 2 1 (No. 154) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 6 16.00 O 364 8.00 N 230 7.00 C 802 6.00 sf(0) = scattering factor at diffraction angle 0. mmtbx.pdb_interpretation /net/rosie/scratch1/rwgk/dist/regression/pdb/ot1_ot2.pdb grep Unexpected atoms libtbx.assert_stdin /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/pdb_interpretation.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.monomer_library import pdb_interpretation /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional mmtbx.pdb_interpretation /net/rosie/scratch1/rwgk/dist/regression/pdb/large_bond.pdb tail -1 libtbx.assert_stdin Sorry: Number of bonds with excessive lengths: 1 mmtbx.geometry_minimization /net/rosie/scratch1/rwgk/dist/regression/pdb/pdb1etn.ent /net/rosie/scratch1/rwgk/dist/regression/misc/multiple_monomers.cif --max_iterations=20 tail -2 head -1 libtbx.assert_stdin Writing: pdb1etn_geometry_minimized.ent /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/geometry_minimization.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx import monomer_library /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import geometry_restraints /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb libtbx.show_dist_paths iotbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/run_tests.py --Quick /net/rosie/scratch1/rwgk/dist/iotbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_wildcard.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_wildcard.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import wildcard /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/wildcard.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_simple_parser.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_simple_parser.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import simple_parser /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phil.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phil.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.phil /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/phil.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_crystal_symmetry_from_any.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_crystal_symmetry_from_any.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/tst_strudat.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/tst_strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/pdb/tst_ext.py /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/pdb/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional u+s,u,s: 0.74 0.66 0.08 libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/tst_pdb.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/tst_pdb.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/space_group_symbols.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/space_group_symbols.py:248: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/tst_cns.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/tst_cns.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.cns.xray_structure /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/sdb_writer.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import adptbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/tst_merge.py P31 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/tst_merge.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.scalepack import merge /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 0.51 0.44 0.07 libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/no_merge_original_index.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/no_merge_original_index.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import mtz /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/extract_from_symop_lib.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/extract_from_symop_lib.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/tst.py P31 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/tst.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import mtz /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 u+s,u,s: 0.70 0.58 0.12 libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_reflection_file_utils.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_reflection_file_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_adsc.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_adsc.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.detectors import adsc /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import os,math /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import os,math /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import approx_equal /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.array_family import flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.detectors import adsc OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/tst_xplormap.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/tst_xplormap.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.xplor.map /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/map.py:32: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phases.py P31 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phases.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.pdb.xray_structure /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Writing tmp.pdb Writing: tmp.phs OK libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/regression/tst_reflection_statistics.py Fdd2 P31m /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/regression/tst_reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.command_line import reflection_statistics /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional F d d 2 P 3 1 m u+s,u,s: 3.96 3.82 0.14 OK iotbx.lattice_symmetry --unit_cell=12.7923,12.7923,29.4356,102.846,102.846,22.7475 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.option_parser import iotbx_option_parser Input ===== Unit cell: (12.7923, 12.7923, 29.4356, 102.846, 102.846, 22.7475) Space group: P 1 (No. 1) Angular tolerance: 3.000 degrees Similar symmetries ================== Symmetry in minimum-lengths cell: Hall: -C 2y (x+y,z,2*x-z) (No. 12) Input minimum-lengths cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374) Symmetry-adapted cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (25.0822, 5.04549, 29.4356, 90, 103.108, 90) Change of basis: 1/2*x+1/2*y,-1/2*x+1/2*y,z Inverse: x-y,x+y,z Maximal angular difference: 0.000 degrees Symmetry in minimum-lengths cell: P -1 (No. 2) Input minimum-lengths cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374) Symmetry-adapted cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374) Conventional setting: P -1 (No. 2) Unit cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374) Change of basis: y-z,x+y-z,-z Inverse: -x+y,x-z,-z Maximal angular difference: 0.000 degrees iotbx.lattice_symmetry --unit_cell=12,12,12.1,89,90,92 F /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.option_parser import iotbx_option_parser cctbx.lattice_symmetry diff lattice_symmetry_py_out lattice_symmetry_cpp_out libtbx.assert_stdin iotbx.lattice_symmetry --unit_cell=78.9 82.3 57.0 90 93.4 90 C --delta=1.4 grep Maximal angular difference: wc -l sed s/ //g libtbx.assert_stdin 5 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.option_parser import iotbx_option_parser iotbx.show_distances /net/rosie/scratch1/rwgk/dist/regression/misc/strudat_zeolite_atlas --tag=EUO --distance_cutoff=3.5 wc -l sed s/ //g libtbx.assert_stdin 71 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.crystal import coordination_sequences /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat iotbx.show_distances /net/rosie/scratch1/rwgk/dist/regression/misc/strudat_zeolite_atlas --tag=NAT --cs=10 tail -2 head -1 libtbx.assert_stdin TD10: 1661.40 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.crystal import coordination_sequences /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat iotbx.show_distances /net/rosie/scratch1/rwgk/dist/regression/pdb/phe.pdb --show_cartesian tail -2 head -1 libtbx.assert_stdin Pair counts: [14, 14, 13, 11, 10, 8, 7, 11, 10, 9, 12, 10, 12, 14, 13] /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.crystal import coordination_sequences /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat iotbx.distance_least_squares /net/rosie/scratch1/rwgk/dist/regression/misc/strudat_zeolite_atlas --tag=AFX grep Final cut -c-36 libtbx.assert_stdin Final target value (i_trial=0): 0.00 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/distance_least_squares.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.geometry_restraints import distance_least_squares /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/distance_least_squares.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.kriber import strudat if ( 1 ) then tail -2 libtbx.show_dist_paths iotbx head -1 libtbx.assert_stdin FOM 17711 100.00% 0.00 0.97 W: weight (of some sort) /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py /net/cci-filer1/vol1/share/structure-lib/nsf-n/resolve-dm/phase_noanom.mtz /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import mtz /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional grep ^ H libtbx.show_dist_paths iotbx tail -1 wc -l sed s/ //g libtbx.assert_stdin 1 /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py --walk /net/cci-filer1/vol1/share/structure-lib --verbose /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import mtz /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional endif iotbx.reflection_file_reader /net/rosie/scratch1/rwgk/dist/regression/reflection_files/cns.inp /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_no_header.cns /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fp_phi_fom.mtz /net/rosie/scratch1/rwgk/dist/regression/reflection_files/heavy_search_1.sdb /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3.shelx=hklf3 /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_alpha.shelx=hklf3 /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_anom.shelx=hklf3 /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hyss.pdb /net/rosie/scratch1/rwgk/dist/regression/reflection_files/i_anomalous.mtz /net/rosie/scratch1/rwgk/dist/regression/reflection_files/madbst.xplor /net/rosie/scratch1/rwgk/dist/regression/reflection_files/merge.sca /net/rosie/scratch1/rwgk/dist/regression/reflection_files/no_merge.sca /net/rosie/scratch1/rwgk/dist/regression/reflection_files/shelx.ins /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve.setup /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve_fpfm.fmt /net/rosie/scratch1/rwgk/dist/regression/reflection_files/xds_ascii_merge.hkl /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_reader.