date
Sun Feb 22 22:57:15 PST 2009
cat /etc/redhat-release
Fedora Core release 6 (Zod)
gcc -v | & tail -1
gcc version 4.1.1 20061011 (Red Hat 4.1.1-30)
$BUILD_PYTHON_EXE -V
Python 2.6.1
libtbx.show_date_and_time -v
Date 2009-02-22 Time 22:57:15 PST -0800 (1235372235.46 s) Seconds since the Epoc
h 1235372235.46
libtbx.show_host_and_user
HOST = leafnose.lbl.gov
HOSTTYPE = i386-linux
VENDOR = intel
USER = rwgk
PID = 17314
boost_adaptbx.show_platform_info
__FILE__ = /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/meta_ext
.cpp
__DATE__ = Feb 21 2009
__TIME__ = 21:33:43
__i386__
__linux
__GNUC__ = 4
__GNUC_MINOR__ = 1
__GNUC_PATCHLEVEL__ = 1
boost::python::cxxabi_cxa_demangle_is_broken(): false
__GXX_WEAK__ = 1
__VERSION__ = 4.1.1 20061011 (Red Hat 4.1.1-30)
FE_INEXACT = 32
FE_DIVBYZERO = 4
FE_UNDERFLOW = 16
FE_OVERFLOW = 8
FE_INVALID = 1
FE_ALL_EXCEPT = 61
PY_VERSION = 2.6.1
PYTHON_API_VERSION = 1013
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) = 2
gnu libc version: 2.5
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/leafnose/scratch1/rwgk/auto_build/sources/libtbx/test_utils.p
y
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/utils.py
### HOST = leafnose.lbl.gov
### HOSTTYPE = i386-linux
### VENDOR = intel
### USER = rwgk
### PID = 17329
OK
libtbx.python /net/leafnose/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/leafnose/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/leafnose/scratch1/rwgk/auto_build/sources/libtbx/introspectio
n.py
number of processors: 4
Virtual memory size: 6,946,816
Resident set size: 4,276,224
Stack size: 139,264
Virtual memory size: 6,946,816 exact max: 10,948,608
Resident set size: 4,292,608 approx. max: 8,294,400
Stack size: 139,264 approx. max: 139,264
Memory total: 2,124,296,192
Memory free: 188,694,528
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/thread_utils
.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/easy_run.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/tst_utils.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/tst_math_uti
ls.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/assert_utils
.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/str_utils.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/table_utils.
py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/tst_dlite.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/phil/tst_tok
enizer.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/phil/tst.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/tst_object_o
riented_patterns.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/tst_itertbx.
py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/libtbx/find_referen
ce_cycles.py
OK
libtbx.python $BOOST_ADAPTBX_DIST/run_tests.py
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_l
ibc_backtrace.py
show_stack(1): /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_
libc_backtrace.py(7) run
show_stack(2): /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_
libc_backtrace.py(13) <module>
libc backtrace (18 frames, most recent call last):
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python [0x8057891]
/lib/libc.so.6(__libc_start_main+0xdc) [0x252f2c]
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python(main+0x22) [0x805
7942]
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python(Py_Main+0xaab) [0
x805871b]
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python(PyRun_SimpleFileE
xFlags+0x1bb) [0x80f2bfb]
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python(PyRun_FileExFlags
+0xac) [0x80f291c]
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python(PyEval_EvalCode+0
x57) [0x80d31b7]
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python(PyEval_EvalCodeEx
+0x82a) [0x80d314a]
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python(PyEval_EvalFrameE
x+0x5691) [0x80d1761]
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python(PyEval_EvalFrameE
x+0x2135) [0x80ce205]
/net/leafnose/scratch1/rwgk/auto_build/build/base/bin/python(PyObject_Call+0x4
5) [0x805c405]
/net/leafnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so [0x171e87]
/net/leafnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::pyt
hon::handle_exception_impl(boost::function0<void>)+0x4b) [0x17c82b]
/net/leafnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::fun
ction0<void>::operator()() const+0x91) [0x17d3a1]
/net/leafnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so [0x175527]
/net/leafnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::pyt
hon::objects::function::call(_object*, _object*) const+0x76) [0x1751a6]
/net/leafnose/scratch1/rwgk/auto_build/build/lib/boost_python_meta_ext.so(boos
t::python::objects::caller_py_function_impl<boost::python::detail::caller<bool
(*)(int), boost::python::default_call_policies, boost::mpl::vector2<bool, int
> > >::operator()(_object*, _object*)+0xbb) [0x142ccb]
/net/leafnose/scratch1/rwgk/auto_build/build/lib/boost_python_meta_ext.so [0x1
3d90d]
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_r
ational.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_r
ational_truediv.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_o
ptional.py
exercise_wstring: <Boost.Python.function object at 0x8f4b3b8>
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_s
td_pair.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_t
uple.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_f
ile.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/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_1
Total OK: 511
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_2
Total OK: 268
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_3
Total OK: 164
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_4
Total OK: 1420
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_5
Total OK: 23
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_vec3
Total OK: 67
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_unsigned_fl
oat_arithmetic
OK
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_mat3
Total OK: 82
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_sym_mat3
Total OK: 71
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_mat_ref
Total OK: 60
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_accessors
Total OK: 1729
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/serialization/tst_base_256
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/error/tst_er
ror.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/stl/tst_map.
py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/stl/tst_set.
py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/stl/tst_vect
or.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/array_family
/boost_python/regression_test.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/array_family
/boost_python/tst_flex.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/array_family
/boost_python/tst_smart_selection.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/array_family
/boost_python/tst_shared.py
OK
libtbx.python /net/leafnose/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 = 0.12 s overhead = 0.00 s (d[*p++] 2.07612e-14)
use_pointers = True
use_iterators = 0 time = 0.11 s overhead = 0.00 s (*dp[i] 0)
use_iterators = 1 time = 0.12 s overhead = 0.00 s (**dpi++ 0)
use_iterators = 2 time = 0.11 s overhead = 0.00 s (**dpp++ 0)
data_size = 10000 n_repeats = 3000
use_pointers = False
use_iterators = 0 time = 0.13 s overhead = 0.00 s (d[p[i]] 5.32896e-12)
use_iterators = 1 time = 0.13 s overhead = 0.00 s (d[*p++] -4.16667e-13)
use_pointers = True
use_iterators = 0 time = 0.12 s overhead = 0.00 s (*dp[i] 5.32896e-12)
use_iterators = 1 time = 0.13 s overhead = 0.00 s (**dpi++ 5.32896e-12)
use_iterators = 2 time = 0.13 s overhead = 0.00 s (**dpp++ 5.32896e-12)
data_size = 100000 n_repeats = 300
use_pointers = False
use_iterators = 0 time = 1.88 s overhead = 0.00 s (d[p[i]] 8.95289e-11)
use_iterators = 1 time = 1.88 s overhead = 0.00 s (d[*p++] 2.60114e-12)
use_pointers = True
use_iterators = 0 time = 1.87 s overhead = 0.00 s (*dp[i] 8.95289e-11)
use_iterators = 1 time = 1.87 s overhead = 0.00 s (**dpi++ 8.95289e-11)
use_iterators = 2 time = 1.87 s overhead = 0.00 s (**dpp++ 8.95289e-11)
data_size = 1000000 n_repeats = 30
use_pointers = False
use_iterators = 0 time = 3.63 s overhead = 0.01 s (d[p[i]] 1.14276e-10)
use_iterators = 1 time = 3.64 s overhead = 0.01 s (d[*p++] -1.11773e-11)
use_pointers = True
use_iterators = 0 time = 3.64 s overhead = 0.01 s (*dp[i] 1.14276e-10)
use_iterators = 1 time = 3.63 s overhead = 0.01 s (**dpi++ 1.14276e-10)
use_iterators = 2 time = 3.63 s overhead = 0.01 s (**dpp++ 1.14276e-10)
data_size = 10000000 n_repeats = 3
use_pointers = False
use_iterators = 0 time = 3.93 s overhead = 0.11 s (d[p[i]] -3.65322e-10)
use_iterators = 1 time = 3.93 s overhead = 0.10 s (d[*p++] -3.88059e-10)
use_pointers = True
use_iterators = 0 time = 3.92 s overhead = 0.10 s (*dp[i] -3.65322e-10)
use_iterators = 1 time = 3.92 s overhead = 0.11 s (**dpi++ -3.65322e-10)
use_iterators = 2 time = 3.92 s overhead = 0.10 s (**dpp++ -3.65322e-10)
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/array_family
/boost_python/tst_cost_of_m_handle_in_af_shared.py
Loop over af::shared<double>:
data_size=1000, n_repeats=30000
size+begin inside loop: 0.09 s
begin outside loop: 0.08 s
size+begin outside loop: 0.05 s
data_size=10000, n_repeats=3000
size+begin inside loop: 0.09 s
begin outside loop: 0.08 s
size+begin outside loop: 0.05 s
data_size=100000, n_repeats=300
size+begin inside loop: 0.27 s
begin outside loop: 0.27 s
size+begin outside loop: 0.27 s
data_size=1000000, n_repeats=30
size+begin inside loop: 0.28 s
begin outside loop: 0.28 s
size+begin outside loop: 0.27 s
data_size=10000000, n_repeats=3
size+begin inside loop: 0.33 s
begin outside loop: 0.31 s
size+begin outside loop: 0.40 s
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/matrix.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/python_utils
/tst_random_transform.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/python_utils
/tst_graph.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_p
ython/tst_math.py
time_eigensystem_real_symmetric: 4.387 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=0.17 s
unimodular range 4: count=2597208, time=1.25 s
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_p
ython/tst_r3_rotation.py
times unit quaternion <-> matrix
py: 0.44 0.32 s
c++: 0.17 0.18 s
ratio: 2.52 1.85
u+s,u,s: 21.93 21.87 0.06 micro-seconds/tick: 0.438
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_p
ython/tst_resample.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_p
ython/tst_line_search.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_p
ython/tst_gaussian.py
u+s,u,s: 51.01 50.92 0.09 micro-seconds/tick: 1.561
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_p
ython/tst_quadrature.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_p
ython/tst_halton.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/tst_eul
er_angles.py
u+s,u,s: 4.76 4.71 0.05 micro-seconds/tick: 0.370
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/tst_sup
erpose.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/sieve_o
f_eratosthenes.py
OK
libtbx.python /net/leafnose/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/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/scale_c
urves.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/math/tst_fit
_peak.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/minpack/tst.
