date Mon Feb 2 23:56:55 PST 2009 cat /etc/fedora-release Fedora Core release 3 (Heidelberg) gcc -v | & tail -1 gcc version 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) $BUILD_PYTHON_EXE -V Python 2.3.4 libtbx.show_date_and_time -v Date 2009-02-02 Time 23:56:55 PST -0800 (1233647815.21 s) Seconds since the Epoch 1233647815.21 libtbx.show_host_and_user HOST = longnose.lbl.gov HOSTTYPE = i386-linux VENDOR = intel USER = rwgk PID = 2827 boost_adaptbx.show_platform_info __FILE__ = /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/meta_ext.cpp __DATE__ = Feb 2 2009 __TIME__ = 23:54:59 __i386__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): true __GXX_WEAK__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 PY_VERSION = 2.3.4 PYTHON_API_VERSION = 1012 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 12 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 sizeof(PY_UNICODE_TYPE) = 4 gnu libc version: 2.3.3 number of processors: 4 sys.byteorder: little import thread: OK boost_adaptbx.int_overflow Now adding int values 2147483647 + 1 ... Result: -2147483648 Now adding long values 2147483647 + 1 ... Result: -2147483648 if ( $status == 0 ) then if ( $SKIP_TESTS != 0 ) then libtbx.python $LIBTBX_DIST/run_tests.py libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/test_utils.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/utils.py ### HOST = longnose.lbl.gov ### HOSTTYPE = i386-linux ### VENDOR = intel ### USER = rwgk ### PID = 2838 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/pbs_utils.py *** MY_PBS_ARRAY_SIZE = None *** MY_PBS_ARRAYID_OFFSET = None *** PBS_ARRAYID = None *** OMPI_MCA_ns_nds_num_procs = None *** OMPI_MCA_ns_nds_vpid = None OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/sge_utils.py *** JOB_ID = None *** SGE_ARCH = None *** SGE_TASK_FIRST = None *** SGE_TASK_LAST = None *** SGE_TASK_ID = None OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/introspection.py number of processors: 4 Virtual memory size: 7,061,504 Resident set size: 3,538,944 Stack size: 1,658,880 Virtual memory size: 7,061,504 approx. max: 11,063,296 Resident set size: 3,547,136 approx. max: 7,548,928 Stack size: 1,658,880 approx. max: 1,658,880 Memory total: 2,122,080,256 Memory free: 259,272,704 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/thread_utils.py multiprocessing requires Python >= 2.6 - skipping these tests. OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/easy_run.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_utils.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_math_utils.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/assert_utils.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/str_utils.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/table_utils.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_dlite.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/phil/tst_tokenizer.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/phil/tst.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_object_oriented_patterns.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_itertbx.py OK libtbx.python $BOOST_ADAPTBX_DIST/run_tests.py libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_libc_backtrace.py show_stack(1): /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_libc_backtrace.py(7) run show_stack(2): /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_libc_backtrace.py(13) ? libc backtrace (20 frames, most recent call last): /usr/bin/python [0x8048501] /lib/tls/libc.so.6(__libc_start_main+0xe3) [0xac4e33] /usr/bin/python(main+0x2a) [0x80485b2] /usr/lib/libpython2.3.so.1.0(Py_Main+0x578) [0xc9c68e] /usr/lib/libpython2.3.so.1.0(PyRun_AnyFileExFlags+0x6e) [0xc97994] /usr/lib/libpython2.3.so.1.0(PyRun_SimpleFileExFlags+0x185) [0xc96942] /usr/lib/libpython2.3.so.1.0 [0xc95817] /usr/lib/libpython2.3.so.1.0(PyEval_EvalCode+0x63) [0xc7c362] /usr/lib/libpython2.3.so.1.0(PyEval_EvalCodeEx+0x679) [0xc7c09e] /usr/lib/libpython2.3.so.1.0 [0xc7b97b] /usr/lib/libpython2.3.so.1.0 [0xc79b7f] /usr/lib/libpython2.3.so.1.0(PyObject_Call+0x33) [0xc24607] /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so [0xf6eceb7f] /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(bool boost::python::handle_exception(boost::python::objects::(anonymous namespace)::bind_return)+0x5d) [0xf6ecfa51] /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0)+0x41) [0xf6ed6b71] /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::function0::operator()() const+0x9a) [0xf6ed7642] /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::detail::function::void_function_ref_invoker0::invoke(boost::detail::function::function_buffer&)+0x25) [0xf6ecf9dd] /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0x150) [0xf6eccc80] /net/longnose/scratch1/rwgk/auto_build/build/lib/boost_python_meta_ext.so(boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*)+0x89) [0xf6f04755] /net/longnose/scratch1/rwgk/auto_build/build/lib/boost_python_meta_ext.so((anonymous namespace)::boost_adptbx_libc_backtrace(int)+0x54) [0xf6efe0ec] OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_rational.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_rational_truediv.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_optional.py exercise_wstring: OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_std_pair.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_tuple.py OK libtbx.python $OMPTBX_DIST/tst.py omptbx.have_stubs_h omtbx.omp_version: None OK libtbx.python $SCITBX_DIST/run_tests.py /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_1 Total OK: 511 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_2 Total OK: 268 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_3 Total OK: 164 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_4 Total OK: 1420 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_5 Total OK: 23 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_vec3 Total OK: 67 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_unsigned_float_arithmetic OK /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_mat3 Total OK: 82 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_sym_mat3 Total OK: 71 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_mat_ref Total OK: 60 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_accessors Total OK: 1729 /net/longnose/scratch1/rwgk/auto_build/build/scitbx/serialization/tst_base_256 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/error/tst_error.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/stl/tst_map.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/stl/tst_set.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/stl/tst_vector.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/regression_test.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_flex.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_smart_selection.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_shared.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py data_size = 1000 n_repeats = 30000 use_pointers = False use_iterators = 0 time = 0.11 s overhead = 0.00 s (d[p[i]] 0) use_iterators = 1 time = 0.11 s overhead = 0.00 s (d[*p++] 0) use_pointers = True use_iterators = 0 time = 0.11 s overhead = 0.00 s (*dp[i] 0) use_iterators = 1 time = 0.14 s overhead = 0.00 s (**dpi++ 0) use_iterators = 2 time = 0.12 s overhead = 0.00 s (**dpp++ 0) data_size = 10000 n_repeats = 3000 use_pointers = False use_iterators = 0 time = 0.12 s overhead = 0.00 s (d[p[i]] 1.8651e-11) use_iterators = 1 time = 0.12 s overhead = 0.00 s (d[*p++] 1.8651e-11) use_pointers = True use_iterators = 0 time = 0.12 s overhead = 0.00 s (*dp[i] 1.8651e-11) use_iterators = 1 time = 0.17 s overhead = 0.00 s (**dpi++ 1.8651e-11) use_iterators = 2 time = 0.12 s overhead = 0.00 s (**dpp++ 1.8651e-11) data_size = 100000 n_repeats = 300 use_pointers = False use_iterators = 0 time = 1.76 s overhead = 0.00 s (d[p[i]] 2.13122e-11) use_iterators = 1 time = 1.76 s overhead = 0.00 s (d[*p++] 2.13122e-11) use_pointers = True use_iterators = 0 time = 1.74 s overhead = 0.00 s (*dp[i] 2.13122e-11) use_iterators = 1 time = 1.75 s overhead = 0.00 s (**dpi++ 2.13122e-11) use_iterators = 2 time = 1.74 s overhead = 0.00 s (**dpp++ 2.13122e-11) data_size = 1000000 n_repeats = 30 use_pointers = False use_iterators = 0 time = 3.64 s overhead = 0.01 s (d[p[i]] 2.132e-10) use_iterators = 1 time = 3.63 s overhead = 0.01 s (d[*p++] 2.132e-10) use_pointers = True use_iterators = 0 time = 3.60 s overhead = 0.01 s (*dp[i] 2.132e-10) use_iterators = 1 time = 3.57 s overhead = 0.01 s (**dpi++ 2.132e-10) use_iterators = 2 time = 3.58 s overhead = 0.01 s (**dpp++ 2.132e-10) data_size = 10000000 n_repeats = 3 use_pointers = False use_iterators = 0 time = 4.45 s overhead = 0.13 s (d[p[i]] -2.15565e-10) use_iterators = 1 time = 4.45 s overhead = 0.13 s (d[*p++] -2.15565e-10) use_pointers = True use_iterators = 0 time = 4.48 s overhead = 0.13 s (*dp[i] -2.15565e-10) use_iterators = 1 time = 4.49 s overhead = 0.13 s (**dpi++ -2.15565e-10) use_iterators = 2 time = 4.52 s overhead = 0.13 s (**dpp++ -2.15565e-10) OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py Loop over af::shared: data_size=1000, n_repeats=30000 size+begin inside loop: 0.42 s begin outside loop: 0.37 s size+begin outside loop: 0.08 s data_size=10000, n_repeats=3000 size+begin inside loop: 0.42 s begin outside loop: 0.37 s size+begin outside loop: 0.08 s data_size=100000, n_repeats=300 size+begin inside loop: 0.45 s begin outside loop: 0.40 s size+begin outside loop: 0.26 s data_size=1000000, n_repeats=30 size+begin inside loop: 0.45 s begin outside loop: 0.39 s size+begin outside loop: 0.26 s data_size=10000000, n_repeats=3 size+begin inside loop: 0.60 s begin outside loop: 0.41 s size+begin outside loop: 0.26 s OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/matrix.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/python_utils/tst_random_transform.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/python_utils/tst_graph.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_math.py time_eigensystem_real_symmetric: 5.311 micro seconds Testing compatibility of cmath_lgamma and slatec_dlngam... OK unimodular range 0: count=0, time=0.00 s unimodular range 1: count=3480, time=0.00 s unimodular range 2: count=67704, time=0.01 s unimodular range 3: count=640824, time=0.20 s unimodular range 4: count=2597208, time=1.42 s OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_r3_rotation.py times unit quaternion <-> matrix py: 0.60 0.46 s c++: 0.25 0.26 s ratio: 2.43 1.72 u+s,u,s: 27.30 27.24 0.06 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_resample.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_line_search.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_gaussian.py u+s,u,s: 62.26 62.06 0.20 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_quadrature.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_halton.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/tst_euler_angles.py u+s,u,s: 6.05 5.99 0.06 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/tst_superpose.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/sieve_of_eratosthenes.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/besselk.py 0.01 1.81901 1.81896284761 0.00259220079084 0.05 1.27752 1.27753829116 0.00143177079474 0.1 0.987739 0.986282193922 0.147488970054 0.5 -0.0404925 -0.0405939006888 0.250418444942 5.0 -5.5961 -5.59611201899 0.000214774434398 50 -51.7321 -51.65017 0.158373621021 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/scale_curves.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/minpack/tst.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/lbfgs/boost_python/tst_lbfgs.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/lbfgsb/boost_python/tst_lbfgsb.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/fftpack/boost_python/tst_fftpack.py usr+sys time: 5.88 seconds wall clock time: 5.88 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/flex_grid.py grid = grid over N-dim box (but there is not array with data!) origin = N-dim indices of lower-left corner of box focus = N-dim indices of upper-right corner of box as we want to use it last = N-dim indices of upper-right corner of box as actually allocated all = actual number or grid points to be allocated in each dimension Motivation for focus/last distinction: padding required by real-to-complex FFT algorithms origin: (0, 0, 0) focus: (3, 4, 6) last: (3, 4, 6) all: (3, 4, 6) origin: (0, 0, 0) focus: (3, 4, 5) last: (3, 4, 6) all: (3, 4, 6) origin: (-2, -3, -4) focus: (3, 4, 6) last: (3, 4, 6) all: (5, 7, 10) origin: (-2, -3, -4) focus: (3, 4, 5) last: (3, 4, 6) all: (5, 7, 10) OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/flex_array_loops.py 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/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/principal_axes_of_inertia.py (7.7966923076923074, 1.3650769230769233, 8.3576923076923073) (38.140037692307693, 97.025267538461534, 79.022219692307701, -19.808558307692309, 35.142585230769235, 7.6620366923076908) [104.22746487361263, 97.266425913775308, 12.69363413568899] [-0.43905397167468402, 0.82221243371028996, -0.36221309171382515, 0.30372167962370772, 0.5152398514117883, 0.80142437999084604, 0.84556770946106941, 0.241856588434883, -0.47594184450140542] libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/lbfgs_recipe.py refinery compute_functional_and_gradients callback_after_step OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/lbfgs_linear_least_squares_fit.py fit.slope: -3.14104556668 fit.y_intercept: 1.78306795976 x_obs y_obs y_calc diff 1.00 -1.33 -1.36 0.02 2.00 -4.47 -4.50 0.03 3.00 -7.67 -7.64 -0.03 4.00 -10.82 -10.78 -0.04 5.00 -13.94 -13.92 -0.02 6.00 -17.05 -17.06 0.02 7.00 -20.20 -20.20 0.00 8.00 -23.35 -23.35 -0.00 9.00 -26.51 -26.49 -0.02 10.00 -29.59 -29.63 0.04 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/chebyshev_lsq_example.py Trying to determine the best number of terms via cross validation techniques Fitting with 12 terms Least Squares residual: 1.988586 R2-value : 0.005655 Maximum deviation between fitted and error free data: 0.180 Mean deviation between fitted and error free data: 0.035 Maximum deviation between fitted and observed data: 0.259 Mean deviation between fitted and observed data: 0.121 Showing 10 points x y_obs y_ideal y_fit 0.010 1.282 1.195 1.252 0.099 1.936 2.061 2.015 0.188 0.832 0.814 0.817 0.277 0.634 0.448 0.495 0.366 2.046 2.025 2.037 0.455 2.386 2.322 2.265 0.545 1.221 0.980 1.024 0.634 1.128 1.301 1.317 0.723 2.798 2.931 2.892 0.812 2.506 2.646 2.623 Preparing output for loggraph in a file called chebyshev.loggraph Coefficients from weighted lsq [4.5241402338890762, -2.0680091197226163, 0.12850863418067884, 0.19943100844005027, -0.090172144930261947] Coefficients from non-weighted lsq [3.4207285988126821, -0.97279683238298753, -1.3518557377924003, 1.6668999570374963, -1.4294103076327269] libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/immoptibox_ports.py u+s,u,s: 38.15 38.07 0.08 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/rigid_body_refinement_core.py an ea: [0.0, 0.0, 0.0] fd ea: [2.9856131013692537e-15, 8.4825039313388431e-16, 3.9566375143884119e-15] an lt: [-0.0, -0.0, -0.0] fd lt: [0.0, 0.0, 0.0] an ea: [1.4293798315070272, -4.7699199336056015, -3.2848275925325994] fd ea: [1.4293798322739804, -4.769919932368083, -3.2848275930419391] an lt: [-2.6395370381698946, 3.8546779254822816, -3.7648774634679576] fd lt: [-2.6395370360532411, 3.8546779257409014, -3.7648774640075544] an ea: [-4.3864544713398521, 2.184889943611112, 5.0802158076235786] fd ea: [-4.386454465432621, 2.1848899418586143, 5.0802158071405756] an lt: [-4.6881328246835459, -10.874759921610867, -1.9393316543209451] fd lt: [-4.6881328277237344, -10.874759922785415, -1.939331655265164] an ea: [-5.0974589936941621, 2.0225151159319288, 4.4791032612277393] fd ea: [-5.0974589882457622, 2.0225151171615607, 4.4791032607349734] an lt: [-2.8154365578392593, -5.1570857812151694, -17.014046644874664] fd lt: [-2.8154365576682494, -5.1570857788618696, -17.014046648000658] OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_utils.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/rigidity.py double banana 3D dof (method=integer): 7 double banana 3D dof (method=float): 7 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_rigidity.py repeat_log = {0: 85} u+s,u,s: 3.73 3.71 0.02 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/rigidity_matrix_symbolic.py u+s,u,s: 4.12 4.10 0.02 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_tardy_tree.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/essence/tst_basic.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/essence/tst_molecules.py OK usr+sys time: 11.04 seconds wall clock time: 11.03 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/free_motion_reference_impl.py e_kin tot ang lin: 0.0406605941304 0.0123105941304 0.02835 e_pot: 0.64030878777 e_tot: 0.680969381901 ang acc 3D: (0.44994052436717469, -0.22736369685250066, -0.68597630003289267) lin acc 3D: (0.2108121283092794, 0.30448143672384792, -0.78243114289474458) e_kin tot ang lin: 0.0433343867202 0.012335145794 0.0309992409262 e_pot: 0.637520443168 e_tot: 0.680854829888 ang acc 3D: (0.44915232838243152, -0.2233952828755118, -0.68836460903992402) lin acc 3D: (0.20633054106767029, 0.30220128126092538, -0.78277910770482562) e_kin tot ang lin: 0.0462449163781 0.0123908412125 0.0338540751655 e_pot: 0.63449664984 e_tot: 0.680741566218 ang acc 3D: (0.4482905223840879, -0.21934640631607011, -0.69061975198037251) lin acc 3D: (0.20168867739512958, 0.29980890029936302, -0.78300792706075406) e_kin tot ang lin: 0.0493898546021 0.0124776322264 0.0369122223756 e_pot: 0.631239827538 e_tot: 0.680629682141 ang acc 3D: (0.44735466644443667, -0.21521902126722914, -0.69274095848332595) lin acc 3D: (0.19688964121862268, 0.29730414639378616, -0.78311556045599717) e_kin tot ang lin: 0.0527666878789 0.0125954480796 0.0401712397993 e_pot: 0.627752580076 e_tot: 0.680519267955 ang acc 3D: (0.4463443200247767, -0.21101512397560779, -0.69472747655310196) lin acc 3D: (0.19193669414908759, 0.29468687861617315, -0.78309994846029196) e_kin tot ang lin: 0.0563727196994 0.0127441954807 0.0436285242187 e_pot: 0.624037693245 e_tot: 0.680410412944 ang acc 3D: (0.44525904268397543, -0.2067367517215091, -0.69657857317890515) lin acc 3D: (0.18683325327725137, 0.29195696483157874, -0.78295901594034689) e_kin tot ang lin: 0.0602050727137 0.0129237586762 0.0472813140375 e_pot: 0.620098132599 e_tot: 0.680303205313 ang acc 3D: (0.44409839480429714, -0.20238598167333133, -0.6982935349568492) lin acc 3D: (0.18158288880693388, 0.2891142841060344, -0.7826906753299725) e_kin tot ang lin: 0.0642606910252 0.0131339995361 0.0511266914891 e_pot: 0.615937041095 e_tot: 0.68019773212 ang acc 3D: (0.4428619383337592, -0.19796492971649071, -0.69987166872353157) lin acc 3D: (0.17618932152521946, 0.28615872924108982, -0.78229282994446914) e_kin tot ang lin: 0.0685363426208 0.013374757653 0.0551615849678 e_pot: 0.611557736598 e_tot: 0.680094079218 ang acc 3D: (0.4415492375442347, -0.19347574925710581, -0.70131230220025587) lin acc 3D: (0.17065642010895676, 0.2830902094290727, -0.78176337733399448) e_kin tot ang lin: 0.0730286219358 0.0136458504521 0.0593827714837 e_pot: 0.606963709255 e_tot: 0.679992331191 ang acc 3D: (0.44015985980451133, -0.18892063000069204, -0.70261478464703297) lin acc 3D: (0.16498819826718966, 0.27990865302275331, -0.78110021267068175) OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_featherstone.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_free_motion.py u+s,u,s: 1.29 1.23 0.06 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_free_motion_hard.py OK usr+sys time: 5.41 seconds wall clock time: 5.41 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_joint_lib.py OK usr+sys time: 4.17 seconds wall clock time: 4.17 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_singular.py OK usr+sys time: 15.15 seconds wall clock time: 15.14 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_spherical_refinement.py OK usr+sys time: 2.38 seconds wall clock time: 2.37 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_molecules.py OK usr+sys time: 10.54 seconds wall clock time: 10.54 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/sparse/tests/tst_sparse.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/sparse/tests/tst_lu_factorization.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/iso_surface/tst_iso_surface.py u+s,u,s: 34.91 34.84 0.07 ( cd tst_featherstone_tmpdir ; "$TST_FEATHERSTONE_PYTHON" tst_featherstone.py ) libtbx.test_utils not available: approx_equal() disabled OK libtbx.python $SCITBX_DIST/rigid_body/essence/make_bundles.py ( cd scitbx_rigid_body_essence ; "$TST_FEATHERSTONE_PYTHON" tst_basic.py ) libtbx.test_utils not available: approx_equal() disabled OK libtbx.python $FFTW3TBX_DIST/tst_ext.py Skipping fftw3tbx tests: Python extension not available. usr+sys time: 0.75 seconds wall clock time: 0.75 seconds libtbx.python $CCTBX_DIST/run_tests.py --Quick libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_adp_aniso_restraints.