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/cns.inp file_type: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz file_type: ccp4_mtz Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:Frem,SIGFrem,DANOrem,SIGDANOrem Observation type: xray.reconstructed_amplitude Type of data: double, size=272 Type of sigmas: double, size=272 Number of Miller indices: 272 Anomalous flag: True Unit cell: (84.511, 104.308, 174.103, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 54 Resolution range: 19.853 15.0015 Completeness in resolution range: 0.989091 Completeness with d_max=infinity: 0.572632 Bijvoet pairs: 109 Lone Bijvoet mates: 0 Anomalous signal: 0.0293 Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:ISYMrem Observation type: None Type of data: int, size=163 Type of sigmas: None Number of Miller indices: 163 Anomalous flag: False Unit cell: (84.511, 104.308, 174.103, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 54 Resolution range: 19.853 15.0015 Completeness in resolution range: 0.981928 Completeness with d_max=infinity: 0.537954 Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:Finf,SIGFinf,DANOinf,SIGDANOinf Observation type: xray.reconstructed_amplitude Type of data: double, size=273 Type of sigmas: double, size=273 Number of Miller indices: 273 Anomalous flag: True Unit cell: (84.577, 104.408, 174.249, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 56 Resolution range: 19.8687 15.0137 Completeness in resolution range: 0.992727 Completeness with d_max=infinity: 0.574737 Bijvoet pairs: 108 Lone Bijvoet mates: 1 Anomalous signal: 0.0281 Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:ISYMinf Observation type: None Type of data: int, size=165 Type of sigmas: None Number of Miller indices: 165 Anomalous flag: False Unit cell: (84.577, 104.408, 174.249, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 56 Resolution range: 19.8687 15.0137 Completeness in resolution range: 0.993976 Completeness with d_max=infinity: 0.544554 Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:Fabs,SIGFabs,DANOabs,SIGDANOabs Observation type: xray.reconstructed_amplitude Type of data: double, size=273 Type of sigmas: double, size=273 Number of Miller indices: 273 Anomalous flag: True Unit cell: (84.572, 104.489, 174.424, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 56 Resolution range: 19.87 15.0207 Completeness in resolution range: 0.992727 Completeness with d_max=infinity: 0.574737 Bijvoet pairs: 108 Lone Bijvoet mates: 1 Anomalous signal: 0.0354 Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:ISYMabs Observation type: None Type of data: int, size=165 Type of sigmas: None Number of Miller indices: 165 Anomalous flag: False Unit cell: (84.572, 104.489, 174.424, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 56 Resolution range: 19.87 15.0207 Completeness in resolution range: 0.993976 Completeness with d_max=infinity: 0.544554 file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns file_type: cns_reflection_file Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns:PA_MOD,PB_MOD,PC_MOD,PD_MOD Observation type: None Type of data: hendrickson_lattman, size=100 Type of sigmas: None Number of Miller indices: 100 Anomalous flag: True Unit cell: None Space group: None Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns:FULL_MOD Observation type: None Type of data: complex_double, size=100 Type of sigmas: None Number of Miller indices: 100 Anomalous flag: True Unit cell: None Space group: None Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns:FOM_MOD Observation type: None Type of data: double, size=100 Type of sigmas: None Number of Miller indices: 100 Anomalous flag: True Unit cell: None Space group: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref file_type: dtrek_reflnlist Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref:Intensity,SigmaI Observation type: xray.intensity Type of data: double, size=100 Type of sigmas: double, size=100 Number of Miller indices: 100 Anomalous flag: False Unit cell: (83.0345, 89.9715, 94.9243, 90, 90, 90) Space group: P 2 2 2 (No. 16) Systematic absences: 0 Centric reflections: 100 Resolution range: 32.6501 2.36571 Completeness in resolution range: 0.00336508 Completeness with d_max=infinity: 0.00336293 Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref:Intensity+-,SigmaI+- Observation type: xray.intensity Type of data: double, size=100 Type of sigmas: double, size=100 Number of Miller indices: 100 Anomalous flag: True Unit cell: (83.0345, 89.9715, 94.9243, 90, 90, 90) Space group: P 2 2 2 (No. 16) Systematic absences: 0 Centric reflections: 100 Resolution range: 32.6501 2.36571 Completeness in resolution range: 0.00178253 Completeness with d_max=infinity: 0.0017818 Bijvoet pairs: 0 Lone Bijvoet mates: 0 Anomalous signal: 0.0000 file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns file_type: cns_reflection_file Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns:FOBS,SIGMA Observation type: xray.amplitude Type of data: double, size=100 Type of sigmas: double, size=100 Number of Miller indices: 100 Anomalous flag: True Unit cell: None Space group: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_no_header.cns file_type: cns_index_fobs_sigma Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_no_header.cns:FOBS,SIGMA Observation type: xray.amplitude Type of data: double, size=100 Type of sigmas: double, size=100 Number of Miller indices: 100 Anomalous flag: False Unit cell: None Space group: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fp_phi_fom.mtz file_type: ccp4_mtz Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fp_phi_fom.mtz:foo,PHIfoo Observation type: xray.amplitude Type of data: complex_double, size=23 Type of sigmas: None Number of Miller indices: 23 Anomalous flag: False Unit cell: (54.723, 76.075, 50.884, 90, 90, 90) Space group: P 21 21 2 (No. 18) Systematic absences: 0 Centric reflections: 17 Resolution range: 50.884 20.3569 Completeness in resolution range: 1 Completeness with d_max=infinity: 1 file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/heavy_search_1.sdb file_type: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3.shelx=hklf3 file_type: shelx_hklf Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3.shelx:Fobs,SigFobs Observation type: xray.amplitude Type of data: double, size=100 Type of sigmas: double, size=100 Number of Miller indices: 100 Anomalous flag: False Unit cell: None Space group: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_alpha.shelx=hklf3 file_type: shelx_hklf Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_alpha.shelx:Fobs,SigFobs Observation type: xray.amplitude Type of data: double, size=100 Type of sigmas: double, size=100 Number of Miller indices: 100 Anomalous flag: False Unit cell: None Space group: None Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_alpha.shelx:alphas Observation type: None Type of data: int, size=100 Type of sigmas: None Number of Miller indices: 100 Anomalous flag: False Unit cell: None Space group: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_anom.shelx=hklf3 file_type: shelx_hklf Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_anom.shelx:Fobs,SigFobs Observation type: xray.amplitude Type of data: double, size=101 Type of sigmas: double, size=101 Number of Miller indices: 101 Anomalous flag: True Unit cell: None Space group: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hyss.pdb file_type: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/i_anomalous.mtz file_type: ccp4_mtz Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/i_anomalous.mtz:i_anomalous(+),SIGi_anomalous(+),i_anomalous(-),SIGi_anomalous(-) Observation type: xray.intensity Type of data: double, size=183 Type of sigmas: double, size=183 Number of Miller indices: 183 Anomalous flag: True Unit cell: (115.986, 115.986, 44.151, 90, 90, 120) Space group: P 6 (No. 168) Systematic absences: 0 Centric reflections: 10 Resolution range: 100.447 2.43475 Completeness in resolution range: 0.00735176 Completeness with d_max=infinity: 0.00735176 Bijvoet pairs: 83 Lone Bijvoet mates: 7 Anomalous signal: 0.0773 file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/madbst.xplor file_type: cns_index_fobs_sigma Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/madbst.xplor:FOBS,SIGMA Observation type: xray.amplitude Type of data: double, size=100 Type of sigmas: double, size=100 Number of Miller indices: 100 Anomalous flag: False Unit cell: None Space group: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/merge.sca file_type: scalepack_merge Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/merge.sca:i_obs,sigma Observation type: xray.intensity Type of data: double, size=183 Type of sigmas: double, size=183 Number of Miller indices: 183 Anomalous flag: True Unit cell: (115.986, 115.986, 44.151, 90, 90, 120) Space group: P 6 (No. 168) Systematic absences: 0 Centric reflections: 10 Resolution range: 100.447 2.43475 Completeness in resolution range: 0.00735176 Completeness with d_max=infinity: 0.00735176 Bijvoet pairs: 83 Lone Bijvoet mates: 7 Anomalous signal: 0.0773 file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/no_merge.sca file_type: scalepack_no_merge_original_index Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/no_merge.sca:i_obs,sigma,merged Observation type: xray.intensity Type of data: double, size=52 Type of sigmas: double, size=52 Number of Miller indices: 52 Anomalous flag: True Unit cell: None Space group: P 2 2 2 (No. 16) Systematic absences: 0 Centric reflections: 52 Bijvoet pairs: 0 Lone Bijvoet mates: 0 Anomalous signal: 0.0000 file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/shelx.ins file_type: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve.setup file_type: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve_fpfm.fmt file_type: solve_fpfm Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve_fpfm.fmt:fpfm,sigma_fpfm Observation type: xray.amplitude Type of data: double, size=160 Type of sigmas: double, size=160 Number of Miller indices: 160 Anomalous flag: True Unit cell: None Space group: None file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/xds_ascii_merge.hkl file_type: xds_ascii Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/xds_ascii_merge.hkl:iobs,sigma_iobs Observation type: xray.intensity Type of data: double, size=100 Type of sigmas: double, size=100 Number of Miller indices: 100 Anomalous flag: True Unit cell: (131.92, 134.49, 203.83, 90, 90, 90) Space group: P 2 2 2 (No. 16) Systematic absences: 0 Centric reflections: 26 Resolution range: 29.3029 24.1946 Completeness in resolution range: 0.877193 Completeness with d_max=infinity: 0.361011 Bijvoet pairs: 35 Lone Bijvoet mates: 4 Anomalous signal: 0.0577 iotbx.reflection_statistics /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional iotbx.reflection_statistics /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns --unit_cell=12,12,12.1,89,90,92 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional iotbx.reflection_statistics /net/rosie/scratch1/rwgk/dist/regression/reflection_files/gpd_nat_resolution_8.mtz grep l,-k,h libtbx.assert_stdin l,-k,h /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional if ( 1 ) then iotbx.reflection_statistics /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz --resolution 4 --bins 8 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional iotbx.reflection_statistics /net/cci-filer1/vol1/share/structure-lib/rnase-s/data/rnase25.mtz --quick /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional iotbx.reflection_statistics /net/cci-filer1/vol1/share/structure-lib/p9/data/infl.sca --unit_cell=114,114,32,90,90,90 --space_group=I4 --weak_symmetry --resolution=4 grep Space group: libtbx.assert_stdin Space group: I 41 (No. 80) /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional iotbx.reflection_statistics /net/cci-filer1/vol1/share/structure-lib/p9/data/infl.sca --unit_cell=114,114,32,90,90,90 --space_group=I4 --resolution=4 grep Space group: libtbx.assert_stdin Space group: I 4 (No. 79) /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional iotbx.reflection_file_converter /net/cci-filer1/vol1/share/structure-lib/p9/data/peak.sca --unit_cell=113.949,113.949,32.474,90,90,90 --mtz=tmpf --write_mtz_amplitudes --non_anomalous --mtz_root_label=FPEAK /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional file_name: /net/cci-filer1/vol1/share/structure-lib/p9/data/peak.sca file_type: scalepack_no_merge_original_index Miller array info: /net/cci-filer1/vol1/share/structure-lib/p9/data/peak.sca:i_obs,sigma Observation type: xray.intensity Type of data: double, size=145453 Type of sigmas: double, size=145453 Number of Miller indices: 145453 Anomalous flag: True Unit cell: None Space group: I 41 (No. 80) Selected data: /net/cci-filer1/vol1/share/structure-lib/p9/data/peak.sca:i_obs,sigma Observation type: xray.intensity Input crystal symmetry: Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 41 (No. 80) Merging symmetry-equivalent values: R-linear = sum(abs(data - mean(data))) / sum(abs(data)) R-square = sum((data - mean(data))**2) / sum(data**2) In these sums single measurements are excluded. Redundancy Mean Mean Min Max Mean R-linear R-square unused: - 28.4910 bin 1: 28.4910 - 3.7555 1 8 3.782 0.0549 0.0105 bin 2: 3.7555 - 2.9819 1 8 3.781 0.0796 0.0253 bin 3: 2.9819 - 2.6052 1 8 3.753 0.1007 0.0343 bin 4: 2.6052 - 2.3672 1 8 3.719 0.1366 0.0554 bin 5: 2.3672 - 2.1976 1 8 3.644 0.1559 0.0685 bin 6: 2.1976 - 2.0680 1 8 3.534 0.1904 0.0906 bin 7: 2.0680 - 1.9645 1 8 3.410 0.2253 0.1156 bin 8: 1.9645 - 1.8790 1 6 3.297 0.2793 0.1542 bin 9: 1.8790 - 1.8067 1 6 3.209 0.3637 0.2270 bin 10: 1.8067 - 1.7443 1 7 3.166 0.4207 0.2714 unused: 1.7443 - Miller array info: None Observation type: xray.intensity Type of data: double, size=41181 Type of sigmas: double, size=41181 Number of Miller indices: 41181 Anomalous flag: True Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 41 (No. 80) Systematic absences: 0 Centric reflections: 1668 Resolution range: 28.4872 1.74434 Completeness in resolution range: 0.990714 Completeness with d_max=infinity: 0.990547 Bijvoet pairs: 19624 Lone Bijvoet mates: 265 Anomalous signal: 0.0835 Converting data array from anomalous to non-anomalous. Writing MTZ file: tmpf.mtz Converting intensities to amplitudes. endif iotbx.cns.sdb_reader /net/rosie/scratch1/rwgk/dist/regression/reflection_files/heavy_search_1.sdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/cns.sdb_reader.