py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/lbfgs/boost_
python/tst_lbfgs.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/lbfgsb/boost
_python/tst_lbfgsb.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/fftpack/boos
t_python/tst_fftpack.py
usr+sys time: 3.79 seconds, ticks: 2905728, micro-seconds/tick: 1.304
wall clock time: 3.79 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/examples/fle
x_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/leafnose/scratch1/rwgk/auto_build/sources/scitbx/examples/fle
x_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/leafnose/scratch1/rwgk/auto_build/sources/scitbx/examples/pri
ncipal_axes_of_inertia.py
(7.7966923076923074, 1.3650769230769231, 8.3576923076923073)
(38.140037692307686, 97.025267538461534, 79.022219692307701, -19.808558307692309
, 35.142585230769235, 7.6620366923076917)
[104.22746487361262, 97.266425913775308, 12.693634135688987]
[-0.43905397167468396, 0.82221243371029007, -0.36221309171382493, 0.303721679623
70789, 0.51523985141178807, 0.80142437999084615, 0.84556770946106952, 0.241856
588434883, -0.47594184450140542]
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/examples/lbf
gs_recipe.py
refinery
compute_functional_and_gradients
callback_after_step
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/examples/lbf
gs_linear_least_squares_fit.py
fit.slope: -3.14309721127
fit.y_intercept: 1.79189945321
x_obs y_obs y_calc diff
1.00 -1.33 -1.35 0.02
2.00 -4.53 -4.49 -0.03
3.00 -7.62 -7.64 0.02
4.00 -10.81 -10.78 -0.03
5.00 -13.91 -13.92 0.01
6.00 -17.02 -17.07 0.04
7.00 -20.24 -20.21 -0.03
8.00 -23.37 -23.35 -0.02
9.00 -26.53 -26.50 -0.03
10.00 -29.60 -29.64 0.04
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/examples/che
byshev_lsq_example.py
Trying to determine the best number of terms
via cross validation techniques
Fitting with 12 terms
Least Squares residual: 1.743886
R2-value : 0.005054
Maximum deviation between fitted and error free data:
0.181
Mean deviation between fitted and error free data:
0.051
Maximum deviation between fitted and observed data:
0.293
Mean deviation between fitted and observed data:
0.113
Showing 10 points
x y_obs y_ideal y_fit
0.010 0.958 1.195 1.025
0.099 1.995 2.061 1.999
0.188 0.999 0.814 0.845
0.277 0.255 0.448 0.444
0.366 1.805 2.025 1.986
0.455 2.284 2.322 2.260
0.545 0.785 0.980 0.963
0.634 1.217 1.301 1.188
0.723 2.843 2.931 2.888
0.812 2.539 2.646 2.708
Preparing output for loggraph in a file called
chebyshev.loggraph
Coefficients from weighted lsq
[6.0145119748267293, -3.6426891719391232, 1.6411568156663754, -0.785481637193231
27, 0.22025959230811321]
Coefficients from non-weighted lsq
[5.8989565176248009, -3.627112603408837, 1.3750985598902132, -0.5431899037984717
6, -0.45281337805613209]
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/examples/imm
optibox_ports.py
Skipping: exercise_lbfgsb() with meyer_function
u+s,u,s: 33.66 33.58 0.08 micro-seconds/tick: 1.223
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/examples/rig
id_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: [1.4293798315070356, -4.7699199336056148, -3.2848275925326007]
fd ea: [1.4293798318298911, -4.7699199341444398, -3.2848275930419391]
an lt: [-2.6395370381698982, 3.8546779254822852, -3.7648774634679576]
fd lt: [-2.6395370369414195, 3.8546779261849906, -3.7648774635634652]
an ea: [-4.3864544713398264, 2.1848899436111231, 5.0802158076235475]
fd ea: [-4.386454476090762, 2.1848899400822575, 5.080215814246003]
an lt: [-4.6881328246835494, -10.874759921610835, -1.9393316543209345]
fd lt: [-4.6881328241710207, -10.874759922785415, -1.9393316534888072]
an ea: [-5.0974589936941257, 2.0225151159319146, 4.4791032612277126]
fd ea: [-5.0974589935748327, 2.0225151153852039, 4.4791032607349734]
an lt: [-2.8154365578392557, -5.1570857812151658, -17.014046644874657]
fd lt: [-2.8154365576682494, -5.1570857824145833, -17.014046648000658]
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_ut
ils.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/graph/rigidi
ty.py
double banana 3D dof (method=integer): 7
double banana 3D dof (method=float): 7
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_ri
gidity.py
repeat_log = {0: 85}
u+s,u,s: 2.36 2.35 0.01
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/graph/rigidi
ty_matrix_symbolic.py
u+s,u,s: 1.85 1.83 0.02
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_ta
rdy_tree_find_paths.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_ta
rdy_tree.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/e
ssence/tst_basic.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/e
ssence/tst_molecules.py
OK
usr+sys time: 20.54 seconds, ticks: 113949077, micro-seconds/tick: 0.180
wall clock time: 20.55 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/p
roto/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/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/p
roto/tst_featherstone.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/p
roto/tst_free_motion.py
u+s,u,s: 0.92 0.87 0.05 micro-seconds/tick: 0.274
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/p
roto/tst_free_motion_hard.py
OK
usr+sys time: 4.03 seconds, ticks: 18795877, micro-seconds/tick: 0.214
wall clock time: 4.03 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/p
roto/tst_joint_lib.py
OK
usr+sys time: 3.16 seconds, ticks: 16812050, micro-seconds/tick: 0.188
wall clock time: 3.16 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/p
roto/tst_singular.py
OK
usr+sys time: 11.34 seconds, ticks: 60761726, micro-seconds/tick: 0.187
wall clock time: 11.34 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/p
roto/tst_spherical_refinement.py
OK
usr+sys time: 1.69 seconds, ticks: 6640926, micro-seconds/tick: 0.254
wall clock time: 1.70 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/p
roto/tst_molecules.py
OK
usr+sys time: 7.90 seconds, ticks: 42790172, micro-seconds/tick: 0.185
wall clock time: 7.90 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/sparse/tests
/tst_sparse.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/sparse/tests
/tst_lu_factorization.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/scitbx/iso_surface/
tst_iso_surface.py
u+s,u,s: 24.00 23.93 0.07 micro-seconds/tick: 0.580
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/fortran_io/tests/tst_numeric
_manipulators
OK
/net/leafnose/scratch1/rwgk/auto_build/build/scitbx/fortran_io/tests/tst_numeric
_parsers
OK
( 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: 0.35 seconds, ticks: 106447, micro-seconds/tick: 3.288
wall clock time: 0.35 seconds
libtbx.python $CCTBX_DIST/run_tests.py --Quick
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_adp_aniso_restraints.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/math/boost_py
thon/tst_math.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/xray/boost_py
thon/tst_f_model.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/array_family/
boost_python/tst_flex.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/uctbx/boost_p
ython/tst_uctbx.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/uctbx/boost_p
ython/tst_crystal_orientation.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/boost_p
ython/tst_sgtbx.py
u+s,u,s: 5.27 5.17 0.10 micro-seconds/tick: 12.250
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/boost_p
ython/tst_N_fold_rot.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/crystal/tst_e
xt.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/adptbx/boost_
python/tst_adptbx.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/miller/boost_
python/tst_miller.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_p
ython/tst_chemical_elements.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_p
ython/tst_xray_scattering.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_p
ython/tst_henke.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_p
ython/tst_icsd_radii.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_p
ython/tst_neutron.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_p
ython/tst_sasaki.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_p
ython/tst_tiny_pse.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_p
ython/tst_wavelengths.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/xray/boost_py
thon/tst_xray.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/maptbx/boost_
python/tst_maptbx.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/dmtbx/boost_p
ython/tst_dmtbx.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/translation_s
earch/boost_python/tst_translation_search.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/geometry_rest
raints/tst_ext.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/geometry_rest
raints/tst_proxy_registry.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/adp_restraint
s/tst_ext.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_math_module.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_krivy_gruber.py --Quick
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_sgtbx.py
u+s,u,s: 3.74 3.67 0.07 micro-seconds/tick: 6.757
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_itvb_2001_table_a1427_hall_symbols.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_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: 3.94 3.89 0.05 micro-seconds/tick: 4.829
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_sgtbx_denominators.py P31
P 31
u+s,u,s: 0.26 0.22 0.04 micro-seconds/tick: 2.451
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_sgtbx_subgroups.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_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: 17.16 17.11 0.05 micro-seconds/tick: 2.144
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_adp_constraints.py P3
P 3
u+s,u,s: 0.45 0.38 0.07 micro-seconds/tick: 2.600
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_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: 0.48 0.40 0.08 micro-seconds/tick: 3.377
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_sgtbx_site_constraints.py
u+s,u,s: 6.00 5.91 0.09 micro-seconds/tick: 1.586
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_reflection_statistics.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_sgtbx_harker.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_twin_target.py
u+s,u,s: 76.85 76.76 0.09 micro-seconds/tick: 2.034
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/symbol_
confidence.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/bravais
_types.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_miller_lookup_utils.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_crystal.py I41/acd
I 41/a c d :2
u+s,u,s: 0.52 0.44 0.08 micro-seconds/tick: 2.606
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_direct_space_asu.py I41/acd
I 41/a c d :2
u+s,u,s: 5.49 5.40 0.09 micro-seconds/tick: 0.756
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_pair_asu_table.py
u+s,u,s: 3.33 3.24 0.09 micro-seconds/tick: 2.714
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_crystal_asu_clusters.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_coordination_sequences.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_crystal_close_packing.py R-3mr
time groel_sampling: 1.58 seconds
R -3 m :R
u+s,u,s: 2.81 2.74 0.07 micro-seconds/tick: 1.102
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_xray.py I41/acd
I 41/a c d :2
u+s,u,s: 10.92 10.83 0.09 micro-seconds/tick: 3.114
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_structure_factors_multithread.py
omptbx.have_stubs_h
Skipping raw multithreaded structure factor computation tests
usr+sys time: 0.65 seconds, ticks: 251833, micro-seconds/tick: 2.581
wall clock time: 0.65 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_miller.py P31
P 31
u+s,u,s: 8.00 7.53 0.47 micro-seconds/tick: 10.880
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_reciprocal_space_asu.py P312
P 3 1 2
u+s,u,s: 0.47 0.41 0.06 micro-seconds/tick: 2.816
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_triplet_generator.py P41
P 41
u+s,u,s: 0.46 0.38 0.08 micro-seconds/tick: 3.400
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_emma.py P31
P 31
u+s,u,s: 1.90 1.83 0.07 micro-seconds/tick: 0.724
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_find_centre_of_inversion.py P31
P 31
u+s,u,s: 0.52 0.45 0.07 micro-seconds/tick: 2.310
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_expand_to_p1.py P31
P 31
u+s,u,s: 0.47 0.39 0.08 micro-seconds/tick: 3.121
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_change_basis.py P31
P 31
u+s,u,s: 0.61 0.53 0.08 micro-seconds/tick: 1.966
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_wilson_plot.py P31
P 31
u+s,u,s: 0.68 0.61 0.07 micro-seconds/tick: 3.320
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_xray_target_functors.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_xray_derivatives.py P31
P 31
u+s,u,s: 6.24 6.14 0.10 micro-seconds/tick: 3.855
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_xray_fast_gradients.py P31
P 31
from_scatterers_direct: 4 calls, 0.09 s
from_scatterers_fft: 15 calls, 0.30 s
gradients_direct: 23 calls, 0.76 s
gradients_fft: 2 calls, 0.13 s
usr+sys time: 3.02 seconds, ticks: 203300, micro-seconds/tick: 14.855
wall clock time: 3.02 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_xray_minimization.py --F P31
Refinement against F
P 31
u+s,u,s: 24.28 24.16 0.12 micro-seconds/tick: 6.252
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_xray_minimization.py --F_sq P31
Refinement against F^2
P 31
u+s,u,s: 10.80 10.70 0.10 micro-seconds/tick: 6.656
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/maptbx/tst_re
al_space_refinement.py
u+s,u,s: 4.96 4.88 0.08 micro-seconds/tick: 5.762
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_maptbx_structure_factors.py P31
P 31
u+s,u,s: 0.60 0.52 0.08 micro-seconds/tick: 2.581
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_miller_merge_equivalents.py P31
P 31
u+s,u,s: 0.51 0.44 0.07 micro-seconds/tick: 2.393
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_grouped_data.py P31
P 31
u+s,u,s: 0.43 0.35 0.08 micro-seconds/tick: 3.527
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_miller_fft_map.py P31
P 31
u+s,u,s: 1.23 1.13 0.10 micro-seconds/tick: 0.955
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_sampled_model_density.py P31
P 31
usr+sys time: 3.24 seconds, ticks: 3023355, micro-seconds/tick: 1.072
wall clock time: 3.24 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_fast_nv1995.py F222
F 2 2 2
u+s,u,s: 0.77 0.69 0.08 micro-seconds/tick: 2.926
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_geometry_restraints.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_geometry_restraints_lbfgs.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_geometry_restraints_2.py
u+s,u,s: 2.27 2.14 0.13 micro-seconds/tick: 0.831
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/development/m
ake_cns_input.py P31
P 31
u+s,u,s: 0.45 0.38 0.07 micro-seconds/tick: 3.389
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/development/t
st_cns_epsilon.py P31
CNS not available.
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/development/t
st_cns_hl.py P31
CNS not available.
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/development/r
un_shelx.py P31
SHELX not available.
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_pointgroup_tools.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/sub_lat
tice_tools.py
u+s,u,s: 0.65 0.59 0.06 micro-seconds/tick: 1.707
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/rationa
l_matrices_point_groups.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/cosets.
py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_find_best_cell.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/regression/ts
t_normalised_amplitudes.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/direct_
space_asu/proto/tst_asu.py
libtbx.python $CCTBX_DIST/run_examples.py --Quick
/net/leafnose/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/leafnose/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/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/gett
ing_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/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/spac
e_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/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/spac
e_subgroups.py
Usage: cctbx.python space_subgroups.py max_index space_group_symbol
Example: cctbx.python space_subgroups.py 2 P41212
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/trig
onal_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/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/quar
tz_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) (-11.3677889425-8.44989154346e-16j)
(1, 0, 1) (-15.044883416-26.0585024704j)
(1, 0, 2) (1.62112316094-2.80786768007j)
(1, 1, 0) (-12.8269388791-5.60868616295e-16j)
(1, 1, 1) (5.53358444868-9.58444941308j)
(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) (-11.3677889425-8.44989154346e-16j)
(1, 0, 1) (-15.044883416-26.0585024704j)
(1, 1, 0) (-12.8269388791-5.60868616295e-16j)
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/anal
yze_adp.py
Input Ucif: (0.17000000000000001, 0.17000000000000001, 0.19, 0.08999999999999999
7, 0, 0)
Warning: ADP tensor is incompatible with site symmetry.