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/math/boost_python/tst_math.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/xray/boost_python/tst_f_model.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/array_family/boost_python/tst_flex.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/uctbx/boost_python/tst_uctbx.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/uctbx/boost_python/tst_crystal_orientation.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/boost_python/tst_sgtbx.py u+s,u,s: 8.82 8.64 0.18 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/boost_python/tst_N_fold_rot.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/crystal/tst_ext.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/adptbx/boost_python/tst_adptbx.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/miller/boost_python/tst_miller.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_chemical_elements.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_xray_scattering.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_henke.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_icsd_radii.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_neutron.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_sasaki.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_tiny_pse.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_wavelengths.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/xray/boost_python/tst_xray.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/maptbx/boost_python/tst_maptbx.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/dmtbx/boost_python/tst_dmtbx.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/translation_search/boost_python/tst_translation_search.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/geometry_restraints/tst_ext.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/geometry_restraints/tst_proxy_registry.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/adp_restraints/tst_ext.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_math_module.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_krivy_gruber.py --Quick OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx.py u+s,u,s: 7.62 7.53 0.09 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py P 4 (No. 75) P 31 1 2 (No. 151) cb_op=x-y,-y,-z -> P 31 1 2 (a,b,c+1/6) cb_op=-y,x-y,z -> P 31 1 2 (a,b,c+1/6) cb_op=-y,-x,-z -> P 31 1 2 (a,b,c+1/3) cb_op=y,x,-z -> P 31 1 2 (a,b,c+1/3) cb_op=-x+y,-x,z -> P 31 1 2 (a,b,c+1/3) cb_op=x-y,x,z -> P 31 1 2 (a,b,c+1/3) cb_op=-x+y,y,-z -> P 31 1 2 (a,b,c+1/6) cb_op=y,-x+y,z -> P 31 1 2 (a,b,c+1/6) u+s,u,s: 6.71 6.65 0.06 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_denominators.py P31 P 31 u+s,u,s: 0.53 0.46 0.07 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_subgroups.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_lattice_symmetry.py 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: 27.59 27.53 0.06 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_adp_constraints.py P3 P 3 u+s,u,s: 0.92 0.84 0.08 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_adp_constraints_cartesian.py 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 I 4/m c m (a+b-1/6,-a+b,c+1/4) u+s,u,s: 1.06 0.96 0.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_site_constraints.py u+s,u,s: 9.17 9.05 0.12 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_reflection_statistics.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_harker.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_twin_target.py u+s,u,s: 117.19 117.07 0.12 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/symbol_confidence.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/bravais_types.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_miller_lookup_utils.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_crystal.py I41/acd I 41/a c d :2 u+s,u,s: 1.14 1.04 0.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_direct_space_asu.py I41/acd I 41/a c d :2 u+s,u,s: 8.40 8.27 0.13 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_pair_asu_table.py u+s,u,s: 5.48 5.37 0.11 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_crystal_asu_clusters.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_coordination_sequences.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_crystal_close_packing.py R-3mr time groel_sampling: 3.13 seconds R -3 m :R u+s,u,s: 5.43 5.33 0.10 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray.py I41/acd I 41/a c d :2 u+s,u,s: 17.08 16.97 0.11 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_structure_factors_multithread.py omptbx.have_stubs_h Skipping raw multithreaded structure factor computation tests usr+sys time: 1.35 seconds wall clock time: 1.35 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_miller.py P31 P 31 u+s,u,s: 11.45 10.86 0.59 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_reciprocal_space_asu.py P312 P 3 1 2 u+s,u,s: 0.94 0.86 0.08 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_triplet_generator.py P41 P 41 u+s,u,s: 1.05 0.96 0.09 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_emma.py P31 P 31 u+s,u,s: 3.28 3.18 0.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_find_centre_of_inversion.py P31 P 31 u+s,u,s: 1.13 1.04 0.09 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_expand_to_p1.py P31 P 31 u+s,u,s: 1.03 0.93 0.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_change_basis.py P31 P 31 u+s,u,s: 1.24 1.14 0.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_wilson_plot.py P31 P 31 u+s,u,s: 1.41 1.31 0.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_target_functors.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_derivatives.py P31 P 31 u+s,u,s: 9.05 8.91 0.14 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_fast_gradients.py P31 P 31 from_scatterers_direct: 4 calls, 0.12 s from_scatterers_fft: 15 calls, 0.68 s gradients_direct: 23 calls, 1.04 s gradients_fft: 2 calls, 0.21 s usr+sys time: 4.95 seconds wall clock time: 4.95 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_minimization.py --F P31 Refinement against F P 31 u+s,u,s: 30.69 30.48 0.21 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_minimization.py --F_sq P31 Refinement against F^2 P 31 u+s,u,s: 13.00 12.87 0.13 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/maptbx/tst_real_space_refinement.py u+s,u,s: 10.32 10.21 0.11 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_maptbx_structure_factors.py P31 P 31 u+s,u,s: 1.22 1.11 0.11 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_miller_merge_equivalents.py P31 P 31 u+s,u,s: 1.10 0.99 0.11 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_grouped_data.py P31 P 31 u+s,u,s: 0.96 0.87 0.09 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_miller_fft_map.py P31 P 31 u+s,u,s: 2.14 2.02 0.12 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sampled_model_density.py P31 P 31 usr+sys time: 5.55 seconds wall clock time: 5.55 seconds libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_fast_nv1995.py F222 F 2 2 2 u+s,u,s: 1.52 1.43 0.09 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_geometry_restraints.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_geometry_restraints_lbfgs.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_geometry_restraints_2.py u+s,u,s: 4.09 3.93 0.16 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/development/make_cns_input.py P31 P 31 u+s,u,s: 1.03 0.94 0.09 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/development/tst_cns_epsilon.py P31 CNS not available. libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/development/tst_cns_hl.py P31 CNS not available. libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/development/run_shelx.py P31 SHELX not available. libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_pointgroup_tools.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/sub_lattice_tools.py u+s,u,s: 1.14 1.06 0.08 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/rational_matrices_point_groups.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/cosets.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_find_best_cell.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_normalised_amplitudes.py OK libtbx.python $CCTBX_DIST/run_examples.py --Quick /net/longnose/scratch1/rwgk/auto_build/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/longnose/scratch1/rwgk/auto_build/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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/getting_started.py 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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/space_group_matrices.py P31 Space group: P 31 (No. 144) [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0] [0.0, -1.0, 0.0, 1.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.33333333333333331] [-1.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.66666666666666663] libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/space_subgroups.py Usage: cctbx.python space_subgroups.py max_index space_group_symbol Example: cctbx.python space_subgroups.py 2 P41212 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/trigonal_r_vs_tetragonal_i.py This is the "tetragonal I" setting humans like: Unit cell: (10, 10, 13, 90, 90, 90) Space group: I 4 (No. 79) Exact same symmetry, but using a basis system that is not very accessible to humans: Change of basis: y+z,x+z,x+y Unit cell: (9.60469, 9.60469, 9.60469, 117.258, 117.258, 94.8191) Space group: I 4 (y+z,x+z,x+y) (No. 79) This is the "trigonal R" setting most humans like best: Unit cell: (10, 10, 13, 90, 90, 120) Space group: R 3 :H (No. 146) Same symmetry, sometimes preferred: Change of basis: x+z,-x+y+z,-y+z Unit cell: (7.2188, 7.2188, 7.2188, 87.6782, 87.6782, 87.6782) Space group: R 3 :R (No. 146) libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/quartz_structure.py Number of scatterers: 2 At special positions: 2 Unit cell: (5.01, 5.01, 5.47, 90, 90, 120) Space group: P 62 2 2 (No. 180) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso Si Si 3 ( 0.5000 0.5000 0.3333) 1.00 0.2000 [ - ] O O 6 ( 0.1970 -0.1970 0.8333) 1.00 0.0000 [ - ] Si: 0.5000 0.5000 0.3333 point group type: 222 special position operator: 1/2,1/2,1/3 O: 0.1970 -0.1970 0.8333 point group type: 2 special position operator: 1/2*x-1/2*y,-1/2*x+1/2*y,5/6 Miller array info: None Observation type: None Type of data: complex_double, size=7 Type of sigmas: None Number of Miller indices: 7 Anomalous flag: False Unit cell: (5.01, 5.01, 5.47, 90, 90, 120) Space group: P 62 2 2 (No. 180) (1, 0, 0) (-11.346254184-1.26748373152e-15j) (1, 0, 1) (-15.047826184-26.0635994942j) (1, 0, 2) (1.61727835827-2.80120828651j) (1, 1, 0) (-12.7983511271-5.60868616295e-16j) (1, 1, 1) (5.52967787492-9.57768302885j) (2, 0, 0) (-2.43055830372+0j) (2, 0, 1) (4.96775720735+8.6044078828j) (1, 0, 0) 4.33878727296 (1, 0, 1) 3.39927502294 (1, 0, 2) 2.31368408207 (1, 1, 0) 2.505 (1, 1, 1) 2.27753582331 (2, 0, 0) 2.16939363648 (2, 0, 1) 2.01658808355 (1, 0, 0) (-11.346254184-1.26748373152e-15j) (1, 0, 1) (-15.047826184-26.0635994942j) (1, 1, 0) (-12.7983511271-5.60868616295e-16j) libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/analyze_adp.py Input Ucif: (0.17000000000000001, 0.17000000000000001, 0.19, 0.089999999999999997, 0, 0) Warning: ADP tensor is incompatible with site symmetry. Averaged Ucif: (0.16666666666666669, 0.16666666666666669, 0.19, 0.083333333333333343, 0.0, 0.0) Eigenvectors and values: v=(0.00000 -0.00000 1.00000) lambda=0.1900 v=(0.85089 -0.52534 -0.00000) lambda=0.1667 v=(0.52534 0.85089 0.00000) lambda=0.1667 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/g_exp_i_partial_derivatives.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_exp_i_alpha_derivatives.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_g_exp_i_alpha_derivatives.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_structure_factor_derivatives.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_structure_factor_derivatives_2.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_structure_factor_derivatives_3.py P31 P 31 u+s,u,s: 23.34 23.24 0.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_structure_factor_derivatives_4.py --tag=internal P 1 strudat tag: EDI u+s,u,s: 16.58 16.49 0.09 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/structure_factor_calculus/site_derivatives.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/structure_factor_calculus/u_star_derivatives.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/structure_factor_calculus/sites_derivatives.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/structure_factor_calculus/sites_least_squares_derivatives.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/all_axes.py P31 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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_phase_o_phrenia.py P2 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, Ustar as 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: 1.01 0.90 0.11 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/map_skewness.py 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, 2.66 fudge factor, phase difference, map skewness: 0.10, 8.75, 2.526 fudge factor, phase difference, map skewness: 0.20, 18.34, 2.182 fudge factor, phase difference, map skewness: 0.30, 26.87, 1.666 fudge factor, phase difference, map skewness: 0.40, 35.17, 1.292 fudge factor, phase difference, map skewness: 0.50, 44.04, 0.6092 fudge factor, phase difference, map skewness: 0.60, 55.57, 0.3374 fudge factor, phase difference, map skewness: 0.70, 62.39, 0.07028 fudge factor, phase difference, map skewness: 0.80, 73.69, -0.01595 fudge factor, phase difference, map skewness: 0.90, 83.53, -0.1369 fudge factor, phase difference, map skewness: 1.00, 88.73, -0.09588 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, 2.458 fudge factor, phase difference, map skewness: 0.10, 11.28, 2.225 fudge factor, phase difference, map skewness: 0.20, 16.92, 1.997 fudge factor, phase difference, map skewness: 0.30, 26.12, 1.589 fudge factor, phase difference, map skewness: 0.40, 33.60, 1.012 fudge factor, phase difference, map skewness: 0.50, 46.53, 0.4876 fudge factor, phase difference, map skewness: 0.60, 52.76, 0.3445 fudge factor, phase difference, map skewness: 0.70, 66.09, 0.08883 fudge factor, phase difference, map skewness: 0.80, 69.27, 0.07266 fudge factor, phase difference, map skewness: 0.90, 81.16, -0.03102 fudge factor, phase difference, map skewness: 1.00, 95.74, -0.04073 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, 2.627 fudge factor, phase difference, map skewness: 0.10, 9.12, 2.241 fudge factor, phase difference, map skewness: 0.20, 19.56, 1.753 fudge factor, phase difference, map skewness: 0.30, 24.31, 1.39 fudge factor, phase difference, map skewness: 0.40, 35.46, 0.8147 fudge factor, phase difference, map skewness: 0.50, 49.14, 0.3868 fudge factor, phase difference, map skewness: 0.60, 52.92, 0.3007 fudge factor, phase difference, map skewness: 0.70, 65.63, -0.003636 fudge factor, phase difference, map skewness: 0.80, 74.38, 0.09175 fudge factor, phase difference, map skewness: 0.90, 80.40, -0.003963 fudge factor, phase difference, map skewness: 1.00, 92.69, -0.1287 Number of scatterers: 20 At special positions: 1 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, 2.594 fudge factor, phase difference, map skewness: 0.10, 8.98, 2.35 fudge factor, phase difference, map skewness: 0.20, 16.21, 2.052 fudge factor, phase difference, map skewness: 0.30, 24.57, 1.612 fudge factor, phase difference, map skewness: 0.40, 33.27, 1.139 fudge factor, phase difference, map skewness: 0.50, 45.66, 0.6064 fudge factor, phase difference, map skewness: 0.60, 55.72, 0.3186 fudge factor, phase difference, map skewness: 0.70, 64.08, -0.004039 fudge factor, phase difference, map skewness: 0.80, 73.95, -0.1258 fudge factor, phase difference, map skewness: 0.90, 81.00, -0.002928 fudge factor, phase difference, map skewness: 1.00, 93.48, 0.1017 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, 2.878 fudge factor, phase difference, map skewness: 0.10, 6.38, 2.705 fudge factor, phase difference, map skewness: 0.20, 18.32, 2.016 fudge factor, phase difference, map skewness: 0.30, 24.99, 1.543 fudge factor, phase difference, map skewness: 0.40, 26.12, 1.504 fudge factor, phase difference, map skewness: 0.50, 45.60, 0.7481 fudge factor, phase difference, map skewness: 0.60, 59.30, 0.1682 fudge factor, phase difference, map skewness: 0.70, 64.27, 0.1207 fudge factor, phase difference, map skewness: 0.80, 76.39, -0.02815 fudge factor, phase difference, map skewness: 0.90, 80.10, 0.07912 fudge factor, phase difference, map skewness: 1.00, 88.55, -0.1605 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/site_symmetry_table.py 0,0,0 1/2,1/2,1/2 x,y,z OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/site_symmetry_constraints.py 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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/adp_symmetry_constraints.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/unit_cell_refinement.py ( 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: 0.00289855 gradient norm: 0.873261 functional: 0.000926904 gradient norm: 0.164675 LBFGS step functional: 0.000721103 gradient norm: 0.10673 LBFGS step functional: 0.000496383 gradient norm: 0.0156637 LBFGS step functional: 0.000436098 gradient norm: 0.0187088 LBFGS step functional: 0.000405012 gradient norm: 0.0141628 LBFGS step functional: 0.000437224 gradient norm: 0.0606773 functional: 0.00040312 gradient norm: 0.0132962 LBFGS step functional: 0.000400413 gradient norm: 0.00486465 LBFGS step functional: 0.000400027 gradient norm: 0.00909807 LBFGS step functional: 0.000399624 gradient norm: 0.00699388 LBFGS step functional: 0.000398287 gradient norm: 0.00462518 LBFGS step functional: 0.000395684 gradient norm: 0.00493147 LBFGS step functional: 0.000391549 gradient norm: 0.00839497 LBFGS step functional: 0.000397073 gradient norm: 0.0313132 functional: 0.000389325 gradient norm: 0.00955155 LBFGS step functional: 0.000387577 gradient norm: 0.0299186 LBFGS step functional: 0.000384514 gradient norm: 0.00250453 LBFGS step functional: 0.000384214 gradient norm: 0.00179241 LBFGS step functional: 0.000384067 gradient norm: 0.00168088 LBFGS step functional: 0.000383912 gradient norm: 0.00139478 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: 0.41 0.36 0.05 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/miller_common_sets.py 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) 0.190996543311 asu a: (1, 2, 3) 0.839368200477 asu a: (2, 3, 4) 0.641108620077 asu a: (3, 4, 5) 0.657120549745 asu a: (4, 5, 6) 0.347894088342 asu b: (5, 6, 7) 0.133592229858 asu b: (0, 1, 2) 0.125840088064 asu b: (3, 4, 5) 0.380366656966 asu b: (1, 2, 3) 0.692508912218 asu b: (4, 5, 6) 0.816294136961 common a: (0, 1, 2) 0.190996543311 common a: (3, 4, 5) 0.657120549745 common a: (1, 2, 3) 0.839368200477 common a: (4, 5, 6) 0.347894088342 common b: (0, 1, 2) 0.125840088064 common b: (3, 4, 5) 0.380366656966 common b: (1, 2, 3) 0.692508912218 common b: (4, 5, 6) 0.816294136961 lone a: (2, 3, 4) 0.641108620077 lone b: (5, 6, 7) 0.133592229858 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/miller_transform.