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.cns import sdb_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/sdb_reader.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional file: heavy_search_1.sdb unit cell: (116.09699999999999, 116.09699999999999, 44.174999999999997, 90.0, 90.0, 120.0) space group: P 6 Number of scatterers: 6 At special positions: 0 Unit cell: (116.097, 116.097, 44.175, 90, 90, 120) Space group: P 6 (No. 168) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso SE_SE Se 6 ( 0.2221 0.1206 0.0037) 1.00 0.8314 SE_SE Se 6 ( 0.2286 0.1400 0.2089) 1.00 0.4283 SE_SE Se 6 ( 0.3687 0.2845 0.2254) 1.00 0.9112 SE_SE Se 6 ( 0.1766 0.0992 0.2504) 1.00 0.5232 SE_SE Se 6 ( 0.3813 0.2748 0.3024) 1.00 0.8433 SE_SE Se 6 ( 0.2107 0.0698 0.9259) 1.00 0.8796 cp /net/rosie/scratch1/rwgk/dist/regression/reflection_files/cns.inp . iotbx.cns.transfer_crystal_symmetry /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz cns.inp libtbx.assert_stdin Info: 5 changes (sg, a, b, c, gamma), writing modified file "cns.inp". /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/cns.transfer_crystal_symmetry.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import cns /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional iotbx.cns.transfer_crystal_symmetry /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz cns.inp libtbx.assert_stdin Info: no changes, "cns.inp" was not modified. /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/cns.transfer_crystal_symmetry.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import cns /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional foreach file ( merge.sca no_merge.sca xds_ascii_merge.hkl dtscale.ref i_anomalous.mtz shelx.ins cns.inp heavy_search_1.sdb hyss.pdb solve.setup ../misc/cns.map ) iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/merge.sca /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(115.986, 115.986, 44.151, 90, 90, 120), space_group_symbol='P 6') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/no_merge.sca /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=None, space_group_symbol='P 2 2 2') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/xds_ascii_merge.hkl /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(131.92, 134.49, 203.83, 90, 90, 90), space_group_symbol='P 2 2 2') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(83.0345, 89.9715, 94.9243, 90, 90, 90), space_group_symbol='P 2 2 2') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/i_anomalous.mtz /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(115.986, 115.986, 44.151, 90, 90, 120), space_group_symbol='P 6') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/shelx.ins /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(87.8432, 155.426, 209.866, 90, 99.2821, 90), space_group_symbol='P 1 21 1') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/cns.inp /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(116.097, 116.097, 44.175, 90, 90, 120), space_group_symbol='P 6') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/heavy_search_1.sdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(116.097, 116.097, 44.175, 90, 90, 120), space_group_symbol='P 6') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hyss.pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(115.986, 115.986, 44.151, 90, 90, 120), space_group_symbol='P 6') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve.setup /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(131.919, 134.489, 203.834, 90, 90, 90), space_group_symbol='P 21 21 21') end iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/../misc/cns.map /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional crystal.symmetry( unit_cell=(7.4141, 7.4141, 12.604, 90, 90, 120), space_group_symbol=None) end libtbx.assert_stdin P 1 21 1 libtbx.show_dist_paths iotbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/shelx_latt_sym_to_space_group_symbol.py /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/shelx_latt_sym_to_space_group_symbol.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.shelx.crystal_symmetry_from_ins import read_shelx_latt /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/shelx/crystal_symmetry_from_ins.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional libtbx.assert_stdin P 1 21 1 libtbx.show_dist_paths iotbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/shelx_latt_sym_to_space_group_symbol.py /net/rosie/scratch1/rwgk/dist/regression/reflection_files/shelx.ins /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/shelx_latt_sym_to_space_group_symbol.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.shelx.crystal_symmetry_from_ins import read_shelx_latt /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/shelx/crystal_symmetry_from_ins.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional libtbx.show_dist_paths iotbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/direct_methods_light.py /net/rosie/scratch1/rwgk/dist/regression/misc/vj1132Isup2.hkl /net/rosie/scratch1/rwgk/dist/regression/misc/vj1132sup1.cif /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/direct_methods_light.py:13: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import acta_c /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/acta_c.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/acta_c.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/PyCifRW': missing __init__.py from PyCifRW.CifFile import CifFile Miller array info: /net/rosie/scratch1/rwgk/dist/regression/misc/vj1132Isup2.hkl:F_meas,F_sigma Observation type: xray.amplitude Type of data: double, size=422 Type of sigmas: double, size=422 Number of Miller indices: 422 Anomalous flag: False Unit cell: (12.0263, 6.0321, 5.8293, 90, 90, 90) Space group: P n a 21 (No. 33) Systematic absences: 0 Centric reflections: 83 Resolution range: 6.01315 0.83382 Completeness in resolution range: 1 Completeness with d_max=infinity: 1 unused: - 6.0133 [ 0/0 ] bin 1: 6.0133 - 1.6574 [57/57] bin 2: 1.6574 - 1.3201 [55/55] bin 3: 1.3201 - 1.1546 [55/55] bin 4: 1.1546 - 1.0496 [45/45] bin 5: 1.0496 - 0.9747 [55/55] bin 6: 0.9747 - 0.9175 [55/55] bin 7: 0.9175 - 0.8717 [48/48] bin 8: 0.8717 - 0.8338 [52/52] unused: 0.8338 - [ 0/0 ] number of large_e_values: 111 triplets per reflection: min,max,mean: 34, 216, 98.40 total number of triplets: 10922 e_map max 11.9186 e_map min -2.87961 e_map mean -2.29868e-17 e_map sigma 1 e_map peak list fractional coordinates peak height ( 0.185597, 0.796808, 0.966541) 12.159 ( 0.093150, 0.511063, 0.086868) 9.072 ( 0.144450, 0.689052, 0.127853) 8.099 ( 0.168054, 0.788814, 0.355261) 6.019 ( 0.136866, 0.605904, 0.547503) 4.943 ( 0.052046, -0.012755, 0.950492) 4.702 ( 0.091541, 0.981652, 0.394957) 4.641 ( 0.137974, 0.656793, 0.767546) 3.277 ( 0.180290, 0.231704, 0.968437) 2.905 (-0.003727, 0.232895, 0.460465) 2.618 Number of scatterers: 13 At special positions: 0 Unit cell: (12.0263, 6.0321, 5.829, 90, 90, 90) Space group: P n a 21 (No. 33) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso O1 O 4 ( 0.5896 0.4862 0.6045) 1.00 0.0356 O2 O 4 ( 0.6861 0.2009 0.7409) 1.00 0.0328 C2 C 4 ( 0.6636 0.2231 0.3380) 1.00 0.0224 H2 H 4 ( 0.7419 0.1804 0.3237) 1.00 0.0270 C1 C 4 ( 0.6443 0.3133 0.5818) 1.00 0.0222 C3 C 4 ( 0.5923 0.0216 0.2916) 1.00 0.0347 H3A H 4 ( 0.6060 -0.0308 0.1387) 1.00 0.0520 H3B H 4 ( 0.5153 0.0605 0.3069) 1.00 0.0520 H3C H 4 ( 0.6104 -0.0930 0.3997) 1.00 0.0520 N1 N 4 ( 0.6395 0.3976 0.1659) 1.00 0.0258 H1A H 4 ( 0.6815 0.5160 0.1942) 1.00 0.0390 H1B H 4 ( 0.5680 0.4351 0.1741) 1.00 0.0390 H1C H 4 ( 0.6544 0.3463 0.0261) 1.00 0.0390 correlation of f_obs and f_calc: 0.9943 Match summary: Operator: rotation: {{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}} translation: {1.98612e-34, 0.5, 0.21909} rms coordinate differences: 0.39 Pairs: 8 O1 peak01 0.168 O2 peak00 0.070 C2 peak03 0.175 C1 peak02 0.057 C3 peak06 0.191 H3B peak05 0.949 N1 peak04 0.050 H1C peak07 0.478 Singles model 1: 5 H2 H3A H3C H1A H1B Singles model 2: 2 peak08 peak09 if ( -d /net/cci/srv/html/cci/cctbx_downloads && /net/rosie/scratch1/rwgk/dist/htdocs != None ) then libtbx.python /net/rosie/scratch1/rwgk/dist/htdocs/siena2005/sort_merge.py /net/cci/srv/html/cci/cctbx_downloads/regression/siena2005_gms_sort_merge_exercise_in_info_and_hkl.data grep Centric reflections libtbx.assert_stdin Centric reflections: 4354 /net/rosie/scratch1/rwgk/dist/htdocs/siena2005/sort_merge.py:15: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional endif grep -i error libtbx.show_dist_paths cctbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/run_tests.py --Verbose /net/rosie/scratch1/rwgk/dist/cctbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_krivy_gruber.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.uctbx import reduction_base /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_denominators.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import sgtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_adp_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 3 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional I 41/a c d :2 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_direct_space_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional I 41/a c d :2 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.crystal import close_packing /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.pdb R -3 m :R /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.development import random_structure /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional I 41/a c d :2 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reciprocal_space_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 3 1 2 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx.test_utils import approx_equal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import dmtbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 41 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import euclidean_model_matching as emma /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_centre_of_inversion.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import find_centre_of_inversion /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_expand_to_p1.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_change_basis.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.xray import minimization /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_wilson_plot.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import statistics /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math.gaussian # base class for gaussian /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_fast_gradients.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_minimization.