Averaged Ucif: (0.16666666666666671, 0.16666666666666671, 0.19, 0.08333333333333
3356, 0.0, 0.0)
Eigenvectors and values:
v=(0.00000 0.00000 1.00000) lambda=0.1900
v=(0.41550 0.90959 -0.00000) lambda=0.1667
v=(0.90959 -0.41550 -0.00000) lambda=0.1667
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/g_ex
p_i_partial_derivatives.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_
exp_i_alpha_derivatives.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_
g_exp_i_alpha_derivatives.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_
structure_factor_derivatives.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_
structure_factor_derivatives_2.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_
structure_factor_derivatives_3.py P31
P 31
u+s,u,s: 16.49 16.41 0.08 micro-seconds/tick: 0.366
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_
structure_factor_derivatives_4.py --tag=internal
P 1
strudat tag: EDI
u+s,u,s: 11.47 11.39 0.08 micro-seconds/tick: 0.360
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/stru
cture_factor_calculus/site_derivatives.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/stru
cture_factor_calculus/u_star_derivatives.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/stru
cture_factor_calculus/sites_derivatives.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/stru
cture_factor_calculus/sites_least_squares_derivatives.py
OK
libtbx.python /net/leafnose/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/leafnose/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: 0.44 0.37 0.07 micro-seconds/tick: 3.403
libtbx.python /net/leafnose/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, 2.782
fudge factor, phase difference, map skewness: 0.10, 8.93, 2.633
fudge factor, phase difference, map skewness: 0.20, 17.45, 2.273
fudge factor, phase difference, map skewness: 0.30, 27.65, 1.731
fudge factor, phase difference, map skewness: 0.40, 35.17, 1.314
fudge factor, phase difference, map skewness: 0.50, 47.35, 0.5118
fudge factor, phase difference, map skewness: 0.60, 55.97, 0.2656
fudge factor, phase difference, map skewness: 0.70, 60.06, 0.1714
fudge factor, phase difference, map skewness: 0.80, 73.74, -0.01987
fudge factor, phase difference, map skewness: 0.90, 80.00, 0.02129
fudge factor, phase difference, map skewness: 1.00, 91.16, -0.00998
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, 2.534
fudge factor, phase difference, map skewness: 0.10, 7.97, 2.409
fudge factor, phase difference, map skewness: 0.20, 17.76, 2.057
fudge factor, phase difference, map skewness: 0.30, 27.96, 1.538
fudge factor, phase difference, map skewness: 0.40, 36.46, 0.8536
fudge factor, phase difference, map skewness: 0.50, 46.53, 0.4687
fudge factor, phase difference, map skewness: 0.60, 53.86, 0.257
fudge factor, phase difference, map skewness: 0.70, 63.07, 0.1243
fudge factor, phase difference, map skewness: 0.80, 69.53, 0.01723
fudge factor, phase difference, map skewness: 0.90, 84.11, -0.06677
fudge factor, phase difference, map skewness: 1.00, 90.73, -0.02715
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, 2.582
fudge factor, phase difference, map skewness: 0.10, 8.60, 2.251
fudge factor, phase difference, map skewness: 0.20, 21.16, 1.516
fudge factor, phase difference, map skewness: 0.30, 29.50, 1.27
fudge factor, phase difference, map skewness: 0.40, 32.77, 1.059
fudge factor, phase difference, map skewness: 0.50, 47.14, 0.467
fudge factor, phase difference, map skewness: 0.60, 50.01, 0.4321
fudge factor, phase difference, map skewness: 0.70, 58.21, 0.1093
fudge factor, phase difference, map skewness: 0.80, 68.98, 0.06266
fudge factor, phase difference, map skewness: 0.90, 79.12, 0.05196
fudge factor, phase difference, map skewness: 1.00, 80.51, 0.01285
Number of scatterers: 20
At special positions: 0
Unit cell: (36.5694, 36.5694, 62.168, 90, 90, 120)
Space group: R 3 2 :H (No. 155)
Miller array info: None
Observation type: None
Type of data: complex_double, size=371
Type of sigmas: None
Number of Miller indices: 371
Anomalous flag: False
Unit cell: (36.5694, 36.5694, 62.168, 90, 90, 120)
Space group: R 3 2 :H (No. 155)
fudge factor, phase difference, map skewness: 0.00, 0.00, 2.529
fudge factor, phase difference, map skewness: 0.10, 7.45, 2.412
fudge factor, phase difference, map skewness: 0.20, 15.39, 2.019
fudge factor, phase difference, map skewness: 0.30, 31.39, 1.265
fudge factor, phase difference, map skewness: 0.40, 41.20, 0.7944
fudge factor, phase difference, map skewness: 0.50, 42.82, 0.657
fudge factor, phase difference, map skewness: 0.60, 57.06, 0.1474
fudge factor, phase difference, map skewness: 0.70, 61.05, 0.1796
fudge factor, phase difference, map skewness: 0.80, 75.85, -0.04234
fudge factor, phase difference, map skewness: 0.90, 75.50, -0.05837
fudge factor, phase difference, map skewness: 1.00, 91.61, -0.03494
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, 2.683
fudge factor, phase difference, map skewness: 0.10, 10.63, 2.016
fudge factor, phase difference, map skewness: 0.20, 20.48, 1.746
fudge factor, phase difference, map skewness: 0.30, 21.80, 1.7
fudge factor, phase difference, map skewness: 0.40, 37.56, 0.7012
fudge factor, phase difference, map skewness: 0.50, 49.28, 0.3219
fudge factor, phase difference, map skewness: 0.60, 58.47, 0.07721
fudge factor, phase difference, map skewness: 0.70, 61.72, 0.0205
fudge factor, phase difference, map skewness: 0.80, 79.03, -0.1657
fudge factor, phase difference, map skewness: 0.90, 85.92, -0.1176
fudge factor, phase difference, map skewness: 1.00, 93.83, 0.01049
libtbx.python /net/leafnose/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/leafnose/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: (0.33333333333333337, 0.66666666666666663, 0.10000000000000001)
independent_gradients: (0.02,)
independent_curvatures: (6.0,)
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/adp_
symmetry_constraints.py
OK
libtbx.python /net/leafnose/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: 0.00289854 gradient norm: 0.87326
functional: 0.000926904 gradient norm: 0.164675
LBFGS step
functional: 0.000721103 gradient norm: 0.10673
LBFGS step
functional: 0.000496383 gradient norm: 0.0156636
LBFGS step
functional: 0.000436098 gradient norm: 0.0187089
LBFGS step
functional: 0.000405012 gradient norm: 0.0141627
LBFGS step
functional: 0.000437223 gradient norm: 0.0606762
functional: 0.00040312 gradient norm: 0.0132963
LBFGS step
functional: 0.000400412 gradient norm: 0.0048646
LBFGS step
functional: 0.000400027 gradient norm: 0.00909764
LBFGS step
functional: 0.000399624 gradient norm: 0.00699398
LBFGS step
functional: 0.000398287 gradient norm: 0.00462531
LBFGS step
functional: 0.000395683 gradient norm: 0.00493111
LBFGS step
functional: 0.000391548 gradient norm: 0.00839572
LBFGS step
functional: 0.000397072 gradient norm: 0.0313129
functional: 0.000389324 gradient norm: 0.00955204
LBFGS step
functional: 0.000387576 gradient norm: 0.0299144
LBFGS step
functional: 0.000384513 gradient norm: 0.00250356
LBFGS step
functional: 0.000384214 gradient norm: 0.00179169
LBFGS step
functional: 0.000384067 gradient norm: 0.00168063
LBFGS step
functional: 0.000383912 gradient norm: 0.00139437
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, 89.988, 89.9857)
u+s,u,s: 0.21 0.17 0.04 micro-seconds/tick: 3.707
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/mill
er_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) 0.80910591266
asu a: (1, 2, 3) 0.187416362544
asu a: (2, 3, 4) 0.990288405684
asu a: (3, 4, 5) 0.519450193207
asu a: (4, 5, 6) 0.984387267702
asu b: (5, 6, 7) 0.102986394833
asu b: (0, 1, 2) 0.400166404547
asu b: (3, 4, 5) 0.729753608881
asu b: (1, 2, 3) 0.530433674659
asu b: (4, 5, 6) 0.884663297434
common a: (0, 1, 2) 0.80910591266
common a: (3, 4, 5) 0.519450193207
common a: (1, 2, 3) 0.187416362544
common a: (4, 5, 6) 0.984387267702
common b: (0, 1, 2) 0.400166404547
common b: (3, 4, 5) 0.729753608881
common b: (1, 2, 3) 0.530433674659
common b: (4, 5, 6) 0.884663297434
lone a: (2, 3, 4) 0.990288405684
lone b: (5, 6, 7) 0.102986394833
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/mill
er_transform.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/chan
ge_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/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/stev
e_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/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/cr2o
3_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/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/cr2o
3_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 ( 0.4442, 0.0558, 0.7500)
O1: 1.9654 ( 0.7500, 0.4442, 0.0558)
O1: 1.9654 ( 0.0558, 0.7500, 0.4442)
O1: 2.0157 ( 0.5558, -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 ( 0.5558, -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 << -0.3476, -0.3476, -0.3476>>
O1: 1.9654 ( -0.4442, -0.0558, -0.7500)
O1: 1.9654 ( -0.7500, -0.4442, -0.0558)
O1: 1.9654 ( -0.0558, -0.7500, -0.4442)
O1: 2.0157 ( -0.5558, 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 ( -0.5558, 0.0558, -0.2500)
O1: 2.0157 ( -0.2500, -0.5558, 0.0558)
O1: 2.0157 ( 0.0558, -0.2500, -0.5558)
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 ( 0.3476, 0.3476, 0.3476)
Cr1: 2.0157 ( 0.1524, 0.1524, 0.1524)
O1 pair count: 4 << -0.5558, 0.0558, -0.2500>>
Cr1: 1.9654 ( -0.8476, 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 ( -0.3476, -0.3476, -0.3476)
Cr1: 2.0157 ( -0.1524, -0.1524, -0.1524)
Coordination sequences for ICSD structure
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
TD10: 1345.00
Coordination sequences for P1 structure
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
TD10: 1345.00
(2, 2, 2) 86.0508424883 86.0508424883
(4, 4, 4) 113.047557719 113.047557719
(3, 2, 3) 40.4154044721 40.4154044721
(3, 3, 2) 40.4154044721 40.4154044721
(2, 3, 3) 40.4154044721 40.4154044721
(1, 0, 1) 95.4889181855 95.4889181855
(1, 1, 0) 95.4889181855 95.4889181855
(0, 1, 1) 95.4889181855 95.4889181855
(2, 1, 1) 162.211900743 162.211900743
(1, 1, 2) 162.211900743 162.211900743
(1, 2, 1) 162.211900743 162.211900743
(4, 3, 3) 155.00906081 155.00906081
(3, 3, 4) 155.00906081 155.00906081
(3, 4, 3) 155.00906081 155.00906081
(0, -1, 1) 169.838481281 169.838481281
(-1, 0, 1) 169.838481281 169.838481281
(1, -1, 0) 169.838481281 169.838481281
(2, 1, 0) 77.6623864446 77.6623864446
(1, 0, 2) 77.6623864446 77.6623864446
(0, 2, 1) 77.6623864446 77.6623864446
(1, 2, 0) 77.6623864446 77.6623864446
(0, 1, 2) 77.6623864446 77.6623864446
(2, 0, 1) 77.6623864446 77.6623864446
(3, 2, 1) 190.423823139 190.423823139
(2, 1, 3) 190.423823139 190.423823139
(1, 3, 2) 190.423823139 190.423823139