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/change_hand_p31.py This example shows that a change of hand ("flipping coordinates") involves changing the space group if the space group is enantimorphic. Note that the interatomic distances do not change if the space group symmetry is transformed correctly, but do change if the original space group symmetry is simply retained. ================== Original structure ================== Number of scatterers: 3 At special positions: 0 Unit cell: (5, 5, 6, 90, 90, 120) Space group: P 31 (No. 144) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso Se1 Se 3 ( 0.7624 0.5887 0.3937) 1.00 0.0000 [ - ] Se2 Se 3 ( 0.2813 0.9896 0.9449) 1.00 0.0000 [ - ] Se3 Se 3 ( 0.4853 0.8980 0.4707) 1.00 0.0000 [ - ] Interatomic distances: Se1 pair count: 3 << 0.7624, 0.5887, 0.3937>> Se2: 1.5428 ( 0.7083, 0.7187, 0.6116) Se3: 2.2165 ( 0.4127, 0.5147, 0.1374) Se2: 2.4626 ( 1.0104, 0.2917, 0.2782) Se2 pair count: 3 << 0.2813, 0.9896, 0.9449>> Se1: 1.5428 ( 0.4113, 1.1737, 0.7270) Se3: 1.9393 ( 0.1020, 0.5873, 0.8040) Se1: 2.4626 ( 0.8263, 1.2376, 1.0604) Se3 pair count: 2 << 0.4853, 0.8980, 0.4707>> Se2: 1.9393 ( 0.7083, 0.7187, 0.6116) Se1: 2.2165 ( 0.4113, 1.1737, 0.7270) ===================================================== Other hand with sites flipped and space group changed ===================================================== Number of scatterers: 3 At special positions: 0 Unit cell: (5, 5, 6, 90, 90, 120) Space group: P 32 (No. 145) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso Se1 Se 3 (-0.7624 -0.5887 -0.3937) 1.00 0.0000 [ - ] Se2 Se 3 (-0.2813 -0.9896 -0.9449) 1.00 0.0000 [ - ] Se3 Se 3 (-0.4853 -0.8980 -0.4707) 1.00 0.0000 [ - ] Interatomic distances: Se1 pair count: 3 << -0.7624, -0.5887, -0.3937>> Se2: 1.5428 ( -0.7083, -0.7187, -0.6116) Se3: 2.2165 ( -0.4127, -0.5147, -0.1374) Se2: 2.4626 ( -1.0104, -0.2917, -0.2782) Se2 pair count: 3 << -0.2813, -0.9896, -0.9449>> Se1: 1.5428 ( -0.4113, -1.1737, -0.7270) Se3: 1.9393 ( -0.1020, -0.5873, -0.8040) Se1: 2.4626 ( -0.8263, -1.2376, -1.0604) Se3 pair count: 2 << -0.4853, -0.8980, -0.4707>> Se2: 1.9393 ( -0.7083, -0.7187, -0.6116) Se1: 2.2165 ( -0.4113, -1.1737, -0.7270) ================================== Other hand with sites flipped only ================================== Number of scatterers: 3 At special positions: 0 Unit cell: (5, 5, 6, 90, 90, 120) Space group: P 31 (No. 144) Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso Se1 Se 3 (-0.7624 -0.5887 -0.3937) 1.00 0.0000 [ - ] Se2 Se 3 (-0.2813 -0.9896 -0.9449) 1.00 0.0000 [ - ] Se3 Se 3 (-0.4853 -0.8980 -0.4707) 1.00 0.0000 [ - ] Interatomic distances: Se1 pair count: 2 << -0.7624, -0.5887, -0.3937>> Se2: 1.0731 ( -0.7083, -0.7187, -0.2782) Se3: 2.2936 ( -1.1020, -0.5873, -0.1374) Se2 pair count: 2 << -0.2813, -0.9896, -0.9449>> Se1: 1.0731 ( -0.4113, -1.1737, -1.0604) Se3: 2.0929 ( -0.1020, -0.5873, -1.1374) Se3 pair count: 2 << -0.4853, -0.8980, -0.4707>> Se2: 2.0929 ( -0.7083, -0.7187, -0.2782) Se1: 2.2936 ( -0.8263, -1.2376, -0.7270) libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/steve_collins.py 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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/cr2o3_primitive_cell.py 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, Ustar as 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, Ustar as 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, Ustar as 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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/cr2o3_consistency_checks.py 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, Ustar as 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, Ustar as 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, Ustar as 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 ( 0.7500, 0.4442, 0.0558) O1: 1.9654 ( 0.0558, 0.7500, 0.4442) O1: 1.9654 ( 0.4442, 0.0558, 0.7500) O1: 2.0157 ( 0.5558, -0.0558, 0.2500) O1: 2.0157 ( 0.2500, 0.5558, -0.0558) O1: 2.0157 ( -0.0558, 0.2500, 0.5558) Cr1 pair count: 6 << 0.1524, 0.1524, 0.1524>> O1: 1.9654 ( -0.2500, 0.4442, 0.0558) O1: 1.9654 ( 0.0558, -0.2500, 0.4442) O1: 1.9654 ( 0.4442, 0.0558, -0.2500) 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 ( -0.7500, -0.4442, -0.0558) O1: 1.9654 ( -0.0558, -0.7500, -0.4442) O1: 1.9654 ( -0.4442, -0.0558, -0.7500) O1: 2.0157 ( -0.5558, 0.0558, -0.2500) O1: 2.0157 ( -0.2500, -0.5558, 0.0558) O1: 2.0157 ( 0.0558, -0.2500, -0.5558) Cr1 pair count: 6 << -0.1524, -0.1524, -0.1524>> O1: 1.9654 ( 0.2500, -0.4442, -0.0558) O1: 1.9654 ( -0.0558, 0.2500, -0.4442) O1: 1.9654 ( -0.4442, -0.0558, 0.2500) 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 ( 0.8476, -0.1524, -0.1524) Cr1: 1.9654 ( 0.6524, -0.3476, 0.6524) Cr1: 2.0157 ( 0.3476, 0.3476, 0.3476) Cr1: 2.0157 ( 0.1524, 0.1524, 0.1524) O1 pair count: 4 << 0.2500, 0.5558, -0.0558>> Cr1: 1.9654 ( -0.1524, 0.8476, -0.1524) Cr1: 1.9654 ( 0.6524, 0.6524, -0.3476) 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 ( 0.1524, 0.1524, 0.1524) Cr1: 2.0157 ( 0.3476, 0.3476, 0.3476) O1 pair count: 4 << -0.5558, 0.0558, -0.2500>> Cr1: 1.9654 ( -0.8476, 0.1524, 0.1524) Cr1: 1.9654 ( -0.6524, 0.3476, -0.6524) Cr1: 2.0157 ( -0.3476, -0.3476, -0.3476) Cr1: 2.0157 ( -0.1524, -0.1524, -0.1524) O1 pair count: 4 << -0.2500, -0.5558, 0.0558>> Cr1: 1.9654 ( 0.1524, -0.8476, 0.1524) Cr1: 1.9654 ( -0.6524, -0.6524, 0.3476) 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 ( -0.1524, -0.1524, -0.1524) Cr1: 2.0157 ( -0.3476, -0.3476, -0.3476) 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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/reduced_cell_two_folds.py (-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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/lebedev_2005_perturbation.py 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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/le_page_1982_vs_lebedev_2005.py OK libtbx.python $CCTBX_DIST/regression/tst_structure_factors_multithread.py --verbose omptbx.have_stubs_h OpenMP # CPU run-time speed-up 1 3.55 x 1.00 2 3.55 x 1.00 Skipping raw multithreaded structure factor computation tests usr+sys time: 11.14 seconds wall clock time: 11.15 seconds libtbx.python $CCTBX_DIST/web/replay.py $BUILD_SRC/phenix_regression/cctbx/web/[a-z]* | grep -i error cctbx Error: Brick is not available for the given space group representation. libtbx.python $RSTBX_DIST/run_tests.py OK libtbx.python $IOTBX_DIST/run_tests.py --Quick /net/longnose/scratch1/rwgk/auto_build/build/iotbx/boost_spirit/tst_parsers OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_wildcard.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_simple_parser.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_phil.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/ranges.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_crystal_symmetry_from_any.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/kriber/tst_strudat.py u+s,u,s: 12.02 11.92 0.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/cif/tst_xray_structure.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/shelx/tst_lex_parse_build.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/shelx/tst_hklf.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/hybrid_36.py exercise OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_hierarchy.py iotbx.pdb.hierarchy.atom.sizeof_data(): 168 u+s,u,s: 5.15 4.96 0.19 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_ext.py time hy36recode_width_4_all: 0.50 s (0.205 micro s per encode-decode cycle) u+s,u,s: 2.68 2.49 0.19 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_atom_selection.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_rna_dna_atom_names.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_atom_name_interpretation.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_pdb.py u+s,u,s: 9.50 9.28 0.22 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/examples/pdb_truncate_to_ala/tst.py total number of: models: 1 chains: 2 alt. conf.: 4 residues: 3 atoms: 23 anisou: 0 number of atom element+charge types: 3 histogram of atom element+charge frequency: " C " 16 " O " 5 " N " 2 residue name classes: "common_amino_acid" 2 "other" 1 number of chain ids: 2 histogram of chain id frequency: " " 1 "A" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 2 "B" 2 residue alt. conf. situations: pure main conf.: 1 pure alt. conf.: 1 proper alt. conf.: 1 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 3 histogram of residue name frequency: "EOH" 1 other "ILE" 1 "SER" 1 total number of: models: 1 chains: 2 alt. conf.: 4 residues: 3 atoms: 23 anisou: 0 number of atom element+charge types: 3 histogram of atom element+charge frequency: " C " 16 " O " 5 " N " 2 residue name classes: "common_amino_acid" 2 "other" 1 number of chain ids: 2 histogram of chain id frequency: " " 1 "A" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 2 "B" 2 residue alt. conf. situations: pure main conf.: 1 pure alt. conf.: 1 proper alt. conf.: 1 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 3 histogram of residue name frequency: "EOH" 1 other "ILE" 1 "SER" 1 resid: " 6 " altloc: "", resname: "SER" N CA C O CB OG resid: " 7 " altloc: "", resname: "ILE" N CA C O CG2 altloc: "A", resname: "ILE" CB CG1 CD1 altloc: "B", resname: "ILE" CB CG1 CD1 resid: " 66 " altloc: "A", resname: "EOH" C1 C2 O altloc: "B", resname: "EOH" C1 C2 O total number of: models: 1 chains: 2 alt. conf.: 4 residues: 3 atoms: 23 anisou: 0 number of atom element+charge types: 3 histogram of atom element+charge frequency: " C " 16 " O " 5 " N " 2 residue name classes: "common_amino_acid" 2 "other" 1 number of chain ids: 2 histogram of chain id frequency: " " 1 "A" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 2 "B" 2 residue alt. conf. situations: pure main conf.: 1 pure alt. conf.: 1 proper alt. conf.: 1 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 3 histogram of residue name frequency: "EOH" 1 other "ILE" 1 "SER" 1 total number of: models: 1 chains: 2 alt. conf.: 4 residues: 3 atoms: 23 anisou: 0 number of atom element+charge types: 3 histogram of atom element+charge frequency: " C " 16 " O " 5 " N " 2 residue name classes: "common_amino_acid" 2 "other" 1 number of chain ids: 2 histogram of chain id frequency: " " 1 "A" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 2 "B" 2 residue alt. conf. situations: pure main conf.: 1 pure alt. conf.: 1 proper alt. conf.: 1 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 3 histogram of residue name frequency: "EOH" 1 other "ILE" 1 "SER" 1 total number of: models: 1 chains: 2 alt. conf.: 4 residues: 3 atoms: 23 anisou: 0 number of atom element+charge types: 3 histogram of atom element+charge frequency: " C " 16 " O " 5 " N " 2 residue name classes: "common_amino_acid" 2 "other" 1 number of chain ids: 2 histogram of chain id frequency: " " 1 "A" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 2 "B" 2 residue alt. conf. situations: pure main conf.: 1 pure alt. conf.: 1 proper alt. conf.: 1 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 3 histogram of residue name frequency: "EOH" 1 other "ILE" 1 "SER" 1 Number of amino acid residues: 2 Number of other residues: 1 Number of atoms removed: 6 Writing file: v4_truncated_to_ala_crambin_pieces.pdb total number of: models: 1 chains: 1 alt. conf.: 2 residues: 3 (1 with mixed residue names) atoms: 31 anisou: 0 number of atom element+charge types: 4 histogram of atom element+charge frequency: " C " 18 " O " 7 " N " 4 " S " 2 residue name classes: "common_amino_acid" 3 "other" 1 number of chain ids: 1 histogram of chain id frequency: "B" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 1 "B" 1 residue alt. conf. situations: pure main conf.: 2 pure alt. conf.: 1 proper alt. conf.: 0 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 4 histogram of residue name frequency: "ALA" 1 "CSD" 1 other "CYS" 1 "TYR" 1 total number of: models: 1 chains: 1 alt. conf.: 2 residues: 3 (1 with mixed residue names) atoms: 31 anisou: 0 number of atom element+charge types: 4 histogram of atom element+charge frequency: " C " 18 " O " 7 " N " 4 " S " 2 residue name classes: "common_amino_acid" 3 "other" 1 number of chain ids: 1 histogram of chain id frequency: "B" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 1 "B" 1 residue alt. conf. situations: pure main conf.: 2 pure alt. conf.: 1 proper alt. conf.: 0 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 4 histogram of residue name frequency: "ALA" 1 "CSD" 1 other "CYS" 1 "TYR" 1 resid: " 110 " altloc: "", resname: "ALA" N CA C O CB resid: " 111 " altloc: "A", resname: "CSD" N CA CB SG C O OD1 OD2 altloc: "B", resname: "CYS" N CA C O CB SG resid: " 112 " altloc: "", resname: "TYR" N CA C O CB CG CD1 CD2 CE1 CE2 CZ OH total number of: models: 1 chains: 1 alt. conf.: 2 residues: 3 (1 with mixed residue names) atoms: 31 anisou: 0 number of atom element+charge types: 4 histogram of atom element+charge frequency: " C " 18 " O " 7 " N " 4 " S " 2 residue name classes: "common_amino_acid" 3 "other" 1 number of chain ids: 1 histogram of chain id frequency: "B" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 1 "B" 1 residue alt. conf. situations: pure main conf.: 2 pure alt. conf.: 1 proper alt. conf.: 0 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 4 histogram of residue name frequency: "ALA" 1 "CSD" 1 other "CYS" 1 "TYR" 1 total number of: models: 1 chains: 1 alt. conf.: 2 residues: 3 (1 with mixed residue names) atoms: 31 anisou: 0 number of atom element+charge types: 4 histogram of atom element+charge frequency: " C " 18 " O " 7 " N " 4 " S " 2 residue name classes: "common_amino_acid" 3 "other" 1 number of chain ids: 1 histogram of chain id frequency: "B" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 1 "B" 1 residue alt. conf. situations: pure main conf.: 2 pure alt. conf.: 1 proper alt. conf.: 0 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 4 histogram of residue name frequency: "ALA" 1 "CSD" 1 other "CYS" 1 "TYR" 1 total number of: models: 1 chains: 1 alt. conf.: 2 residues: 3 (1 with mixed residue names) atoms: 31 anisou: 0 number of atom element+charge types: 4 histogram of atom element+charge frequency: " C " 18 " O " 7 " N " 4 " S " 2 residue name classes: "common_amino_acid" 3 "other" 1 number of chain ids: 1 histogram of chain id frequency: "B" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 1 "B" 1 residue alt. conf. situations: pure main conf.: 2 pure alt. conf.: 1 proper alt. conf.: 0 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 4 histogram of residue name frequency: "ALA" 1 "CSD" 1 other "CYS" 1 "TYR" 1 Number of amino acid residues: 3 Number of other residues: 0 Number of atoms removed: 11 Writing file: v4_truncated_to_ala_resname_mix.pdb OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/cns/space_group_symbols.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/cns/tst_cns.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/scalepack/tst_merge.py P31 P 31 u+s,u,s: 1.25 1.14 0.11 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/scalepack/no_merge_original_index.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/ccp4_map/tst.py u+s,u,s: 0.67 0.57 0.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/mtz/tst_ext.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/mtz/extract_from_symop_lib.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/mtz/tst.py P31 P 31 u+s,u,s: 1.80 1.68 0.12 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/examples/tst_mtz_free_flipper.py Reading file: /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/reflection_files/l.mtz Number of 0: 13469 Number of 1: 1065 Writing file: free_flipped_l.mtz Reading file: free_flipped_l.mtz Number of 0: 1065 Number of 1: 13469 Writing file: free_flipped_free_flipped_l.mtz Reading file: /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/reflection_files/l.mtz Input number of free reflections: 1065 Input number of work reflections: 13469 Number of reflections converted from free to work: 533 Output number of free reflections: 532 Output number of work reflections: 14002 Writing file: less_free_l.mtz u+s,u,s: 12.97 12.84 0.13 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_reflection_file_utils.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/detectors/tst_adsc.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/detectors/tst_debug_write.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/xplor/tst_xplormap.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_phases.py P31 Writing tmp.pdb Writing: tmp.phs OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/regression/tst_lattice_symmetry.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/regression/tst_reflection_statistics.py Fdd2 P31m F d d 2 P 3 1 m u+s,u,s: 11.79 11.61 0.18 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_data_plots.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_csv_utils.py OK libtbx.python $PYCIFRW_DIST/example_quartz.py 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, Ustar as 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) 16.3662770268 (1, 0, 1) 36.7226624914 (1, 0, 2) 6.96161334665 (1, 1, 0) 14.716747416 (1, 1, 1) 0.539734721891 (2, 0, 0) 14.6748185743 (2, 0, 1) 12.9746389785 OK libtbx.python $CLIPPER_ADAPTBX_DIST/clipper/tst_sigmaa.py 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 I 4/m c m (a+b-1/6,-a+b,c+1/4) u+s,u,s: 3.78 3.63 0.15 libtbx.python $SMTBX_DIST/run_tests.py --Quick libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/smtbx/ab_initio/tests/tst_ab_initio_ext.py u+s,u,s: 4.55 4.46 0.09 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/smtbx/ab_initio/tests/tst_charge_flipping.py 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 u+s,u,s: 139.35 138.23 1.12 16 test cases: 16 successes 16 phase transitions 16 Euclidean matches with correct structure in P1 16 found shifts 16 Euclidean matches with correct structure in original spacegroup libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/smtbx/refinement/constraints/tests/tst_constraints.py OK libtbx.python $MMTBX_DIST/run_tests.py --Quick libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/chemical_components/tst.py ________________________________________________________________________________ HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH Atom names ['O', 'H1', 'H2'] Alternate atom names ['O', '1H', '2H'] Hydrogen names ['H1', 'H2'] Alternate hydrogen names ['1H', '2H'] Wrapped hydrogen names ['H1', 'H2'] Bond pairs [['O', 'H1'], ['O', 'H2']] Alternate name bond pairs [['O', '1H'], ['O', '2H']] ________________________________________________________________________________ ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP Atom names ['PG', 'O1G', 'O2G', 'O3G', 'PB', 'O1B', 'O2B', 'O3B', 'PA', 'O1A', 'O2A', 'O3A', "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "O2'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', 'HOG2', 'HOG3', 'HOB2', 'HOA2', "H5'1", "H5'2", "H4'", "H3'", "HO3'", "H2'", "HO2'", "H1'", 'H8', 'HN61', 'HN62', 'H2'] Alternate atom names ['PG', 'O1G', 'O2G', 'O3G', 'PB', 'O1B', 'O2B', 'O3B', 'PA', 'O1A', 'O2A', 'O3A', 'O5*', 'C5*', 'C4*', 'O4*', 'C3*', 'O3*', 'C2*', 'O2*', 'C1*', 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', '2HOG', '3HOG', '2HOB', '2HOA', '1H5*', '2H5*', 'H4*', 'H3*', '*HO3', 'H2*', '*HO2', 'H1*', 'H8', '1HN6', '2HN6', 'H2'] Hydrogen names ['HOG2', 'HOG3', 'HOB2', 'HOA2', "H5'1", "H5'2", "H4'", "H3'", "HO3'", "H2'", "HO2'", "H1'", 'H8', 'HN61', 'HN62', 'H2'] Alternate hydrogen names ['2HOG', '3HOG', '2HOB', '2HOA', '1H5*', '2H5*', 'H4*', 'H3*', '*HO3', 'H2*', '*HO2', 'H1*', 'H8', '1HN6', '2HN6', 'H2'] Wrapped hydrogen names ['2HOG', '3HOG', '2HOB', '2HOA', "1H5'", "2H5'", "H4'", "H3'", "'HO3", "H2'", "'HO2", "H1'", 'H8', '1HN6', '2HN6', 'H2'] Bond pairs [['PG', 'O1G'], ['PG', 'O2G'], ['PG', 'O3G'], ['PG', 'O3B'], ['O2G', 'HOG2'], ['O3G', 'HOG3'], ['PB', 'O1B'], ['PB', 'O2B'], ['PB', 'O3B'], ['PB', 'O3A'], ['O2B', 'HOB2'], ['PA', 'O1A'], ['PA', 'O2A'], ['PA', 'O3A'], ['PA', "O5'"], ['O2A', 'HOA2'], ["O5'", "C5'"], ["C5'", "C4'"], ["C5'", "H5'1"], ["C5'", "H5'2"], ["C4'", "O4'"], ["C4'", "C3'"], ["C4'", "H4'"], ["O4'", "C1'"], ["C3'", "O3'"], ["C3'", "C2'"], ["C3'", "H3'"], ["O3'", "HO3'"], ["C2'", "O2'"], ["C2'", "C1'"], ["C2'", "H2'"], ["O2'", "HO2'"], ["C1'", 'N9'], ["C1'", "H1'"], ['N9', 'C8'], ['N9', 'C4'], ['C8', 'N7'], ['C8', 'H8'], ['N7', 'C5'], ['C5', 'C6'], ['C5', 'C4'], ['C6', 'N6'], ['C6', 'N1'], ['N6', 'HN61'], ['N6', 'HN62'], ['N1', 'C2'], ['C2', 'N3'], ['C2', 'H2'], ['N3', 'C4']] Alternate name bond pairs [['PG', 'O1G'], ['PG', 'O2G'], ['PG', 'O3G'], ['PG', 'O3B'], ['O2G', '2HOG'], ['O3G', '3HOG'], ['PB', 'O1B'], ['PB', 'O2B'], ['PB', 'O3B'], ['PB', 'O3A'], ['O2B', '2HOB'], ['PA', 'O1A'], ['PA', 'O2A'], ['PA', 'O3A'], ['PA', 'O5*'], ['O2A', '2HOA'], ['O5*', 'C5*'], ['C5*', 'C4*'], ['C5*', '1H5*'], ['C5*', '2H5*'], ['C4*', 'O4*'], ['C4*', 'C3*'], ['C4*', 'H4*'], ['O4*', 'C1*'], ['C3*', 'O3*'], ['C3*', 'C2*'], ['C3*', 'H3*'], ['O3*', '*HO3'], ['C2*', 'O2*'], ['C2*', 'C1*'], ['C2*', 'H2*'], ['O2*', '*HO2'], ['C1*', 'N9'], ['C1*', 'H1*'], ['N9', 'C8'], ['N9', 'C4'], ['C8', 'N7'], ['C8', 'H8'], ['N7', 'C5'], ['C5', 'C6'], ['C5', 'C4'], ['C6', 'N6'], ['C6', 'N1'], ['N6', '1HN6'], ['N6', '2HN6'], ['N1', 'C2'], ['C2', 'N3'], ['C2', 'H2'], ['N3', 'C4']] ________________________________________________________________________________ hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem Atom names ['FE', 'CHA', 'CHB', 'CHC', 'CHD', 'NA', 'C1A', 'C2A', 'C3A', 'C4A', 'CMA', 'CAA', 'CBA', 'CGA', 'O1A', 'O2A', 'NB', 'C1B', 'C2B', 'C3B', 'C4B', 'CMB', 'CAB', 'CBB', 'NC', 'C1C', 'C2C', 'C3C', 'C4C', 'CMC', 'CAC', 'CBC', 'ND', 'C1D', 'C2D', 'C3D', 'C4D', 'CMD', 'CAD', 'CBD', 'CGD', 'O1D', 'O2D', 'HHA', 'HHB', 'HHC', 'HHD', 'HMA1', 'HMA2', 'HMA3', 'HAA1', 'HAA2', 'HBA1', 'HBA2', 'H2A', 'HMB1', 'HMB2', 'HMB3', 'HAB', 'HBB1', 'HBB2', 'HMC1', 'HMC2', 'HMC3', 'HAC', 'HBC1', 'HBC2', 'HMD1', 'HMD2', 'HMD3', 'HAD1', 'HAD2', 'HBD1', 'HBD2', 'H2D'] Alternate atom names ['FE', 'CHA', 'CHB', 'CHC', 'CHD', 'N A', 'C1A', 'C2A', 'C3A', 'C4A', 'CMA', 'CAA', 'CBA', 'CGA', 'O1A', 'O2A', 'N B', 'C1B', 'C2B', 'C3B', 'C4B', 'CMB', 'CAB', 'CBB', 'N C', 'C1C', 'C2C', 'C3C', 'C4C', 'CMC', 'CAC', 'CBC', 'N D', 'C1D', 'C2D', 'C3D', 'C4D', 'CMD', 'CAD', 'CBD', 'CGD', 'O1D', 'O2D', 'HHA', 'HHB', 'HHC', 'HHD', '1HMA', '2HMA', '3HMA', '1HAA', '2HAA', '1HBA', '2HBA', 'H2A', '1HMB', '2HMB', '3HMB', 'HAB', '1HBB', '2HBB', '1HMC', '2HMC', '3HMC', 'HAC', '1HBC', '2HBC', '1HMD', '2HMD', '3HMD', '1HAD', '2HAD', '1HBD', '2HBD', 'H2D'] Hydrogen names ['HHA', 'HHB', 'HHC', 'HHD', 'HMA1', 'HMA2', 'HMA3', 'HAA1', 'HAA2', 'HBA1', 'HBA2', 'H2A', 'HMB1', 'HMB2', 'HMB3', 'HAB', 'HBB1', 'HBB2', 'HMC1', 'HMC2', 'HMC3', 'HAC', 'HBC1', 'HBC2', 'HMD1', 'HMD2', 'HMD3', 'HAD1', 'HAD2', 'HBD1', 'HBD2', 'H2D'] Alternate hydrogen names ['HHA', 'HHB', 'HHC', 'HHD', '1HMA', '2HMA', '3HMA', '1HAA', '2HAA', '1HBA', '2HBA', 'H2A', '1HMB', '2HMB', '3HMB', 'HAB', '1HBB', '2HBB', '1HMC', '2HMC', '3HMC', 'HAC', '1HBC', '2HBC', '1HMD', '2HMD', '3HMD', '1HAD', '2HAD', '1HBD', '2HBD', 'H2D'] Wrapped hydrogen names ['HHA', 'HHB', 'HHC', 'HHD', '1HMA', '2HMA', '3HMA', '1HAA', '2HAA', '1HBA', '2HBA', 'H2A', '1HMB', '2HMB', '3HMB', 'HAB', '1HBB', '2HBB', '1HMC', '2HMC', '3HMC', 'HAC', '1HBC', '2HBC', '1HMD', '2HMD', '3HMD', '1HAD', '2HAD', '1HBD', '2HBD', 'H2D'] Bond pairs [['FE', 'NA'], ['FE', 'NB'], ['FE', 'NC'], ['FE', 'ND'], ['CHA', 'C1A'], ['CHA', 'C4D'], ['CHA', 'HHA'], ['CHB', 'C4A'], ['CHB', 'C1B'], ['CHB', 'HHB'], ['CHC', 'C4B'], ['CHC', 'C1C'], ['CHC', 'HHC'], ['CHD', 'C4C'], ['CHD', 'C1D'], ['CHD', 'HHD'], ['NA', 'C1A'], ['NA', 'C4A'], ['C1A', 'C2A'], ['C2A', 'C3A'], ['C2A', 'CAA'], ['C3A', 'C4A'], ['C3A', 'CMA'], ['CMA', 'HMA1'], ['CMA', 'HMA2'], ['CMA', 'HMA3'], ['CAA', 'CBA'], ['CAA', 'HAA1'], ['CAA', 'HAA2'], ['CBA', 'CGA'], ['CBA', 'HBA1'], ['CBA', 'HBA2'], ['CGA', 'O1A'], ['CGA', 'O2A'], ['O2A', 'H2A'], ['NB', 'C1B'], ['NB', 'C4B'], ['C1B', 'C2B'], ['C2B', 'C3B'], ['C2B', 'CMB'], ['C3B', 'C4B'], ['C3B', 'CAB'], ['CMB', 'HMB1'], ['CMB', 'HMB2'], ['CMB', 'HMB3'], ['CAB', 'CBB'], ['CAB', 'HAB'], ['CBB', 'HBB1'], ['CBB', 'HBB2'], ['NC', 'C1C'], ['NC', 'C4C'], ['C1C', 'C2C'], ['C2C', 'C3C'], ['C2C', 'CMC'], ['C3C', 'C4C'], ['C3C', 'CAC'], ['CMC', 'HMC1'], ['CMC', 'HMC2'], ['CMC', 'HMC3'], ['CAC', 'CBC'], ['CAC', 'HAC'], ['CBC', 'HBC1'], ['CBC', 'HBC2'], ['ND', 'C1D'], ['ND', 'C4D'], ['C1D', 'C2D'], ['C2D', 'C3D'], ['C2D', 'CMD'], ['C3D', 'C4D'], ['C3D', 'CAD'], ['CMD', 'HMD1'], ['CMD', 'HMD2'], ['CMD', 'HMD3'], ['CAD', 'CBD'], ['CAD', 'HAD1'], ['CAD', 'HAD2'], ['CBD', 'CGD'], ['CBD', 'HBD1'], ['CBD', 'HBD2'], ['CGD', 'O1D'], ['CGD', 'O2D'], ['O2D', 'H2D']] Alternate name bond pairs [['FE', 'N A'], ['FE', 'N B'], ['FE', 'N C'], ['FE', 'N D'], ['CHA', 'C1A'], ['CHA', 'C4D'], ['CHA', 'HHA'], ['CHB', 'C4A'], ['CHB', 'C1B'], ['CHB', 'HHB'], ['CHC', 'C4B'], ['CHC', 'C1C'], ['CHC', 'HHC'], ['CHD', 'C4C'], ['CHD', 'C1D'], ['CHD', 'HHD'], ['N A', 'C1A'], ['N A', 'C4A'], ['C1A', 'C2A'], ['C2A', 'C3A'], ['C2A', 'CAA'], ['C3A', 'C4A'], ['C3A', 'CMA'], ['CMA', '1HMA'], ['CMA', '2HMA'], ['CMA', '3HMA'], ['CAA', 'CBA'], ['CAA', '1HAA'], ['CAA', '2HAA'], ['CBA', 'CGA'], ['CBA', '1HBA'], ['CBA', '2HBA'], ['CGA', 'O1A'], ['CGA', 'O2A'], ['O2A', 'H2A'], ['N B', 'C1B'], ['N B', 'C4B'], ['C1B', 'C2B'], ['C2B', 'C3B'], ['C2B', 'CMB'], ['C3B', 'C4B'], ['C3B', 'CAB'], ['CMB', '1HMB'], ['CMB', '2HMB'], ['CMB', '3HMB'], ['CAB', 'CBB'], ['CAB', 'HAB'], ['CBB', '1HBB'], ['CBB', '2HBB'], ['N C', 'C1C'], ['N C', 'C4C'], ['C1C', 'C2C'], ['C2C', 'C3C'], ['C2C', 'CMC'], ['C3C', 'C4C'], ['C3C', 'CAC'], ['CMC', '1HMC'], ['CMC', '2HMC'], ['CMC', '3HMC'], ['CAC', 'CBC'], ['CAC', 'HAC'], ['CBC', '1HBC'], ['CBC', '2HBC'], ['N D', 'C1D'], ['N D', 'C4D'], ['C1D', 'C2D'], ['C2D', 'C3D'], ['C2D', 'CMD'], ['C3D', 'C4D'], ['C3D', 'CAD'], ['CMD', '1HMD'], ['CMD', '2HMD'], ['CMD', '3HMD'], ['CAD', 'CBD'], ['CAD', '1HAD'], ['CAD', '2HAD'], ['CBD', 'CGD'], ['CBD', '1HBD'], ['CBD', '2HBD'], ['CGD', 'O1D'], ['CGD', 'O2D'], ['O2D', 'H2D']] OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/regression/tst_add_h_to_water.py Number of H added: 9 X-H deviation from ideal before regularization (bond): mean= 0.013 max= 0.020 X-H deviation from ideal after regularization (bond): mean= 0.000 max= 0.000 u+s,u,s: 16.30 15.99 0.31 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/rotamer/rotamer_eval.py Processing data files in "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/rotarama_data": rota500-cys.data -> rota500-cys.pickle: already up to date. rota500-asp.data -> rota500-asp.pickle: already up to date. rota500-ser.data -> rota500-ser.pickle: already up to date. rota500-gln.data -> rota500-gln.pickle: already up to date. rota500-ile.data -> rota500-ile.pickle: already up to date. rota500-pro.data -> rota500-pro.pickle: already up to date. rota500-lys.data -> rota500-lys.pickle: already up to date. rota500-thr.data -> rota500-thr.pickle: already up to date. rota500-phetyr.data -> rota500-phetyr.pickle: already up to date. rota500-asn.data -> rota500-asn.pickle: already up to date. rota500-met.data -> rota500-met.pickle: already up to date. rota500-his.data -> rota500-his.pickle: already up to date. rota500-leu.data -> rota500-leu.pickle: already up to date. rota500-arg.data -> rota500-arg.pickle: already up to date. rota500-trp.data -> rota500-trp.pickle: already up to date. rota500-glu.data -> rota500-glu.pickle: already up to date. rota500-phetyr.data -> rota500-phetyr.pickle: already up to date. rota500-val.data -> rota500-val.pickle: already up to date. Processing data files in "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/rotarama_data": rama500-prepro.data -> rama500-prepro.pickle: already up to date. rama500-pro.data -> rama500-pro.pickle: already up to date. rama500-gly-sym.data -> rama500-gly-sym.pickle: already up to date. rama500-general.data -> rama500-general.pickle: already up to date. u+s,u,s: 2.10 1.92 0.18 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/wwpdb/tst_standard_geometry_cif.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_pdbtools.py OK usr+sys time: 33.52 seconds wall clock time: 2 minutes 53.30 seconds (173.30 seconds total) libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/real_space/tst.py OK: real_space: u+s,u,s: 166.41 162.06 4.35 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/ias/tst_ias.py >>> Adding IAS.......... Total number of covalent bonds = 40 IAS considered: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS selected: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS scattering dictionary: Number of scattering types: 1 Type Number sf(0) Gaussians D10 4 0.05 1 sf(0) = scattering factor at diffraction angle 0. HETATM 1 D10 IAS 1 2.370 3.660 -0.690 1.00 0.83 D1 HETATM 2 D10 IAS 2 2.614 3.609 -1.283 1.00 0.83 D1 HETATM 3 D10 IAS 3 1.345 4.997 2.883 1.00 0.91 D1 HETATM 4 D10 IAS 4 1.076 4.418 2.809 1.00 0.91 D1 Scattering dictionary for combined xray_structure: Number of scattering types: 5 Type Number sf(0) Gaussians O 6 8.00 6 N 3 7.00 6 C 13 6.00 6 H 19 1.00 6 D10 4 0.05 1 sf(0) = scattering factor at diffraction angle 0. >>> Adding IAS.......... Total number of covalent bonds = 40 IAS considered: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS selected: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS scattering dictionary: Number of scattering types: 1 Type Number sf(0) Gaussians D9 1 -0.30 1 sf(0) = scattering factor at diffraction angle 0. HETATM 1 D9 IAS 1 1.075 0.334 -2.554 1.00 0.95 D9 Scattering dictionary for combined xray_structure: Number of scattering types: 5 Type Number sf(0) Gaussians O 6 8.00 6 N 3 7.00 6 C 13 6.00 6 H 19 1.00 6 D9 1 -0.30 1 sf(0) = scattering factor at diffraction angle 0. >>> Adding IAS.......... Total number of covalent bonds = 40 IAS considered: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS selected: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS scattering dictionary: Number of scattering types: 5 Type Number sf(0) Gaussians D5 6 0.20 1 D4 5 0.14 1 D8 4 0.11 1 D6 5 0.08 1 D7 1 0.07 1 sf(0) = scattering factor at diffraction angle 0. HETATM 1 D7 IAS 1 1.630 -1.554 -1.815 1.00 1.27 D7 HETATM 2 D5 IAS 2 1.733 -0.685 -2.660 1.00 1.03 D5 HETATM 3 D5 IAS 3 0.997 -0.542 -1.713 1.00 1.03 D5 HETATM 4 D5 IAS 4 1.817 0.185 -3.486 1.00 1.03 D5 HETATM 5 D5 IAS 5 0.343 0.464 -1.605 1.00 1.03 D5 HETATM 6 D5 IAS 6 1.158 1.204 -3.380 1.00 0.95 D5 HETATM 7 D5 IAS 7 0.420 1.340 -2.446 1.00 0.95 D5 HETATM 8 D4 IAS 8 0.477 2.272 -3.299 1.00 0.91 D4 HETATM 9 D4 IAS 9 0.677 3.542 -3.289 1.00 0.91 D4 HETATM 10 D6 IAS 10 1.816 4.161 -3.359 1.00 0.91 D6 HETATM 11 D4 IAS 11 1.192 4.075 -2.265 1.00 0.83 D4 HETATM 12 D8 IAS 12 1.752 3.869 -1.311 1.00 0.99 D8 HETATM 13 D6 IAS 13 0.749 4.146 -1.136 1.00 0.83 D6 HETATM 14 D8 IAS 14 1.042 4.890 2.030 1.00 0.99 D8 HETATM 15 D4 IAS 15 0.584 4.487 1.090 1.00 0.91 D4 HETATM 16 D6 IAS 16 1.092 5.584 1.239 1.00 0.95 D6 HETATM 17 D6 IAS 17 0.217 4.137 -0.109 1.00 0.91 D6 HETATM 18 D8 IAS 18 1.410 8.867 2.122 1.00 0.99 D8 HETATM 19 D8 IAS 19 0.653 8.303 2.249 1.00 1.03 D8 HETATM 20 D6 IAS 20 1.592 6.648 1.254 1.00 1.07 D6 HETATM 21 D4 IAS 21 1.576 7.806 1.851 1.00 0.99 D4 Scattering dictionary for combined xray_structure: Number of scattering types: 9 Type Number sf(0) Gaussians O 6 8.00 6 N 3 7.00 6 C 13 6.00 6 H 19 1.00 6 D5 6 0.20 1 D4 5 0.14 1 D8 4 0.11 1 D6 5 0.08 1 D7 1 0.07 1 sf(0) = scattering factor at diffraction angle 0. >>> Adding IAS.......... Total number of covalent bonds = 40 IAS considered: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS selected: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS scattering dictionary: Number of scattering types: 3 Type Number sf(0) Gaussians D1 11 0.22 1 D2 5 0.16 1 D3 3 0.09 1 sf(0) = scattering factor at diffraction angle 0. HETATM 1 D3 IAS 1 2.387 -2.396 -1.821 1.00 1.34 D3 HETATM 2 D1 IAS 2 2.576 -0.898 -3.654 1.00 1.19 D1 HETATM 3 D1 IAS 3 0.253 -0.476 -0.641 1.00 1.19 D1 HETATM 4 D1 IAS 4 1.974 1.097 -4.424 1.00 1.19 D1 HETATM 5 D1 IAS 5 -0.384 1.541 -1.402 1.00 1.19 D1 HETATM 6 D1 IAS 6 0.333 2.962 -4.401 1.00 1.10 D1 HETATM 7 D1 IAS 7 -0.539 3.079 -3.350 1.00 1.10 D1 HETATM 8 D1 IAS 8 0.677 4.846 -3.199 1.00 0.99 D1 HETATM 9 D2 IAS 9 2.896 4.727 -3.371 1.00 1.10 D2 HETATM 10 D2 IAS 10 2.849 3.558 -3.510 1.00 1.10 D2 HETATM 11 D2 IAS 11 2.394 4.228 -4.408 1.00 1.10 D2 HETATM 12 D1 IAS 12 0.619 3.240 0.828 1.00 1.10 D1 HETATM 13 D1 IAS 13 -0.568 3.906 0.916 1.00 1.10 D1 HETATM 14 D2 IAS 14 -0.470 4.416 -1.090 1.00 1.06 D2 HETATM 15 D2 IAS 15 1.099 6.286 0.217 1.00 1.15 D2 HETATM 16 D1 IAS 16 2.366 6.934 2.309 1.00 1.27 D1 HETATM 17 D1 IAS 17 2.565 7.521 1.061 1.00 1.27 D1 HETATM 18 D3 IAS 18 0.918 1.686 3.084 1.00 1.46 D3 HETATM 19 D3 IAS 19 0.782 2.788 3.272 1.00 1.46 D3 Scattering dictionary for combined xray_structure: Number of scattering types: 7 Type Number sf(0) Gaussians O 6 8.00 6 N 3 7.00 6 C 13 6.00 6 H 19 1.00 6 D1 11 0.22 1 D2 5 0.16 1 D3 3 0.09 1 sf(0) = scattering factor at diffraction angle 0. >>> Adding IAS.......... Total number of covalent bonds = 40 IAS considered: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS selected: Number of IAS built: total: 45 bond (X-X): 21 bond (X-H): 19 ring centers: 1 lone pairs: 4 IAS scattering dictionary: Number of scattering types: 10 Type Number sf(0) Gaussians D1 11 0.22 1 D5 6 0.20 1 D2 5 0.16 1 D4 5 0.14 1 D8 4 0.11 1 D3 3 0.09 1 D6 5 0.08 1 D7 1 0.07 1 D10 4 0.05 1 D9 1 -0.30 1 sf(0) = scattering factor at diffraction angle 0. HETATM 1 D7 IAS 1 1.630 -1.554 -1.815 1.00 1.27 D7 HETATM 2 D3 IAS 2 2.387 -2.396 -1.821 1.00 1.34 D3 HETATM 3 D5 IAS 3 1.733 -0.685 -2.660 1.00 1.03 D5 HETATM 4 D5 IAS 4 0.997 -0.542 -1.713 1.00 1.03 D5 HETATM 5 D5 IAS 5 1.817 0.185 -3.486 1.00 1.03 D5 HETATM 6 D1 IAS 6 2.576 -0.898 -3.654 1.00 1.19 D1 HETATM 7 D5 IAS 7 0.343 0.464 -1.605 1.00 1.03 D5 HETATM 8 D1 IAS 8 0.253 -0.476 -0.641 1.00 1.19 D1 HETATM 9 D5 IAS 9 1.158 1.204 -3.380 1.00 0.95 D5 HETATM 10 D1 IAS 10 1.974 1.097 -4.424 1.00 1.19 D1 HETATM 11 D5 IAS 11 0.420 1.340 -2.446 1.00 0.95 D5 HETATM 12 D1 IAS 12 -0.384 1.541 -1.402 1.00 1.19 D1 HETATM 13 D4 IAS 13 0.477 2.272 -3.299 1.00 0.91 D4 HETATM 14 D4 IAS 14 0.677 3.542 -3.289 1.00 0.91 D4 HETATM 15 D1 IAS 15 0.333 2.962 -4.401 1.00 1.10 D1 HETATM 16 D1 IAS 16 -0.539 3.079 -3.350 1.00 1.10 D1 HETATM 17 D6 IAS 17 1.816 4.161 -3.359 1.00 0.91 D6 HETATM 18 D1 IAS 18 0.677 4.846 -3.199 1.00 0.99 D1 HETATM 19 D4 IAS 19 1.192 4.075 -2.265 1.00 0.83 D4 HETATM 20 D2 IAS 20 2.896 4.727 -3.371 1.00 1.10 D2 HETATM 21 D2 IAS 21 2.849 3.558 -3.510 1.00 1.10 D2 HETATM 22 D2 IAS 22 2.394 4.228 -4.408 1.00 1.10 D2 HETATM 23 D8 IAS 23 1.752 3.869 -1.311 1.00 0.99 D8 HETATM 24 D6 IAS 24 0.749 4.146 -1.136 1.00 0.83 D6 HETATM 25 D8 IAS 25 1.042 4.890 2.030 1.00 0.99 D8 HETATM 26 D4 IAS 26 0.584 4.487 1.090 1.00 0.91 D4 HETATM 27 D6 IAS 27 1.092 5.584 1.239 1.00 0.95 D6 HETATM 28 D6 IAS 28 0.217 4.137 -0.109 1.00 0.91 D6 HETATM 29 D1 IAS 29 0.619 3.240 0.828 1.00 1.10 D1 HETATM 30 D1 IAS 30 -0.568 3.906 0.916 1.00 1.10 D1 HETATM 31 D2 IAS 31 -0.470 4.416 -1.090 1.00 1.06 D2 HETATM 32 D8 IAS 32 1.410 8.867 2.122 1.00 0.99 D8 HETATM 33 D8 IAS 33 0.653 8.303 2.249 1.00 1.03 D8 HETATM 34 D6 IAS 34 1.592 6.648 1.254 1.00 1.07 D6 HETATM 35 D2 IAS 35 1.099 6.286 0.217 1.00 1.15 D2 HETATM 36 D4 IAS 36 1.576 7.806 1.851 1.00 0.99 D4 HETATM 37 D1 IAS 37 2.366 6.934 2.309 1.00 1.27 D1 HETATM 38 D1 IAS 38 2.565 7.521 1.061 1.00 1.27 D1 HETATM 39 D3 IAS 39 0.918 1.686 3.084 1.00 1.46 D3 HETATM 40 D3 IAS 40 0.782 2.788 3.272 1.00 1.46 D3 HETATM 41 D9 IAS 41 1.075 0.334 -2.554 1.00 0.95 D9 HETATM 42 D10 IAS 42 2.370 3.660 -0.690 1.00 0.83 D1 HETATM 43 D10 IAS 43 2.614 3.609 -1.283 1.00 0.83 D1 HETATM 44 D10 IAS 44 1.345 4.997 2.883 1.00 0.91 D1 HETATM 45 D10 IAS 45 1.076 4.418 2.809 1.00 0.91 D1 Scattering dictionary for combined xray_structure: Number of scattering types: 14 Type Number sf(0) Gaussians O 6 8.00 6 N 3 7.00 6 C 13 6.00 6 H 19 1.00 6 D1 11 0.22 1 D5 6 0.20 1 D2 5 0.16 1 D4 5 0.14 1 D8 4 0.11 1 D3 3 0.09 1 D6 5 0.08 1 D7 1 0.07 1 D10 4 0.05 1 D9 1 -0.30 1 sf(0) = scattering factor at diffraction angle 0. OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/refinement/tst_anomalous_scatterer_groups.py P3 P 3 u+s,u,s: 2.73 2.57 0.16 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/refinement/tst_rigid_body.py test 1: xyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 1 Resulting number of reflections: 100 Requested low-resolution limit: None Final number of reflections: 100 Data resolution: 11.14 - 2.00 (256 reflections) Resolution for rigid body refinement: 11.14 - 3.01 (80 reflections) WARNING: Final number of reflections for first resolution zone is greater than the number of available reflections (100 > 80). INFO: Number of resolution zones reset to 1. |-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------| | | | r_work= 0.6176 r_free= 0.1832 ksol= 0.00 Bsol= 0.00 scale= 0.703 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 3.01 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 -0.50 -0.70 -0.90 1.24 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 -0.50 -0.70 -0.90 1.24 | |-----------------------------------------------------------------------------| test 2: xyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 1 Resulting number of reflections: 100 Requested low-resolution limit: None Final number of reflections: 100 Data resolution: 11.14 - 2.00 (256 reflections) Resolution for rigid body refinement: 11.14 - 3.01 (80 reflections) WARNING: Final number of reflections for first resolution zone is greater than the number of available reflections (100 > 80). INFO: Number of resolution zones reset to 1. |-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 3.01 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| test 3: xyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 1 Resulting number of reflections: 100 Requested low-resolution limit: None Final number of reflections: 100 Data resolution: 11.14 - 2.00 (256 reflections) Resolution for rigid body refinement: 11.14 - 2.00 (256 reflections) Resolution cutoffs for multiple zones: number of zone resolution reflections target 1 11.14 - 2.75 100 ls_wunit_k1 2 11.14 - 2.75 101 ls_wunit_k1 3 11.14 - 2.69 110 ls_wunit_k1 4 11.14 - 2.42 149 ls_wunit_k1 5 11.14 - 2.00 256 ls_wunit_k1 zone number of reflections = 100 + 0.609375 * (zone-1)**4 |-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------| | | | r_work= 0.1885 r_free= 0.1410 ksol= 0.00 Bsol= 0.00 scale= 0.974 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.75 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.036 -1.945 -1.104 3.76 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.75 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.036 -1.945 -1.104 3.76 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.69 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.036 -1.945 -1.104 3.76 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.42 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.036 -1.945 -1.104 3.76 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.00 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.036 -1.945 -1.104 3.76 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.036 -1.945 -1.104 3.76 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| test 4: xyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 1 Resulting number of reflections: 100 Requested low-resolution limit: None Final number of reflections: 100 Data resolution: 41.94 - 2.00 (7315 reflections) Resolution for rigid body refinement: 41.94 - 2.00 (7315 reflections) Resolution cutoffs for multiple zones: number of zone resolution reflections target 1 41.94 - 9.06 100 ls_wunit_k1 2 41.94 - 8.29 128 ls_wunit_k1 3 41.94 - 4.92 551 ls_wunit_k1 4 41.94 - 2.95 2383 ls_wunit_k1 5 41.94 - 2.00 7315 ls_wunit_k1 zone number of reflections = 100 + 28.1836 * (zone-1)**4 |-Start-(resolution: 2.00 - 41.94 A; n_refl. = 7389)--------------------------| | | | r_work= 0.5468 r_free= 0.5461 ksol= 0.00 Bsol= 0.00 scale= 0.848 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 9.06 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0177 r_free= 0.0163 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.060 -1.913 -1.190 3.78 -0.48 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 8.29 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0110 r_free= 0.0124 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.002 -1.985 -1.172 3.77 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 4.92 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0025 r_free= 0.0026 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.036 -1.943 -1.099 3.75 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 2.95 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0006 r_free= 0.0007 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.039 -1.940 -1.105 3.76 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 2.00 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0002 r_free= 0.0003 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.039 -1.940 -1.102 3.76 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 41.94 A; n_refl. = 7389)-----------------| | | | r_work= 0.0002 r_free= 0.0003 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.039 -1.940 -1.102 3.76 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| test 5: xyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 2 Resulting number of reflections: 200 Requested low-resolution limit: None Final number of reflections: 200 Data resolution: 41.94 - 2.00 (7315 reflections) Resolution for rigid body refinement: 41.94 - 2.00 (7315 reflections) Resolution cutoffs for multiple zones: number of zone resolution reflections target 1 41.94 - 7.02 200 ls_wunit_k1 2 41.94 - 6.73 228 ls_wunit_k1 3 41.94 - 4.65 645 ls_wunit_k1 4 41.94 - 2.92 2451 ls_wunit_k1 5 41.94 - 2.00 7315 ls_wunit_k1 zone number of reflections = 200 + 27.793 * (zone-1)**4 |-Start-(resolution: 2.00 - 41.94 A; n_refl. = 7389)--------------------------| | | | r_work= 0.5519 r_free= 0.4926 ksol= 0.00 Bsol= 0.00 scale= 0.833 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | | group 2: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 7.02 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0078 r_free= 0.0103 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.012 -1.953 -1.160 3.76 -0.50 -1.00 -1.50 1.87 | | group 2: -1.095 -1.936 -3.061 3.77 -1.50 -0.50 -0.99 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 6.73 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0062 r_free= 0.0068 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.027 -1.943 -1.144 3.76 -0.50 -1.00 -1.49 1.87 | | group 2: -1.088 -1.950 -3.045 3.76 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 4.65 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0047 