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_maptbx_structure_factors.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import maptbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_merge_equivalents.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_fft_map.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import crystal /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sampled_model_density.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_fast_nv1995.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import translation_search /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional F 2 2 2 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/make_cns_input.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.eltbx.xray_scattering /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.math.gaussian # base class for gaussian /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python P 31 /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.cns import reflection_reader /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.cns import reflection_reader /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import adptbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.shelx.write_ins import LATT_SYMM sh: shelxl: command not found mean_weighted_phase_error: 1.10 direct/fft_regression mean weighted phase error: 0.04 direct/fft_xray mean weighted phase error: 0.04 direct/fft_regression mean weighted phase error: 0.31 direct/fft_xray mean weighted phase error: 0.31 direct/fft_regression mean weighted phase error: 0.09 direct/fft_xray mean weighted phase error: 0.09 direct/fft_regression mean weighted phase error: 0.26 direct/fft_xray mean weighted phase error: 0.26 direct/fft_regression mean weighted phase error: 0.10 direct/fft_xray mean weighted phase error: 0.10 direct/fft_regression mean weighted phase error: 0.05 direct/fft_xray mean weighted phase error: 0.04 direct/fft_regression mean weighted phase error: 0.68 direct/fft_xray mean weighted phase error: 0.68 direct/fft_regression mean weighted phase error: 0.15 direct/fft_xray mean weighted phase error: 0.14 direct/fft_regression mean weighted phase error: 0.04 direct/fft_xray mean weighted phase error: 0.04 direct/fft_regression mean weighted phase error: 0.05 direct/fft_xray mean weighted phase error: 0.05 direct/fft_regression mean weighted phase error: 0.21 direct/fft_xray mean weighted phase error: 0.21 direct/fft_regression mean weighted phase error: 0.03 direct/fft_xray mean weighted phase error: 0.04 direct/fft_regression mean weighted phase error: 0.42 direct/fft_xray mean weighted phase error: 0.42 direct/fft_regression mean weighted phase error: 0.17 direct/fft_xray mean weighted phase error: 0.16 direct/fft_regression mean weighted phase error: 0.71 direct/fft_xray mean weighted phase error: 0.71 direct/fft_regression mean weighted phase error: 0.10 direct/fft_xray mean weighted phase error: 0.10 grep -i error libtbx.show_dist_paths iotbx /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/run_tests.py --Verbose /net/rosie/scratch1/rwgk/dist/iotbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/tst_merge.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.scalepack import merge /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/tst.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import mtz /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional P 31 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phases.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.pdb.xray_structure /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/regression/tst_reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx.command_line import reflection_statistics /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional F d d 2 P 3 1 m /net/rosie/scratch1/rwgk/dist/regression/misc/tst_iotbx_emma.csh /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/find_in_repositories.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import uctbx /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK /net/rosie/scratch1/rwgk/dist/regression/misc/tst_iotbx_reflection_file.csh /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/find_in_repositories.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_converter /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/mtz.dump.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import mtz /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional OK iotbx.pdb.hierarchy /net/rosie/scratch1/rwgk/dist/regression/pdb/pdb13gs.ent --details=conformer --prefix=T@ grep -v ^T@ libtbx.assert_stdin /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/pdb.hierarchy.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional libtbx.show_dist_paths phenix grep -i error /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env phenix.python /net/rosie/scratch1/rwgk/dist/phenix/run_tests.py --Verbose /net/rosie/scratch1/rwgk/dist/phenix/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import test_utils /net/rosie/scratch1/rwgk/dist/phenix/phenix/regression/tst_heavy_search.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex C 1 2 1 if ( 1 ) then mmtbx.xtriage file=/net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz obs_labels=SEpeak log=gre_MAD.log /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/xtriage.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.scaling import xtriage /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/xtriage.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.phil ############################################################# ## mmtbx.xtriage ## ## ## ## P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams ## ## ## ############################################################# Date 2006-06-25 Time 20:09:04 PDT -0700 ##-------------------------------------------## ## WARNING: ## ## Number of residues unspecified ## ##-------------------------------------------## Effective parameters: scaling.input { parameters { asu_contents { n_residues = None n_bases = None n_copies_per_asu = None } misc_twin_parameters { missing_symmetry { tanh_location = 0.08 tanh_slope = 50 } twinning_with_ncs { perform_analyses = False n_bins = 7 } twin_test_cuts { low_resolution = 10 high_resolution = None isigi_cut = 3 completeness_cut = 0.85 } } reporting { verbose = 1 log = "gre_MAD.log" ccp4_style_graphs = True } } xray_data { file_name = "/net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz" obs_labels = SEpeak calc_labels = None unit_cell = 108.7419968 61.67900085 71.65200043 90 97.15100098 90 space_group = "C 1 2 1" high_resolution = None low_resolution = None } } Symmetry, cell and reflection file content summary Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak Observation type: xray.amplitude Type of data: double, size=23010 Type of sigmas: double, size=23010 Number of Miller indices: 23010 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 766 Resolution range: 29.664 2.74731 Completeness in resolution range: 0.955763 Completeness with d_max=infinity: 0.955049 Bijvoet pairs: 11010 Lone Bijvoet mates: 224 Anomalous signal: 0.1207 ##----------------------------------------------------## ## Basic statistics ## ##----------------------------------------------------## Matthews coefficient and Solvent content statistics Number of residues unknown, assuming 50% solvent content ---------------------------------------------------------------- | Best guess : 436 residues in the asu | ---------------------------------------------------------------- Completeness and data strength analyses The following table lists the completeness in various resolution ranges, after applying a I/sigI cut. Miller indices for which individual I/sigI values are larger than the value specified in the top row of the table, are retained, while other intensities are discarded. The resulting completeness profiles are an indication of the strength of the data. ---------------------------------------------------------------------------------------- | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | ---------------------------------------------------------------------------------------- | 29.67 - 6.75 | 93.3% | 91.2% | 90.0% | 87.4% | 81.7% | 74.7% | | 6.75 - 5.37 | 96.1% | 89.3% | 86.9% | 80.5% | 63.7% | 45.5% | | 5.37 - 4.69 | 97.0% | 90.0% | 87.4% | 81.0% | 63.8% | 40.8% | | 4.69 - 4.27 | 97.7% | 92.8% | 90.8% | 87.2% | 75.2% | 58.9% | | 4.27 - 3.96 | 98.2% | 90.5% | 87.1% | 81.0% | 65.4% | 48.2% | | 3.96 - 3.73 | 97.9% | 87.9% | 84.1% | 76.4% | 58.5% | 35.5% | | 3.73 - 3.54 | 97.3% | 86.8% | 82.6% | 73.5% | 48.2% | 16.7% | | 3.54 - 3.39 | 97.5% | 81.2% | 74.9% | 62.1% | 41.2% | 23.8% | | 3.39 - 3.26 | 99.0% | 79.2% | 70.9% | 56.6% | 31.2% | 13.7% | | 3.26 - 3.14 | 97.5% | 71.1% | 62.1% | 46.4% | 20.8% | 7.7% | | 3.14 - 3.05 | 97.0% | 66.8% | 58.2% | 40.3% | 15.6% | 4.0% | | 3.05 - 2.96 | 98.5% | 61.1% | 50.1% | 33.0% | 7.5% | 0.4% | | 2.96 - 2.88 | 96.3% | 54.1% | 43.2% | 26.9% | 8.9% | 2.5% | | 2.88 - 2.81 | 94.1% | 45.0% | 35.6% | 22.0% | 6.9% | 2.4% | ---------------------------------------------------------------------------------------- Maximum likelihood isotropic Wilson scaling ML estimate of overall B value of /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak: 37.29 A**(-2) Estimated -log of scale factor of /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak: -0.44 Maximum likelihood anisotropic Wilson scaling ML estimate of overall B_cart value of /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak: 35.85, 0.00, 7.66 36.31, 0.00 41.02 Equivalent representation as U_cif: 0.48, -0.00, 0.16 0.46, 0.00 0.52 ML estimate of -log of scale factor of /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak: -0.44 Correcting for anisotropy in the data Some basic intensity statistics follow. Low resolution completeness analyses The following table shows the completeness of the data to 5 Angstrom. unused: - 29.6645 [ 0/18 ] 0.000 bin 1: 29.6645 - 10.6221 [368/402] 0.915 bin 2: 10.6221 - 8.4963 [383/408] 0.939 bin 3: 8.4963 - 7.4416 [368/388] 0.948 bin 4: 7.4416 - 6.7701 [367/389] 0.943 bin 5: 6.7701 - 6.2898 [381/396] 0.962 bin 6: 6.2898 - 5.9221 [392/409] 0.958 bin 7: 5.9221 - 5.6276 [375/382] 0.982 bin 8: 5.6276 - 5.3841 [417/434] 0.961 bin 9: 5.3841 - 5.1780 [367/371] 0.989 bin 10: 5.1780 - 5.0002 [389/407] 0.956 unused: 5.0002 - [ 0/0 ] Mean intensity analyses Analyses of the mean intensity. Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. The following resolution shells are worrisome: ------------------------------------------------ | d_spacing | z_score | compl. | / | ------------------------------------------------ | 8.445 | 4.76 | 0.96 | 1.463 | | 5.771 | 6.23 | 0.98 | 0.713 | | 5.422 | 5.85 | 0.97 | 0.742 | | 5.128 | 9.65 | 0.97 | 0.626 | | 4.878 | 7.50 | 0.99 | 0.689 | | 3.676 | 6.04 | 0.99 | 1.304 | ------------------------------------------------ Possible reasons for the presence of the reported unexpected low or elevated mean intensity in a given resolution bin are : - missing overloaded or weak reflections - suboptimal data processing - satelite (ice) crystals - NCS - translational pseudo symmetry (detected elsewhere) - outliers (detected elsewhere) - ice rings (detected elsewhere) - other problems Note that the presence of abnormalities in a certain region of reciprocal space might confuse the data validation algorithm throughout a large region of reciprocal space, even though the data is acceptable in those areas. Possible outliers Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 Acentric reflections: None Centric reflections: None Ice ring related problems The following statistics were obtained from ice-ring insensitive resolution ranges mean bin z_score : 2.54 ( rms deviation : 2.47 ) mean bin completeness : 0.92 ( rms deviation : 0.18 ) The following table shows the z-scores and completeness in ice-ring sensitive areas. Large z-scores and high completeness in these resolution ranges might be a reason to re-assess your data processsing if ice rings were present. ------------------------------------------------ | d_spacing | z_score | compl. | Rel. Ice int. | ------------------------------------------------ | 3.897 | 0.45 | 0.98 | 1.000 | | 3.669 | 1.13 | 0.97 | 0.750 | | 3.441 | 2.48 | 0.97 | 0.530 | ------------------------------------------------ Abnormalities in mean intensity or completeness at resolution ranges with a relative ice ring intensity lower then 0.10 will be ignored. No ice ring related problems detected. If ice rings were present, the data does not look worse at ice ring related d_spacings as compared to the rest of the data set Analyses of anomalous differences Table of measurability as a function of resolution The measurability is defined as the fraction of Bijvoet related intensity differences for which |delta_I|/sigma_delta_I > 3.0 min[I(+)/sigma_I(+), I(-)/sigma_I(-)] > 3.0 holds. The measurability provides an intuitive feeling of the quality of the data, as it is related to the number of reliable Bijvoet differences. When the data is processed properly and the standard deviations have been estimated accurately, values larger than 0.05 are encouraging. unused: - 29.6657 [ 0/18 ] bin 1: 29.6657 - 5.9049 [2279/2412] 0.3837 bin 2: 5.9049 - 4.6929 [2342/2404] 0.2224 bin 3: 4.6929 - 4.1014 [2356/2397] 0.1292 bin 4: 4.1014 - 3.7272 [2394/2432] 0.0857 bin 5: 3.7272 - 3.4605 [2341/2380] 0.0451 bin 6: 3.4605 - 3.2567 [2375/2403] 0.0373 bin 7: 3.2567 - 3.0938 [2396/2428] 0.0138 bin 8: 3.0938 - 2.9593 [2348/2390] 0.0035 bin 9: 2.9593 - 2.8454 [2334/2396] 0.0124 bin 10: 2.8454 - 2.7473 [1845/2433] 0.0059 unused: 2.7473 - [ 0/0 ] The anomalous signal seems to extend to about 3.7 A (or to 3.5 A, from a more optimistic point of view) The quoted resolution limits can be used as a guideline to decide where to cut the resolution for phenix.hyss Basic analyses completed ##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------## Using data between 10.00 to 3.96 Angstrom. Determining possible twin laws. 0 merohedral twin operators found 0 pseudo-merohedral twin operators found In total, 0 twin operator were found Number of centrics : 315 Number of acentrics : 7022 Largest patterson peak with length larger then 15 Angstrom Frac. coord. : 0.086 0.000 -0.475 Distance to origin : 36.425 Height (origin=100) : 7.995 p_value(height) : 3.396e-01 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 3.396e-01 p_values smaller then 0.05 might indicate weak translation pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller then 1e-3 are a very strong indication for the presence of translational pseudo symmetry. Wilson ratio and moments Acentric reflections /^2 :1.992 (untwinned: 2.000; perfect twin 1.500) ^2/ :0.787 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.736 (untwinned: 0.736; perfect twin 0.541) Centric reflections /^2 :2.726 (untwinned: 3.000; perfect twin 2.000) ^2/ :0.690 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :0.946 (untwinned: 0.968; perfect twin 0.736) NZ test (0<=z<1) to detect twinning and possible translational NCS ----------------------------------------------- | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | ----------------------------------------------- | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | | 0.1 | 0.096 | 0.095 | 0.187 | 0.248 | | 0.2 | 0.183 | 0.181 | 0.254 | 0.345 | | 0.3 | 0.260 | 0.259 | 0.317 | 0.419 | | 0.4 | 0.330 | 0.330 | 0.384 | 0.474 | | 0.5 | 0.390 | 0.394 | 0.444 | 0.520 | | 0.6 | 0.451 | 0.451 | 0.508 | 0.561 | | 0.7 | 0.507 | 0.503 | 0.540 | 0.597 | | 0.8 | 0.557 | 0.551 | 0.587 | 0.629 | | 0.9 | 0.599 | 0.593 | 0.629 | 0.657 | | 1.0 | 0.639 | 0.632 | 0.660 | 0.683 | ----------------------------------------------- | Maximum deviation acentric : 0.007 | | Maximum deviation centric : 0.101 | | | | _acentric : +0.002 | | _centric : -0.057 | ----------------------------------------------- L test for acentric data using difference vectors (dh,dk,dl) of the form: (2hp,2kp,2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.496 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.328 (untwinned: 0.333; perfect twin: 0.200) The distribution of |L| values indicates a twin fraction of 0.01. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available. ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - /^2 : 1.992 - ^2/ : 0.787 - <|E^2-1|> : 0.736 - <|L|>, : 0.496, 0.328 Multivariate Z score L-test: 1.059 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 7.995 (correpsonding p value : 3.396e-01) The largest off-origin peak in the Patterson function is 8.00% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. ------------------------------------------------------------------------------- mmtbx.xtriage file=/net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca log=sec17.log /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/xtriage.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py from mmtbx.scaling import xtriage /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/xtriage.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.phil ############################################################# ## mmtbx.xtriage ## ## ## ## P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams ## ## ## ############################################################# Date 2006-06-25 Time 20:09:08 PDT -0700 ##-------------------------------------------## ## WARNING: ## ## Number of residues unspecified ## ##-------------------------------------------## Effective parameters: scaling.input { parameters { asu_contents { n_residues = None n_bases = None n_copies_per_asu = None } misc_twin_parameters { missing_symmetry { tanh_location = 0.08 tanh_slope = 50 } twinning_with_ncs { perform_analyses = False n_bins = 7 } twin_test_cuts { low_resolution = 10 high_resolution = None isigi_cut = 3 completeness_cut = 0.85 } } reporting { verbose = 1 log = "sec17.log" ccp4_style_graphs = True } } xray_data { file_name = "/net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca" obs_labels = None calc_labels = None unit_cell = 108.18 108.18 46.509 90 90 90 space_group = "P 41" high_resolution = None low_resolution = None } } Symmetry, cell and reflection file content summary Miller array info: /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma Observation type: xray.amplitude Type of data: double, size=15372 Type of sigmas: double, size=15372 Number of Miller indices: 15372 Anomalous flag: True Unit cell: (108.18, 108.18, 46.509, 90, 90, 90) Space group: P 41 (No. 76) Systematic absences: 0 Centric reflections: 763 Resolution range: 19.8701 3.3032 Completeness in resolution range: 0.975319 Completeness with d_max=infinity: 0.971129 Bijvoet pairs: 7171 Lone Bijvoet mates: 267 Anomalous signal: 0.1071 ##----------------------------------------------------## ## Basic statistics ## ##----------------------------------------------------## Matthews coefficient and Solvent content statistics Number of residues unknown, assuming 50% solvent content ---------------------------------------------------------------- | Best guess : 498 residues in the asu | ---------------------------------------------------------------- Completeness and data strength analyses The following table lists the completeness in various resolution ranges, after applying a I/sigI cut. Miller indices for which individual I/sigI values are larger than the value specified in the top row of the table, are retained, while other intensities are discarded. The resulting completeness profiles are an indication of the strength of the data. ---------------------------------------------------------------------------------------- | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | ---------------------------------------------------------------------------------------- | 19.87 - 7.98 | 96.4% | 95.3% | 94.5% | 93.6% | 91.7% | 89.3% | | 7.98 - 6.40 | 99.2% | 98.2% | 97.1% | 95.5% | 90.9% | 84.7% | | 6.40 - 5.61 | 97.8% | 95.4% | 93.3% | 87.1% | 76.6% | 66.8% | | 5.61 - 5.11 | 98.2% | 95.9% | 94.0% | 87.9% | 74.1% | 58.0% | | 5.11 - 4.75 | 97.9% | 96.2% | 94.5% | 91.1% | 79.2% | 62.5% | | 4.75 - 4.47 | 97.4% | 95.4% | 93.1% | 88.9% | 76.6% | 56.9% | | 4.47 - 4.25 | 96.5% | 94.5% | 92.1% | 88.0% | 75.3% | 56.5% | | 4.25 - 4.07 | 96.6% | 94.0% | 91.2% | 85.4% | 69.3% | 44.9% | | 4.07 - 3.91 | 95.6% | 92.1% | 87.8% | 80.1% | 61.9% | 34.8% | | 3.91 - 3.78 | 94.3% | 89.6% | 83.7% | 71.1% | 48.7% | 20.5% | | 3.78 - 3.66 | 95.7% | 90.9% | 85.6% | 71.5% | 42.4% | 14.8% | | 3.66 - 3.56 | 91.6% | 85.0% | 78.0% | 63.3% | 34.1% | 9.5% | | 3.56 - 3.46 | 89.8% | 80.4% | 70.2% | 52.8% | 22.2% | 3.8% | | 3.46 - 3.38 | 87.4% | 76.3% | 64.6% | 46.7% | 15.5% | 1.7% | ---------------------------------------------------------------------------------------- Maximum likelihood isotropic Wilson scaling ML estimate of overall B value of /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma: 75.85 A**(-2) Estimated -log of scale factor of /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma: -2.43 Maximum likelihood anisotropic Wilson scaling ML estimate of overall B_cart value of /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma: 68.92, 0.00, 0.00 68.92, 0.00 91.87 Equivalent representation as U_cif: 0.87, -0.00, -0.00 0.87, 0.00 1.16 ML estimate of -log of scale factor of /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma: -2.42 Correcting for anisotropy in the data Some basic intensity statistics follow. Low resolution completeness analyses The following table shows the completeness of the data to 5 Angstrom. unused: - 19.8702 [ 0/68 ] 0.000 bin 1: 19.8702 - 10.3027 [425/455] 0.934 bin 2: 10.3027 - 8.3766 [443/446] 0.993 bin 3: 8.3766 - 7.3796 [446/447] 0.998 bin 4: 7.3796 - 6.7336 [447/449] 0.996 bin 5: 6.7336 - 6.2673 [450/454] 0.991 bin 6: 6.2673 - 5.9080 [428/429] 0.998 bin 7: 5.9080 - 5.6192 [459/466] 0.985 bin 8: 5.6192 - 5.3796 [446/450] 0.991 bin 9: 5.3796 - 5.1763 [437/440] 0.993 bin 10: 5.1763 - 5.0006 [460/462] 0.996 unused: 5.0006 - [ 0/0 ] Mean intensity analyses Analyses of the mean intensity. Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. The following resolution shells are worrisome: ------------------------------------------------ | d_spacing | z_score | compl. | / | ------------------------------------------------ | 5.773 | 7.95 | 0.99 | 0.658 | | 5.423 | 8.62 | 0.99 | 0.654 | | 5.130 | 6.31 | 0.99 | 0.744 | | 4.879 | 5.36 | 0.99 | 0.775 | | 4.662 | 4.52 | 0.99 | 0.803 | | 3.676 | 5.45 | 0.99 | 1.248 | ------------------------------------------------ Possible reasons for the presence of the reported unexpected low or elevated mean intensity in a given resolution bin are : - missing overloaded or weak reflections - suboptimal data processing - satelite (ice) crystals - NCS - translational pseudo symmetry (detected elsewhere) - outliers (detected elsewhere) - ice rings (detected elsewhere) - other problems Note that the presence of abnormalities in a certain region of reciprocal space might confuse the data validation algorithm throughout a large region of reciprocal space, even though the data is acceptable in those areas. Possible outliers Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 Acentric reflections: None Centric reflections: None Ice ring related problems The following statistics were obtained from ice-ring insensitive resolution ranges mean bin z_score : 3.47 ( rms deviation : 2.83 ) mean bin completeness : 0.99 ( rms deviation : 0.00 ) The following table shows the z-scores and completeness in ice-ring sensitive areas. Large z-scores and high completeness in these resolution ranges might be a reason to re-assess your data processsing if ice rings were present. ------------------------------------------------ | d_spacing | z_score | compl. | Rel. Ice int. | ------------------------------------------------ | 3.897 | 0.12 | 0.97 | 1.000 | | 3.669 | 0.96 | 0.95 | 0.750 | | 3.441 | 2.14 | 0.94 | 0.530 | ------------------------------------------------ Abnormalities in mean intensity or