(2, 3, 1) 190.423823139 190.423823139
(1, 2, 3) 190.423823139 190.423823139
(3, 1, 2) 190.423823139 190.423823139
(4, 3, 2) 47.1902503064 47.1902503064
(3, 2, 4) 47.1902503064 47.1902503064
(2, 4, 3) 47.1902503064 47.1902503064
(3, 4, 2) 47.1902503064 47.1902503064
(2, 3, 4) 47.1902503064 47.1902503064
(4, 2, 3) 47.1902503064 47.1902503064
(5, 4, 3) 38.7011643914 38.7011643914
(4, 3, 5) 38.7011643914 38.7011643914
(3, 5, 4) 38.7011643914 38.7011643914
(4, 5, 3) 38.7011643914 38.7011643914
(3, 4, 5) 38.7011643914 38.7011643914
(5, 3, 4) 38.7011643914 38.7011643914
(4, 2, 4) 126.854496289 126.854496289
(4, 4, 2) 126.854496289 126.854496289
(2, 4, 4) 126.854496289 126.854496289
(2, 0, 2) 159.758114444 159.758114444
(2, 2, 0) 159.758114444 159.758114444
(0, 2, 2) 159.758114444 159.758114444
(2, 0, 0) 52.4585599646 52.4585599646
(0, 0, 2) 52.4585599646 52.4585599646
(0, 2, 0) 52.4585599646 52.4585599646
(4, 2, 2) 19.175305094 19.175305094
(2, 2, 4) 19.175305094 19.175305094
(2, 4, 2) 19.175305094 19.175305094
(3, 1, 4) 22.6189348657 22.6189348657
(4, 3, 1) 22.6189348657 22.6189348657
(1, 4, 3) 22.6189348657 22.6189348657
(1, 3, 4) 22.6189348657 22.6189348657
(3, 4, 1) 22.6189348657 22.6189348657
(4, 1, 3) 22.6189348657 22.6189348657
(2, 0, 3) 16.0896242359 16.0896242359
(3, 2, 0) 16.0896242359 16.0896242359
(0, 3, 2) 16.0896242359 16.0896242359
(0, 2, 3) 16.0896242359 16.0896242359
(2, 3, 0) 16.0896242359 16.0896242359
(3, 0, 2) 16.0896242359 16.0896242359
(-1, -2, 1) 53.0970522234 53.0970522234
(1, -1, 2) 53.0970522234 53.0970522234
(-1, 2, 1) 53.0970522234 53.0970522234
(-1, 1, 2) 53.0970522234 53.0970522234
(2, -1, 1) 53.0970522234 53.0970522234
(-2, -1, 1) 53.0970522234 53.0970522234
(0, -1, 2) 18.7461313511 18.7461313511
(0, -2, 1) 18.7461313511 18.7461313511
(-2, 0, 1) 18.7461313511 18.7461313511
(1, -2, 0) 18.7461313511 18.7461313511
(-1, 0, 2) 18.7461313511 18.7461313511
(2, -1, 0) 18.7461313511 18.7461313511
(3, 1, 0) 132.488142531 132.488142531
(1, 0, 3) 132.488142531 132.488142531
(0, 3, 1) 132.488142531 132.488142531
(1, 3, 0) 132.488142531 132.488142531
(0, 1, 3) 132.488142531 132.488142531
(3, 0, 1) 132.488142531 132.488142531
(4, 2, 1) 14.1831500279 14.1831500279
(2, 1, 4) 14.1831500279 14.1831500279
(1, 4, 2) 14.1831500279 14.1831500279
(2, 4, 1) 14.1831500279 14.1831500279
(1, 2, 4) 14.1831500279 14.1831500279
(4, 1, 2) 14.1831500279 14.1831500279
(5, 3, 2) 121.452908825 121.452908825
(3, 2, 5) 121.452908825 121.452908825
(2, 5, 3) 121.452908825 121.452908825
(3, 5, 2) 121.452908825 121.452908825
(2, 3, 5) 121.452908825 121.452908825
(5, 2, 3) 121.452908825 121.452908825
(0, -2, 2) 121.476041154 121.476041154
(-2, 0, 2) 121.476041154 121.476041154
(2, -2, 0) 121.476041154 121.476041154
(1, -1, 3) 39.0693132248 39.0693132248
(-1, 3, 1) 39.0693132248 39.0693132248
(-1, -3, 1) 39.0693132248 39.0693132248
(-3, -1, 1) 39.0693132248 39.0693132248
(-1, 1, 3) 39.0693132248 39.0693132248
(3, -1, 1) 39.0693132248 39.0693132248
(4, 2, 0) 133.588352208 133.588352208
(2, 0, 4) 133.588352208 133.588352208
(0, 4, 2) 133.588352208 133.588352208
(2, 4, 0) 133.588352208 133.588352208
(0, 2, 4) 133.588352208 133.588352208
(4, 0, 2) 133.588352208 133.588352208
(3, 0, 3) 75.3123159831 75.3123159831
(3, 3, 0) 75.3123159831 75.3123159831
(0, 3, 3) 75.3123159831 75.3123159831
(-1, -1, 2) 219.874202958 219.874202958
(1, -2, 1) 219.874202958 219.874202958
(-2, 1, 1) 219.874202958 219.874202958
(4, 1, 1) 75.3123159831 75.3123159831
(1, 1, 4) 75.3123159831 75.3123159831
(1, 4, 1) 75.3123159831 75.3123159831
(3, 0, 4) 7.74006832091 7.74006832091
(4, 3, 0) 7.74006832091 7.74006832091
(0, 4, 3) 7.74006832091 7.74006832091
(0, 3, 4) 7.74006832091 7.74006832091
(3, 4, 0) 7.74006832091 7.74006832091
(4, 0, 3) 7.74006832091 7.74006832091
(-2, -3, 1) 92.880272839 92.880272839
(2, -1, 3) 92.880272839 92.880272839
(-1, 3, 2) 92.880272839 92.880272839
(-1, 2, 3) 92.880272839 92.880272839
(3, -1, 2) 92.880272839 92.880272839
(-3, -2, 1) 92.880272839 92.880272839
(-1, -2, 2) 9.22539071273 9.22539071273
(1, -2, 2) 9.22539071273 9.22539071273
(-2, 2, 1) 9.22539071273 9.22539071273
(-2, 1, 2) 9.22539071273 9.22539071273
(2, -2, 1) 9.22539071273 9.22539071273
(-2, -1, 2) 9.22539071273 9.22539071273
(0, -1, 3) 58.7597521751 58.7597521751
(0, -3, 1) 58.7597521751 58.7597521751
(-3, 0, 1) 58.7597521751 58.7597521751
(1, -3, 0) 58.7597521751 58.7597521751
(-1, 0, 3) 58.7597521751 58.7597521751
(3, -1, 0) 58.7597521751 58.7597521751
(4, 1, 0) 8.38469863314 8.38469863314
(1, 0, 4) 8.38469863314 8.38469863314
(0, 4, 1) 8.38469863314 8.38469863314
(1, 4, 0) 8.38469863314 8.38469863314
(0, 1, 4) 8.38469863314 8.38469863314
(4, 0, 1) 8.38469863314 8.38469863314
(-2, -2, 2) 63.3334064079 63.3334064079
(2, -2, 2) 63.3334064079 63.3334064079
(-2, 2, 2) 63.3334064079 63.3334064079
(4, 0, 0) 76.9075882126 76.9075882126
(0, 0, 4) 76.9075882126 76.9075882126
(0, 4, 0) 76.9075882126 76.9075882126
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/redu
ced_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/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/lebe
dev_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/leafnose/scratch1/rwgk/auto_build/sources/cctbx/examples/le_p
age_1982_vs_lebedev_2005.py
OK
libtbx.python $CCTBX_DIST/regression/tst_structure_factors_multithread.py --verb
ose
omptbx.have_stubs_h
OpenMP
# CPU run-time speed-up
1 2.14 x 1.00
2 2.14 x 1.00
Skipping raw multithreaded structure factor computation tests
usr+sys time: 6.88 seconds, ticks: 4206394, micro-seconds/tick: 1.636
wall clock time: 6.88 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
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/tst_wildcard.
py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/tst_simple_pa
rser.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/tst_phil.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/ranges.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/tst_crystal_s
ymmetry_from_any.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/kriber/tst_st
rudat.py
u+s,u,s: 7.91 7.84 0.07 micro-seconds/tick: 0.831
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/cif/tst_xray_
structure.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/shelx/tst_lex
_parse_build.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/shelx/tst_hkl
f.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/hybrid_36
.py exercise
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_hiera
rchy.py
iotbx.pdb.hierarchy.atom.sizeof_data(): 168
u+s,u,s: 3.66 3.49 0.17 micro-seconds/tick: 3.863
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_ext.p
y
time hy36recode_width_4_all: 0.20 s (0.082 micro s per encode-decode cycle)
u+s,u,s: 1.37 1.24 0.13 micro-seconds/tick: 1.091
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_atom_
selection.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_rna_d
na_atom_names.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_atom_
name_interpretation.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_extra
ct_rfactors_resolutions_sigma.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_pdb.p
y
u+s,u,s: 6.41 6.25 0.16 micro-seconds/tick: 2.055
libtbx.python /net/leafnose/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/leafnose/scratch1/rwgk/auto_build/sources/iotbx/cns/space_gro
up_symbols.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/cns/tst_cns.p
y
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/scalepack/tst
_merge.py P31
P 31
u+s,u,s: 0.63 0.54 0.09 micro-seconds/tick: 1.376
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/scalepack/no_
merge_original_index.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/ccp4_map/tst.
py
u+s,u,s: 0.31 0.25 0.06 micro-seconds/tick: 2.771
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/mtz/tst_ext.p
y
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/mtz/extract_f
rom_symop_lib.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/mtz/tst.py P3
1
P 31
u+s,u,s: 0.99 0.91 0.08 micro-seconds/tick: 1.815
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/examples/tst_
mtz_free_flipper.py
Reading file: /net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/r
eflection_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/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/r
eflection_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: 8.68 8.57 0.11 micro-seconds/tick: 1.674
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/tst_reflectio
n_file_utils.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/detectors/tst
_adsc.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/detectors/tst
_debug_write.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/xplor/tst_xpl
ormap.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/tst_phases.py
P31
Writing tmp.pdb
Writing: tmp.phs
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/regression/ts
t_lattice_symmetry.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/regression/ts
t_reflection_statistics.py Fdd2 P31m
F d d 2
P 3 1 m
u+s,u,s: 7.28 7.14 0.14 micro-seconds/tick: 4.047
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/iotbx/tst_data_plot
s.py
OK
libtbx.python /net/leafnose/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: 1.78 1.66 0.12 micro-seconds/tick: 8.685
libtbx.python $SMTBX_DIST/run_tests.py --Quick
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/smtbx/ab_initio/tes
ts/tst_ab_initio_ext.py
u+s,u,s: 2.80 2.72 0.08 micro-seconds/tick: 1.008
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/smtbx/ab_initio/tes
ts/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: 70.58 70.22 0.36 micro-seconds/tick: 1.071
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/leafnose/scratch1/rwgk/auto_build/sources/smtbx/refinement/co
nstraints/tests/tst_constraints.py
OK
libtbx.python $MMTBX_DIST/run_tests.py --Quick
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/polygon/tst.p
y
EXAMPLE 1:
rfact
0.1775 0.1902 516
0.1902 0.2030 799
0.2030 0.2157 896
0.2157 0.2284 787
0.2284 0.2412 524
0.2412 0.2539 299
0.2539 0.2666 155
0.2666 0.2793 77
0.2793 0.2921 41
0.2921 0.3048 19
rfree
0.1913 0.2058 33
0.2058 0.2203 199
0.2203 0.2347 548
0.2347 0.2492 825
0.2492 0.2637 934
0.2637 0.2782 707
0.2782 0.2927 481
0.2927 0.3071 241
0.3071 0.3216 91
0.3216 0.3361 54
bndav
0.0020 0.0039 3
0.0039 0.0058 173
0.0058 0.0077 1280
0.0077 0.0096 745
0.0096 0.0115 528
0.0115 0.0134 467
0.0134 0.0153 348
0.0153 0.0172 249
0.0172 0.0191 193
0.0191 0.0210 127
angav
0.7000 0.8430 11
0.8430 0.9860 66
0.9860 1.1290 225
1.1290 1.2720 878
1.2720 1.4150 1171
1.4150 1.5580 772
1.5580 1.7010 481
1.7010 1.8440 277
1.8440 1.9870 143
1.9870 2.1300 89
adpav
2.1000 7.3200 8
7.3200 12.5400 38
12.5400 17.7600 120
17.7600 22.9800 358