r_free= 0.0047 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.034 -1.949 -1.082 3.75 -0.50 -1.00 -1.51 1.88 | | group 2: -1.093 -1.949 -3.043 3.76 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 2.92 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0012 r_free= 0.0012 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.038 -1.940 -1.108 3.76 -0.50 -1.00 -1.50 1.87 | | group 2: -1.103 -1.946 -3.043 3.76 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 2.00 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0003 r_free= 0.0003 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.039 -1.941 -1.105 3.76 -0.50 -1.00 -1.50 1.87 | | group 2: -1.105 -1.944 -3.036 3.76 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 41.94 A; n_refl. = 7389)-----------------| | | | r_work= 0.0003 r_free= 0.0003 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -3.039 -1.941 -1.105 3.76 -0.50 -1.00 -1.50 1.87 | | group 2: -1.105 -1.944 -3.036 3.76 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| test 1: zyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 1 Resulting number of reflections: 100 Requested low-resolution limit: None Final number of reflections: 100 Data resolution: 11.14 - 2.00 (256 reflections) Resolution for rigid body refinement: 11.14 - 3.01 (80 reflections) WARNING: Final number of reflections for first resolution zone is greater than the number of available reflections (100 > 80). INFO: Number of resolution zones reset to 1. |-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------| | | | r_work= 0.6176 r_free= 0.1832 ksol= 0.00 Bsol= 0.00 scale= 0.703 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 3.01 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 -0.50 -0.70 -0.90 1.24 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 -0.50 -0.70 -0.90 1.24 | |-----------------------------------------------------------------------------| test 2: zyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 1 Resulting number of reflections: 100 Requested low-resolution limit: None Final number of reflections: 100 Data resolution: 11.14 - 2.00 (256 reflections) Resolution for rigid body refinement: 11.14 - 3.01 (80 reflections) WARNING: Final number of reflections for first resolution zone is greater than the number of available reflections (100 > 80). INFO: Number of resolution zones reset to 1. |-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 3.01 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| test 3: zyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 1 Resulting number of reflections: 100 Requested low-resolution limit: None Final number of reflections: 100 Data resolution: 11.14 - 2.00 (256 reflections) Resolution for rigid body refinement: 11.14 - 2.00 (256 reflections) Resolution cutoffs for multiple zones: number of zone resolution reflections target 1 11.14 - 2.75 100 ls_wunit_k1 2 11.14 - 2.75 101 ls_wunit_k1 3 11.14 - 2.69 110 ls_wunit_k1 4 11.14 - 2.42 149 ls_wunit_k1 5 11.14 - 2.00 256 ls_wunit_k1 zone number of reflections = 100 + 0.609375 * (zone-1)**4 |-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------| | | | r_work= 0.2132 r_free= 0.1989 ksol= 0.00 Bsol= 0.00 scale= 0.966 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.75 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.035 -2.000 -4.001 4.47 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.75 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.035 -2.000 -4.001 4.47 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.69 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.035 -2.000 -4.001 4.47 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.42 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.035 -2.000 -4.001 4.47 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 11.14 - 2.00 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.035 -2.000 -4.001 4.47 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.035 -2.000 -4.001 4.47 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| test 4: zyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 1 Resulting number of reflections: 100 Requested low-resolution limit: None Final number of reflections: 100 Data resolution: 41.94 - 2.00 (7315 reflections) Resolution for rigid body refinement: 41.94 - 2.00 (7315 reflections) Resolution cutoffs for multiple zones: number of zone resolution reflections target 1 41.94 - 9.06 100 ls_wunit_k1 2 41.94 - 8.29 128 ls_wunit_k1 3 41.94 - 4.92 551 ls_wunit_k1 4 41.94 - 2.95 2383 ls_wunit_k1 5 41.94 - 2.00 7315 ls_wunit_k1 zone number of reflections = 100 + 28.1836 * (zone-1)**4 |-Start-(resolution: 2.00 - 41.94 A; n_refl. = 7389)--------------------------| | | | r_work= 0.5392 r_free= 0.4766 ksol= 0.00 Bsol= 0.00 scale= 0.850 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 9.06 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0206 r_free= 0.0190 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.052 -1.973 -4.107 4.56 -0.48 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 8.29 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0116 r_free= 0.0129 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.001 -2.051 -4.074 4.56 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 4.92 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0027 r_free= 0.0028 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.034 -2.004 -3.996 4.47 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 2.95 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0006 r_free= 0.0006 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.038 -2.000 -4.002 4.47 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 2.00 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0002 r_free= 0.0003 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.037 -2.000 -4.000 4.47 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 41.94 A; n_refl. = 7389)-----------------| | | | r_work= 0.0002 r_free= 0.0003 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.037 -2.000 -4.000 4.47 -0.50 -1.00 -1.50 1.87 | |-----------------------------------------------------------------------------| test 5: zyz Rigid body refinement: Requested number of resolution zones: 5 Calculation for first resolution zone: Requested number of reflections per body: 100 Requested factor per body: 1.0 Number of bodies: 2 Resulting number of reflections: 200 Requested low-resolution limit: None Final number of reflections: 200 Data resolution: 41.94 - 2.00 (7315 reflections) Resolution for rigid body refinement: 41.94 - 2.00 (7315 reflections) Resolution cutoffs for multiple zones: number of zone resolution reflections target 1 41.94 - 7.02 200 ls_wunit_k1 2 41.94 - 6.73 228 ls_wunit_k1 3 41.94 - 4.65 645 ls_wunit_k1 4 41.94 - 2.92 2451 ls_wunit_k1 5 41.94 - 2.00 7315 ls_wunit_k1 zone number of reflections = 200 + 27.793 * (zone-1)**4 |-Start-(resolution: 2.00 - 41.94 A; n_refl. = 7389)--------------------------| | | | r_work= 0.5539 r_free= 0.4628 ksol= 0.00 Bsol= 0.00 scale= 0.830 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | | group 2: 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 7.02 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0085 r_free= 0.0108 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.008 -2.008 -4.060 4.53 -0.50 -1.00 -1.49 1.87 | | group 2: -0.096 -1.988 -4.019 4.48 -1.50 -0.50 -0.99 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 6.73 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0066 r_free= 0.0075 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.023 -2.004 -4.047 4.52 -0.50 -1.00 -1.49 1.87 | | group 2: -0.087 -2.006 -4.014 4.49 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 4.65 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0043 r_free= 0.0043 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.033 -2.009 -3.980 4.46 -0.50 -1.00 -1.51 1.88 | | group 2: -0.093 -2.003 -4.009 4.48 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 2.92 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0012 r_free= 0.0012 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.037 -1.999 -4.004 4.48 -0.50 -1.00 -1.50 1.87 | | group 2: -0.103 -1.999 -4.009 4.48 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| ----------Refinement at resolution: 41.94 - 2.00 target=ls_wunit_k1---------- |-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------| | | | r_work= 0.0002 r_free= 0.0003 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.037 -2.000 -4.001 4.47 -0.50 -1.00 -1.50 1.87 | | group 2: -0.105 -1.997 -4.002 4.47 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| |-Rigid body end-(resolution: 2.00 - 41.94 A; n_refl. = 7389)-----------------| | | | r_work= 0.0002 r_free= 0.0003 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | Rigid body shift (Euler angles xyz): | | rotation (deg) translation (A) | | xyz total xyz total | | group 1: -0.037 -2.000 -4.001 4.47 -0.50 -1.00 -1.50 1.87 | | group 2: -0.105 -1.997 -4.002 4.47 -1.50 -0.50 -1.00 1.87 | |-----------------------------------------------------------------------------| finite_differences_test: u+s,u,s: 215.47 212.37 3.10 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/refinement/tst_refinement_flags.py u+s,u,s: 2.31 2.16 0.15 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_model.py |-Geometry statistics---------------------------------------------------------| | Histogram of deviations from ideal values for | | Bonds | Angles | Nonbonded contacts | | 0.000 - 0.041: 40 | 0.004 - 3.586: 52 | 2.642 - 2.868: 15 | | 0.041 - 0.082: 0 | 3.586 - 7.169: 0 | 2.868 - 3.094: 15 | | 0.082 - 0.123: 0 | 7.169 - 10.751: 0 | 3.094 - 3.319: 21 | | 0.123 - 0.165: 0 | 10.751 - 14.334: 0 | 3.319 - 3.545: 33 | | 0.165 - 0.206: 0 | 14.334 - 17.916: 0 | 3.545 - 3.770: 50 | | 0.206 - 0.247: 0 | 17.916 - 21.499: 1 | 3.770 - 3.996: 71 | | 0.247 - 0.288: 0 | 21.499 - 25.081: 0 | 3.996 - 4.222: 59 | | 0.288 - 0.329: 0 | 25.081 - 28.663: 0 | 4.222 - 4.447: 78 | | 0.329 - 0.370: 0 | 28.663 - 32.246: 0 | 4.447 - 4.673: 91 | | 0.370 - 0.412: 1 | 32.246 - 35.828: 1 | 4.673 - 4.899: 108 | |-----------------------------------------------------------------------------| |-Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 41 | 0.064 0.412 0.000 | 10.330 | | | angle | 54 | 5.564 35.828 0.004 | 3.441 | | | chirality | 4 | 0.002 0.003 0.001 | 0.000 | 1.228 | | planarity | 7 | 0.052 0.138 0.000 | 27.185 | | | dihedral | 11 | 22.383 69.790 0.067 | 0.667 | | | nonbonded | 41 | 4.176 4.899 2.642 | 0.028 | | |-----------------------------------------------------------------------------| |-Geometry statistics---------------------------------------------------------| | Histogram of deviations from ideal values for | | Bonds | Angles | Nonbonded contacts | | 0.000 - 0.041: 40 | 0.004 - 3.586: 52 | 2.642 - 2.868: 15 | | 0.041 - 0.082: 0 | 3.586 - 7.169: 0 | 2.868 - 3.094: 15 | | 0.082 - 0.123: 0 | 7.169 - 10.751: 0 | 3.094 - 3.319: 21 | | 0.123 - 0.165: 0 | 10.751 - 14.334: 0 | 3.319 - 3.545: 33 | | 0.165 - 0.206: 0 | 14.334 - 17.916: 0 | 3.545 - 3.770: 50 | | 0.206 - 0.247: 0 | 17.916 - 21.499: 1 | 3.770 - 3.996: 71 | | 0.247 - 0.288: 0 | 21.499 - 25.081: 0 | 3.996 - 4.222: 59 | | 0.288 - 0.329: 0 | 25.081 - 28.663: 0 | 4.222 - 4.447: 78 | | 0.329 - 0.370: 0 | 28.663 - 32.246: 0 | 4.447 - 4.673: 91 | | 0.370 - 0.412: 1 | 32.246 - 35.828: 1 | 4.673 - 4.899: 108 | |-----------------------------------------------------------------------------| |-Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 41 | 0.064 0.412 0.000 | 10.330 | | | angle | 54 | 5.564 35.828 0.004 | 3.441 | | | chirality | 4 | 0.002 0.003 0.001 | 0.000 | 1.228 | | planarity | 7 | 0.052 0.138 0.000 | 27.185 | | | dihedral | 11 | 22.383 69.790 0.067 | 0.667 | | | nonbonded | 41 | 4.176 4.899 2.642 | 0.028 | | |-----------------------------------------------------------------------------| |-Geometry statistics---------------------------------------------------------| | Histogram of deviations from ideal values for | | Bonds | Angles | Nonbonded contacts | | 0.000 - 0.041: 40 | 0.004 - 3.586: 52 | 1.157 - 1.532: 1 | | 0.041 - 0.082: 0 | 3.586 - 7.169: 0 | 1.532 - 1.906: 0 | | 0.082 - 0.123: 0 | 7.169 - 10.751: 0 | 1.906 - 2.280: 0 | | 0.123 - 0.165: 0 | 10.751 - 14.334: 0 | 2.280 - 2.654: 3 | | 0.165 - 0.206: 0 | 14.334 - 17.916: 0 | 2.654 - 3.028: 29 | | 0.206 - 0.247: 0 | 17.916 - 21.499: 1 | 3.028 - 3.402: 59 | | 0.247 - 0.288: 0 | 21.499 - 25.081: 0 | 3.402 - 3.776: 86 | | 0.288 - 0.329: 0 | 25.081 - 28.663: 0 | 3.776 - 4.150: 125 | | 0.329 - 0.370: 0 | 28.663 - 32.246: 0 | 4.150 - 4.524: 158 | | 0.370 - 0.412: 1 | 32.246 - 35.828: 1 | 4.524 - 4.899: 197 | |-----------------------------------------------------------------------------| |-Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 41 | 0.064 0.412 0.000 | 10.330 | | | angle | 54 | 5.564 35.828 0.004 | 3.441 | | | chirality | 4 | 0.002 0.003 0.001 | 0.000 | 1.329 | | planarity | 7 | 0.052 0.138 0.000 | 27.185 | | | dihedral | 11 | 22.383 69.790 0.067 | 0.667 | | | nonbonded | 41 | 4.147 4.899 1.157 | 5.430 | | |-----------------------------------------------------------------------------| |-Geometry statistics---------------------------------------------------------| | Histogram of deviations from ideal values for | | Bonds | Angles | Nonbonded contacts | | 0.000 - 0.041: 40 | 0.004 - 3.586: 52 | 2.642 - 2.868: 15 | | 0.041 - 0.082: 0 | 3.586 - 7.169: 0 | 2.868 - 3.094: 15 | | 0.082 - 0.123: 0 | 7.169 - 10.751: 0 | 3.094 - 3.319: 21 | | 0.123 - 0.165: 0 | 10.751 - 14.334: 0 | 3.319 - 3.545: 33 | | 0.165 - 0.206: 0 | 14.334 - 17.916: 0 | 3.545 - 3.770: 50 | | 0.206 - 0.247: 0 | 17.916 - 21.499: 1 | 3.770 - 3.996: 71 | | 0.247 - 0.288: 0 | 21.499 - 25.081: 0 | 3.996 - 4.222: 59 | | 0.288 - 0.329: 0 | 25.081 - 28.663: 0 | 4.222 - 4.447: 78 | | 0.329 - 0.370: 0 | 28.663 - 32.246: 0 | 4.447 - 4.673: 91 | | 0.370 - 0.412: 1 | 32.246 - 35.828: 1 | 4.673 - 4.899: 108 | |-----------------------------------------------------------------------------| |-Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 41 | 0.064 0.412 0.000 | 10.330 | | | angle | 54 | 5.564 35.828 0.004 | 3.441 | | | chirality | 4 | 0.002 0.003 0.001 | 0.000 | 1.228 | | planarity | 7 | 0.052 0.138 0.000 | 27.185 | | | dihedral | 11 | 22.383 69.790 0.067 | 0.667 | | | nonbonded | 41 | 4.176 4.899 2.642 | 0.028 | | |-----------------------------------------------------------------------------| |-ADP statistics-------------------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 40 0 0.85 1.88 1.20 None None None | | all(noH): 40 0 0.85 1.88 1.20 None None None | | Sol. : 0 0 None None None None None None | | Mac. : 40 0 0.85 1.88 1.20 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 0.850 - 0.953: 9 | 5: 1.365 - 1.468: 4 | | 1: 0.953 - 1.056: 6 | 6: 1.468 - 1.571: 4 | | 2: 1.056 - 1.159: 8 | 7: 1.571 - 1.674: 2 | | 3: 1.159 - 1.262: 3 | 8: 1.674 - 1.777: 0 | | 4: 1.262 - 1.365: 2 | 9: 1.777 - 1.880: 2 | | =>continue=> | |----------------------------------------------------------------------| |-ADP statistics-------------------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 40 0 0.85 1.88 1.20 None None None | | all(noH): 40 0 0.85 1.88 1.20 None None None | | Sol. : 0 0 None None None None None None | | Mac. : 40 0 0.85 1.88 1.20 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 0.850 - 0.953: 9 | 5: 1.365 - 1.468: 4 | | 1: 0.953 - 1.056: 6 | 6: 1.468 - 1.571: 4 | | 2: 1.056 - 1.159: 8 | 7: 1.571 - 1.674: 2 | | 3: 1.159 - 1.262: 3 | 8: 1.674 - 1.777: 0 | | 4: 1.262 - 1.365: 2 | 9: 1.777 - 1.880: 2 | | =>continue=> | |----------------------------------------------------------------------| Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 46 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Modifications used: {'NH3': 1} Chain: "S" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 20 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 0.09, per 1000 atoms: 1.96 Number of scatterers: 46 At special positions: 0 Unit cell: (15.343, 15.541, 15.674, 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 10 8.00 N 4 7.00 C 6 6.00 H 26 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: 0.54 - 0.77: 2 0.77 - 1.01: 11 1.01 - 1.24: 8 1.24 - 1.48: 11 1.48 - 1.72: 4 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual pdb=" O HOH S 7 " - pdb=" H1 HOH S 7 " 0.980 1.476 -0.496 2.50e+03 6.14e+02 pdb=" CG ARG A 1 " - pdb=" HG3 ARG A 1 " 0.970 0.537 0.433 2.50e+03 4.70e+02 pdb=" O HOH S 9 " - pdb=" H2 HOH S 9 " 0.980 1.323 -0.343 2.50e+03 2.95e+02 pdb=" CA ARG A 1 " - pdb=" HA ARG A 1 " 0.980 1.263 -0.283 2.50e+03 2.00e+02 pdb=" O HOH S 1 " - pdb=" H1 HOH S 1 " 0.980 1.262 -0.282 2.50e+03 1.99e+02 ... (remaining 31 not shown) Histogram of nonbonded interaction distances: 0.71 - 1.55: 14 1.55 - 2.38: 25 2.38 - 3.22: 86 3.22 - 4.05: 56 4.05 - 4.89: 108 Warning: very small nonbonded interaction distances. Nonbonded interactions sorted by model distance: atom i - atom j model vdw pdb="HH12 ARG A 1 " - pdb=" H1 HOH S 4 " 0.712 2.400 pdb="HH11 ARG A 1 " - pdb=" H2 HOH S 4 " 0.791 2.400 pdb=" H1 HOH S 1 " - pdb=" H1 HOH S 9 " 0.840 2.400 pdb=" O HOH S 5 " - pdb=" H1 HOH S 8 " 0.902 2.720 pdb=" H2 HOH S 1 " - pdb=" H2 HOH S 9 " 0.914 2.400 ... (remaining 284 not shown) Histogram of dihedral angle deviations from ideal: 3.91 - 6.53: 3 6.53 - 9.16: 1 9.16 - 11.79: 1 11.79 - 14.42: 1 14.42 - 17.04: 1 Dihedral angle restraints sorted by residual: pdb=" CD ARG A 1 " pdb=" NE ARG A 1 " pdb=" CZ ARG A 1 " pdb=" NH2 ARG A 1 " ideal model delta periodicty weight residual 0.00 170.11 9.89 2 1.00e-02 9.78e-01 pdb=" NE ARG A 1 " pdb=" CZ ARG A 1 " pdb=" NH1 ARG A 1 " pdb="HH12 ARG A 1 " ideal model delta periodicty weight residual 0.00 17.04 -17.04 2 2.50e-03 7.26e-01 pdb=" NE ARG A 1 " pdb=" CZ ARG A 1 " pdb=" NH2 ARG A 1 " pdb="HH22 ARG A 1 " ideal model delta periodicty weight residual 0.00 167.09 12.91 2 2.50e-03 4.16e-01 ... (remaining 4 not shown) Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 1191 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 1191 Unusual residues: {'AU ': 1} Inner-chain residues flagged as termini: ['pdbres="CYS 127 "'] Classifications: {'undetermined': 1, 'water': 208, 'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, None: 209, 'TRANS': 124} Time building chain proxies: 2.44, per 1000 atoms: 2.05 Number of scatterers: 1191 At special positions: 0 Unit cell: (28.174, 52.857, 68.929, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Au 1 78.96 S 10 16.00 O 391 8.00 N 188 7.00 C 601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS 6 " - pdb=" SG CYS 127 " distance=1.99 Simple disulfide: pdb=" SG CYS 30 " - pdb=" SG CYS 115 " distance=1.98 Simple disulfide: pdb=" SG CYS 64 " - pdb=" SG CYS 80 " distance=1.98 Simple disulfide: pdb=" SG CYS 76 " - pdb=" SG CYS 94 " distance=1.98 Time building geometry restraints manager: 0.13 seconds Histogram of bond lengths: 1.19 - 1.35: 352 1.35 - 1.51: 579 1.51 - 1.67: 59 1.67 - 1.83: 12 1.83 - 1.99: 4 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual pdb=" CA TYR 53 " - pdb=" C TYR 53 " 1.525 1.451 0.074 2.27e+03 1.25e+01 pdb=" CA TRP 63 " - pdb=" C TRP 63 " 1.525 1.451 0.074 2.27e+03 1.23e+01 pdb=" CB CYS 76 " - pdb=" SG CYS 76 " 1.808 1.697 0.111 9.18e+02 1.14e+01 pdb=" CG MET 12 " - pdb=" SD MET 12 " 1.803 1.719 0.084 1.60e+03 1.12e+01 pdb=" CB TRP 123 " - pdb=" CG TRP 123 " 1.498 1.401 0.097 1.04e+03 9.71e+00 ... (remaining 1001 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 565 2.72 - 3.26: 1653 3.26 - 3.81: 3296 3.81 - 4.35: 4089 4.35 - 4.90: 5786 Nonbonded interactions sorted by model distance: atom i - atom j model vdw sym.op. j pdb=" O THR 43 " - pdb=" O HOH 164 " 2.172 3.040 pdb=" NH2 ARG 61 " - pdb=" O GLY 102 " 2.237 3.120 x-1/2,-y-1/2,-z+1 pdb=" O HOH 81 " - pdb=" O HOH 91 " 2.251 3.040 pdb=" O HOH 191 " - pdb=" O HOH 195 " 2.271 3.040 pdb=" O HOH 21 " - pdb=" O HOH 139 " 2.273 3.040 ... (remaining 15384 not shown) Histogram of dihedral angle deviations from ideal: 0.04 - 16.72: 305 16.72 - 33.40: 32 33.40 - 50.08: 7 50.08 - 66.75: 6 66.75 - 83.43: 3 Dihedral angle restraints sorted by residual: pdb=" CA TRP 62 " pdb=" C TRP 62 " pdb=" N TRP 63 " pdb=" CA TRP 63 " ideal model delta periodicty weight residual 180.00 -155.81 -24.19 1 4.00e-02 2.34e+01 pdb=" CA PHE 3 " pdb=" C PHE 3 " pdb=" N GLY 4 " pdb=" CA GLY 4 " ideal model delta periodicty weight residual 180.00 160.44 19.56 1 4.00e-02 1.53e+01 pdb=" CA ASN 113 " pdb=" C ASN 113 " pdb=" N ARG 114 " pdb=" CA ARG 114 " ideal model delta periodicty weight residual 180.00 -161.24 -18.76 1 4.00e-02 1.41e+01 ... (remaining 350 not shown) u+s,u,s: 10.57 10.38 0.19 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_fmodel.py P 1 P 4 C 1 2/c 1 u+s,u,s: 196.44 193.26 3.18 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_utils.py u+s,u,s: 20.86 20.62 0.24 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_alignment.py testError (__main__.test_blosum62) ... ok testSelected (__main__.test_blosum62) ... ok testSymmetric (__main__.test_blosum62) ... ok ---------------------------------------------------------------------- Ran 3 tests in 0.002s OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_fmodel_fd.py P31 P 31 ls_wexp_kunit lsm_kunit ls_wff_k1 ls_wff_k2 ls_wunit_k1 ls_wunit_k2 ls_wunit_k1_fixed ls_wunit_kunit lsm_k2 lsm_k1 lsm_k1_fixed mlhl ls_wunit_k1ask3_fixed ml ls_wff_k1_fixed ls_wff_kunit ls_wexp_k2 ls_wff_k1ask3_fixed lsm_k1ask3_fixed ls_wexp_k1 ls_wexp_kunit lsm_kunit ls_wff_k1 ls_wff_k2 ls_wunit_k1 ls_wunit_k2 ls_wunit_k1_fixed ls_wunit_kunit lsm_k2 lsm_k1 lsm_k1_fixed ls_wunit_k1ask3_fixed ml ls_wff_k1_fixed ls_wff_kunit ls_wexp_k2 ls_wff_k1ask3_fixed lsm_k1ask3_fixed ls_wexp_k1 u+s,u,s: 14.50 14.23 0.27 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/ncs/tst_restraints.py u+s,u,s: 3.31 3.16 0.15 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/ncs/tst_restraints.py u+s,u,s: 3.28 3.12 0.16 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/ncs/ncs.py exercise Reading NCS information from: TEST.NCS based on TEST.NCS GROUP 1 Summary of NCS group with 2 operators: ID of chain/residue where these apply: [['A', 'B'], [[[1, 26]], [[101, 126]]]] RMSD (A) from chain A: 0.2 0.1 Number of residues matching chain A:[12.0, 15.0] Source of NCS info: TEST.NCS NCS domains represented by: TEST.NCS Correlation of NCS: 0.92 OPERATOR 1 CENTER: 30.2920 -2.8923 16.6160 ROTA 1: 1.0000 0.0000 0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 0.0000 0.0000 0.0000 OPERATOR 2 CENTER: 39.8735 3.8824 16.7239 ROTA 1: -0.9971 0.0424 -0.0635 ROTA 2: -0.0297 -0.9816 -0.1889 ROTA 3: -0.0703 -0.1864 0.9800 TRANS: 70.9461 5.2622 3.7549 GROUP 2 Summary of NCS group with 2 operators: ID of chain/residue where these apply: [['A', 'B'], [[[1, 25]], [[101, 124]]]] RMSD (A) from chain A: 0.6 0.5 Number of residues matching chain A:[13.0, 11.0] Source of NCS info: TEST.NCS NCS domains represented by: TEST.NCS Correlation of NCS: 0.95 OPERATOR 1 CENTER: 31.2920 -2.8923 16.6160 ROTA 1: 1.0000 0.0000 0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 0.0000 0.0000 0.0001 OPERATOR 2 CENTER: 38.8735 3.8824 16.7239 ROTA 1: -0.9970 0.0424 -0.0635 ROTA 2: -0.0297 -0.9816 -0.1889 ROTA 3: -0.0703 -0.1864 0.9800 TRANS: 70.9461 5.2622 3.7549 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/regression/tst_adp_restraints.py u+s,u,s: 3.11 2.94 0.17 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/tst_scaling.py very_quick_erf*15000000 optimized=False: 14.20 s very_quick_erf*15000000 optimized=True: 1.36 s quick_ei0*5000000 optimized=False: 1.85 s quick_ei0*5000000 optimized=True: 0.83 s OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/tst_outlier.