[phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS
Jan Gebauer
jan.gebauer at uni-koeln.de
Thu Oct 31 08:48:01 PDT 2013
Dear all,
I'm trying to get rosetta_refine working on ubuntu 12.04 LTS.
This was the (latest) way I tried it:
1) Downloaded phenix-dev-1523 binary & installed it via installer in
/usr/local/science/phenix4rosetta/phenix-dev-1523
2) Downloaded rosetta 2031wk42 and extracted it in
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle
3) Inserted into phenix_env.sh
export
ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin
export
PHENIX_ROSETTA_PATH=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/
export
ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/database
4) sources phenix_env.sh
5) build the interface via
rosetta.build_phenix_interface nproc=4
6) exceute the refinement via phenix.rosetta_refine phasermodel.pdb
data.mtz nproc=4
The programm runs fine, up to the point where it should generate models
via rosetta, it then stops and crashes.
I have attached some logfiles
Has anyone managed to run rosetta_refine on Ubuntu? Which phenix and
rosetta versions did you use? Ist there anything wrong on my above
mentioned build protocol?
I'm thankful for any help.
Regards,
Jan Gebauer
--
Dr. Jan Gebauer
AG Prof. Baumann
Institut für Biochemie / Uni-Köln
Otto-Fischer-Str. 12-14 / 50674 Köln
Fon: +49 (221) 470 3212
Fax: +49 (221) 470 5066
http://px.uni-koeln.de/
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Output directory:
/home/gebauer/tmp/rosetta_6
=========================== Importing data and flags ==========================
WARNING: data are incomplete (73.9% of possible reflections measured to
3.52A). This may cause problems if you plan to use the maps for building
and/or ligand fitting!
----------Setting up input files for Rosetta----------
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source
----------Loading model and data----------
=========================== ROSETTA X-ray refinement ==========================
|-starting model--------------------------------------------------------------|
| target_work(ml) = 7.62563 r_work = 0.4769 r_free = 0.4887 |
|-----------------------------------------------------------------------------|
Validation statistics (starting model):
Ramachandran outliers = 0.27 %
favored = 95.25 %
Rotamer outliers = 9.45 %
C-beta deviations = 20
Clashscore = 14.46
Molprobity score = 2.74
Generating 5 models on 4 processors...
DEBUG dumping error message
ERROR: Rosetta exited with status 1
stderr output:
show_stack(1): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/boost_adaptbx/boost/python.py(25) import_ext
show_stack(2): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/scitbx/math/ext.py(6) <module>
show_stack(3): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/scitbx/math/__init__.py(2) <module>
show_stack(4): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/cctbx/maptbx/__init__.py(17) <module>
show_stack(5): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/cctbx/miller/__init__.py(10) <module>
show_stack(6): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/mmtbx/utils/__init__.py(2) <module>
show_stack(7): /usr/local/science/phenix4rosetta/phenix-dev-1523/phenix/phenix/rosetta/xray_target.py(3) <module>
libc backtrace (106 frames, most recent call last):
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x401e31]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fad8d97c76d]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x401c7e]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(utility::pointer::owning_ptr<protocols::moves::Mover>)+0x35) [0x7fad8f0239b5]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(utility::pointer::owning_ptr<protocols::moves::Mover>)+0xbdb) [0x7fad8f04abcb]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x27e) [0x7fad8efd075e]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> > const*, std::vector<std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> >, std::allocator<std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> > > > >)+0x30) [0x7fad8efcfda0]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover_filter_pair(core::pose::Pose&, std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> > const&)+0x126) [0x7fad8efcf916]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.6.so(protocols::cryst::TagPoseWithRefinementStatsMover::apply(core::pose::Pose&)+0x27) [0x7fad8797d9c7]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libcore.3.so(core::scoring::cryst::PhenixInterface::getScore(core::pose::Pose const&)+0x1a6) [0x7fad8a3a0686]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libcore.3.so(core::scoring::cryst::PhenixInterface::initialize_target_evaluator(core::pose::Pose