22.9800 28.2000 585
28.2000 33.4200 735
33.4200 38.6400 739
38.6400 43.8600 705
43.8600 49.0800 504
49.0800 54.3000 321
EXAMPLE 2:
rfact
0.1660 0.1823 2139
0.1823 0.1987 3650
0.1987 0.2150 4015
0.2150 0.2314 3092
0.2314 0.2477 1863
0.2477 0.2640 946
0.2640 0.2804 437
0.2804 0.2967 192
0.2967 0.3131 61
0.3131 0.3294 5
rfree
0.1683 0.1852 48
0.1852 0.2021 706
0.2021 0.2191 2051
0.2191 0.2360 3071
0.2360 0.2529 3450
0.2529 0.2698 2998
0.2698 0.2867 2045
0.2867 0.3037 1209
0.3037 0.3206 570
0.3206 0.3375 252
bndav
0.0000 0.0025 8
0.0025 0.0050 188
0.0050 0.0075 4778
0.0075 0.0100 2827
0.0100 0.0125 3067
0.0125 0.0150 2483
0.0150 0.0175 1070
0.0175 0.0200 824
0.0200 0.0225 791
0.0225 0.0250 364
angav
0.0000 0.2870 4
0.2870 0.5740 3
0.5740 0.8610 84
0.8610 1.1480 1256
1.1480 1.4350 7471
1.4350 1.7220 4673
1.7220 2.0090 1779
2.0090 2.2960 702
2.2960 2.5830 276
2.5830 2.8700 152
adpav
2.0000 7.9900 48
7.9900 13.9800 501
13.9800 19.9700 2166
19.9700 25.9600 3374
25.9600 31.9500 3162
31.9500 37.9400 2478
37.9400 43.9300 1886
43.9300 49.9200 1309
49.9200 55.9100 844
55.9100 61.9000 632
EXAMPLE 3:
rfact
0.1415 0.1548 9
0.1548 0.1681 35
0.1681 0.1814 82
0.1814 0.1947 152
0.1947 0.2079 177
0.2079 0.2212 158
0.2212 0.2345 113
0.2345 0.2478 42
0.2478 0.2611 13
0.2611 0.2744 3
rfree
0.1732 0.1849 8
0.1849 0.1965 14
0.1965 0.2082 41
0.2082 0.2199 91
0.2199 0.2315 134
0.2315 0.2432 138
0.2432 0.2549 135
0.2549 0.2666 103
0.2666 0.2782 80
0.2782 0.2899 40
bndav
0.0040 0.0066 175
0.0066 0.0092 214
0.0092 0.0118 79
0.0118 0.0144 118
0.0144 0.0170 64
0.0170 0.0196 70
0.0196 0.0222 45
0.0222 0.0248 8
0.0248 0.0274 5
0.0274 0.0300 6
angav
0.7900 0.9210 6
0.9210 1.0520 25
1.0520 1.1830 96
1.1830 1.3140 155
1.3140 1.4450 188
1.4450 1.5760 119
1.5760 1.7070 84
1.7070 1.8380 61
1.8380 1.9690 30
1.9690 2.1000 20
adpav
6.5000 10.1300 5
10.1300 13.7600 17
13.7600 17.3900 49
17.3900 21.0200 77
21.0200 24.6500 112
24.6500 28.2800 136
28.2800 31.9100 128
31.9100 35.5400 117
35.5400 39.1700 82
39.1700 42.8000 61
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/chemical_comp
onents/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', 'HN
62', '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', '2H
N6', 'H2']
Hydrogen names
['HOG2', 'HOG3', 'HOB2', 'HOA2', "H5'1", "H5'2", "H4'", "H3'", "HO3'", "H2'", "H
O2'", "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'], ['O
2B', 'HOB2'], ['PA', 'O1A'], ['PA', 'O2A'], ['PA', 'O3A'], ['PA', "O5'"], ['O2
A', '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'", "C
1'"], ["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'], ['O
2B', '2HOB'], ['PA', 'O1A'], ['PA', 'O2A'], ['PA', 'O3A'], ['PA', 'O5*'], ['O2
A', '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*', 'C
1*'], ['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', 'C
2D', 'C3D', 'C4D', 'CMD', 'CAD', 'CBD', 'CGD', 'O1D', 'O2D', 'HHA', 'HHB', 'HH
C', 'HHD', 'HMA1', 'HMA2', 'HMA3', 'HAA1', 'HAA2', 'HBA1', 'HBA2', 'H2A', 'HMB
1', 'HMB2', 'HMB3', 'HAB', 'HBB1', 'HBB2', 'HMC1', 'HMC2', 'HMC3', 'HAC', 'HBC
1', 'HBC2', 'HMD1', 'HMD2', 'HMD3', 'HAD1', 'HAD2', 'HBD1', 'HBD2', 'H2D']
Alternate atom names
['FE', 'CHA', 'CHB', 'CHC', 'CHD', 'N A', 'C1A', 'C2A', 'C3A', 'C4A', 'CMA', 'CA
A', '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', 'HB
A2', 'H2A', 'HMB1', 'HMB2', 'HMB3', 'HAB', 'HBB1', 'HBB2', 'HMC1', 'HMC2', 'HM
C3', 'HAC', 'HBC1', 'HBC2', 'HMD1', 'HMD2', 'HMD3', 'HAD1', 'HAD2', 'HBD1', 'H
BD2', 'H2D']
Alternate hydrogen names
['HHA', 'HHB', 'HHC', 'HHD', '1HMA', '2HMA', '3HMA', '1HAA', '2HAA', '1HBA', '2H
BA', 'H2A', '1HMB', '2HMB', '3HMB', 'HAB', '1HBB', '2HBB', '1HMC', '2HMC', '3H
MC', 'HAC', '1HBC', '2HBC', '1HMD', '2HMD', '3HMD', '1HAD', '2HAD', '1HBD', '2
HBD', 'H2D']
Wrapped hydrogen names
['HHA', 'HHB', 'HHC', 'HHD', '1HMA', '2HMA', '3HMA', '1HAA', '2HAA', '1HBA', '2H
BA', 'H2A', '1HMB', '2HMB', '3HMB', 'HAB', '1HBB', '2HBB', '1HMC', '2HMC', '3H
MC', 'HAC', '1HBC', '2HBC', '1HMD', '2HMD', '3HMD', '1HAD', '2HAD', '1HBD', '2
HBD', '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'], ['C
HD', 'HHD'], ['NA', 'C1A'], ['NA', 'C4A'], ['C1A', 'C2A'], ['C2A', 'C3A'], ['C
2A', 'CAA'], ['C3A', 'C4A'], ['C3A', 'CMA'], ['CMA', 'HMA1'], ['CMA', 'HMA2'],
['CMA', 'HMA3'], ['CAA', 'CBA'], ['CAA', 'HAA1'], ['CAA', 'HAA2'], ['CBA', 'C
GA'], ['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'], ['C3
D', 'C4D'], ['C3D', 'CAD'], ['CMD', 'HMD1'], ['CMD', 'HMD2'], ['CMD', 'HMD3'],
['CAD', 'CBD'], ['CAD', 'HAD1'], ['CAD', 'HAD2'], ['CBD', 'CGD'], ['CBD', 'HB
D1'], ['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'], ['C
HA', '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', '2
HMA'], ['CMA', '3HMA'], ['CAA', 'CBA'], ['CAA', '1HAA'], ['CAA', '2HAA'], ['CB
A', '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', '2H
MB'], ['CMB', '3HMB'], ['CAB', 'CBB'], ['CAB', 'HAB'], ['CBB', '1HBB'], ['CBB'
, '2HBB'], ['N C', 'C1C'], ['N C', 'C4C'], ['C1C', 'C2C'], ['C2C', 'C3C'], ['C
2C', 'CMC'], ['C3C', 'C4C'], ['C3C', 'CAC'], ['CMC', '1HMC'], ['CMC', '2HMC'],
['CMC', '3HMC'], ['CAC', 'CBC'], ['CAC', 'HAC'], ['CBC', '1HBC'], ['CBC', '2H
BC'], ['N D', 'C1D'], ['N D', 'C4D'], ['C1D', 'C2D'], ['C2D', 'C3D'], ['C2D',
'CMD'], ['C3D', 'C4D'], ['C3D', 'CAD'], ['CMD', '1HMD'], ['CMD', '2HMD'], ['CM
D', '3HMD'], ['CAD', 'CBD'], ['CAD', '1HAD'], ['CAD', '2HAD'], ['CBD', 'CGD'],
['CBD', '1HBD'], ['CBD', '2HBD'], ['CGD', 'O1D'], ['CGD', 'O2D'], ['O2D', 'H2
D']]
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/regression/ts
t_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: 6.91 6.71 0.20 micro-seconds/tick: 1.779
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/rotamer/rotam
er_eval.py
Processing data files in "/net/leafnose/scratch1/rwgk/auto_build/sources/chem_da
ta/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-glu.data -> rota500-glu.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-asn.data -> rota500-asn.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/leafnose/scratch1/rwgk/auto_build/sources/chem_da
ta/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: 0.94 0.81 0.13 micro-seconds/tick: 0.789
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/wwpdb/tst_sta
ndard_geometry_cif.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_pdbtools.
py
OK
usr+sys time: 22.11 seconds, ticks: 34923927, micro-seconds/tick: 0.633
wall clock time: 95.34 seconds
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/real_space/ts
t.py
OK: real_space: u+s,u,s: 107.88 104.37 3.51 micro-seconds/tick: 84.137
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/ias/tst_ias.p
y
>>> 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 7.805 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 7.805 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/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/refinement/ts
t_anomalous_scatterer_groups.py P3
P 3
u+s,u,s: 1.38 1.28 0.10 micro-seconds/tick: 1.116
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/refinement/ts
t_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: 131.18 129.13 2.05 micro-seconds/tick: 2.470
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/refinement/ts
t_refinement_flags.py
u+s,u,s: 1.07 0.96 0.11 micro-seconds/tick: 0.844
libtbx.python /net/leafnose/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/leafnose/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: 0.07, per 1000 atoms: 1.52
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 res
idual
pdb=" O HOH S 7 " - pdb=" H1 HOH S 7 " 0.980 1.476 -0.496 2.50e+03 6.1
4e+02
pdb=" CG ARG A 1 " - pdb=" HG3 ARG A 1 " 0.970 0.537 0.433 2.50e+03 4.7
0e+02
pdb=" O HOH S 9 " - pdb=" H2 HOH S 9 " 0.980 1.323 -0.343 2.50e+03 2.9
5e+02
pdb=" CA ARG A 1 " - pdb=" HA ARG A 1 " 0.980 1.263 -0.283 2.50e+03 2.0
0e+02
pdb=" O HOH S 1 " - pdb=" H1 HOH S 1 " 0.980 1.262 -0.282 2.50e+03 1.9
9e+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/leafnose/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: 1.84, per 1000 atoms: 1.54
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=1.9
9
Simple disulfide: pdb=" SG CYS 30 " - pdb=" SG CYS 115 " distance=1.9
8
Simple disulfide: pdb=" SG CYS 64 " - pdb=" SG CYS 80 " distance=1.9
8
Simple disulfide: pdb=" SG CYS 76 " - pdb=" SG CYS 94 " distance=1.9
8
Time building geometry restraints manager: 0.09 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 res
idual
pdb=" CA TYR 53 " - pdb=" C TYR 53 " 1.525 1.451 0.074 2.27e+03 1.2
5e+01
pdb=" CA TRP 63 " - pdb=" C TRP 63 " 1.525 1.451 0.074 2.27e+03 1.2
3e+01
pdb=" CB CYS 76 " - pdb=" SG CYS 76 " 1.808 1.697 0.111 9.18e+02 1.1
4e+01
pdb=" CG MET 12 " - pdb=" SD MET 12 " 1.803 1.719 0.084 1.60e+03 1.1
2e+01
pdb=" CB TRP 123 " - pdb=" CG TRP 123 " 1.498 1.401 0.097 1.04e+03 9.7
1e+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: 6.80 6.64 0.16 micro-seconds/tick: 0.820
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_fmodel.py
P 1
P 4
C 1 2/c 1
u+s,u,s: 122.25 119.82 2.43 micro-seconds/tick: 1.829
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_utils.py
u+s,u,s: 13.55 13.38 0.17 micro-seconds/tick: 0.544
libtbx.python /net/leafnose/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/leafnose/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: 9.22 9.05 0.17 micro-seconds/tick: 2.542
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/ncs/tst_restr
aints.py
u+s,u,s: 1.72 1.61 0.11 micro-seconds/tick: 0.930
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/ncs/tst_restr
aints.py
u+s,u,s: 1.71 1.59 0.12 micro-seconds/tick: 0.924
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/ncs/ncs.py ex
ercise
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/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/regression/ts
t_adp_restraints.py
u+s,u,s: 1.59 1.46 0.13 micro-seconds/tick: 0.647
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/tst_s
caling.py
very_quick_erf*15000000 optimized=False: 11.68 s
very_quick_erf*15000000 optimized=True: 0.82 s
quick_ei0*5000000 optimized=False: 1.72 s
quick_ei0*5000000 optimized=True: 0.77 s
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/tst_o
utlier.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/absen
ce_likelihood.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/thoro
ugh_outlier_test.py P21
P 1 21 1
u+s,u,s: 22.37 22.03 0.34 micro-seconds/tick: 4.479
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/twinning/prob
abalistic_detwinning.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_libra
ry/tst_rna_sugar_pucker_analysis.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_libra
ry/tst_cif_types.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_libra
ry/tst_motif.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_libra