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/absence_likelihood.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/thorough_outlier_test.py P21 P 1 21 1 u+s,u,s: 30.83 30.40 0.43 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/twinning/probabalistic_detwinning.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_rna_sugar_pucker_analysis.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_cif_types.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_motif.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_selection.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_tyr_from_gly_and_bnz.py Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 12 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Time building chain proxies: 0.02, per 1000 atoms: 1.67 Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 12 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 12 Number of conformers: 1 Conformer: "" 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 "ATOM 145 CB GLY 1 .*. C " Time building chain proxies: 0.04, per 1000 atoms: 3.33 geo_tyr Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.03 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 pdb=" CD1 TYR 1 " - pdb=" CE1 TYR 1 " 1.382 1.394 -0.012 1.11e+03 1.67e-01 pdb=" CD2 TYR 1 " - pdb=" CE2 TYR 1 " 1.382 1.393 -0.011 1.11e+03 1.31e-01 pdb=" CE2 TYR 1 " - pdb=" CZ TYR 1 " 1.378 1.386 -0.008 1.74e+03 1.09e-01 pdb=" N TYR 1 " - pdb=" CA TYR 1 " 1.458 1.453 0.005 2.77e+03 6.34e-02 pdb=" CG TYR 1 " - pdb=" 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 - 3.19: 4 3.19 - 3.60: 7 3.60 - 4.02: 7 4.02 - 4.44: 5 4.44 - 4.85: 7 Nonbonded interactions sorted by model distance: atom i - atom j model vdw pdb=" CD2 TYR 1 " - pdb=" CE1 TYR 1 " 2.772 2.912 pdb=" CD1 TYR 1 " - pdb=" CE2 TYR 1 " 2.773 2.912 pdb=" CG TYR 1 " - pdb=" CZ TYR 1 " 2.797 2.784 pdb=" C TYR 1 " - pdb=" CG TYR 1 " 2.865 2.792 pdb=" O TYR 1 " - pdb=" CG TYR 1 " 3.226 3.260 ... (remaining 25 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: pdb=" N TYR 1 " pdb=" CA TYR 1 " pdb=" CB TYR 1 " pdb=" CG TYR 1 " ideal model delta periodicty weight residual 180.00 170.12 9.88 3 4.44e-03 4.34e-01 pdb=" CA TYR 1 " pdb=" CB TYR 1 " pdb=" CG TYR 1 " pdb=" CD1 TYR 1 " ideal model delta periodicty weight residual 90.00 78.11 11.89 2 2.50e-03 3.53e-01 target: 3.72568 bond_residual_sum (n=12): 0.630997 nonbonded_residual_sum (n=30): 0.155571 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: 0.02 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 pdb=" CA GLY 1 " - pdb=" C GLY 1 " 1.516 1.527 -0.011 3.09e+03 3.98e-01 pdb=" CD1 BNZ 2 " - pdb=" CE1 BNZ 2 " 1.382 1.394 -0.012 1.11e+03 1.67e-01 pdb=" CD2 BNZ 2 " - pdb=" CE2 BNZ 2 " 1.382 1.393 -0.011 1.11e+03 1.31e-01 pdb=" CE2 BNZ 2 " - pdb=" CZ BNZ 2 " 1.378 1.386 -0.008 1.74e+03 1.09e-01 pdb=" CG BNZ 2 " - pdb=" 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 pdb=" CA GLY 1 " - pdb=" CB GLY 1 " 1.529 1.000 pdb=" N GLY 1 " - pdb=" CB GLY 1 " 2.455 1.000 pdb=" C GLY 1 " - pdb=" CB GLY 1 " 2.498 1.000 pdb=" CA GLY 1 " - pdb=" CG BNZ 2 " 2.534 3.660 pdb=" CD2 BNZ 2 " - pdb=" CE1 BNZ 2 " 2.772 2.912 ... (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: pdb=" N GLY 1 " pdb=" CA GLY 1 " pdb=" CB GLY 1 " pdb=" CG BNZ 2 " ideal model delta periodicty weight residual 180.00 170.12 9.88 3 4.44e-03 4.34e-01 pdb=" CA GLY 1 " pdb=" CB GLY 1 " pdb=" CG BNZ 2 " pdb=" CD1 BNZ 2 " ideal model delta periodicty weight residual 90.00 78.11 11.89 2 2.50e-03 3.53e-01 target: 32.4767 bond_residual_sum (n=11): 0.970446 nonbonded_residual_sum (n=33): 29.2511 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/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_pdb_interpretation.py u+s,u,s: 7.64 7.47 0.17 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_rna_dna_interpretation.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_protein_interpretation.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/regression/tst_altloc_chain_break.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/hydrogens/build_hydrogens.py @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/arg.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 12 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.05, per 1000 atoms: 4.17 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 24 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.05, per 1000 atoms: 2.08 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: 0.02 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 pdb=" CA ARG 1 " - pdb="HA ARG 1 " 0.980 1.062 -0.082 2.50e+03 1.69e+01 pdb=" NE ARG 1 " - pdb=" CZ ARG 1 " 1.329 1.367 -0.038 5.10e+03 7.42e+00 pdb=" CA ARG 1 " - pdb=" N ARG 1 " 1.458 1.507 -0.049 2.77e+03 6.52e+00 pdb=" NE ARG 1 " - pdb="HE ARG 1 " 0.970 1.010 -0.040 2.50e+03 4.09e+00 pdb=" CB ARG 1 " - pdb=" 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 - 2.70: 28 2.70 - 3.25: 34 3.25 - 3.80: 33 3.80 - 4.34: 28 4.34 - 4.89: 30 Nonbonded interactions sorted by model distance: atom i - atom j model vdw pdb="HD2 ARG 1 " - pdb="HH12 ARG 1 " 2.158 2.400 pdb="HE ARG 1 " - pdb="HH21 ARG 1 " 2.266 2.400 pdb="HD1 ARG 1 " - pdb="HG2 ARG 1 " 2.275 1.920 pdb="HE ARG 1 " - pdb="HD1 ARG 1 " 2.285 1.920 pdb="HH22 ARG 1 " - pdb="HH11 ARG 1 " 2.294 2.400 ... (remaining 148 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: pdb=" OXT ARG 1 " pdb=" C ARG 1 " pdb=" CA ARG 1 " pdb=" N ARG 1 " ideal model delta periodicty weight residual 160.00 132.82 27.18 2 1.11e-03 8.21e-01 pdb=" CB ARG 1 " pdb=" CG ARG 1 " pdb=" CD ARG 1 " pdb=" NE ARG 1 " ideal model delta periodicty weight residual 180.00 71.06 -11.06 3 4.44e-03 5.44e-01 pdb=" CG ARG 1 " pdb=" CB ARG 1 " pdb=" CA ARG 1 " pdb=" 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: 60.28 bond_residual_sum (n=23): 43.5818 nonbonded_residual_sum (n=153): 1.14145 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: 60.28 bond_residual_sum (n=23): 43.5818 nonbonded_residual_sum (n=153): 1.14145 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: 781.811 Energies after minimization: target: 4.23207 bond_residual_sum (n=23): 0.058584 nonbonded_residual_sum (n=153): 3.00516 angle_residual_sum (n=39): 0.93043 dihedral_residual_sum (n=8): 0.22035 chirality_residual_sum (n=1): 0.0173148 planarity_residual_sum (n=2): 0.00022968 norm of gradients: 9.08072e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/lys.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 10 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.04, per 1000 atoms: 4.00 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 25 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Duplicate atoms: {'LYS%COO,HB1': 3} Classifications: {'peptide': 1} Modifications used: {'COO': 1} Number of atoms with unknown scattering type symbols: 3 "ATOM 22 HB2 LYS 1 .*. " "ATOM 23 HB1 LYS 1 .*. " "ATOM 24 HB2 LYS 1 .*. " Number of atoms with unknown nonbonded energy type symbols: 3 "ATOM 22 HB2 LYS 1 .*. " "ATOM 23 HB1 LYS 1 .*. " "ATOM 24 HB2 LYS 1 .*. " Time building chain proxies: 0.04, per 1000 atoms: 1.60 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: 0.02 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 pdb=" CA LYS 1 " - pdb=" N LYS 1 " 1.458 1.506 -0.048 2.77e+03 6.37e+00 pdb=" CA LYS 1 " - pdb="HA LYS 1 " 0.980 1.020 -0.040 2.50e+03 4.08e+00 pdb=" CB LYS 1 " - pdb=" CA LYS 1 " 1.530 1.555 -0.025 2.50e+03 1.52e+00 pdb=" C LYS 1 " - pdb=" OXT LYS 1 " 1.231 1.250 -0.019 2.50e+03 8.82e-01 pdb=" C LYS 1 " - pdb=" 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 - 1.57: 8 1.57 - 2.39: 26 2.39 - 3.21: 65 3.21 - 4.03: 44 4.03 - 4.85: 42 Warning: very small nonbonded interaction distances. Nonbonded interactions sorted by model distance: atom i - atom j model vdw pdb="HB1 LYS 1 " - pdb="HB2 LYS 1 " 0.754 1.000 pdb="HB2 LYS 1 " - pdb="HB1 LYS 1 " 0.795 1.000 pdb=" CB LYS 1 " - pdb="HB1 LYS 1 " 0.970 1.000 pdb=" CB LYS 1 " - pdb="HB2 LYS 1 " 0.970 1.000 pdb=" CB LYS 1 " - pdb="HB2 LYS 1 " 0.970 1.000 ... (remaining 180 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: pdb=" CD LYS 1 " pdb=" CE LYS 1 " pdb=" NZ LYS 1 " pdb="HZ3 LYS 1 " ideal model delta periodicty weight residual 60.00 141.07 38.93 3 1.11e-03 1.68e+00 pdb=" OXT LYS 1 " pdb=" C LYS 1 " pdb=" CA LYS 1 " pdb=" N LYS 1 " ideal model delta periodicty weight residual 160.00 -49.77 29.77 2 1.11e-03 9.85e-01 pdb=" CA LYS 1 " pdb=" CB LYS 1 " pdb=" CG LYS 1 " pdb=" 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: 668.898 bond_residual_sum (n=21): 14.6924 nonbonded_residual_sum (n=185): 10.7633 angle_residual_sum (n=39): 638.229 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: 668.898 bond_residual_sum (n=21): 14.6924 nonbonded_residual_sum (n=185): 10.7633 angle_residual_sum (n=39): 638.229 dihedral_residual_sum (n=6): 4.52202 chirality_residual_sum (n=1): 0.690449 planarity_residual_sum (n=1): 0.000506488 norm of gradients: 1336.79 Energies after minimization: target: 1.47913 bond_residual_sum (n=21): 0.0112116 nonbonded_residual_sum (n=182): 0.626626 angle_residual_sum (n=39): 0.419968 dihedral_residual_sum (n=6): 0.397743 chirality_residual_sum (n=1): 0.0235834 planarity_residual_sum (n=1): 7.35854e-15 norm of gradients: 2.11422e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/ala.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 6 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.03, per 1000 atoms: 5.00 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 10 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 2.00 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 pdb=" CA ALA 1 " - pdb="HA ALA 1 " 0.980 1.050 -0.070 2.50e+03 1.23e+01 pdb=" CA ALA 1 " - pdb=" N ALA 1 " 1.458 1.503 -0.045 2.77e+03 5.55e+00 pdb=" C ALA 1 " - pdb=" OXT ALA 1 " 1.231 1.250 -0.019 2.50e+03 9.41e-01 pdb=" C ALA 1 " - pdb=" O ALA 1 " 1.231 1.249 -0.018 2.50e+03 7.81e-01 pdb=" C ALA 1 " - pdb=" 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 pdb="HA ALA 1 " - pdb="HB3 ALA 1 " 2.298 1.920 pdb=" OXT ALA 1 " - pdb="HA ALA 1 " 2.457 2.176 pdb="HA ALA 1 " - pdb="HB1 ALA 1 " 2.473 1.920 pdb=" N ALA 1 " - pdb="HB1 ALA 1 " 2.586 2.240 pdb=" C ALA 1 " - pdb="HB2 ALA 1 " 2.615 2.360 ... (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: pdb=" N ALA 1 " pdb=" CB ALA 1 " pdb=" CA ALA 1 " pdb="HB3 ALA 1 " ideal model delta periodicty weight residual -60.00 163.29 16.71 3 4.44e-03 1.24e+00 pdb=" OXT ALA 1 " pdb=" C ALA 1 " pdb=" CA ALA 1 " pdb=" 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): 1.76642e-12 chirality_residual_sum (n=1): 0.0188403 planarity_residual_sum (n=1): 3.55183e-15 norm of gradients: 9.04354e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/gly.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 5 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.01, per 1000 atoms: 2.00 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 7 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 7 Number of conformers: 1 Conformer: "" 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: 0.01 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 pdb=" CA GLY 1 " - pdb=" N GLY 1 " 1.451 1.491 -0.040 3.91e+03 6.31e+00 pdb=" C GLY 1 " - pdb=" O GLY 1 " 1.231 1.250 -0.019 2.50e+03 8.56e-01 pdb=" OXT GLY 1 " - pdb=" C GLY 1 " 1.231 1.249 -0.018 2.50e+03 7.95e-01 pdb=" C GLY 1 " - pdb=" CA GLY 1 " 1.516 1.524 -0.008 3.09e+03 2.10e-01 pdb=" CA GLY 1 " - pdb="HA2 GLY 1 " 0.970 0.970 0.000 2.50e+03 4.41e-04 pdb=" CA GLY 1 " - pdb="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 pdb=" OXT GLY 1 " - pdb="HA2 GLY 1 " 2.435 2.176 pdb=" O GLY 1 " - pdb="HA1 GLY 1 " 2.646 2.176 pdb=" O GLY 1 " - pdb=" N GLY 1 " 2.924 2.496 pdb=" OXT GLY 1 " - pdb="HA1 GLY 1 " 2.983 2.176 pdb=" O GLY 1 " - pdb="HA2 GLY 1 " 3.158 2.176 pdb=" OXT GLY 1 " - pdb=" N GLY 1 " 3.421 2.496 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: pdb=" OXT GLY 1 " pdb=" C GLY 1 " pdb=" CA GLY 1 " pdb=" 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): 2.73974e-15 nonbonded_residual_sum (n=6): 0 angle_residual_sum (n=9): 0.13971 dihedral_residual_sum (n=1): 1.01429e-14 chirality_residual_sum (n=0): 0 planarity_residual_sum (n=1): 5.24466e-16 norm of gradients: 8.48013e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/his.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 11 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.04, per 1000 atoms: 3.64 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 18 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.04, per 1000 atoms: 2.22 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: 0.01 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 pdb=" CA HIS 1 " - pdb=" N HIS 1 " 1.458 1.505 -0.047 2.77e+03 6.20e+00 pdb=" CA HIS 1 " - pdb="HA HIS 1 " 0.980 1.028 -0.048 2.50e+03 5.66e+00 pdb=" CB HIS 1 " - pdb=" CA HIS 1 " 1.530 1.557 -0.027 2.50e+03 1.76e+00 pdb=" C HIS 1 " - pdb=" OXT HIS 1 " 1.231 1.250 -0.019 2.50e+03 9.07e-01 pdb=" C HIS 1 " - pdb=" 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 - 2.87: 14 2.87 - 3.38: 21 3.38 - 3.88: 22 3.88 - 4.39: 12 4.39 - 4.90: 18 Nonbonded interactions sorted by model distance: atom i - atom j model vdw pdb="HE1 HIS 1 " - pdb="HD1 HIS 1 " 2.363 1.920 pdb="HE2 HIS 1 " - pdb="HE1 HIS 1 " 2.364 1.920 pdb="HE2 HIS 1 " - pdb="HD2 HIS 1 " 2.426 1.920 pdb=" OXT HIS 1 " - pdb="HA HIS 1 " 2.462 2.176 pdb="HD1 HIS 1 " - pdb="HB1 HIS 1 " 2.486 2.400 ... (remaining 82 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: pdb=" CG HIS 1 " pdb=" CB HIS 1 " pdb=" CA HIS 1 " pdb=" N HIS 1 " ideal model delta periodicty weight residual 180.00 -160.63 -19.37 3 4.44e-03 1.67e+00 pdb=" CA HIS 1 " pdb=" CB HIS 1 " pdb=" CG HIS 1 " pdb=" ND1 HIS 1 " ideal model delta periodicty weight residual 90.00 110.09 -20.09 2 2.50e-03 1.01e+00 pdb=" OXT HIS 1 " pdb=" C HIS 1 " pdb=" CA HIS 1 " pdb=" N HIS 1 " ideal model delta periodicty weight residual 160.00 130.66 29.34 2 1.11e-03 9.57e-01 target: 27.8229 bond_residual_sum (n=18): 16.2986 nonbonded_residual_sum (n=87): 7.16918e-05 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: 27.8229 bond_residual_sum (n=18): 16.2986 nonbonded_residual_sum (n=87): 7.16918e-05 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: 0.340824 bond_residual_sum (n=18): 0.00284261 nonbonded_residual_sum (n=87): 0.0382526 angle_residual_sum (n=30): 0.253362 dihedral_residual_sum (n=3): 0.0251822 chirality_residual_sum (n=1): 0.0211128 planarity_residual_sum (n=2): 7.20967e-05 norm of gradients: 1.50079e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/ile.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 9 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.04, per 1000 atoms: 4.44 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 20 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Duplicate atoms: {'ILE%COO,HG11': 1} Classifications: {'peptide': 1} Modifications used: {'COO': 1} Number of atoms with unknown scattering type symbols: 1 "ATOM 14 HG12 ILE 1 .*. " Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 14 HG12 ILE 1 .*. " Time building chain proxies: 0.04, per 1000 atoms: 2.00 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: 0.02 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 pdb=" CA ILE 1 " - pdb="HA ILE 1 " 0.980 1.117 -0.137 2.50e+03 4.71e+01 pdb=" CB ILE 1 " - pdb="HB ILE 1 " 0.970 1.035 -0.065 2.50e+03 1.07e+01 pdb=" CA ILE 1 " - pdb=" N ILE 1 " 1.458 1.506 -0.048 2.77e+03 6.33e+00 pdb=" CB ILE 1 " - pdb=" CA ILE 1 " 1.540 1.588 -0.048 1.37e+03 3.18e+00 pdb=" CB ILE 1 " - pdb=" CG1 ILE 1 " 1.530 1.565 -0.035 2.50e+03 3.08e+00 ... (remaining 13 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.41: 5 1.41 - 2.26: 6 2.26 - 3.11: 39 3.11 - 3.96: 46 3.96 - 4.80: 35 Warning: very small nonbonded interaction distances. Nonbonded interactions sorted by model distance: atom i - atom j model vdw pdb=" CD1 ILE 1 " - pdb="HG12 ILE 1 " 0.566 1.000 pdb=" CG1 ILE 1 " - pdb="HG12 ILE 1 " 0.970 1.000 pdb="HG12 ILE 1 " - pdb="HD11 ILE 1 " 1.196 1.000 pdb="HG12 ILE 1 " - pdb="HD12 ILE 1 " 1.284 1.000 pdb="HG12 ILE 1 " - pdb="HD13 ILE 1 " 1.320 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: pdb=" CB ILE 1 " pdb=" CD1 ILE 1 " pdb=" CG1 ILE 1 " pdb="HD13 ILE 1 " ideal model delta periodicty weight residual -60.00 104.34 -44.34 3 1.11e-03 2.18e+00 pdb=" CA ILE 1 " pdb=" CB ILE 1 " pdb=" CG1 ILE 1 " pdb=" CD1 ILE 1 " ideal model delta periodicty weight residual 180.00 74.80 -14.80 3 4.44e-03 9.73e-01 pdb=" N ILE 1 " pdb=" CB ILE 1 " pdb=" CA ILE 1 " pdb=" 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: 95.5006 bond_residual_sum (n=18): 73.456 nonbonded_residual_sum (n=131): 1.23375 angle_residual_sum (n=33): 16.1902 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: 95.5006 bond_residual_sum (n=18): 73.456 nonbonded_residual_sum (n=131): 1.23375 angle_residual_sum (n=33): 16.1902 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: 1071.14 Energies after minimization: target: 6.15839 bond_residual_sum (n=18): 0.0539857 nonbonded_residual_sum (n=131): 2.25277 angle_residual_sum (n=33): 0.944518 dihedral_residual_sum (n=5): 2.87315 chirality_residual_sum (n=2): 0.0320489 planarity_residual_sum (n=1): 0.00191259 norm of gradients: 7.23681e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/leu.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 9 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.04, per 1000 atoms: 4.44 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 22 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Duplicate atoms: {'LEU%COO,HB1': 3} 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 "ATOM 18 HB2 LEU 1 .*. C " "ATOM 19 HB1 LEU 1 .*. C " "ATOM 20 HB2 LEU 1 .