const&, std::string)+0x5bc) [0x7fad8a39cf4c]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_Import+0xbd) [0x7fad8508b4dd]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_CallFunction+0x7e) [0x7fad84fcc8fe]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x4c82b) [0x7fad84fcc82b]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x324) [0x7fad8508ac04]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a700) [0x7fad8508a700]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x324) [0x7fad8508ac04]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a700) [0x7fad8508a700]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x57f8) [0x7fad850703a8]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x59dd) [0x7fad8507058d]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1da) [0x7fad8508aaba]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x98) [0x7fad8508c028]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(_PyImport_GetDynLoadFunc+0x12d) [0x7fad850a56dd]
/lib/x86_64-linux-gnu/libdl.so.2(dlopen+0x31) [0x7fad8483cfc1]
/lib/x86_64-linux-gnu/libdl.so.2(+0x152f) [0x7fad8483d52f]
/lib64/ld-linux-x86-64.so.2(+0xf176) [0x7fad8feb9176]
/lib/x86_64-linux-gnu/libdl.so.2(+0xf26) [0x7fad8483cf26]
/lib64/ld-linux-x86-64.so.2(+0x1331a) [0x7fad8febd31a]
/lib64/ld-linux-x86-64.so.2(+0xf176) [0x7fad8feb9176]
/lib64/ld-linux-x86-64.so.2(+0x13ada) [0x7fad8febdada]
/lib64/ld-linux-x86-64.so.2(+0xf3df) [0x7fad8feb93df]
/lib64/ld-linux-x86-64.so.2(+0xf306) [0x7fad8feb9306]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(+0x17f799) [0x7fad77433799]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(boost::math::detail::erf_inv_initializer<long double, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> >::init::do_init()+0x12) [0x7fad7751ab92]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(+0x259c7a) [0x7fad7750dc7a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(long double boost::math::detail::erf_inv_imp<long double, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> >(long double const&, long double const&, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> const&, mpl_::int_<64> const*)+0x3a7) [0x7fad77514747]
/lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7fad8d9914a0]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/boost_python_meta_ext.so(init_module_boost_python_meta_ext()+0) [0x7fad7db89250]
Segmentation fault (Python and libc call stacks above)
This crash may be due to a problem in any imported
Python module, including modules which are not part
of the cctbx project. To disable the traps leading
to this message, define these environment variables
(e.g. assign the value 1):
BOOST_ADAPTBX_FPE_DEFAULT
BOOST_ADAPTBX_SIGNALS_DEFAULT
This will NOT solve the problem, just mask it, but
may allow you to proceed in case it is not critical.
Traceback (most recent call last):
File "/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/rosetta_refine.py", line 350, in <module>
run(sys.argv[1:], create_dir=True)
File "/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/rosetta_refine.py", line 347, in run
create_dir=create_dir)
File "/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/rosetta_refine.py", line 141, in __init__
self.run_rosetta_scripts()
File "/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/rosetta_refine.py", line 199, in run_rosetta_scripts
debug=self.params.runtime.debug)
File "/usr/local/science/phenix4rosetta/phenix-dev-1523/phenix/phenix/rosetta/refine.py", line 307, in __init__
self.run_jobs()
File "/usr/local/science/phenix4rosetta/phenix-dev-1523/phenix/phenix/rosetta/refine.py", line 381, in run_jobs
check_result(result)
File "/usr/local/science/phenix4rosetta/phenix-dev-1523/phenix/phenix/rosetta/refine.py", line 363, in check_result
raise RuntimeError("Aborted due to error in job %d." % result.job_id)
RuntimeError: Aborted due to error in job 1.
-------------- next part --------------
show_stack(1): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/boost_adaptbx/boost/python.py(25) import_ext
show_stack(2): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/scitbx/math/ext.py(6) <module>
show_stack(3): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/scitbx/math/__init__.py(2) <module>
show_stack(4): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/cctbx/maptbx/__init__.py(17) <module>
show_stack(5): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/cctbx/miller/__init__.py(10) <module>
show_stack(6): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/mmtbx/utils/__init__.py(2) <module>
show_stack(7): /usr/local/science/phenix4rosetta/phenix-dev-1523/phenix/phenix/rosetta/xray_target.py(3) <module>
libc backtrace (106 frames, most recent call last):