ry/tst_selection.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_libra
ry/tst_tyr_from_gly_and_bnz.py
Monomer Library directory:
"/net/leafnose/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/leafnose/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: 0.03, per 1000 atoms: 2.50
geo_tyr
Number of disulfides: simple=0, symmetry=0
Time building geometry restraints manager: 0.01 seconds
Histogram of bond lengths:
1.23 - 1.29: 1
1.29 - 1.35: 0
1.35 - 1.41: 7
1.41 - 1.47: 1
1.47 - 1.53: 3
Bond restraints sorted by residual:
atom i - atom j ideal model delta weight res
idual
pdb=" CD1 TYR 1 " - pdb=" CE1 TYR 1 " 1.382 1.394 -0.012 1.11e+03 1.6
7e-01
pdb=" CD2 TYR 1 " - pdb=" CE2 TYR 1 " 1.382 1.393 -0.011 1.11e+03 1.3
1e-01
pdb=" CE2 TYR 1 " - pdb=" CZ TYR 1 " 1.378 1.386 -0.008 1.74e+03 1.0
9e-01
pdb=" N TYR 1 " - pdb=" CA TYR 1 " 1.458 1.453 0.005 2.77e+03 6.3
4e-02
pdb=" CG TYR 1 " - pdb=" CD1 TYR 1 " 1.389 1.394 -0.005 2.27e+03 4.8
4e-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 res
idual
pdb=" CA GLY 1 " - pdb=" C GLY 1 " 1.516 1.527 -0.011 3.09e+03 3.9
8e-01
pdb=" CD1 BNZ 2 " - pdb=" CE1 BNZ 2 " 1.382 1.394 -0.012 1.11e+03 1.6
7e-01
pdb=" CD2 BNZ 2 " - pdb=" CE2 BNZ 2 " 1.382 1.393 -0.011 1.11e+03 1.3
1e-01
pdb=" CE2 BNZ 2 " - pdb=" CZ BNZ 2 " 1.378 1.386 -0.008 1.74e+03 1.0
9e-01
pdb=" CG BNZ 2 " - pdb=" CD1 BNZ 2 " 1.389 1.394 -0.005 2.27e+03 4.8
4e-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/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_libra
ry/tst_pdb_interpretation.py
u+s,u,s: 4.76 4.61 0.15 micro-seconds/tick: 0.705
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_libra
ry/tst_rna_dna_interpretation.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_libra
ry/tst_protein_interpretation.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/regression/ts
t_altloc_chain_break.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/hydrogens/bui
ld_hydrogens.py
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/arg.p
db
Monomer Library directory:
"/net/leafnose/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/leafnose/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: 0.03, per 1000 atoms: 1.25
Number of scatterers: 24
At special positions: 0
Unit cell: (10, 10, 10, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
O 2 8.00
N 4 7.00
C 6 6.00
H 12 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Time building geometry restraints manager: 0.01 seconds
Histogram of bond lengths:
0.86 - 1.00: 10
1.00 - 1.14: 2
1.14 - 1.28: 2
1.28 - 1.42: 3
1.42 - 1.56: 6
Bond restraints sorted by residual:
atom i - atom j ideal model delta weight res
idual
pdb=" CA ARG 1 " - pdb="HA ARG 1 " 0.980 1.062 -0.082 2.50e+03 1.6
9e+01
pdb=" NE ARG 1 " - pdb=" CZ ARG 1 " 1.329 1.367 -0.038 5.10e+03 7.4
2e+00
pdb=" CA ARG 1 " - pdb=" N ARG 1 " 1.458 1.507 -0.049 2.77e+03 6.5
2e+00
pdb=" NE ARG 1 " - pdb="HE ARG 1 " 0.970 1.010 -0.040 2.50e+03 4.0
9e+00
pdb=" CB ARG 1 " - pdb=" CA ARG 1 " 1.530 1.559 -0.029 2.50e+03 2.1
4e+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: 8.10796e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/lys.p
db
Monomer Library directory:
"/net/leafnose/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/leafnose/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: 0.01 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 res
idual
pdb=" CA LYS 1 " - pdb=" N LYS 1 " 1.458 1.506 -0.048 2.77e+03 6.3
7e+00
pdb=" CA LYS 1 " - pdb="HA LYS 1 " 0.980 1.020 -0.040 2.50e+03 4.0
8e+00
pdb=" CB LYS 1 " - pdb=" CA LYS 1 " 1.530 1.555 -0.025 2.50e+03 1.5
2e+00
pdb=" C LYS 1 " - pdb=" OXT LYS 1 " 1.231 1.250 -0.019 2.50e+03 8.8
2e-01
pdb=" C LYS 1 " - pdb=" O LYS 1 " 1.231 1.249 -0.018 2.50e+03 8.3
3e-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): 0.0112115
nonbonded_residual_sum (n=182): 0.626625
angle_residual_sum (n=39): 0.419967
dihedral_residual_sum (n=6): 0.397744
chirality_residual_sum (n=1): 0.0235834
planarity_residual_sum (n=1): 1.74641e-15
norm of gradients: 2.19871e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/ala.p
db
Monomer Library directory:
"/net/leafnose/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: 0.02, per 1000 atoms: 3.33
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/leafnose/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: 0.01, per 1000 atoms: 1.00
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 res
idual
pdb=" CA ALA 1 " - pdb="HA ALA 1 " 0.980 1.050 -0.070 2.50e+03 1.2
3e+01
pdb=" CA ALA 1 " - pdb=" N ALA 1 " 1.458 1.503 -0.045 2.77e+03 5.5
5e+00
pdb=" C ALA 1 " - pdb=" OXT ALA 1 " 1.231 1.250 -0.019 2.50e+03 9.4
1e-01
pdb=" C ALA 1 " - pdb=" O ALA 1 " 1.231 1.249 -0.018 2.50e+03 7.8
1e-01
pdb=" C ALA 1 " - pdb=" CA ALA 1 " 1.525 1.534 -0.009 2.27e+03 1.7
5e-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): 4.68146e-13
chirality_residual_sum (n=1): 0.0188403
planarity_residual_sum (n=1): 3.96226e-15
norm of gradients: 8.06482e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/gly.p
db
Monomer Library directory:
"/net/leafnose/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: 0.02, per 1000 atoms: 4.00
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/leafnose/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 res
idual
pdb=" CA GLY 1 " - pdb=" N GLY 1 " 1.451 1.491 -0.040 3.91e+03 6.3
1e+00
pdb=" C GLY 1 " - pdb=" O GLY 1 " 1.231 1.250 -0.019 2.50e+03 8.5
6e-01
pdb=" OXT GLY 1 " - pdb=" C GLY 1 " 1.231 1.249 -0.018 2.50e+03 7.9
5e-01
pdb=" C GLY 1 " - pdb=" CA GLY 1 " 1.516 1.524 -0.008 3.09e+03 2.1
0e-01
pdb=" CA GLY 1 " - pdb="HA2 GLY 1 " 0.970 0.970 0.000 2.50e+03 4.4
1e-04
pdb=" CA GLY 1 " - pdb="HA1 GLY 1 " 0.970 0.970 -0.000 2.50e+03 3.5
4e-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): 2.77979e-15
nonbonded_residual_sum (n=6): 0
angle_residual_sum (n=9): 0.13971
dihedral_residual_sum (n=1): 1.03248e-14
chirality_residual_sum (n=0): 0
planarity_residual_sum (n=1): 4.96267e-16
norm of gradients: 8.51012e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/his.p
db
Monomer Library directory:
"/net/leafnose/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: 0.03, per 1000 atoms: 2.73
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/leafnose/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: 0.03, per 1000 atoms: 1.67
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 res
idual
pdb=" CA HIS 1 " - pdb=" N HIS 1 " 1.458 1.505 -0.047 2.77e+03 6.2
0e+00
pdb=" CA HIS 1 " - pdb="HA HIS 1 " 0.980 1.028 -0.048 2.50e+03 5.6
6e+00
pdb=" CB HIS 1 " - pdb=" CA HIS 1 " 1.530 1.557 -0.027 2.50e+03 1.7
6e+00
pdb=" C HIS 1 " - pdb=" OXT HIS 1 " 1.231 1.250 -0.019 2.50e+03 9.0
7e-01
pdb=" C HIS 1 " - pdb=" O HIS 1 " 1.231 1.249 -0.018 2.50e+03 7.8
3e-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): 0.01
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): 0.0028426
nonbonded_residual_sum (n=87): 0.0382528
angle_residual_sum (n=30): 0.253362
dihedral_residual_sum (n=3): 0.025182
chirality_residual_sum (n=1): 0.0211127
planarity_residual_sum (n=2): 7.20954e-05
norm of gradients: 1.51136e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/ile.p
db
Monomer Library directory:
"/net/leafnose/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', 'HD
12', '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/leafnose/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: 0.03, per 1000 atoms: 1.50
Number of scatterers: 20
At special positions: 0
Unit cell: (10, 10, 10, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
O 2 8.00
N 1 7.00
C 6 6.00
H 10 1.00
? 1 0.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Time building geometry restraints manager: 0.01 seconds
Histogram of bond lengths:
0.96 - 1.09: 9
1.09 - 1.21: 1
1.21 - 1.34: 2
1.34 - 1.46: 0
1.46 - 1.59: 6
Bond restraints sorted by residual:
atom i - atom j ideal model delta weight res
idual
pdb=" CA ILE 1 " - pdb="HA ILE 1 " 0.980 1.117 -0.137 2.50e+03 4.7
1e+01
pdb=" CB ILE 1 " - pdb="HB ILE 1 " 0.970 1.035 -0.065 2.50e+03 1.0
7e+01
pdb=" CA ILE 1 " - pdb=" N ILE 1 " 1.458 1.506 -0.048 2.77e+03 6.3
3e+00
pdb=" CB ILE 1 " - pdb=" CA ILE 1 " 1.540 1.588 -0.048 1.37e+03 3.1
8e+00
pdb=" CB ILE 1 " - pdb=" CG1 ILE 1 " 1.530 1.565 -0.035 2.50e+03 3.0
8e+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): 0.0539856
nonbonded_residual_sum (n=131): 2.25277
angle_residual_sum (n=33): 0.944517
dihedral_residual_sum (n=5): 2.87315
chirality_residual_sum (n=2): 0.0320489
planarity_residual_sum (n=1): 0.00191259
norm of gradients: 1.2261e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/leu.p
db
Monomer Library directory:
"/net/leafnose/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: 0.03, per 1000 atoms: 3.33
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/leafnose/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: 0.01 seconds
Histogram of bond lengths:
0.96 - 1.08: 10
1.08 - 1.20: 0
1.20 - 1.32: 2
1.32 - 1.44: 0
1.44 - 1.56: 6
Bond restraints sorted by residual:
atom i - atom j ideal model delta weight res
idual
pdb=" CG LEU 1 " - pdb="HG LEU 1 " 0.970 1.055 -0.085 2.50e+03 1.8
1e+01
pdb=" CA LEU 1 " - pdb="HA LEU 1 " 0.980 1.032 -0.052 2.50e+03 6.7
2e+00
pdb=" CA LEU 1 " - pdb=" N LEU 1 " 1.458 1.503 -0.045 2.77e+03 5.5
2e+00
pdb=" CB LEU 1 " - pdb=" CG LEU 1 " 1.530 1.565 -0.035 2.50e+03 2.9
9e+00
pdb=" CB LEU 1 " - pdb=" CA LEU 1 " 1.530 1.563 -0.033 2.50e+03 2.6
8e+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): 0.0497748
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): 1.86362e-14
norm of gradients: 1.92114e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/phe.p
db
Monomer Library directory:
"/net/leafnose/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: 0.04, per 1000 atoms: 3.33
Residue name: PHE%COO PHE
Missing hydrogen atoms: ['HZ', 'HE2', 'HE1', 'HD1', 'H', 'HD2', 'HA', 'HB1', 'H
B2']
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/leafnose/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 res
idual
pdb=" CA PHE 1 " - pdb=" N PHE 1 " 1.458 1.491 -0.033 2.77e+03 3.0
5e+00
pdb=" CD2 PHE 1 " - pdb=" CE2 PHE 1 " 1.382 1.430 -0.048 1.11e+03 2.5
3e+00
pdb=" CD1 PHE 1 " - pdb=" CE1 PHE 1 " 1.382 1.430 -0.048 1.11e+03 2.5
1e+00
pdb=" CG PHE 1 " - pdb=" CD1 PHE 1 " 1.384 1.414 -0.030 2.27e+03 2.0
4e+00
pdb=" CA PHE 1 " - pdb="HA PHE 1 " 0.980 1.008 -0.028 2.50e+03 1.9
2e+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): 0.0368482
angle_residual_sum (n=33): 0.268212
dihedral_residual_sum (n=3): 0.0036681
chirality_residual_sum (n=1): 0.0190864
planarity_residual_sum (n=2): 4.26707e-15
norm of gradients: 1.48819e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/tyr.p
db
Monomer Library directory:
"/net/leafnose/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
Residue name: TYR%COO TYR