*. C " Time building chain proxies: 0.04, per 1000 atoms: 1.82 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: 0.02 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 pdb=" CG LEU 1 " - pdb="HG LEU 1 " 0.970 1.055 -0.085 2.50e+03 1.81e+01 pdb=" CA LEU 1 " - pdb="HA LEU 1 " 0.980 1.032 -0.052 2.50e+03 6.72e+00 pdb=" CA LEU 1 " - pdb=" N LEU 1 " 1.458 1.503 -0.045 2.77e+03 5.52e+00 pdb=" CB LEU 1 " - pdb=" CG LEU 1 " 1.530 1.565 -0.035 2.50e+03 2.99e+00 pdb=" CB LEU 1 " - pdb=" 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 pdb="HB1 LEU 1 " - pdb="HB2 LEU 1 " 0.021 1.000 pdb="HB2 LEU 1 " - pdb="HB3 LEU 1 " 0.143 1.000 pdb=" CG LEU 1 " - pdb="HB1 LEU 1 " 0.630 1.000 pdb=" CB LEU 1 " - pdb="HB2 LEU 1 " 0.970 1.000 pdb=" CB LEU 1 " - pdb="HB2 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: pdb=" CA LEU 1 " pdb=" CB LEU 1 " pdb=" CG LEU 1 " pdb=" CD2 LEU 1 " ideal model delta periodicty weight residual 180.00 82.11 -22.11 3 4.44e-03 2.17e+00 pdb=" CB LEU 1 " pdb=" CG LEU 1 " pdb=" CD2 LEU 1 " pdb="HD23 LEU 1 " ideal model delta periodicty weight residual 60.00 149.28 30.72 3 1.11e-03 1.05e+00 pdb=" OXT LEU 1 " pdb=" C LEU 1 " pdb=" CA LEU 1 " pdb=" 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: 82.4974 bond_residual_sum (n=18): 38.445 nonbonded_residual_sum (n=166): 24.1 angle_residual_sum (n=33): 14.8442 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: 82.4974 bond_residual_sum (n=18): 38.445 nonbonded_residual_sum (n=166): 24.1 angle_residual_sum (n=33): 14.8442 dihedral_residual_sum (n=5): 4.4702 chirality_residual_sum (n=2): 0.637222 planarity_residual_sum (n=1): 0.000879497 norm of gradients: 805.49 Energies after minimization: target: 4.15158 bond_residual_sum (n=18): 0.0497747 nonbonded_residual_sum (n=164): 1.89993 angle_residual_sum (n=33): 1.12896 dihedral_residual_sum (n=5): 1.0388 chirality_residual_sum (n=2): 0.0341183 planarity_residual_sum (n=1): 1.48221e-15 norm of gradients: 2.22707e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/phe.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 12 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.05, per 1000 atoms: 4.17 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 20 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.04, per 1000 atoms: 2.00 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 pdb=" CA PHE 1 " - pdb=" N PHE 1 " 1.458 1.491 -0.033 2.77e+03 3.05e+00 pdb=" CD2 PHE 1 " - pdb=" CE2 PHE 1 " 1.382 1.430 -0.048 1.11e+03 2.53e+00 pdb=" CD1 PHE 1 " - pdb=" CE1 PHE 1 " 1.382 1.430 -0.048 1.11e+03 2.51e+00 pdb=" CG PHE 1 " - pdb=" CD1 PHE 1 " 1.384 1.414 -0.030 2.27e+03 2.04e+00 pdb=" CA PHE 1 " - pdb="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 - 2.84: 20 2.84 - 3.35: 24 3.35 - 3.85: 16 3.85 - 4.35: 11 4.35 - 4.85: 26 Nonbonded interactions sorted by model distance: atom i - atom j model vdw pdb="HD2 PHE 1 " - pdb="HB2 PHE 1 " 2.341 2.400 pdb="HZ PHE 1 " - pdb="HE1 PHE 1 " 2.353 1.920 pdb="HZ PHE 1 " - pdb="HE2 PHE 1 " 2.353 1.920 pdb="HE1 PHE 1 " - pdb="HD1 PHE 1 " 2.354 1.920 pdb="HE2 PHE 1 " - pdb="HD2 PHE 1 " 2.354 1.920 ... (remaining 92 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: pdb=" OXT PHE 1 " pdb=" C PHE 1 " pdb=" CA PHE 1 " pdb=" N PHE 1 " ideal model delta periodicty weight residual 160.00 120.83 39.17 2 1.11e-03 1.70e+00 pdb=" CA PHE 1 " pdb=" CB PHE 1 " pdb=" CG PHE 1 " pdb=" CD1 PHE 1 " ideal model delta periodicty weight residual 90.00 70.30 19.70 2 2.50e-03 9.71e-01 pdb=" CG PHE 1 " pdb=" CB PHE 1 " pdb=" CA PHE 1 " pdb=" N PHE 1 " ideal model delta periodicty weight residual 180.00 -61.50 1.50 3 4.44e-03 9.94e-03 target: 29.5196 bond_residual_sum (n=20): 19.3992 nonbonded_residual_sum (n=97): 0.509062 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: 29.5196 bond_residual_sum (n=20): 19.3992 nonbonded_residual_sum (n=97): 0.509062 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: 454.835 Energies after minimization: target: 0.339579 bond_residual_sum (n=20): 0.0117639 nonbonded_residual_sum (n=97): 0.0368481 angle_residual_sum (n=33): 0.268212 dihedral_residual_sum (n=3): 0.00366822 chirality_residual_sum (n=1): 0.0190864 planarity_residual_sum (n=2): 5.70301e-14 norm of gradients: 1.39329e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/tyr.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 13 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.05, per 1000 atoms: 3.85 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 21 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.04, per 1000 atoms: 1.90 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 pdb=" CA TYR 1 " - pdb=" N TYR 1 " 1.458 1.507 -0.049 2.77e+03 6.73e+00 pdb=" CA TYR 1 " - pdb="HA TYR 1 " 0.980 1.021 -0.041 2.50e+03 4.14e+00 pdb=" CD2 TYR 1 " - pdb=" CG TYR 1 " 1.389 1.429 -0.040 2.27e+03 3.69e+00 pdb=" CG TYR 1 " - pdb=" CD1 TYR 1 " 1.389 1.429 -0.040 2.27e+03 3.65e+00 pdb=" CZ TYR 1 " - pdb=" 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 - 2.79: 18 2.79 - 3.31: 23 3.31 - 3.83: 22 3.83 - 4.35: 12 4.35 - 4.87: 28 Nonbonded interactions sorted by model distance: atom i - atom j model vdw pdb="HE2 TYR 1 " - pdb="HH TYR 1 " 2.274 2.400 pdb="HE1 TYR 1 " - pdb="HD1 TYR 1 " 2.340 1.920 pdb="HE2 TYR 1 " - pdb="HD2 TYR 1 " 2.341 1.920 pdb=" CE2 TYR 1 " - pdb="HH TYR 1 " 2.402 2.416 pdb="HA TYR 1 " - pdb="HB2 TYR 1 " 2.442 1.920 ... (remaining 98 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: pdb=" CE1 TYR 1 " pdb=" OH TYR 1 " pdb=" CZ TYR 1 " pdb="HH TYR 1 " ideal model delta periodicty weight residual -60.00 -179.97 -60.03 2 1.11e-03 4.00e+00 pdb=" OXT TYR 1 " pdb=" C TYR 1 " pdb=" CA TYR 1 " pdb=" N TYR 1 " ideal model delta periodicty weight residual 160.00 -49.67 29.67 2 1.11e-03 9.78e-01 pdb=" CG TYR 1 " pdb=" CB TYR 1 " pdb=" CA TYR 1 " pdb=" N TYR 1 " ideal model delta periodicty weight residual 180.00 -68.78 8.78 3 4.44e-03 3.42e-01 pdb=" CA TYR 1 " pdb=" CB TYR 1 " pdb=" CG TYR 1 " pdb=" CD1 TYR 1 " ideal model delta periodicty weight residual 90.00 -85.51 -4.49 2 2.50e-03 5.04e-02 target: 40.7003 bond_residual_sum (n=21): 28.8817 nonbonded_residual_sum (n=103): 0.00538344 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: 40.7003 bond_residual_sum (n=21): 28.8817 nonbonded_residual_sum (n=103): 0.00538344 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: 573.508 Energies after minimization: target: 0.330276 bond_residual_sum (n=21): 0.00424817 nonbonded_residual_sum (n=103): 0.031871 angle_residual_sum (n=34): 0.272515 dihedral_residual_sum (n=4): 0.00247102 chirality_residual_sum (n=1): 0.0191155 planarity_residual_sum (n=2): 5.49542e-05 norm of gradients: 9.49242e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/trp.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 15 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.06, per 1000 atoms: 4.00 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 24 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.05, per 1000 atoms: 2.08 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: 0.02 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 pdb=" CA TRP 1 " - pdb=" N TRP 1 " 1.458 1.507 -0.049 2.77e+03 6.78e+00 pdb=" CE3 TRP 1 " - pdb=" CD2 TRP 1 " 1.398 1.433 -0.035 3.91e+03 4.74e+00 pdb=" CA TRP 1 " - pdb="HA TRP 1 " 0.980 1.020 -0.040 2.50e+03 4.09e+00 pdb=" CZ2 TRP 1 " - pdb=" CH2 TRP 1 " 1.368 1.403 -0.035 2.77e+03 3.34e+00 pdb=" CZ2 TRP 1 " - pdb=" 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 - 2.85: 20 2.85 - 3.36: 33 3.36 - 3.87: 26 3.87 - 4.38: 22 4.38 - 4.90: 35 Nonbonded interactions sorted by model distance: atom i - atom j model vdw pdb="HH2 TRP 1 " - pdb="HZ2 TRP 1 " 2.339 1.920 pdb="HH2 TRP 1 " - pdb="HZ3 TRP 1 " 2.347 1.920 pdb="HE3 TRP 1 " - pdb="HZ3 TRP 1 " 2.349 1.920 pdb="HE1 TRP 1 " - pdb="HD1 TRP 1 " 2.411 1.920 pdb="HA TRP 1 " - pdb="HB2 TRP 1 " 2.445 1.920 ... (remaining 131 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: pdb=" N TRP 1 " pdb=" C TRP 1 " pdb=" CA TRP 1 " pdb=" OXT TRP 1 " ideal model delta periodicty weight residual -160.00 -130.62 -29.38 2 1.11e-03 9.59e-01 pdb=" CG TRP 1 " pdb=" CB TRP 1 " pdb=" CA TRP 1 " pdb=" N TRP 1 " ideal model delta periodicty weight residual 180.00 -69.24 9.24 3 4.44e-03 3.79e-01 pdb=" CA TRP 1 " pdb=" CB TRP 1 " pdb=" CG TRP 1 " pdb=" 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=136): 3.30721e-05 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=136): 3.30721e-05 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: 676.857 Energies after minimization: target: 0.281772 bond_residual_sum (n=25): 0.0065275 nonbonded_residual_sum (n=136): 0.00317817 angle_residual_sum (n=42): 0.252815 dihedral_residual_sum (n=3): 6.65914e-07 chirality_residual_sum (n=1): 0.0192505 planarity_residual_sum (n=2): 6.86899e-16 norm of gradients: 9.41684e-06 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/thr.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 8 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.03, per 1000 atoms: 3.75 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 13 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.03, per 1000 atoms: 2.31 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: 0.01 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 pdb=" CB THR 1 " - pdb="HB THR 1 " 0.970 1.029 -0.059 2.50e+03 8.81e+00 pdb=" CA THR 1 " - pdb=" N THR 1 " 1.458 1.508 -0.050 2.77e+03 6.87e+00 pdb=" CA THR 1 " - pdb="HA THR 1 " 0.980 1.031 -0.051 2.50e+03 6.60e+00 pdb=" C THR 1 " - pdb=" OXT THR 1 " 1.231 1.250 -0.019 2.50e+03 8.89e-01 pdb=" C THR 1 " - pdb=" 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 pdb="HG21 THR 1 " - pdb="HB THR 1 " 2.165 1.920 pdb="HA THR 1 " - pdb="HG22 THR 1 " 2.360 2.400 pdb=" OG1 THR 1 " - pdb="HG23 THR 1 " 2.377 2.176 pdb="HA THR 1 " - pdb="HB THR 1 " 2.451 1.920 pdb=" O THR 1 " - pdb="HA THR 1 " 2.459 2.176 ... (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: pdb=" CA THR 1 " pdb=" CB THR 1 " pdb=" CG2 THR 1 " pdb="HG23 THR 1 " ideal model delta periodicty weight residual 60.00 100.94 -40.94 3 1.11e-03 1.86e+00 pdb=" OXT THR 1 " pdb=" C THR 1 " pdb=" CA THR 1 " pdb=" N THR 1 " ideal model delta periodicty weight residual 160.00 -49.57 29.57 2 1.11e-03 9.72e-01 pdb=" N THR 1 " pdb=" CB THR 1 " pdb=" CA THR 1 " pdb=" CG2 THR 1 " ideal model delta periodicty weight residual -180.00 68.60 -8.60 3 4.44e-03 3.28e-01 target: 41.9254 bond_residual_sum (n=12): 24.73 nonbonded_residual_sum (n=44): 8.6912e-05 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: 41.9254 bond_residual_sum (n=12): 24.73 nonbonded_residual_sum (n=44): 8.6912e-05 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: 845.061 Energies after minimization: target: 0.316755 bond_residual_sum (n=12): 0.00186294 nonbonded_residual_sum (n=44): 0.0106859 angle_residual_sum (n=21): 0.279242 dihedral_residual_sum (n=3): 0.00149716 chirality_residual_sum (n=2): 0.0234672 planarity_residual_sum (n=1): 6.68696e-17 norm of gradients: 1.04277e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/val.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 8 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.04, per 1000 atoms: 5.00 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 16 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.04, per 1000 atoms: 2.50 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: 0.01 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 pdb=" CA VAL 1 " - pdb="HA VAL 1 " 0.980 1.091 -0.111 2.50e+03 3.07e+01 pdb=" CA VAL 1 " - pdb=" N VAL 1 " 1.458 1.505 -0.047 2.77e+03 6.17e+00 pdb=" CB VAL 1 " - pdb="HB VAL 1 " 0.980 1.026 -0.046 2.50e+03 5.22e+00 pdb=" CB VAL 1 " - pdb=" CA VAL 1 " 1.540 1.581 -0.041 1.37e+03 2.30e+00 pdb=" C VAL 1 " - pdb=" 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 pdb="HG23 VAL 1 " - pdb="HG13 VAL 1 " 2.050 2.400 pdb="HG12 VAL 1 " - pdb="HB VAL 1 " 2.164 1.920 pdb="HG21 VAL 1 " - pdb="HB VAL 1 " 2.186 1.920 pdb="HG11 VAL 1 " - pdb="HA VAL 1 " 2.372 2.400 pdb=" CG2 VAL 1 " - pdb="HG13 VAL 1 " 2.458 2.512 ... (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: pdb=" CA VAL 1 " pdb=" CB VAL 1 " pdb=" CG1 VAL 1 " pdb="HG13 VAL 1 " ideal model delta periodicty weight residual 60.00 123.81 -63.81 2 1.11e-03 4.52e+00 pdb=" OXT VAL 1 " pdb=" C VAL 1 " pdb=" CA VAL 1 " pdb=" N VAL 1 " ideal model delta periodicty weight residual 160.00 135.14 24.86 2 1.11e-03 6.87e-01 pdb=" CA VAL 1 " pdb=" CB VAL 1 " pdb=" CG2 VAL 1 " pdb="HG23 VAL 1 " ideal model delta periodicty weight residual 60.00 -135.02 15.02 2 1.11e-03 2.51e-01 pdb=" N VAL 1 " pdb=" CB VAL 1 " pdb=" CA VAL 1 " pdb=" CG2 VAL 1 " ideal model delta periodicty weight residual -180.00 -55.39 -4.61 3 4.44e-03 9.44e-02 target: 64.3136 bond_residual_sum (n=15): 47.3506 nonbonded_residual_sum (n=74): 0.352835 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: 64.3136 bond_residual_sum (n=15): 47.3506 nonbonded_residual_sum (n=74): 0.352835 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: 882.162 Energies after minimization: target: 0.463554 bond_residual_sum (n=15): 0.00177692 nonbonded_residual_sum (n=74): 0.184628 angle_residual_sum (n=27): 0.241823 dihedral_residual_sum (n=4): 0.0197403 chirality_residual_sum (n=2): 0.0155556 planarity_residual_sum (n=1): 2.97146e-05 norm of gradients: 1.62062e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/cys.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 7 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.03, per 1000 atoms: 4.29 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 11 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 1.82 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 pdb=" CA CYS 1 " - pdb="HA CYS 1 " 0.980 1.072 -0.092 2.50e+03 2.12e+01 pdb=" CA CYS 1 " - pdb=" N CYS 1 " 1.458 1.506 -0.048 2.77e+03 6.44e+00 pdb=" CB CYS 1 " - pdb=" CA CYS 1 " 1.530 1.561 -0.031 2.50e+03 2.47e+00 pdb=" C CYS 1 " - pdb=" OXT CYS 1 " 1.231 1.250 -0.019 2.50e+03 9.05e-01 pdb=" C CYS 1 " - pdb=" 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 pdb="HA CYS 1 " - pdb="HB1 CYS 1 " 2.369 1.920 pdb="HA CYS 1 " - pdb="HB2 CYS 1 " 2.402 1.920 pdb=" OXT CYS 1 " - pdb="HA CYS 1 " 2.467 2.176 pdb=" O CYS 1 " - pdb="HG CYS 1 " 2.593 2.720 pdb=" C CYS 1 " - pdb="HB2 CYS 1 " 2.721 2.360 ... (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: pdb=" CA CYS 1 " pdb=" CB CYS 1 " pdb=" SG CYS 1 " pdb="HG CYS 1 " ideal model delta periodicty weight residual 180.00 -0.01 -59.99 3 4.44e-03 1.60e+01 pdb=" OXT CYS 1 " pdb=" C CYS 1 " pdb=" CA CYS 1 " pdb=" N CYS 1 " ideal model delta periodicty weight residual 160.00 133.17 26.83 2 1.11e-03 8.00e-01 pdb=" N CYS 1 " pdb=" CB CYS 1 " pdb=" CA CYS 1 " pdb=" SG CYS 1 " ideal model delta periodicty weight residual -180.00 -59.31 -0.69 3 4.44e-03 2.14e-03 target: 59.9793 bond_residual_sum (n=10): 32.5394 nonbonded_residual_sum (n=29): 0.00698155 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: 59.9793 bond_residual_sum (n=10): 32.5394 nonbonded_residual_sum (n=29): 0.00698155 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: 705.658 Energies after minimization: target: 0.29813 bond_residual_sum (n=10): 0.00163257 nonbonded_residual_sum (n=29): 5.90638e-05 angle_residual_sum (n=16): 0.2772 dihedral_residual_sum (n=3): 4.26806e-07 chirality_residual_sum (n=1): 0.0192382 planarity_residual_sum (n=1): 8.51102e-15 norm of gradients: 1.28033e-05 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/ser.pdb Monomer Library directory: "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 7 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.03, per 1000 atoms: 4.29 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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib" Total number of atoms: 11 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.02, per 1000 atoms: 1.82 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 pdb=" CA SER 1 " - pdb=" N SER 1 " 1.458 1.504 -0.046 2.77e+03 5.86e+00 pdb=" CA SER 1 " - pdb="HA SER 1 " 0.980 1.027 -0.047 2.50e+03 5.50e+00 pdb=" C SER 1 " - pdb=" OXT SER 1 " 1.231 1.249 -0.018 2.50e+03 8.06e-01 pdb=" C SER 1 " - pdb=" O SER 1 " 1.231 1.249 -0.018 2.50e+03 7.75e-01 pdb=" CB SER 1 " - pdb=" 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 pdb="HA SER 1 " - pdb="HB1 SER 1 " 2.352 1.920 pdb=" CA SER 1 " - pdb="HG SER 1 " 2.363 2.520 pdb="HA SER 1 " - pdb="HB2 SER 1 " 2.400 1.920 pdb=" O SER 1 " - pdb="HG SER 1 " 2.419 2.720 pdb=" OXT SER 1 " - pdb="HA SER 1 " 2.458 2.176 ... (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: pdb=" N SER 1 " pdb=" C SER 1 " pdb=" CA SER 1 " pdb=" OXT SER 1 " ideal model delta periodicty weight residual -160.00 -131.41 -28.59 2 1.11e-03 9.08e-01 pdb=" OG SER 1 " pdb=" CB SER 1 " pdb=" CA SER 1 " pdb=" N SER 1 " ideal model delta periodicty weight residual 180.00 57.04 2.96 3 4.44e-03 3.89e-02 pdb=" CA SER 1 " pdb=" OG SER 1 " pdb=" CB SER 1 " pdb="HG SER 1 " ideal model delta periodicty weight residual -180.00 -0.03 0.03 2 1.11e-03 1.32e-06 target: 21.382 bond_residual_sum (n=10): 13.8342 nonbonded_residual_sum (n=29): 0.277467 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: 21.382 bond_residual_sum (n=10): 13.8342 nonbonded_residual_sum (n=29): 0.277467 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: 480.001 Energies after minimization: target: 0.502005 bond_residual_sum (n=10): 0.00103528 nonbonded_residual_sum (n=29): 0.230399 angle_residual_sum (n=16): 0.246422 dihedral_residual_sum (n=3): 0.00957638 chirality_residual_sum (n=1): 0.0145721 planarity_residual_sum (n=1): 2.53367e-15 norm of gradients: 6.3777e-06 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/max_lik/tst_maxlik.py u+s,u,s: 35.14 34.99 0.15 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/masks/tst_masks.py 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 I 4/m c m (a+b-1/6,-a+b,c+1/4) u+s,u,s: 18.09 16.84 1.25 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/max_lik/tst_max_lik.py 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 I 4/m c m (a+b-1/6,-a+b,c+1/4) u+s,u,s: 31.30 30.68 0.62 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 I 4/m c m (a+b-1/6,-a+b,c+1/4) u+s,u,s: 97.86 93.76 4.10 OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/dynamics/tst_cartesian_dynamics.py u+s,u,s: 6.36 6.19 0.17 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tls/tst_tls.py |-----------------------------------------------------------------------------| |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: 1658.52 1631.91 26.61 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tls/tst_get_t_scheme.py P 1 (6.76703, 8.79714, 11.504, 83, 109, 129) .............................. P 1 i= 10000 out of 100000 branch_0 = 2006 branch_1 = 7994 branch_1_1 = 2478 branch_1_2 = 5516 branch_1_2_1 = 246 branch_1_2_2 = 1996 branch_1_2_3 = 3274 branch_1_2_3_1 = 1466 branch_1_2_3_2 = 1808 .............................. P 1 i= 20000 out of 100000 branch_0 = 3938 branch_1 = 16062 branch_1_1 = 4979 branch_1_2 = 11083 branch_1_2_1 = 481 branch_1_2_2 = 3961 branch_1_2_3 = 6641 branch_1_2_3_1 = 3090 branch_1_2_3_2 = 3551 .............................. P 1 i= 30000 out of 100000 branch_0 = 5944 branch_1 = 24056 branch_1_1 = 7510 branch_1_2 = 16546 branch_1_2_1 = 705 branch_1_2_2 = 6021 branch_1_2_3 = 9820 branch_1_2_3_1 = 4570 branch_1_2_3_2 = 5250 .............................. P 1 i= 40000 out of 100000 branch_0 = 7884 branch_1 = 32116 branch_1_1 = 10037 branch_1_2 = 22079 branch_1_2_1 = 933 branch_1_2_2 = 8024 branch_1_2_3 = 13122 branch_1_2_3_1 = 6091 branch_1_2_3_2 = 7031 .............................. P 1 i= 50000 out of 100000 branch_0 = 9910 branch_1 = 40090 branch_1_1 = 12475 branch_1_2 = 27615 branch_1_2_1 = 1172 branch_1_2_2 = 10047 branch_1_2_3 = 16396 branch_1_2_3_1 = 7591 branch_1_2_3_2 = 8805 .............................. P 1 i= 60000 out of 100000 branch_0 = 11886 branch_1 = 48114 branch_1_1 = 14922 branch_1_2 = 33192 branch_1_2_1 = 1411 branch_1_2_2 = 12083 branch_1_2_3 = 19698 branch_1_2_3_1 = 8955 branch_1_2_3_2 = 10743 .............................. P 1 i= 70000 out of 100000 branch_0 = 13893 branch_1 = 56107 branch_1_1 = 17321 branch_1_2 = 38786 branch_1_2_1 = 1642 branch_1_2_2 = 14113 branch_1_2_3 = 23031 branch_1_2_3_1 = 10339 branch_1_2_3_2 = 12692 .............................. P 1 i= 80000 out of 100000 branch_0 = 15889 branch_1 = 64111 branch_1_1 = 19746 branch_1_2 = 44365 branch_1_2_1 = 1873 branch_1_2_2 = 16150 branch_1_2_3 = 26342 branch_1_2_3_1 = 11719 branch_1_2_3_2 = 14623 .............................. P 1 i= 90000 out of 100000 branch_0 = 17832 branch_1 = 72168 branch_1_1 = 22255 branch_1_2 = 49913 branch_1_2_1 = 2130 branch_1_2_2 = 18141 branch_1_2_3 = 29642 branch_1_2_3_1 = 13073 branch_1_2_3_2 = 16569 .............................. P 1 i= 100000 out of 100000 branch_0 = 19836 branch_1 = 80164 branch_1_1 = 24732 branch_1_2 = 55432 branch_1_2_1 = 2352 branch_1_2_2 = 20129 branch_1_2_3 = 32951 branch_1_2_3_1 = 14392 branch_1_2_3_2 = 18559 .............................. i= 10000 out of 100000 branch_0 = 9 branch_1 = 9991 branch_1_1 = 124 branch_1_2 = 9867 branch_1_2_1 = 7813 branch_1_2_2 = 0 branch_1_2_3 = 2054 branch_1_2_3_1 = 1265 branch_1_2_3_2 = 789 .............................. i= 20000 out of 100000 branch_0 = 12 branch_1 = 19988 branch_1_1 = 262 branch_1_2 = 19726 branch_1_2_1 = 15651 branch_1_2_2 = 0 branch_1_2_3 = 4075 branch_1_2_3_1 = 2551 branch_1_2_3_2 = 1524 .............................. i= 30000 out of 100000 branch_0 = 17 branch_1 = 29983 branch_1_1 = 378 branch_1_2 = 29605 branch_1_2_1 = 23460 branch_1_2_2 = 0 branch_1_2_3 = 6145 branch_1_2_3_1 = 3852 branch_1_2_3_2 = 2293 .............................. i= 40000 out of 100000 branch_0 = 23 branch_1 = 39977 branch_1_1 = 512 branch_1_2 = 39465 branch_1_2_1 = 31303 branch_1_2_2 = 1 branch_1_2_3 = 8161 branch_1_2_3_1 = 5123 branch_1_2_3_2 = 3038 .............................. i= 50000 out of 100000 branch_0 = 30 branch_1 = 49970 branch_1_1 = 632 branch_1_2 = 49338 branch_1_2_1 = 39151 branch_1_2_2 = 1 branch_1_2_3 = 10186 branch_1_2_3_1 = 6369 branch_1_2_3_2 = 3817 .............................. i= 60000 out of 100000 branch_0 = 32 branch_1 = 59968 branch_1_1 = 740 branch_1_2 = 59228 branch_1_2_1 = 46958 branch_1_2_2 = 1 branch_1_2_3 = 12269 branch_1_2_3_1 = 7551 branch_1_2_3_2 = 4718 *********************************************** Start values: M= 19.9997 10 10.0003 0 0 0 N= 20 10.0004 19.9996 2.31836e-05 -1.53405e-07 0.0661665 myu= 19.9997 10.0003 10 nyu= 20 20 10 Current values: myu= 5.00864 3.01139e-08 -4.99071 nyu= 5.00897 5.00897 0 M= 5.00864 -4.99071 3.02203e-08 9.95662e-12 -2.31834e-05 -2.14337e-06 N= 5.00897 5.00897 0 1.29519e-26 0 0 T= 14.991 10.0002 14.9908 1.1571e-05 -7.65647e-08 0.0330239 T1= 0 0 0 0 0 0 T2= 4.99103 4.99103 0 0 0 0 T3= 10 10 10 0 0 0 myu(M-T)= 5.00864 3.01139e-08 -4.99071 nyu(N-T)= 5.00897 5.00897 -8.01047e-16 PD(M)= 0 PD(N)= 1 branch_0 = 0 branch_1 = 1 branch_1_1 = 0 branch_1_2 = 1 branch_1_2_1 = 0 branch_1_2_2 = 0 branch_1_2_3 = 1 branch_1_2_3_1 = 0 branch_1_2_3_2 = 1 *********************************************** .............................. i= 70000 out of 100000 branch_0 = 36 branch_1 = 69963 branch_1_1 = 858 branch_1_2 = 69105 branch_1_2_1 = 54789 branch_1_2_2 = 1 branch_1_2_3 = 14315 branch_1_2_3_1 = 8705 branch_1_2_3_2 = 5610 .............................. i= 80000 out of 100000 branch_0 = 37 branch_1 = 79962 branch_1_1 = 982 branch_1_2 = 78980 branch_1_2_1 = 62691 branch_1_2_2 = 1 branch_1_2_3 = 16288 branch_1_2_3_1 = 9829 branch_1_2_3_2 = 6459 *********************************************** Start values: M= 19.9996 10 10.0004 -0 0 -0 N= 20 10.0055 19.9945 8.66993e-05 0 -0.234903 myu= 19.9996 10.0004 10 nyu= 20 20 10 Current values: myu= 5.00966 3.76909e-07 -4.98961 nyu= 5.01002 5.01002 0 M= 5.00966 -4.98961 3.78393e-07 2.9535e-10 8.66722e-05 8.53645e-06 N= 5.01002 5.01002 0 2.03715e-06 0 0 T= 14.99 10.0028 14.9872 4.32389e-05 1.01625e-06 -0.117216 T1= 0 0 0 0 0 0 T2= 4.98998 4.98998 0 0 0 0 T3= 10 10 10 0 0 0 myu(M-T)= 5.00966 3.76909e-07 -4.98961 nyu(N-T)= 5.01002 5.01002 9.63912e-16 PD(M)= 0 PD(N)= 1 branch_0 = 0 branch_1 = 1 branch_1_1 = 0 branch_1_2 = 1 branch_1_2_1 = 0 branch_1_2_2 = 0 branch_1_2_3 = 1 branch_1_2_3_1 = 0 branch_1_2_3_2 = 1 *********************************************** .............................. i= 90000 out of 100000 branch_0 = 42 branch_1 = 89956 branch_1_1 = 1114 branch_1_2 = 88842 branch_1_2_1 = 70495 branch_1_2_2 = 1 branch_1_2_3 = 18346 branch_1_2_3_1 = 10957 branch_1_2_3_2 = 7389 .............................. i= 100000 out of 100000 branch_0 = 44 branch_1 = 99954 branch_1_1 = 1235 branch_1_2 = 98719 branch_1_2_1 = 78288 branch_1_2_2 = 1 branch_1_2_3 = 20430 branch_1_2_3_1 = 12113 branch_1_2_3_2 = 8317 OK: u+s,u,s: 113.00 112.85 0.15 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tls/tst_tls_refinement_fft.py random_seed: 1279104071 |-----------------------------------------------------------------------------| | 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 = 17.09 max = 53.74 mean = 35.10 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | 17.095 - 20.759: 12 | 17.095 - 20.759: 12 | | 20.759 - 24.423: 0 | 20.759 - 24.423: 0 | | 24.423 - 28.088: 0 | 24.423 - 28.088: 0 | | 28.088 - 31.752: 0 | 28.088 - 31.752: 0 | | 31.752 - 35.416: 8 | 31.752 - 35.416: 8 | | 35.416 - 39.080: 4 | 35.416 - 39.080: 4 | | 39.080 - 42.744: 0 | 39.080 - 42.744: 0 | | 42.744 - 46.409: 0 | 42.744 - 46.409: 0 | | 46.409 - 50.073: 0 | 46.409 - 50.073: 0 | | 50.073 - 53.737: 12 | 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 | |-----------------------------------------------------------------------------| |--(resolution: 1.50 - 11.82 A; n_refl. = 957)--------------------------------| | | | r_work= 0.0000 r_free= 0.0000 ksol= 0.00 Bsol= 0.00 scale= 1.000 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: -0.00 A | | x-ray target function (ls_wunit_k1) for work reflections: 0.000000 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 11.8227 - 1.5003 1.00 947 10 0.0000 0.0000 2.9276e-31 1.2225e-31| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 Scale Alpha Beta | | # range work test error factor | | 1: 11.8227 - 1.5003 947 10 1.00 0.00 1.00 1.00 0.00| |alpha: min = 1.00 max = 1.00 mean = 1.00| |beta: min = 0.00 max = 0.00 mean = 0.00| |figures of merit: min = 1.00 max = 1.00 mean = 1.00| |phase err.(work): min = 0.00 max = 0.00 mean = 0.00| |phase err.(test): min = 0.00 max = 0.00 mean = 0.00| |-----------------------------------------------------------------------------| |--(resolution: 1.50 - 11.82 A; n_refl. = 957)--------------------------------| | | | r_work= 0.4872 r_free= 0.3832 ksol= 0.00 Bsol= 0.00 scale= 1.066 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.52 A | | x-ray target function (ls_wunit_k1) for work reflections: 0.164911 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 11.8227 - 1.5003 1.00 947 10 0.4872 0.3832 26.991 18.982| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 Scale Alpha Beta | | # range work test error factor | | 1: 11.8227 - 1.5003 947 10 0.38 60.73 1.07 0.95 28.51| |alpha: min = 0.95 max = 0.95 mean = 0.95| |beta: min = 28.51 max = 28.51 mean = 28.51| |figures of merit: min = 0.00 max = 1.00 mean = 0.38| |phase err.(work): min = 0.00 max = 89.98 mean = 60.73| |phase err.(test): min = 0.00 max = 88.11 mean = 55.21| |-----------------------------------------------------------------------------| ******************************************************************************** None |-TLS refinement: start model-------------------------------------------------| | target_work(ls_wunit_k1) = 0.164911 r_work = 0.4872 r_free = 0.3832 | |-----------------------------------------------------------------------------| |-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 = 25.00 max = 25.00 mean = 25.00 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | 25.000 - 25.000: 36 | 25.000 - 25.000: 36 | | 25.000 - 25.000: 0 | 25.000 - 25.000: 0 | | 25.000 - 25.000: 0 | 25.000 - 25.000: 0 | | 25.000 - 25.000: 0 | 25.000 - 25.000: 0 | | 25.000 - 25.000: 0 | 25.000 - 25.000: 0 | | 25.000 - 25.000: 0 | 25.000 - 25.000: 0 | | 25.000 - 25.000: 0 | 25.000 - 25.000: 0 | | 25.000 - 25.000: 0 | 25.000 - 25.000: 0 | | 25.000 - 25.000: 0 | 25.000 - 25.000: 0 | | 25.000 - 25.000: 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= 0.2603 T22= 0.2983 T33= 0.3045 T12= 0.0209 T13= 0.0054 T23= -0.0117| |L11= 2.0000 L22= 2.0000 L33= 2.0000 L12= 2.0000 L13= 2.0000 L23= 2.0000| |S11= 0.1402 S22= -0.2801 S33= 0.1399 S12= -0.0936 S13= -0.0276 S21= -0.0453| |S23= -0.2169 S31= -0.0269 S32= 0.2420 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.2817 T22= 0.2620 T33= 0.3016 T12= 0.0274 T13= -0.0026 T23= -0.0175| |L11= 2.0000 L22= 2.0000 L33= 2.0000 L12= 2.0000 L13= 2.0000 L23= 2.0000| |S11= -0.0366 S22= -0.1932 S33= 0.2298 S12= -0.2463 S13= -0.1538 S21= -0.2040| |S23= -0.2247 S31= 0.0799 S32= 0.4319 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.2985 T22= 0.2801 T33= 0.3047 T12= 0.0126 T13= -0.0028 T23= -0.0131| |L11= 2.0000 L22= 2.0000 L33= 2.0000 L12= 2.0000 L13= 2.0000 L23= 2.0000| |S11= 0.0075 S22= -0.1145 S33= 0.1069 S12= -0.1756 S13= -0.0750 S21= -0.1185| |S23= -0.1022 S31= 0.0367 S32= 0.2639 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| | iso = 0 aniso = 36 pos. def. = 36 non-pos. def. = 0 | | Total B(isotropic equivalent): min = 15.98 max = 23.20 mean = 19.52 | | Isotropic B only: min = 15.98 max = 23.20 mean = 19.52 | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic B-factors: | | Isotropic | Total | | 15.983 - 16.704: 6 | 15.983 - 16.704: 6 | | 16.704 - 17.426: 6 | 16.704 - 17.426: 6 | | 17.426 - 18.148: 0 | 17.426 - 18.148: 0 | | 18.148 - 18.870: 1 | 18.148 - 18.870: 1 | | 18.870 - 19.592: 9 | 18.870 - 19.592: 9 | | 19.592 - 20.313: 2 | 19.592 - 20.313: 2 | | 20.313 - 21.035: 0 | 20.313 - 21.035: 0 | | 21.035 - 21.757: 0 | 21.035 - 21.757: 0 | | 21.757 - 22.479: 3 | 21.757 - 22.479: 3 | | 22.479 - 23.201: 9 | 22.479 - 23.201: 9 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.1239 T22= 0.2289 T33= 0.2688 T12= 0.0981 T13= 0.0765 T23= 0.1363| |L11= 2.0000 L22= 1.9999 L33= 1.9998 L12= 1.9999 L13= 1.9999 L23= 1.9997| |S11= 0.1415 S22= -0.2814 S33= 0.1399 S12= -0.0943 S13= -0.0272 S21= -0.0402| |S23= -0.2170 S31= -0.0213 S32= 0.2411 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.1957 T22= 0.2251 T33= 0.2991 T12= 0.1269 T13= 0.0451 T23= 0.1543| |L11= 2.0000 L22= 1.9999 L33= 1.9999 L12= 1.9997 L13= 1.9999 L23= 1.9997| |S11= -0.0354 S22= -0.1930 S33= 0.2298 S12= -0.2463 S13= -0.1526 S21= -0.2023| |S23= -0.2259 S31= 0.0816 S32= 0.4314 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.2553 T22= 0.2734 T33= 0.3205 T12= 0.0820 T13= 0.0475 T23= 0.1333| |L11= 2.0001 L22= 2.0000 L33= 1.9999 L12= 1.9998 L13= 1.9999 L23= 1.9998| |S11= 0.0079 S22= -0.1151 S33= 0.1069 S12= -0.1754 S13= -0.0739 S21= -0.1170| |S23= -0.1030 S31= 0.0382 S32= 0.2636 | |-----------------------------------------------------------------------------| |-TLS refinement: after macrocycle 1------------------------------------------| | target_work(ls_wunit_k1) = 0.0426172 r_work = 0.2472 r_free = 0.1737 | |-----------------------------------------------------------------------------| |-TLS refinement: final values------------------------------------------------| |TLS group number 1: | | Origin (x,y,z) = 5.4095 5.5841 7.5222 | |T11= 0.1239 T22= 0.2289 T33= 0.2688 T12= 0.0981 T13= 0.0765 T23= 0.1363| |L11= 2.0000 L22= 1.9999 L33= 1.9998 L12= 1.9999 L13= 1.9999 L23= 1.9997| |S11= 0.1415 S22= -0.2814 S33= 0.1399 S12= -0.0943 S13= -0.0272 S21= -0.0402| |S23= -0.2170 S31= -0.0213 S32= 0.2411 | |TLS group number 2: | | Origin (x,y,z) = 10.8834 4.8200 7.3685 | |T11= 0.1957 T22= 0.2251 T33= 0.2991 T12= 0.1269 T13= 0.0451 T23= 0.1543| |L11= 2.0000 L22= 1.9999 L33= 1.9999 L12= 1.9997 L13= 1.9999 L23= 1.9997| |S11= -0.0354 S22= -0.1930 S33= 0.2298 S12= -0.2463 S13= -0.1526 S21= -0.2023| |S23= -0.2259 S31= 0.0816 S32= 0.4314 | |TLS group number 3: | | Origin (x,y,z) = 10.4142 10.1560 8.5901 | |T11= 0.2553 T22= 0.2734 T33= 0.3205 T12= 0.0820 T13= 0.0475 T23= 0.1333| |L11= 2.0001 L22= 2.0000 L33= 1.9999 L12= 1.9998 L13= 1.9999 L23= 1.9998| |S11= 0.0079 S22= -0.1151 S33= 0.1069 S12= -0.1754 S13= -0.0739 S21= -0.1170| |S23= -0.1030 S31= 0.0382 S32= 0.2636 | |-----------------------------------------------------------------------------| u+s,u,s: 15.62 15.45 0.17 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/examples/f_model_manager.py |--(resolution: 2.00 - 36.80 A; n_refl. = 7168)-------------------------------| | | | r_work= 0.2715 r_free= 0.2582 ksol= 0.00 Bsol= 0.00 scale= 0.996 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.18 A | | x-ray target function (ml) for work reflections: 5.094793 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.8046 - 3.4193 1.00 1379 144 0.2703 0.2757 5.4467 5.4664| | 2: 3.4193 - 2.7143 1.00 1296 139 0.2607 0.2385 5.2158 5.1916| | 3: 2.7143 - 2.3713 1.00 1261 153 0.2707 0.2585 5.0201 5.0422| | 4: 2.3713 - 2.1545 1.00 1258 147 0.2772 0.2290 4.9312 4.7391| | 5: 2.1545 - 2.0001 1.00 1257 134 0.2861 0.2886 4.8226 4.811| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 Scale Alpha Beta | | # range work test error factor | | 1: 36.8046 - 3.4193 1379 144 0.80 24.42 0.99 0.97 7091.12| | 2: 3.4193 - 2.7143 1296 139 0.81 24.45 1.00 0.98 4750.46| | 3: 2.7143 - 2.3713 1261 153 0.82 24.56 1.00 0.98 3124.95| | 4: 2.3713 - 2.1545 1258 147 0.83 23.75 0.99 0.96 2335.56| | 5: 2.1545 - 2.0001 1257 134 0.81 25.26 0.99 0.96 2114.06| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2114.06 max = 7091.12 mean = 3948.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 90.00 mean = 24.49| |phase err.(test): min = 0.00 max = 89.65 mean = 24.18| |-----------------------------------------------------------------------------| 0.271520875931 0.258211729842 |--(resolution: 2.00 - 36.80 A; n_refl. = 7168)-------------------------------| | | | r_work= 0.2715 r_free= 0.2582 ksol= 0.00 Bsol= 0.00 scale= 0.996 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.18 A | | x-ray target function (ml) for work reflections: 5.094793 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.8046 - 3.4193 1.00 1379 144 0.2703 0.2757 5.4467 5.4664| | 2: 3.4193 - 2.7143 1.00 1296 139 0.2607 0.2385 5.2158 5.1916| | 3: 2.7143 - 2.3713 1.00 1261 153 0.2707 0.2585 5.0201 5.0422| | 4: 2.3713 - 2.1545 1.00 1258 147 0.2772 0.2290 4.9312 4.7391| | 5: 2.1545 - 2.0001 1.00 1257 134 0.2861 0.2886 4.8226 4.811| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 Scale Alpha Beta | | # range work test error factor | | 1: 36.8046 - 3.4193 1379 144 0.80 24.42 0.99 0.97 7091.12| | 2: 3.4193 - 2.7143 1296 139 0.81 24.45 1.00 0.98 4750.46| | 3: 2.7143 - 2.3713 1261 153 0.82 24.56 1.00 0.98 3124.95| | 4: 2.3713 - 2.1545 1258 147 0.83 23.75 0.99 0.96 2335.56| | 5: 2.1545 - 2.0001 1257 134 0.81 25.26 0.99 0.96 2114.06| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2114.06 max = 7091.12 mean = 3948.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 90.00 mean = 24.49| |phase err.(test): min = 0.00 max = 89.65 mean = 24.18| |-----------------------------------------------------------------------------| |--(resolution: 2.00 - 36.80 A; n_refl. = 7168)-------------------------------| | | | r_work= 0.5013 r_free= 0.4699 ksol= 1.20 Bsol= 30.00 scale= 0.646 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.44 A | | x-ray target function (ml) for work reflections: 5.300042 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.8046 - 3.4193 1.00 1379 144 0.6257 0.6350 5.9193 5.8373| | 2: 3.4193 - 2.7143 1.00 1296 139 0.3667 0.4064 5.564 5.6956| | 3: 2.7143 - 2.3713 1.00 1261 153 0.2870 0.2733 5.159 5.1916| | 4: 2.3713 - 2.1545 1.00 1258 147 0.2814 0.2368 4.9455 4.7852| | 5: 2.1545 - 2.0001 1.00 1257 134 0.2944 0.2921 4.8448 4.815| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 Scale Alpha Beta | | # range work test error factor | | 1: 36.8046 - 3.4193 1379 144 0.34 63.37 0.47 0.39 29597.42| | 2: 3.4193 - 2.7143 1296 139 0.53 49.41 1.28 0.84 14636.65| | 3: 2.7143 - 2.3713 1261 153 0.74 31.27 0.92 0.98 5543.60| | 4: 2.3713 - 2.1545 1258 147 0.81 25.07 0.85 0.83 2619.18| | 5: 2.1545 - 2.0001 1257 134 0.81 25.51 0.85 0.83 2132.04| |alpha: min = 0.39 max = 0.98 mean = 0.77| |beta: min = 2132.04 max = 29597.42 mean = 11277.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.64| |phase err.(work): min = 0.00 max = 90.00 mean = 39.44| |phase err.(test): min = 0.00 max = 89.75 mean = 39.35| |-----------------------------------------------------------------------------| OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling.py OK: u+s,u,s: 372.24 361.50 10.74 libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/alignment.py D A A A T T 0.0 0.0 0.0 0.0 0.0 0.0 A 0.0 -4.0 -5.0 -6.0 -7.0 -8.0 A 0.0 -1.0 -3.0 -4.0 -5.0 -6.0 A 0.0 -2.0 0.0 -2.0 -3.0 -4.0 G 0.0 -3.0 -1.0 1.0 -1.0 -2.0 G 0.0 -4.0 -2.0 0.0 1.0 -1.0 T 0.0 -5.0 -3.0 -1.0 0.0 1.0 T 0.0 -6.0 -4.0 -2.0 -1.0 0.0 I A A A T T 0.0 0.0 0.0 0.0 0.0 0.0 A 0.0 -4.0 -1.0 -2.0 -3.0 -4.0 A 0.0 -5.0 -3.0 0.0 -1.0 -2.0 A 0.0 -6.0 -4.0 -2.0 1.0 0.0 G 0.0 -7.0 -5.0 -3.0 -1.0 1.0 G 0.0 -8.0 -6.0 -4.0 -2.0 -1.0 T 0.0 -9.0 -7.0 -5.0 -3.0 -1.0 T 0.0 -10.0 -8.0 -6.0 -4.0 -2.0 M A A A T T 0.0 -2.0 -3.0 -4.0 -5.0 -6.0 A -2.0 1.0 -1.0 -2.0 -3.0 -4.0 A -3.0 -1.0 2.0 0.0 -1.0 -2.0 A -4.0 -2.0 0.0 3.0 1.0 0.0 G -5.0 -3.0 -1.0 1.0 3.0 1.0 G -6.0 -4.0 -2.0 0.0 1.0 3.0 T -7.0 -5.0 -3.0 -1.0 1.0 2.0 T -8.0 -6.0 -4.0 -2.0 0.0 2.0 E A A A T T 0.0 0.0 0.0 0.0 0.0 0.0 A 0.0 0.0 -1.0 -1.0 -1.0 -1.0 A 0.0 1.0 0.0 -1.0 -1.0 -1.0 A 0.0 1.0 1.0 0.0 -1.0 -1.0 G 0.0 1.0 1.0 1.0 0.0 -1.0 G 0.0 1.0 1.0 1.0 1.0 0.0 T 0.0 1.0 1.0 1.0 0.0 0.0 T 0.0 1.0 1.0 1.0 0.0 0.0 score=2.0 mmmddmm AAAGGTT ||| || AAA--TT 1rra vs. 1bli; GLOBAL allignment; mdm78 score=1773.0 mmmmmmmmmmmmmmmmmmmmmmmdmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmmdmmmmmdmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmmiiii AESSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNGRNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV---- **| | || |* ***** ||* *|*|*|*| **|| *|||*|* ***||| *** * |*| * | |****| |*| |*| | |*| *|** *****||* | *|||*| |* DNSRYTHFLTQHYDAKPQGRDDR-YCESIMRRRGLT-SPCKDINTFIHGNKRSIKAIC-ENKNG-NPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSIFRRP 1rra vs. 1bli; LOCAL allignment; mdm78 score=2009.0 mmmmmmmmmmmmmmmmdmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmmdmmmmmdmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmm FKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNGRNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV | || |* ***** ||* *|*|*|*| **|| *|||*|* ***||| *** * |*| * | |****| |*| |*| | |*| *|** *****||* | *|||*| |* FLTQHYDAKPQGRDDR-YCESIMRRRGLT-SPCKDINTFIHGNKRSIKAIC-ENKNG-NPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSI 1rra vs. 1bli; GLOBAL allignment; blosum50 score=267.0 mmmmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmddddmmmiiimmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmmiiii AESSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNG---RNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV---- | | || | * | || *|*|*|*| || *|||*| **||| * ||| | | | |****| |*| | | *| | | | *****||* | *|||*| |* DNSRYTHFLTQHYDAK-PQGRDDRYCESIMRRRGLTS-PCKDINTFIHGNKRSIKAIC-EN----KNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSIFRRP 1rra vs. 1bli; LOCAL allignment; blosum50 score=287.0 mmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmddddmmmiiimmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmm SSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNG---RNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV | | || | * | || *|*|*|*| || *|||*| **||| * ||| | | | |****| |*| | | *| | | | *****||* | *|||*| |* SRYTHFLTQHYDAK-PQGRDDRYCESIMRRRGLTS-PCKDINTFIHGNKRSIKAIC-EN----KNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSI pretty_print is pretty pretty 12345678901234567890123456789012345678901234567890 1rra SSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLE | | || | * | || *|*|*|*| || *|||*| 1bli SRYTHFLTQHYDAK-PQGRDDRYCESIMRRRGLTS-PCKDINTFIHGNKR 1rra DVQAICSQGQVTCKNG---RNNCHKSSSTLRITDCRLKGSSKYPNCDYTT **||| * ||| | | | |****| |*| | | *| | | 1bli SIKAIC-EN----KNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRA 1rra TDSQKHIIIACDGNPYVPVHFDASV | *****||* | *|||*| |* 1bli TAGFRNVVVACE-NG-LPVHLDQSI OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/invariant_domain.py OK libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_bioinformatics.py testEquality (__main__.test_sequence) ... ok testNonEquality (__main__.test_sequence) ... ok testFormat (__main__.test_fasta_sequence) ... ok testStr (__main__.test_fasta_sequence) ... ok testFormat (__main__.test_pir_sequence) ... ok testStr (__main__.test_pir_sequence) ... ok testConservationCode (__main__.test_midline) ... ok testMidline (__main__.test_midline) ... ok testError (__main__.test_alignment) ... ok testIdentityCount (__main__.test_alignment) ... ok testError (__main__.test_fasta_alignment) ... ok testFormat (__main__.test_fasta_alignment) ... ok testStr (__main__.test_fasta_alignment) ... ok testError (__main__.test_pir_alignment) ... ok testFormat (__main__.test_pir_alignment) ... ok testStr (__main__.test_pir_alignment) ... ok testFormat (__main__.test_clustal_alignment) ... ok testStr (__main__.test_clustal_alignment) ... ok testFasta (__main__.test_sequence_parse) ... ok testPir (__main__.test_sequence_parse) ... ok testSequence (__main__.test_sequence_parse) ... ok test_filename_selection (__main__.test_sequence_parse) ... ok test_known_formats (__main__.test_sequence_parse) ... ok testAli (__main__.test_alignment_parse) ... ok testClustal (__main__.test_alignment_parse) ... ok testFasta (__main__.test_alignment_parse) ... ok testPir (__main__.test_alignment_parse) ... ok test_filename_selection (__main__.test_alignment_parse) ... ok test_known_formats (__main__.test_alignment_parse) ... ok ---------------------------------------------------------------------- Ran 29 tests in 0.016s OK endif endif libtbx.show_date_and_time -v Date 2009-02-03 Time 01:15:16 PST -0800 (1233652516.46 s) Seconds since the Epoch 1233652516.46