completeness at resolution ranges with a relative ice ring intensity lower then 0.10 will be ignored. At 3.67 A there is an lower occupancy then expected from the rest of the data set. Even though the completeness is lower as expected, the mean instensity is still reasonable at this resolution At 3.44 A there is an lower occupancy then expected from the rest of the data set. Even though the completeness is lower as expected, the mean instensity is still reasonable at this resolution There were 2 ice ring related warnings This could indicate the presence of ice rings. Analyses of anomalous differences Table of measurability as a function of resolution The measurability is defined as the fraction of Bijvoet related intensity differences for which |delta_I|/sigma_delta_I > 3.0 min[I(+)/sigma_I(+), I(-)/sigma_I(-)] > 3.0 holds. The measurability provides an intuitive feeling of the quality of the data, as it is related to the number of reliable Bijvoet differences. When the data is processed properly and the standard deviations have been estimated accurately, values larger than 0.05 are encouraging. unused: - 19.8704 [ 0/68 ] bin 1: 19.8704 - 7.0211 [1551/1585] 0.1924 bin 2: 7.0211 - 5.6142 [1560/1575] 0.0814 bin 3: 5.6142 - 4.9168 [1546/1555] 0.0261 bin 4: 4.9168 - 4.4729 [1563/1582] 0.0081 bin 5: 4.4729 - 4.1554 [1557/1577] 0.0095 bin 6: 4.1554 - 3.9124 [1531/1570] 0.0083 bin 7: 3.9124 - 3.7178 [1541/1585] 0.0069 bin 8: 3.7178 - 3.5569 [1509/1552] 0.0028 bin 9: 3.5569 - 3.4207 [1522/1606] 0.0085 bin 10: 3.4207 - 3.3032 [1492/1574] 0.0044 unused: 3.3032 - [ 0/0 ] The anomalous signal seems to extend to about 5.9 A (or to 5.2 A, from a more optimistic point of view) The quoted resolution limits can be used as a guideline to decide where to cut the resolution for phenix.hyss As the anomalous signal is not very strong in this dataset substructire solution via SAD might prove to be a challenge. Especially if only low resolution reflections are used, the resulting substructures could contain a significant amount of of false positives. Basic analyses completed ##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------## Using data between 10.00 to 3.66 Angstrom. Determining possible twin laws. The following twin laws have been found: ------------------------------------------------------------------------------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------------- | M | 2-fold | 0.000 | 0.000 | 0.000 | -h,k,-l | ------------------------------------------------------------------------------- M: Merohedral twin law PM: Pseudomerohedral twin law 1 merohedral twin operators found 0 pseudo-merohedral twin operators found In total, 1 twin operator were found Number of centrics : 559 Number of acentrics : 10332 Largest patterson peak with length larger then 15 Angstrom Frac. coord. : 0.027 0.057 0.345 Distance to origin : 17.444 Height (origin=100) : 3.886 p_value(height) : 9.982e-01 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 9.982e-01 p_values smaller then 0.05 might indicate weak translation pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller then 1e-3 are a very strong indication for the presence of translational pseudo symmetry. Wilson ratio and moments Acentric reflections /^2 :1.969 (untwinned: 2.000; perfect twin 1.500) ^2/ :0.792 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.732 (untwinned: 0.736; perfect twin 0.541) Centric reflections /^2 :2.442 (untwinned: 3.000; perfect twin 2.000) ^2/ :0.698 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :0.889 (untwinned: 0.968; perfect twin 0.736) NZ test (0<=z<1) to detect twinning and possible translational NCS ----------------------------------------------- | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | ----------------------------------------------- | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | | 0.1 | 0.086 | 0.095 | 0.179 | 0.248 | | 0.2 | 0.171 | 0.181 | 0.301 | 0.345 | | 0.3 | 0.251 | 0.259 | 0.363 | 0.419 | | 0.4 | 0.322 | 0.330 | 0.438 | 0.474 | | 0.5 | 0.395 | 0.394 | 0.488 | 0.520 | | 0.6 | 0.452 | 0.451 | 0.537 | 0.561 | | 0.7 | 0.505 | 0.503 | 0.576 | 0.597 | | 0.8 | 0.553 | 0.551 | 0.608 | 0.629 | | 0.9 | 0.591 | 0.593 | 0.635 | 0.657 | | 1.0 | 0.632 | 0.632 | 0.664 | 0.683 | ----------------------------------------------- | Maximum deviation acentric : 0.011 | | Maximum deviation centric : 0.069 | | | | _acentric : -0.003 | | _centric : -0.031 | ----------------------------------------------- L test for acentric data using difference vectors (dh,dk,dl) of the form: (2hp,2kp,2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.485 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.318 (untwinned: 0.333; perfect twin: 0.200) The distribution of |L| values indicates a twin fraction of 0.00. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available. --------------------------------------------- Analysing possible twin law : -h,k,-l --------------------------------------------- Results of the H-test on a-centric data: (Only 50.0% of the strongest twin pairs were used) mean |H| : 0.458 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.299 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.042 Estimation of twin fraction via cum. dist. of H: 0.034 Britton analyses Extrapolation performed on 0.00 < alpha < 0.495 Estimated twin fraction: 0.011 Correlation: 0.9990 R vs R statistic: R_abs_twin = <|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 R_abs_twin observed data : 0.457 R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> R_sq_twin observed data : 0.297 No calculated data available. R_twin for calculated data not determined. Maximum Likelihood twin fraction determination Zwart, Read, Grosse-Kunstleve & Adams, to be published. The estimated twin fraction is equal to 0.022 Exploring higher metric symmetry The point group of data as dictated by the space group is P 4 the point group in the niggli setting is Hall: P 4 (z,x,y) The point group of the lattice is Hall: P 4 2 (z,x,y) A summary of R values for various possible point groups follow. ------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | choice | ------------------------------------------------------------------------------------------- | Hall: P 4 (z,x,y) | None | None | 0.457 | 0.457 | <--- | | Hall: P 4 2 (z,x,y) | 0.457 | 0.457 | None | None | | ------------------------------------------------------------------------------------------- R_used: mean and maximum R value for symmetry operators *used* in this point group R_unused: mean and minimum R value for symmetry operators *not used* in this point group The likely point group of the data is: Hall: P 4 (z,x,y) Possible space groups in this point groups are: Unit cell: (108.18, 108.18, 46.509, 90, 90, 90) Space group: P 41 (No. 76) Unit cell: (108.18, 108.18, 46.509, 90, 90, 90) Space group: P 43 (No. 78) Note that this analyses does not take into account the effects of twinning. If the data is (allmost) perfectly twinned, the symmetry will appear to be higher than it actually is. ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - /^2 : 1.969 - ^2/ : 0.792 - <|E^2-1|> : 0.732 - <|L|>, : 0.485, 0.318 Multivariate Z score L-test: 0.983 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it. Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -h,k,-l | M | 0.457 | 0.011 | 0.034 | 0.022 | ----------------------------------------------------------------- Patterson analyses - Largest peak height : 3.886 (correpsonding p value : 9.982e-01) The largest off-origin peak in the Patterson function is 3.89% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. Even though no twinning is suspected, it might be worthwhile carrying out a refinement using a dedicated twin target anyway, as twinned structures with low twin fractions are difficult to distinguish from non-twinned structures. ------------------------------------------------------------------------------- phenix.hyss /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz 2 se --molecular_weight=8000 --solvent_content=0.70 /net/rosie/scratch1/rwgk/dist/phenix/phenix/command_line/hyss.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx.array_family import flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional /net/rosie/scratch1/rwgk/dist/phenix/phenix/command_line/hyss.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader Command line arguments: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz 2 se --molecular_weight=8000 --solvent_content=0.70 ------------------------------------------------------------------------------ PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography User: rwgk ------------------------------------------------------------------------------ HySS: Hybrid Substructure Search ------------------------------------------------------------------------------ Phenix developers include: P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, E.W. McKee, N.W. Moriarty, R.K. Pai, R.J. Read, T.D. Romo, J.C. Sacchettini, N.K. Sauter, J.N. Smith, L.C. Storoni, T.C. Terwilliger, P.H. Zwart Phenix home page: http://www.phenix-online.org/ ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Phenix components are copyrighted by: - Lawrence Berkeley National Laboratory - Los Alamos National Laboratory - University of Cambridge - Texas Agricultural Experiment Station & Texas Engineering Experiment Station ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Major third-party components of Phenix include: Python, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------ Reading reflection file: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz Input Miller array: Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:FSEinfl,SIGFSEinfl,DSEinfl,SIGDSEinfl Observation type: xray.reconstructed_amplitude Type of data: double, size=22062 Type of sigmas: double, size=22062 Number of Miller indices: 22062 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 722 Resolution range: 28.2923 2.74876 Completeness in resolution range: 0.91753 Completeness with d_max=infinity: 0.916691 Bijvoet pairs: 10497 Lone Bijvoet mates: 346 Anomalous signal: 0.1065 Removing systematic absences: Number of reflections: 22062 Removing zero or negative observations: Number of reflections: 22062 ************************ Anomalous signal: 0.1065 ************************ Applying resolution limits: 15 3.24876 Number of reflections: 13427 Applying sigma cutoff: 1 Number of reflections: 13427 Computing anomalous differences Number of reflections: 6391 Applying difference sigma cutoff: 0.5 Number of reflections: 5647 Applying rms outlier cutoff: 4 Number of reflections: 5641 Final anomalous difference array: Miller array info: None Observation type: None Type of data: double, size=5641 Type of sigmas: double, size=5641 Number of Miller indices: 5641 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.9539 3.24877 Completeness in resolution range: 0.753842 Completeness with d_max=infinity: 0.745277 Fraction of original data: 1/1.96 = 51.1% Input Miller array: Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEinfl,SIGF(+)SEinfl,F(-)SEinfl,SIGF(-)SEinfl Observation type: xray.amplitude Type of data: double, size=22062 Type of sigmas: double, size=22062 Number of Miller indices: 22062 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 722 Resolution range: 28.2923 2.74876 Completeness in resolution range: 0.91753 Completeness with d_max=infinity: 0.916691 Bijvoet pairs: 10497 Lone Bijvoet mates: 346 Anomalous signal: 0.1018 Removing systematic absences: Number of reflections: 22062 Removing zero or negative observations: Number of reflections: 22062 ************************ Anomalous signal: 0.1018 ************************ Applying resolution limits: 15 3.24876 Number of reflections: 13427 Applying sigma cutoff: 1 Number of reflections: 13427 Computing anomalous differences Number of reflections: 6391 Applying difference sigma cutoff: 0.5 Number of reflections: 4511 Applying rms outlier cutoff: 4 Number of reflections: 4508 