Missing hydrogen atoms: ['HE2', 'HE1', 'HD1', 'H', 'HH', 'HD2', 'HA', 'HB1', 'H
B2']
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/leafnose/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: 0.03, per 1000 atoms: 1.43
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 res
idual
pdb=" CA TYR 1 " - pdb=" N TYR 1 " 1.458 1.507 -0.049 2.77e+03 6.7
3e+00
pdb=" CA TYR 1 " - pdb="HA TYR 1 " 0.980 1.021 -0.041 2.50e+03 4.1
4e+00
pdb=" CD2 TYR 1 " - pdb=" CG TYR 1 " 1.389 1.429 -0.040 2.27e+03 3.6
9e+00
pdb=" CG TYR 1 " - pdb=" CD1 TYR 1 " 1.389 1.429 -0.040 2.27e+03 3.6
5e+00
pdb=" CZ TYR 1 " - pdb=" CE2 TYR 1 " 1.378 1.414 -0.036 1.74e+03 2.2
2e+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): 0.0318709
angle_residual_sum (n=34): 0.272515
dihedral_residual_sum (n=4): 0.00247108
chirality_residual_sum (n=1): 0.0191155
planarity_residual_sum (n=2): 5.49548e-05
norm of gradients: 9.61878e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/trp.p
db
Monomer Library directory:
"/net/leafnose/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: 0.04, per 1000 atoms: 2.67
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/leafnose/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: 0.03, per 1000 atoms: 1.25
Number of scatterers: 24
At special positions: 0
Unit cell: (10, 10, 10, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
O 2 8.00
N 2 7.00
C 11 6.00
H 9 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Time building geometry restraints manager: 0.01 seconds
Histogram of bond lengths:
0.86 - 1.00: 8
1.00 - 1.14: 1
1.14 - 1.27: 2
1.27 - 1.41: 4
1.41 - 1.55: 10
Bond restraints sorted by residual:
atom i - atom j ideal model delta weight res
idual
pdb=" CA TRP 1 " - pdb=" N TRP 1 " 1.458 1.507 -0.049 2.77e+03 6.7
8e+00
pdb=" CE3 TRP 1 " - pdb=" CD2 TRP 1 " 1.398 1.433 -0.035 3.91e+03 4.7
4e+00
pdb=" CA TRP 1 " - pdb="HA TRP 1 " 0.980 1.020 -0.040 2.50e+03 4.0
9e+00
pdb=" CZ2 TRP 1 " - pdb=" CH2 TRP 1 " 1.368 1.403 -0.035 2.77e+03 3.3
4e+00
pdb=" CZ2 TRP 1 " - pdb=" CE2 TRP 1 " 1.394 1.427 -0.033 2.27e+03 2.4
7e+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): 0.00652751
nonbonded_residual_sum (n=136): 0.00317817
angle_residual_sum (n=42): 0.252815
dihedral_residual_sum (n=3): 6.65921e-07
chirality_residual_sum (n=1): 0.0192505
planarity_residual_sum (n=2): 5.89282e-15
norm of gradients: 9.03878e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/thr.p
db
Monomer Library directory:
"/net/leafnose/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/leafnose/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 res
idual
pdb=" CB THR 1 " - pdb="HB THR 1 " 0.970 1.029 -0.059 2.50e+03 8.8
1e+00
pdb=" CA THR 1 " - pdb=" N THR 1 " 1.458 1.508 -0.050 2.77e+03 6.8
7e+00
pdb=" CA THR 1 " - pdb="HA THR 1 " 0.980 1.031 -0.051 2.50e+03 6.6
0e+00
pdb=" C THR 1 " - pdb=" OXT THR 1 " 1.231 1.250 -0.019 2.50e+03 8.8
9e-01
pdb=" C THR 1 " - pdb=" O THR 1 " 1.231 1.250 -0.019 2.50e+03 8.6
6e-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): 0.0106858
angle_residual_sum (n=21): 0.279242
dihedral_residual_sum (n=3): 0.00149726
chirality_residual_sum (n=2): 0.0234672
planarity_residual_sum (n=1): 6.63118e-17
norm of gradients: 1.15395e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/val.p
db
Monomer Library directory:
"/net/leafnose/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: VAL%COO VAL
Missing hydrogen atoms: ['HG22', 'H', 'HG21', 'HG11', 'HG12', 'HG13', 'HB', 'HG
23', '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/leafnose/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: 0.03, per 1000 atoms: 1.88
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 res
idual
pdb=" CA VAL 1 " - pdb="HA VAL 1 " 0.980 1.091 -0.111 2.50e+03 3.0
7e+01
pdb=" CA VAL 1 " - pdb=" N VAL 1 " 1.458 1.505 -0.047 2.77e+03 6.1
7e+00
pdb=" CB VAL 1 " - pdb="HB VAL 1 " 0.980 1.026 -0.046 2.50e+03 5.2
2e+00
pdb=" CB VAL 1 " - pdb=" CA VAL 1 " 1.540 1.581 -0.041 1.37e+03 2.3
0e+00
pdb=" C VAL 1 " - pdb=" O VAL 1 " 1.231 1.250 -0.019 2.50e+03 9.1
3e-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): 0.00177693
nonbonded_residual_sum (n=74): 0.184628
angle_residual_sum (n=27): 0.241823
dihedral_residual_sum (n=4): 0.0197402
chirality_residual_sum (n=2): 0.0155555
planarity_residual_sum (n=1): 2.97164e-05
norm of gradients: 1.22773e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/cys.p
db
Monomer Library directory:
"/net/leafnose/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: 0.02, per 1000 atoms: 2.86
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/leafnose/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 res
idual
pdb=" CA CYS 1 " - pdb="HA CYS 1 " 0.980 1.072 -0.092 2.50e+03 2.1
2e+01
pdb=" CA CYS 1 " - pdb=" N CYS 1 " 1.458 1.506 -0.048 2.77e+03 6.4
4e+00
pdb=" CB CYS 1 " - pdb=" CA CYS 1 " 1.530 1.561 -0.031 2.50e+03 2.4
7e+00
pdb=" C CYS 1 " - pdb=" OXT CYS 1 " 1.231 1.250 -0.019 2.50e+03 9.0
5e-01
pdb=" C CYS 1 " - pdb=" O CYS 1 " 1.231 1.249 -0.018 2.50e+03 8.4
6e-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): 5.90648e-05
angle_residual_sum (n=16): 0.2772
dihedral_residual_sum (n=3): 4.2592e-07
chirality_residual_sum (n=1): 0.0192382
planarity_residual_sum (n=1): 4.57174e-15
norm of gradients: 7.49218e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/leafnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/ser.p
db
Monomer Library directory:
"/net/leafnose/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: 0.02, per 1000 atoms: 2.86
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/leafnose/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 res
idual
pdb=" CA SER 1 " - pdb=" N SER 1 " 1.458 1.504 -0.046 2.77e+03 5.8
6e+00
pdb=" CA SER 1 " - pdb="HA SER 1 " 0.980 1.027 -0.047 2.50e+03 5.5
0e+00
pdb=" C SER 1 " - pdb=" OXT SER 1 " 1.231 1.249 -0.018 2.50e+03 8.0
6e-01
pdb=" C SER 1 " - pdb=" O SER 1 " 1.231 1.249 -0.018 2.50e+03 7.7
5e-01
pdb=" CB SER 1 " - pdb=" CA SER 1 " 1.530 1.545 -0.015 2.50e+03 5.7
8e-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): 0.00103527
nonbonded_residual_sum (n=29): 0.230399
angle_residual_sum (n=16): 0.246422
dihedral_residual_sum (n=3): 0.00957633
chirality_residual_sum (n=1): 0.0145721
planarity_residual_sum (n=1): 1.93827e-15
norm of gradients: 6.42944e-06
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/max_lik/tst_m
axlik.py
u+s,u,s: 20.28 20.15 0.13 micro-seconds/tick: 3.860
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/masks/tst_mas
ks.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: 12.84 11.90 0.94 micro-seconds/tick: 7.330
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/max_lik/tst_m
ax_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: 24.86 24.30 0.56 micro-seconds/tick: 3.546
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: 75.74 72.33 3.41 micro-seconds/tick: 10.100
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/dynamics/tst_
cartesian_dynamics.py
u+s,u,s: 3.81 3.69 0.12 micro-seconds/tick: 0.959
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/tls/tst_tls.p
y
|-----------------------------------------------------------------------------|
|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: 769.59 769.19 0.40 micro-seconds/tick: 29.759
libtbx.python /net/leafnose/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 = 2021
branch_1 = 7979
branch_1_1 = 2478
branch_1_2 = 5501
branch_1_2_1 = 254
branch_1_2_2 = 1996
branch_1_2_3 = 3251
branch_1_2_3_1 = 1450
branch_1_2_3_2 = 1801
.............................. P 1
i= 20000 out of 100000
branch_0 = 4011
branch_1 = 15989
branch_1_1 = 4979
branch_1_2 = 11010
branch_1_2_1 = 466
branch_1_2_2 = 3961
branch_1_2_3 = 6583
branch_1_2_3_1 = 3033
branch_1_2_3_2 = 3550
.............................. P 1
i= 30000 out of 100000
branch_0 = 6028
branch_1 = 23972
branch_1_1 = 7510
branch_1_2 = 16462
branch_1_2_1 = 684
branch_1_2_2 = 6021
branch_1_2_3 = 9757
branch_1_2_3_1 = 4513
branch_1_2_3_2 = 5244
.............................. P 1
i= 40000 out of 100000
branch_0 = 7994
branch_1 = 32006
branch_1_1 = 10037
branch_1_2 = 21969
branch_1_2_1 = 895
branch_1_2_2 = 8024
branch_1_2_3 = 13050
branch_1_2_3_1 = 6029
branch_1_2_3_2 = 7021
.............................. P 1
i= 50000 out of 100000
branch_0 = 10044
branch_1 = 39956
branch_1_1 = 12475
branch_1_2 = 27481
branch_1_2_1 = 1119
branch_1_2_2 = 10047
branch_1_2_3 = 16315
branch_1_2_3_1 = 7529
branch_1_2_3_2 = 8786
.............................. P 1
i= 60000 out of 100000
branch_0 = 12023
branch_1 = 47977
branch_1_1 = 14922
branch_1_2 = 33055
branch_1_2_1 = 1347
branch_1_2_2 = 12083
branch_1_2_3 = 19625
branch_1_2_3_1 = 8898
branch_1_2_3_2 = 10727
.............................. P 1
i= 70000 out of 100000
branch_0 = 14023
branch_1 = 55977
branch_1_1 = 17321
branch_1_2 = 38656
branch_1_2_1 = 1579
branch_1_2_2 = 14113
branch_1_2_3 = 22964
branch_1_2_3_1 = 10285
branch_1_2_3_2 = 12679
.............................. P 1
i= 80000 out of 100000
branch_0 = 16041
branch_1 = 63959
branch_1_1 = 19746
branch_1_2 = 44213
branch_1_2_1 = 1799
branch_1_2_2 = 16150
branch_1_2_3 = 26264
branch_1_2_3_1 = 11646
branch_1_2_3_2 = 14618
.............................. P 1
i= 90000 out of 100000
branch_0 = 17992
branch_1 = 72008
branch_1_1 = 22255
branch_1_2 = 49753
branch_1_2_1 = 2042
branch_1_2_2 = 18141
branch_1_2_3 = 29570
branch_1_2_3_1 = 13000
branch_1_2_3_2 = 16570
.............................. P 1
i= 100000 out of 100000
branch_0 = 20018
branch_1 = 79982
branch_1_1 = 24732
branch_1_2 = 55250
branch_1_2_1 = 2257
branch_1_2_2 = 20129
branch_1_2_3 = 32864
branch_1_2_3_1 = 14319
branch_1_2_3_2 = 18545
..............................
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 = 1267
branch_1_2_3_2 = 787
..............................
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 = 2552
branch_1_2_3_2 = 1523
..............................
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 = 3853
branch_1_2_3_2 = 2292
..............................
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 = 5122
branch_1_2_3_2 = 3039
..............................
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 = 6366
branch_1_2_3_2 = 3820
..............................
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 1.34288e-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 -8.13786e-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 = 8707
branch_1_2_3_2 = 5608
..............................
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 = 9832
branch_1_2_3_2 = 6456
***********************************************
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 1.80892e-15
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 = 10960
branch_1_2_3_2 = 7386
..............................