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x401e31]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fad8d97c76d]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x401c7e]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(utility::pointer::owning_ptr<protocols::moves::Mover>)+0x35) [0x7fad8f0239b5]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(utility::pointer::owning_ptr<protocols::moves::Mover>)+0xbdb) [0x7fad8f04abcb]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x27e) [0x7fad8efd075e]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> > const*, std::vector<std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> >, std::allocator<std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> > > > >)+0x30) [0x7fad8efcfda0]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover_filter_pair(core::pose::Pose&, std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> > const&)+0x126) [0x7fad8efcf916]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.6.so(protocols::cryst::TagPoseWithRefinementStatsMover::apply(core::pose::Pose&)+0x27) [0x7fad8797d9c7]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libcore.3.so(core::scoring::cryst::PhenixInterface::getScore(core::pose::Pose const&)+0x1a6) [0x7fad8a3a0686]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libcore.3.so(core::scoring::cryst::PhenixInterface::initialize_target_evaluator(core::pose::Pose const&, std::string)+0x5bc) [0x7fad8a39cf4c]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_Import+0xbd) [0x7fad8508b4dd]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_CallFunction+0x7e) [0x7fad84fcc8fe]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x4c82b) [0x7fad84fcc82b]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x324) [0x7fad8508ac04]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a700) [0x7fad8508a700]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x324) [0x7fad8508ac04]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a700) [0x7fad8508a700]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x57f8) [0x7fad850703a8]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x59dd) [0x7fad8507058d]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1da) [0x7fad8508aaba]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x98) [0x7fad8508c028]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(_PyImport_GetDynLoadFunc+0x12d) [0x7fad850a56dd]
/lib/x86_64-linux-gnu/libdl.so.2(dlopen+0x31) [0x7fad8483cfc1]
/lib/x86_64-linux-gnu/libdl.so.2(+0x152f) [0x7fad8483d52f]
/lib64/ld-linux-x86-64.so.2(+0xf176) [0x7fad8feb9176]
/lib/x86_64-linux-gnu/libdl.so.2(+0xf26) [0x7fad8483cf26]
/lib64/ld-linux-x86-64.so.2(+0x1331a) [0x7fad8febd31a]
/lib64/ld-linux-x86-64.so.2(+0xf176) [0x7fad8feb9176]
/lib64/ld-linux-x86-64.so.2(+0x13ada) [0x7fad8febdada]
/lib64/ld-linux-x86-64.so.2(+0xf3df) [0x7fad8feb93df]
/lib64/ld-linux-x86-64.so.2(+0xf306) [0x7fad8feb9306]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(+0x17f799) [0x7fad77433799]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(boost::math::detail::erf_inv_initializer<long double, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> >::init::do_init()+0x12) [0x7fad7751ab92]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(+0x259c7a) [0x7fad7750dc7a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(long double boost::math::detail::erf_inv_imp<long double, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> >(long double const&, long double const&, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> const&, mpl_::int_<64> const*)+0x3a7) [0x7fad77514747]
/lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7fad8d9914a0]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/boost_python_meta_ext.so(init_module_boost_python_meta_ext()+0) [0x7fad7db89250]
Segmentation fault (Python and libc call stacks above)
This crash may be due to a problem in any imported
Python module, including modules which are not part
of the cctbx project. To disable the traps leading
to this message, define these environment variables
(e.g. assign the value 1):
BOOST_ADAPTBX_FPE_DEFAULT
BOOST_ADAPTBX_SIGNALS_DEFAULT
This will NOT solve the problem, just mask it, but
may allow you to proceed in case it is not critical.
-------------- next part --------------
core.init: Rosetta version unknown from unknown
core.init: command: /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease -parser:protocol /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s phasermodel_in.pdb -mtzfile /home/gebauer/tmp/rosetta_6/phasermodel_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=phasermodel.symm -set_weights cart_bonded 0.5 pro_close 0 -nstruct 1 -out:suffix _1
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1830876912 seed_offset=0 real_seed=1830876912
core.init.random: RandomGenerator:init: Normal mode, seed=1830876912 RG_type=mt19937
core.init: found database environment variable ROSETTA3_DB: /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/database
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed phasermodel_in.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.JobDistributor: Parser is present. Input mover will be overwritten with whatever the parser creates.