Final anomalous difference array: Miller array info: None Observation type: None Type of data: double, size=4508 Type of sigmas: double, size=4508 Number of Miller indices: 4508 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.9539 3.24877 Completeness in resolution range: 0.602432 Completeness with d_max=infinity: 0.595587 Fraction of original data: 1/2.45 = 40.9% Input Miller array: Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:FSElrm,SIGFSElrm,DSElrm,SIGDSElrm Observation type: xray.reconstructed_amplitude Type of data: double, size=22797 Type of sigmas: double, size=22797 Number of Miller indices: 22797 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 760 Resolution range: 28.2923 2.76136 Completeness in resolution range: 0.961007 Completeness with d_max=infinity: 0.960116 Bijvoet pairs: 10902 Lone Bijvoet mates: 233 Anomalous signal: 0.1019 Removing systematic absences: Number of reflections: 22797 Removing zero or negative observations: Number of reflections: 22797 ************************ Anomalous signal: 0.1019 ************************ Applying resolution limits: 15 3.26136 Number of reflections: 13953 Applying sigma cutoff: 1 Number of reflections: 13953 Computing anomalous differences Number of reflections: 6676 Applying difference sigma cutoff: 0.5 Number of reflections: 5996 Applying rms outlier cutoff: 4 Number of reflections: 5993 Final anomalous difference array: Miller array info: None Observation type: None Type of data: double, size=5993 Type of sigmas: double, size=5993 Number of Miller indices: 5993 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.9539 3.26151 Completeness in resolution range: 0.8114 Completeness with d_max=infinity: 0.802061 Fraction of original data: 1/1.9 = 52.6% Input Miller array: Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SElrm,SIGF(+)SElrm,F(-)SElrm,SIGF(-)SElrm Observation type: xray.amplitude Type of data: double, size=22797 Type of sigmas: double, size=22797 Number of Miller indices: 22797 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 760 Resolution range: 28.2923 2.76136 Completeness in resolution range: 0.961007 Completeness with d_max=infinity: 0.960116 Bijvoet pairs: 10902 Lone Bijvoet mates: 233 Anomalous signal: 0.0987 Removing systematic absences: Number of reflections: 22797 Removing zero or negative observations: Number of reflections: 22797 ************************ Anomalous signal: 0.0987 ************************ Applying resolution limits: 15 3.26136 Number of reflections: 13953 Applying sigma cutoff: 1 Number of reflections: 13953 Computing anomalous differences Number of reflections: 6676 Applying difference sigma cutoff: 0.5 Number of reflections: 5023 Applying rms outlier cutoff: 4 Number of reflections: 5020 Final anomalous difference array: Miller array info: None Observation type: None Type of data: double, size=5020 Type of sigmas: double, size=5020 Number of Miller indices: 5020 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.9539 3.26151 Completeness in resolution range: 0.679664 Completeness with d_max=infinity: 0.671842 Fraction of original data: 1/2.27 = 44% Input Miller array: Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:FSEpeak,SIGFSEpeak,DSEpeak,SIGDSEpeak Observation type: xray.reconstructed_amplitude Type of data: double, size=23010 Type of sigmas: double, size=23010 Number of Miller indices: 23010 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 766 Resolution range: 29.664 2.74731 Completeness in resolution range: 0.955763 Completeness with d_max=infinity: 0.955049 Bijvoet pairs: 11010 Lone Bijvoet mates: 224 Anomalous signal: 0.1237 Removing systematic absences: Number of reflections: 23010 Removing zero or negative observations: Number of reflections: 23010 ************************ Anomalous signal: 0.1237 ************************ Applying resolution limits: 15 3.24731 Number of reflections: 14110 Applying sigma cutoff: 1 Number of reflections: 14110 Computing anomalous differences Number of reflections: 6755 Applying difference sigma cutoff: 0.5 Number of reflections: 6167 Applying rms outlier cutoff: 4 Number of reflections: 6165 Final anomalous difference array: Miller array info: None Observation type: None Type of data: double, size=6165 Type of sigmas: double, size=6165 Number of Miller indices: 6165 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.9539 3.24736 Completeness in resolution range: 0.823097 Completeness with d_max=infinity: 0.813754 Fraction of original data: 1/1.87 = 53.6% Input Miller array: Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak Observation type: xray.amplitude Type of data: double, size=23010 Type of sigmas: double, size=23010 Number of Miller indices: 23010 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 766 Resolution range: 29.664 2.74731 Completeness in resolution range: 0.955763 Completeness with d_max=infinity: 0.955049 Bijvoet pairs: 11010 Lone Bijvoet mates: 224 Anomalous signal: 0.1207 Removing systematic absences: Number of reflections: 23010 Removing zero or negative observations: Number of reflections: 23010 ************************ Anomalous signal: 0.1207 ************************ Applying resolution limits: 15 3.24731 Number of reflections: 14110 Applying sigma cutoff: 1 Number of reflections: 14110 Computing anomalous differences Number of reflections: 6755 Applying difference sigma cutoff: 0.5 Number of reflections: 5250 Applying rms outlier cutoff: 4 Number of reflections: 5246 Final anomalous difference array: Miller array info: None Observation type: None Type of data: double, size=5246 Type of sigmas: double, size=5246 Number of Miller indices: 5246 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.9539 3.24766 Completeness in resolution range: 0.700494 Completeness with d_max=infinity: 0.692541 Fraction of original data: 1/2.19 = 45.6% Input Miller array: Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:FSEhrm,SIGFSEhrm,DSEhrm,SIGDSEhrm Observation type: xray.reconstructed_amplitude Type of data: double, size=25745 Type of sigmas: double, size=25745 Number of Miller indices: 25745 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 823 Resolution range: 29.664 2.66232 Completeness in resolution range: 0.972611 Completeness with d_max=infinity: 0.97195 Bijvoet pairs: 12399 Lone Bijvoet mates: 124 Anomalous signal: 0.1061 Removing systematic absences: Number of reflections: 25745 Removing zero or negative observations: Number of reflections: 25745 ************************ Anomalous signal: 0.1061 ************************ Applying resolution limits: 15 3.16232 Number of reflections: 15328 Applying sigma cutoff: 1 Number of reflections: 15328 Computing anomalous differences Number of reflections: 7337 Applying difference sigma cutoff: 0.5 Number of reflections: 6426 Applying rms outlier cutoff: 4 Number of reflections: 6417 Final anomalous difference array: Miller array info: None Observation type: None Type of data: double, size=6417 Type of sigmas: double, size=6417 Number of Miller indices: 6417 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.9539 3.16242 Completeness in resolution range: 0.790368 Completeness with d_max=infinity: 0.782084 Fraction of original data: 1/2.01 = 49.9% Input Miller array: Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEhrm,SIGF(+)SEhrm,F(-)SEhrm,SIGF(-)SEhrm Observation type: xray.amplitude Type of data: double, size=25745 Type of sigmas: double, size=25745 Number of Miller indices: 25745 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 823 Resolution range: 29.664 2.66232 Completeness in resolution range: 0.972611 Completeness with d_max=infinity: 0.97195 Bijvoet pairs: 12399 Lone Bijvoet mates: 124 Anomalous signal: 0.1004 Removing systematic absences: Number of reflections: 25745 Removing zero or negative observations: Number of reflections: 25745 ************************ Anomalous signal: 0.1004 ************************ Applying resolution limits: 15 3.16232 Number of reflections: 15328 Applying sigma cutoff: 1 Number of reflections: 15328 Computing anomalous differences Number of reflections: 7337 Applying difference sigma cutoff: 0.5 Number of reflections: 4867 Applying rms outlier cutoff: 4 Number of reflections: 4865 Final anomalous difference array: Miller array info: None Observation type: None Type of data: double, size=4865 Type of sigmas: double, size=4865 Number of Miller indices: 4865 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.827 3.16335 Completeness in resolution range: 0.599803 Completeness with d_max=infinity: 0.59322 Fraction of original data: 1/2.65 = 37.8% Selecting anomalous differences derived from this input array: Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak Observation type: xray.amplitude Type of data: double, size=23010 Type of sigmas: double, size=23010 Number of Miller indices: 23010 Anomalous flag: True Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 766 Resolution range: 29.664 2.74731 Completeness in resolution range: 0.955763 Completeness with d_max=infinity: 0.955049 Bijvoet pairs: 11010 Lone Bijvoet mates: 224 Anomalous signal: 0.1207 The corresponding anomalous differences again: Miller array info: Strongest anomalous signal: 0.121 Observation type: None Type of data: double, size=5246 Type of sigmas: double, size=5246 Number of Miller indices: 5246 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.9539 3.24766 Completeness in resolution range: 0.700494 Completeness with d_max=infinity: 0.692541 #---------------------------------------------------------------------------# | Formula for calculating the number of molecules given a molecular weight. | |---------------------------------------------------------------------------| | n_mol = ((1.0-solvent_content)*v_cell)/(molecular_weight*n_sym*.783) | #---------------------------------------------------------------------------# Number of molecules: 6 Number of sites: 12 Values used in calculation: Solvent content: 0.70 Unit cell volume: 476839 Molecular weight: 8000.00 Number of symmetry operators: 4 Writing anomalous differences as SHELX HKLF file: gere_MAD_anom_diffs.hkl Writing SHELXD ins file: gere_MAD_anom_diffs.ins Starting the search procedure (fast mode): Miller array info: Strongest anomalous signal: 0.121 Observation type: None Type of data: double, size=5246 Type of sigmas: double, size=5246 Number of Miller indices: 5246 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Transformation to Niggli cell: x-y,2*x,z Miller array info: Primitive Niggli setting Observation type: None Type of data: double, size=5246 Type of sigmas: double, size=5246 Number of Miller indices: 5246 Anomalous flag: False Unit cell: (61.679, 62.5082, 71.652, 96.2161, 90, 119.562) Space group: Hall: C 2y (x-y,2*x,z) (No. 5) Substructure parameter: n_sites: 12 Substructure parameter: min_cross_distance: 3.5 Substructure parameter: min_distance_sym_equiv: 3.5 Substructure parameter: general_positions_only: True Substructure parameter: min_distance: 3.5 hyss: using shelxd.q_value_estimation Search parameter: n_high_extrapolation_scan_correlation_group: 0 Search parameter: min_low_correlation: 0.1 Search parameter: n_chunk: 1 Search parameter: real_space_squaring: None Search parameter: high_low_correlation_factor: 2 Search parameter: peak_search_effective_resolution: None Search parameter: site_recycling_min_use: 0 Search parameter: n_candidate_sites: 11 Search parameter: n_use_sites: 8 Search parameter: enable_early_termination: True Search parameter: n_recycling_cycles: 10 Search parameter: occupancy_minimization: True Search parameter: site_recycling_candidate_factor: 0.9 Search parameter: truncate_consensus_model: True Search parameter: n_patterson_vectors: 33 Search parameter: max_relative_spread_top_correlations: 0.1 Search parameter: n_sites_final_factor: 1.3 Search parameter: min_top_n_matches: 8 Search parameter: e_min: 1.5 Search parameter: p1_n_recycling_cycles: 10 Search parameter: cos_sin_table: True Search parameter: n_fragments: 3 Search parameter: i_chunk: 0 Search parameter: site_recycling_use_heights_as_occupancies: False Search parameter: factor_top_n_matches: 0.666666666667 Search parameter: n_sites_final: 16 Search parameter: site_recycling_use_factor: 0.666666666667 Search parameter: n_top_models_to_compare: 3 Search parameter: minimize_consensus_model: True Search parameter: compare_sites_if_correlation_is_over: 0.2 Patterson: harker_plane_min_distance: 1.75 Patterson: keep_map: False Patterson: origin_peak_removal: False Patterson: grid_resolution_factor: 0.333333333333 Patterson: number of reflections: 5246 Patterson: suppressing peaks near Harker planes. Patterson: map gridding: (60, 60, 72) Patterson: map min: -13.66 sigma Patterson: map max: 91.68 sigma Two-site translation: grid_resolution_factor: 0.333333333333 Two-site translation: number of reflections: 5246 Tangent refinement: use_fixed_only: True Tangent refinement: reuse_results: True Tangent refinement: n_cycles: 1 Tangent refinement: fraction_fixed_phases: 0.4 Tangent refinement: number of reflections: 595 Tangent refinement: n_fixed: 238 Tangent refinement: n_variable: 357 Tangent refinement: time triplet generation: 0.02 seconds Tangent refinement: number of triplet phase relations: Tangent refinement: min: 40 Tangent refinement: max: 226 Tangent refinement: mean: 106.02 Tangent refinement: total number of triplets: 63084 Tangent refinement: use_fixed_only: True Tangent refinement: reuse_results: True Tangent refinement: n_cycles: 1 Tangent refinement: fraction_fixed_phases: 0.4 Tangent refinement: number of reflections: 1190 Tangent refinement: n_fixed: 476 Tangent refinement: n_variable: 714 Tangent refinement: time triplet generation: 0.03 seconds Tangent refinement: number of triplet phase relations: Tangent refinement: min: 40 Tangent refinement: max: 226 Tangent refinement: mean: 106.02 Tangent refinement: total number of triplets: 126168 Entering search loop: p = peaklist index in Patterson map f = peaklist index in two-site translation function cc = correlation coefficient after extrapolation scan r = number of dual-space recycling cycles cc = final correlation coefficient p=000 f=000 cc=0.241 r=010 cc=0.411 [ best cc: 0.411 ] p=000 f=001 cc=0.237 r=010 cc=0.398 [ best cc: 0.411 0.398 ] Number of matching sites of top 2 structures: 13 p=000 f=002 cc=0.182 r=010 cc=0.405 [ best cc: 0.411 0.405 0.398 ] Number of matching sites of top 2 structures: 13 Number of matching sites of top 3 structures: 11 Top 3 correlations: p=000 f=000 cc=0.241 r=010 cc=0.411 p=000 f=002 cc=0.182 r=010 cc=0.405 p=000 f=001 cc=0.237 r=010 cc=0.398 Match summary: Operator: rotation: {{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}} translation: {-3.56175e-36, -0.224884, 0.5} rms coordinate differences: 0.27 Pairs: 11 site001 site004 0.158 site002 site002 0.182 site003 site003 0.110 site004 site005 0.199 site005 site001 0.145 site006 site011 0.145 site007 site007 0.240 site008 site009 0.345 site009 site008 0.589 site010 site006 0.192 site011 site010 0.333 Singles model 1: 2 site013 site014 Singles model 2: 5 site012 site013 site014 site015 site016 Minimizing consensus model (11 sites). Correlation coefficient for consensus model (11 sites): 0.400 Search finished. time_log: label: n accumulation delta average time_log: patterson_peaks: 1 0.21 0.21 0.21 time_log: two_site_search: 1 0.12 0.12 0.12 time_log: extrapolation_scan: 3 0.31 0.1 0.103 time_log: p1_recycling: 3 1.70 0.55 0.567 time_log: p1_recycling q_large_calc: 30 0.02 0 0.000667 time_log: p1_recycling tangent_refinement: 30 0.20 0.01 0.00667 time_log: p1_recycling squaring: 0 0.00 0 0 time_log: p1_recycling fft_map: 30 0.40 0.01 0.0133 time_log: p1_recycling peak_search: 30 0.61 0.02 0.0203 time_log: p1_recycling random_omit: 30 0.01 0 0.000333 time_log: p1_recycling recover_origin: 3 0.43 0.14 0.143 time_log: p1_recycling combine_duplicates: 3 0.03 0.01 0.01 time_log: p1_recycling total: 3 1.70 0.55 0.567 p1_recycling time unaccounted for: 0.00 time_log: compute_correlation: 3 0.05 0.02 0.0167 time_log: q_large_calc: 27 0.00 0 0 time_log: tangent_refinement: 27 0.09 0 0.00333 time_log: squaring: 0 0.00 0 0 time_log: fft_map: 30 0.43 0.01 0.0143 time_log: peak_search: 30 0.93 0.04 0.031 time_log: random_omit: 27 0.00 0 0 time_log: minimization: 4 1.43 0.66 0.357 time_log: euclidean_model_matching: 2 0.33 0.2 0.165 time_log: hyss total: 1 6.25 6.25 6.25 time unaccounted for: 0.65 Storing all substructures found: gere_MAD_hyss_models.pickle Storing consensus model: gere_MAD_hyss_consensus_model.pickle Writing consensus model as PDB file: gere_MAD_hyss_consensus_model.pdb Writing consensus model as CNS SDB file: gere_MAD_hyss_consensus_model.sdb Writing consensus model as SOLVE xyz records: gere_MAD_hyss_consensus_model.xyz The fractional coordinates may also be useful in other programs. If HySS was helpful please cite: Acta Cryst. 2003, D59, 1966-1973 http://cci.lbl.gov/publications/download/ba5048_reprint.pdf See also: http://www.phenix-online.org/download/documentation/cci_apps/hyss/ For help enter: phenix.hyss --help Send bug reports to: bugs@phenix-online.org For help write to: help@phenix-online.org Total CPU time: 7.57 seconds iotbx.pdb.insert_scale_records /net/rosie/scratch1/rwgk/dist/regression/pdb/phe.pdb grep SCALE3 libtbx.assert_stdin SCALE3 0.000000 0.000000 0.066667 0.00000 /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/pdb.insert_scale_records.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional iotbx.pdb.superpose_centers_of_mass /net/rosie/scratch1/rwgk/dist/regression/pdb/phe.pdb /net/rosie/scratch1/rwgk/dist/regression/pdb/phe.pdb reference.atom_selection=name ca other.atom_selection=name c output.file=tmp.pdb output.atom_selection=name c* --space_group=p4 --unit_cell=20,20,21 grep Rotation libtbx.assert_stdin Rotation in fractional space: x,y,z /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/pdb.superpose_centers_of_mass.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional iotbx.pdb.as_xray_structure --symmetry=gere_MAD_anom_diffs.ins /net/cci-filer1/vol1/share/structure-lib/gere/sites/12_se.pdb --pickle=12_se /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/pdb.as_xray_structure.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import pdb /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional file_name: /net/cci-filer1/vol1/share/structure-lib/gere/sites/12_se.pdb Number of scatterers: 12 At special positions: 0 Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Writing all xray structures to file: 12_se.pickle cctbx.euclidean_model_matching 12_se.pickle gere_MAD_hyss_consensus_model.pickle /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/euclidean_model_matching.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py from libtbx import easy_pickle /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/euclidean_model_matching.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py from scitbx.python_utils import dicts /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/euclidean_model_matching.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import euclidean_model_matching as emma /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional Reference model: Number of scatterers: 12 At special positions: 0 Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Number of scatterers: 11 At special positions: 0 Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) Match summary: Operator: rotation: {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}} translation: {-2.91523e-36, -0.242927, 0} rms coordinate differences: 0.53 Pairs: 11 PEAK369 site002 0.235 PEAK937 site005 0.586 PEAK1076 site010 0.776 PEAK1482 site003 0.142 PEAK1617 site004 0.254 PEAK2021 site001 0.361 PEAK2156 site008 0.267 PEAK2551 site009 0.987 PEAK2686 site007 0.266 PEAK2951 site006 0.333 PEAK3086 site011 0.822 Singles model 1: 1 PEAK504 Singles model 2: 0 match_list: [11/11] matches: frequency 11: 1 = 100.0%, 100.0% iotbx.reflection_file_reader gere_MAD_anom_diffs.hkl=amplitudes --symmetry=gere_MAD_hyss_consensus_model.pdb --pickle=gere_MAD_anom_diffs.pickle /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_reader.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py from iotbx import reflection_file_reader /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py import cctbx.array_family.flex /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.optional file_name: gere_MAD_anom_diffs.hkl=amplitudes file_type: shelx_hklf Miller array info: gere_MAD_anom_diffs.hkl:Fobs,SigFobs Observation type: xray.amplitude Type of data: double, size=5246 Type of sigmas: double, size=5246 Number of Miller indices: 5246 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.15, 90) Space group: C 1 2 1 (No. 5) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.9539 3.24766 Completeness in resolution range: 0.700494 Completeness with d_max=infinity: 0.692541 Writing all Miller arrays to file: gere_MAD_anom_diffs.pickle libtbx.show_dist_paths phenix /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env phenix.python /net/rosie/scratch1/rwgk/dist/phenix/phenix/heavy_search/pc_multi.py gere_MAD_anom_diffs.pickle gere_MAD_hyss_consensus_model.pickle /net/rosie/scratch1/rwgk/dist/phenix/phenix/heavy_search/pc_multi.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import xray /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex Miller array info: gere_MAD_anom_diffs.hkl:Fobs,SigFobs Observation type: xray.amplitude Type of data: double, size=5246 Type of sigmas: double, size=5246 Number of Miller indices: 5246 Anomalous flag: False Unit cell: (108.742, 61.679, 71.652, 90, 97.15, 90) Space group: C 1 2 1 (No. 5) Number of scatterers: 11 At special positions: 0 Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90) Space group: C 1 2 1 (No. 5) gere_MAD_hyss_consensus_model.pickle: correlation after site refinement: 0.393 gere_MAD_hyss_consensus_model.pickle: correlation after occupancy refinement: 0.394 gere_MAD_hyss_consensus_model.pickle: correlation after site+occupancy refinement: 0.394 u+s,u,s: 1.59 1.53 0.06 endif rm -rf tst_pdb2xplor mkdir tst_pdb2xplor cd tst_pdb2xplor cp /net/rosie/scratch1/rwgk/dist/regression/misc/1CL7I.pdb . libtbx.show_dist_paths phenix /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py import libtbx.load_env phenix.python /net/rosie/scratch1/rwgk/dist/phenix/phenix/pdb_tools/pdb2xplor.py . /net/rosie/scratch1/rwgk/dist/phenix/phenix/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py try: import libtbx.forward_compatibility /net/rosie/scratch1/rwgk/dist/phenix/phenix/foundation/Structure.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/phenix/phenix/foundation/Structure.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py import math /net/rosie/scratch1/rwgk/dist/phenix/phenix/pdb_tools/pdb2xplor.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py import iotbx.xplor.map /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py import boost.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/map.py:32: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py from cctbx import miller /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py import scitbx.array_family.flex ________________________________________________________________________________ 1CL7I.pdb Class : PDBClass 606 atoms 0 bonds and 0 conect records 0 angles 0 diherals 0 impropers 0 residues Minimum and maximum B-factors: 2.00 51.89 Minimum and maximum occupancies: 1.00 1.00 Scatterers: {'C': 381, 'S': 4, 'O': 121, 'N': 100} [36.895000000000003, 39.993000000000002, 44.993000000000002] Map gridding: (40, 45, 50) Number of scatterers: 606 At special positions: 0 Unit cell: (36.895, 39.993, 44.993, 90, 90, 90) Space group: P 1 (No. 1) PDB # 0 in 0.152448177338 seconds if ( ! -f 1CL7I.xplor ) then cd .. set time_end=`libtbx.seconds_since_the_epoch` libtbx.seconds_since_the_epoch echo print 'Total time tests: %.2f seconds' % (1151291364.82-1151290469.09) python Total time tests: 895.73 seconds