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: 79.27 79.13 0.14 micro-seconds/tick: 0.449
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/tls/tst_tls_r
efinement_fft.py
random_seed: 2093839616
|-----------------------------------------------------------------------------|
| 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 4.2271e-31 1.8939e-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= 0.4866 r_free= 0.4678 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: -0.00 A |
| x-ray target function (ls_wunit_k1) for work reflections: 0.163603 |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| 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 0.4866 0.4678 26.919 25.727|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|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 0.33 64.20 1.07 1.01 42.11|
|alpha: min = 1.01 max = 1.01 mean = 1.01|
|beta: min = 42.11 max = 42.11 mean = 42.11|
|figures of merit: min = 0.00 max = 1.00 mean = 0.33|
|phase err.(work): min = 0.00 max = 89.98 mean = 64.20|
|phase err.(test): min = 7.46 max = 89.90 mean = 58.18|
|-----------------------------------------------------------------------------|
********************************************************************************
None
|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 0.163603 r_work = 0.4866 r_free = 0.4678 |
|-----------------------------------------------------------------------------|
|-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= 0.2670 T22= 0.2959 T33= 0.2992 T12= 0.0149 T13= 0.0003 T23= -0.0148|
|L11= 2.0000 L22= 2.0000 L33= 2.0000 L12= 2.0000 L13= 2.0000 L23= 2.0000|
|S11= 0.1687 S22= -0.3098 S33= 0.1412 S12= -0.1068 S13= -0.0205 S21= -0.0349|
|S23= -0.1993 S31= -0.0256 S32= 0.2990 |
|TLS group number 2: |
| Origin (x,y,z) = 10.8834 4.8200 7.3685 |
|T11= 0.2757 T22= 0.2587 T33= 0.3011 T12= 0.0313 T13= -0.0035 T23= -0.0170|
|L11= 2.0000 L22= 2.0000 L33= 2.0000 L12= 2.0000 L13= 2.0000 L23= 2.0000|
|S11= -0.0276 S22= -0.1927 S33= 0.2203 S12= -0.2461 S13= -0.1469 S21= -0.1911|
|S23= -0.2213 S31= 0.0538 S32= 0.4457 |
|TLS group number 3: |
| Origin (x,y,z) = 10.4142 10.1560 8.5901 |
|T11= 0.2991 T22= 0.2856 T33= 0.3089 T12= 0.0149 T13= -0.0018 T23= -0.0091|
|L11= 2.0000 L22= 2.0000 L33= 2.0000 L12= 2.0000 L13= 2.0000 L23= 2.0000|
|S11= 0.0041 S22= -0.1078 S33= 0.1038 S12= -0.1810 S13= -0.0813 S21= -0.1046|
|S23= -0.1072 S31= 0.0222 S32= 0.2493 |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 0 aniso = 36 pos. def. = 36 non-pos. def. = 0 |
| Total B(isotropic equivalent): min = 16.30 max = 23.47 mean = 19.64 |
| Isotropic B only: min = 16.30 max = 23.47 mean = 19.64 |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Distribution of isotropic B-factors: |
| Isotropic | Total |
| 16.303 - 17.019: 4 | 16.303 - 17.019: 4 |
| 17.019 - 17.735: 8 | 17.019 - 17.735: 8 |
| 17.735 - 18.452: 1 | 17.735 - 18.452: 1 |
| 18.452 - 19.168: 7 | 18.452 - 19.168: 7 |
| 19.168 - 19.884: 4 | 19.168 - 19.884: 4 |
| 19.884 - 20.600: 0 | 19.884 - 20.600: 0 |
| 20.600 - 21.317: 0 | 20.600 - 21.317: 0 |
| 21.317 - 22.033: 0 | 21.317 - 22.033: 0 |
| 22.033 - 22.749: 2 | 22.033 - 22.749: 2 |
| 22.749 - 23.465: 10 | 22.749 - 23.465: 10 |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1: |
| Origin (x,y,z) = 5.4095 5.5841 7.5222 |
|T11= 0.1363 T22= 0.2325 T33= 0.2676 T12= 0.0864 T13= 0.0707 T23= 0.1243|
|L11= 2.0000 L22= 1.9999 L33= 1.9998 L12= 1.9999 L13= 1.9999 L23= 1.9997|
|S11= 0.1699 S22= -0.3109 S33= 0.1412 S12= -0.1075 S13= -0.0202 S21= -0.0302|
|S23= -0.1994 S31= -0.0204 S32= 0.2982 |
|TLS group number 2: |
| Origin (x,y,z) = 10.8834 4.8200 7.3685 |
|T11= 0.1878 T22= 0.2215 T33= 0.2983 T12= 0.1284 T13= 0.0426 T23= 0.1499|
|L11= 2.0000 L22= 1.9999 L33= 1.9999 L12= 1.9997 L13= 1.9999 L23= 1.9997|
|S11= -0.0263 S22= -0.1924 S33= 0.2203 S12= -0.2461 S13= -0.1458 S21= -0.1896|
|S23= -0.2226 S31= 0.0555 S32= 0.4453 |
|TLS group number 3: |
| Origin (x,y,z) = 10.4142 10.1560 8.5901 |
|T11= 0.2589 T22= 0.2784 T33= 0.3231 T12= 0.0751 T13= 0.0448 T23= 0.1258|
|L11= 2.0001 L22= 2.0000 L33= 1.9999 L12= 1.9998 L13= 1.9999 L23= 1.9998|
|S11= 0.0043 S22= -0.1086 S33= 0.1038 S12= -0.1810 S13= -0.0803 S21= -0.1030|
|S23= -0.1077 S31= 0.0236 S32= 0.2489 |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 0.0460934 r_work = 0.2573 r_free = 0.2333 |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1: |
| Origin (x,y,z) = 5.4095 5.5841 7.5222 |
|T11= 0.1363 T22= 0.2325 T33= 0.2676 T12= 0.0864 T13= 0.0707 T23= 0.1243|
|L11= 2.0000 L22= 1.9999 L33= 1.9998 L12= 1.9999 L13= 1.9999 L23= 1.9997|
|S11= 0.1699 S22= -0.3109 S33= 0.1412 S12= -0.1075 S13= -0.0202 S21= -0.0302|
|S23= -0.1994 S31= -0.0204 S32= 0.2982 |
|TLS group number 2: |
| Origin (x,y,z) = 10.8834 4.8200 7.3685 |
|T11= 0.1878 T22= 0.2215 T33= 0.2983 T12= 0.1284 T13= 0.0426 T23= 0.1499|
|L11= 2.0000 L22= 1.9999 L33= 1.9999 L12= 1.9997 L13= 1.9999 L23= 1.9997|
|S11= -0.0263 S22= -0.1924 S33= 0.2203 S12= -0.2461 S13= -0.1458 S21= -0.1896|
|S23= -0.2226 S31= 0.0555 S32= 0.4453 |
|TLS group number 3: |
| Origin (x,y,z) = 10.4142 10.1560 8.5901 |
|T11= 0.2589 T22= 0.2784 T33= 0.3231 T12= 0.0751 T13= 0.0448 T23= 0.1258|
|L11= 2.0001 L22= 2.0000 L33= 1.9999 L12= 1.9998 L13= 1.9999 L23= 1.9998|
|S11= 0.0043 S22= -0.1086 S33= 0.1038 S12= -0.1810 S13= -0.0803 S21= -0.1030|
|S23= -0.1077 S31= 0.0236 S32= 0.2489 |
|-----------------------------------------------------------------------------|
u+s,u,s: 9.61 9.46 0.15 micro-seconds/tick: 2.470
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/examples/f_mo
del_manager.py
|--(resolution: 2.00 - 36.80 A; n_refl. = 7168)-------------------------------|
| |
| r_work= 0.2621 r_free= 0.2792 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: 0.22 A |
| x-ray target function (ml) for work reflections: 5.052736 |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| Bin Resolution Compl. No. Refl. R-factors Targets |
|number range work test work test work test|
| 1: 36.8046 - 3.4193 1.00 1358 165 0.2564 0.2939 5.441 5.4182|
| 2: 3.4193 - 2.7143 1.00 1311 124 0.2549 0.2438 5.1643 5.193|
| 3: 2.7143 - 2.3713 1.00 1250 164 0.2596 0.2706 4.9791 4.9755|
| 4: 2.3713 - 2.1545 1.00 1269 136 0.2722 0.2917 4.8929 4.986|
| 5: 2.1545 - 2.0001 1.00 1263 128 0.2768 0.2919 4.753 4.7312|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|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 1358 165 0.81 24.06 1.00 0.93 7320.26|
| 2: 3.4193 - 2.7143 1311 124 0.81 24.88 1.00 0.95 4735.59|
| 3: 2.7143 - 2.3713 1250 164 0.82 24.23 0.98 0.96 3084.67|
| 4: 2.3713 - 2.1545 1269 136 0.81 25.48 1.01 0.94 2375.10|
| 5: 2.1545 - 2.0001 1263 128 0.81 25.77 0.99 0.94 1849.14|
|alpha: min = 0.93 max = 0.96 mean = 0.94|
|beta: min = 1849.14 max = 7320.26 mean = 3930.33|
|figures of merit: min = 0.00 max = 1.00 mean = 0.81|
|phase err.(work): min = 0.00 max = 89.94 mean = 24.88|
|phase err.(test): min = 0.00 max = 89.24 mean = 25.53|
|-----------------------------------------------------------------------------|
0.26210769558
0.279155407752
|--(resolution: 2.00 - 36.80 A; n_refl. = 7168)-------------------------------|
| |
| r_work= 0.2621 r_free= 0.2792 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: 0.22 A |
| x-ray target function (ml) for work reflections: 5.052736 |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| Bin Resolution Compl. No. Refl. R-factors Targets |
|number range work test work test work test|
| 1: 36.8046 - 3.4193 1.00 1358 165 0.2564 0.2939 5.441 5.4182|
| 2: 3.4193 - 2.7143 1.00 1311 124 0.2549 0.2438 5.1643 5.193|
| 3: 2.7143 - 2.3713 1.00 1250 164 0.2596 0.2706 4.9791 4.9755|
| 4: 2.3713 - 2.1545 1.00 1269 136 0.2722 0.2917 4.8929 4.986|
| 5: 2.1545 - 2.0001 1.00 1263 128 0.2768 0.2919 4.753 4.7312|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|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 1358 165 0.81 24.06 1.00 0.93 7320.26|
| 2: 3.4193 - 2.7143 1311 124 0.81 24.88 1.00 0.95 4735.59|
| 3: 2.7143 - 2.3713 1250 164 0.82 24.23 0.98 0.96 3084.67|
| 4: 2.3713 - 2.1545 1269 136 0.81 25.48 1.01 0.94 2375.10|
| 5: 2.1545 - 2.0001 1263 128 0.81 25.77 0.99 0.94 1849.14|
|alpha: min = 0.93 max = 0.96 mean = 0.94|
|beta: min = 1849.14 max = 7320.26 mean = 3930.33|
|figures of merit: min = 0.00 max = 1.00 mean = 0.81|
|phase err.(work): min = 0.00 max = 89.94 mean = 24.88|
|phase err.(test): min = 0.00 max = 89.24 mean = 25.53|
|-----------------------------------------------------------------------------|
|--(resolution: 2.00 - 36.80 A; n_refl. = 7168)-------------------------------|
| |
| r_work= 0.5079 r_free= 0.5423 ksol= 1.20 Bsol= 30.00 scale= 0.612 |
| |
| 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 (ml) for work reflections: 5.290916 |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| Bin Resolution Compl. No. Refl. R-factors Targets |
|number range work test work test work test|
| 1: 36.8046 - 3.4193 1.00 1358 165 0.6164 0.6518 5.9611 5.7869|
| 2: 3.4193 - 2.7143 1.00 1311 124 0.3818 0.3494 5.571 5.6129|
| 3: 2.7143 - 2.3713 1.00 1250 164 0.2795 0.3023 5.1723 5.2016|
| 4: 2.3713 - 2.1545 1.00 1269 136 0.2799 0.2942 4.9155 5.005|
| 5: 2.1545 - 2.0001 1.00 1263 128 0.2822 0.2829 4.7742 4.729|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|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 1358 165 0.32 64.82 0.46 0.30 26709.72|
| 2: 3.4193 - 2.7143 1311 124 0.52 49.74 1.28 0.81 13677.47|
| 3: 2.7143 - 2.3713 1250 164 0.75 31.15 0.90 0.98 5614.46|
| 4: 2.3713 - 2.1545 1269 136 0.79 27.23 0.86 0.82 2762.07|
| 5: 2.1545 - 2.0001 1263 128 0.81 25.31 0.86 0.81 1811.55|
|alpha: min = 0.30 max = 0.98 mean = 0.74|
|beta: min = 1811.55 max = 26709.72 mean = 10388.17|
|figures of merit: min = 0.00 max = 1.00 mean = 0.63|
|phase err.(work): min = 0.00 max = 89.99 mean = 40.10|
|phase err.(test): min = 0.00 max = 89.96 mean = 40.87|
|-----------------------------------------------------------------------------|
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/bulk_solvent/
tst_bulk_solvent_and_scaling.py
OK: u+s,u,s: 241.38 232.62 8.76 micro-seconds/tick: 9.000
libtbx.python /net/leafnose/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
mmmmmmmmmmmmmmmmmmmmmmmdmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmmdmmmmmdmmmmmmmmmmmmmmm
mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmmiiii
AESSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNGRNNCHKSSSTLR
ITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV----
**| | || |* ***** ||* *|*|*|*| **|| *|||*|* ***||| *** * |*| * | |***
*| |*| |*| | |*| *|** *****||* | *|||*| |*
DNSRYTHFLTQHYDAKPQGRDDR-YCESIMRRRGLT-SPCKDINTFIHGNKRSIKAIC-ENKNG-NPHRENLRISKSSFQ
VTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSIFRRP
1rra vs. 1bli; LOCAL allignment; mdm78
score=2009.0
mmmmmmmmmmmmmmmmdmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmmdmmmmmdmmmmmmmmmmmmmmmmmmmmmm
mmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmm
FKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNGRNNCHKSSSTLRITDCRLK
GSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV
| || |* ***** ||* *|*|*|*| **|| *|||*|* ***||| *** * |*| * | |****| |*|
|*| | |*| *|** *****||* | *|||*| |*
FLTQHYDAKPQGRDDR-YCESIMRRRGLT-SPCKDINTFIHGNKRSIKAIC-ENKNG-NPHRENLRISKSSFQVTTCKLH
GGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSI
1rra vs. 1bli; GLOBAL allignment; blosum50
score=267.0
mmmmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmddddmmmiiimmmmmmmmm
mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmmiiii
AESSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNG---RNNCHKSSS
TLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV----
| | || | * | || *|*|*|*| || *|||*| **||| * ||| | | | |
****| |*| | | *| | | | *****||* | *|||*| |*
DNSRYTHFLTQHYDAK-PQGRDDRYCESIMRRRGLTS-PCKDINTFIHGNKRSIKAIC-EN----KNGNPHRENLRISKS
SFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSIFRRP
1rra vs. 1bli; LOCAL allignment; blosum50
score=287.0
mmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmddddmmmiiimmmmmmmmmmm
mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmm
SSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNG---RNNCHKSSSTL
RITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV
| | || | * | || *|*|*|*| || *|||*| **||| * ||| | | | |**
**| |*| | | *| | | | *****||* | *|||*| |*
SRYTHFLTQHYDAK-PQGRDDRYCESIMRRRGLTS-PCKDINTFIHGNKRSIKAIC-EN----KNGNPHRENLRISKSSF
QVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-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/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/invariant_dom
ain.py
OK
libtbx.python /net/leafnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_bioinform
atics.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 0.012s
OK
endif
endif
libtbx.show_date_and_time -v
Date 2009-02-22 Time 23:47:03 PST -0800 (1235375223.45 s) Seconds since the Epoc
h 1235375223.45