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB phasermodel_in.pdb
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4369 residue types
core.io.pdb.file_data: [ WARNING ] missing density found at residue (rosetta number) 146
core.io.pdb.file_data: [ WARNING ] missing density found at residue (rosetta number) 524
core.io.pdb.file_data: [ WARNING ] missing density found at residue (rosetta number) 902
core.io.pdb.file_data: [ WARNING ] missing density found at residue (rosetta number) 1280
core.pack.task: Packer task: initialize from command line()
protocols.jd2.DockDesignParser: dock_design_filename=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml
protocols.jd2.DockDesignParser: Variable substitution will occur with the following values: '%%symmdef%%'='phasermodel.symm';
protocols.jd2.DockDesignParser: Substituted script:
<ROSETTASCRIPTS>
<TASKOPERATIONS>
<ExtraRotamersGeneric name=extra ex1=1 ex2=1 extrachi_cutoff=0/>
<RestrictToRepacking name=restrict/>
<IncludeCurrent name=keep_curr/>
</TASKOPERATIONS>
<SCOREFXNS>
<xtal weights="talaris2013" symmetric=1>
<Reweight scoretype=cart_bonded weight=0.5/>
<Reweight scoretype=pro_close weight=0.0/>
</xtal>
<dens_soft weights=soft_rep symmetric=1>
<Reweight scoretype=fa_elec weight=0.7/>
<Reweight scoretype=cart_bonded weight=0.5/>
<Reweight scoretype=pro_close weight=0.0/>
<Reweight scoretype=elec_dens_fast weight=20.0/>
</dens_soft>
<dens weights="talaris2013" symmetric=1>
<Reweight scoretype=cart_bonded weight=0.5/>
<Reweight scoretype=pro_close weight=0.0/>
<Reweight scoretype=elec_dens_fast weight=20.0/>
</dens>
</SCOREFXNS>
<MOVERS>
<SetRefinementOptions name=setup_opts prime_and_switch=1/>
<SetupForSymmetry name=setup_symm definition="phasermodel.symm"/>
<ExtractAsymmetricUnit name=extract_asu/>
<RecomputeDensityMap name=recompute_dens/>
<FitBfactors name=fit_bs adp_strategy=individual/>
<TagPoseWithRefinementStats name=tag_i tag=input/>
<TagPoseWithRefinementStats name=tag_c tag=cycle/>
<TagPoseWithRefinementStats name=tag_f tag=final/>
<SetCrystWeight name=set_cryst_wt_cart weight_scale=0.5 scorefxn=xtal scorefxn_ref=xtal cartesian=1 bb=1 chi=1/>
<SetCrystWeight name=set_cryst_wt_tors weight_scale=0.5 scorefxn=xtal scorefxn_ref=xtal bb=1 chi=1 jump=ALL bondangle=1/>
<SymMinMover name=min_tors_xtal scorefxn=xtal type=lbfgs_armijo_rescored tolerance=0.0001 max_iter=100 bb=1 chi=1 jump=ALL bondangle=1/>
<SymMinMover name=min_cart_xtal cartesian=1 scorefxn=xtal type=lbfgs_armijo_rescored tolerance=0.0001 max_iter=100 bb=1 chi=1/>
<SymMinMover name=min_dens scorefxn=dens type=lbfgs_armijo tolerance=0.00001 max_iter=25 bb=1 chi=1 jump=ALL bondangle=1/>
<SymPackRotamersMover name=screpack_soft scorefxn=dens_soft task_operations=extra,restrict,keep_curr />
<SymPackRotamersMover name=screpack scorefxn=dens task_operations=extra,restrict,keep_curr />
<ParsedProtocol name=stage1cycle>
<Add mover=recompute_dens/>
<Add mover=screpack_soft/>
<Add mover=set_cryst_wt_tors/>
<Add mover=min_tors_xtal/>
<Add mover=fit_bs/>
<Add mover=tag_c/>
</ParsedProtocol>
<ParsedProtocol name=stage2cycle>
<Add mover=recompute_dens/>
<Add mover=screpack/>
<Add mover=min_dens/>
<Add mover=set_cryst_wt_tors/>
<Add mover=min_tors_xtal/>
<Add mover=fit_bs/>
<Add mover=tag_c/>
</ParsedProtocol>
<ParsedProtocol name=stage3cycle>
<Add mover=recompute_dens/>
<Add mover=screpack/>
<Add mover=set_cryst_wt_cart/>
<Add mover=min_cart_xtal/>
<Add mover=fit_bs/>
<Add mover=tag_c/>
</ParsedProtocol>
</MOVERS>
<PROTOCOLS>
<Add mover=setup_opts/>
<Add mover=setup_symm/>
<Add mover=tag_i/>
<Add mover=stage1cycle/>
<Add mover=stage1cycle/>
<Add mover=stage1cycle/>
<Add mover=stage2cycle/>
<Add mover=stage2cycle/>
<Add mover=stage2cycle/>
<Add mover=stage2cycle/>
<Add mover=stage2cycle/>
<Add mover=stage3cycle/>
<Add mover=stage3cycle/>
<Add mover=tag_f/>
<Add mover=extract_asu/>
</PROTOCOLS>
</ROSETTASCRIPTS>
protocols.jd2.DockDesignParser: Parsed script:
<ROSETTASCRIPTS>
<TASKOPERATIONS>
<ExtraRotamersGeneric ex1=1 ex2=1 extrachi_cutoff=0 name=extra/>
<RestrictToRepacking name=restrict/>
<IncludeCurrent name=keep_curr/>
</TASKOPERATIONS>
<SCOREFXNS>
<xtal symmetric=1 weights=talaris2013>
<Reweight scoretype=cart_bonded weight=0.5/>
<Reweight scoretype=pro_close weight=0.0/>
</xtal>
<dens_soft symmetric=1 weights=soft_rep>
<Reweight scoretype=fa_elec weight=0.7/>
<Reweight scoretype=cart_bonded weight=0.5/>
<Reweight scoretype=pro_close weight=0.0/>
<Reweight scoretype=elec_dens_fast weight=20.0/>
</dens_soft>
<dens symmetric=1 weights=talaris2013>
<Reweight scoretype=cart_bonded weight=0.5/>
<Reweight scoretype=pro_close weight=0.0/>
<Reweight scoretype=elec_dens_fast weight=20.0/>
</dens>
</SCOREFXNS>
<MOVERS>
<SetRefinementOptions name=setup_opts prime_and_switch=1/>
<SetupForSymmetry definition=phasermodel.symm name=setup_symm/>
<ExtractAsymmetricUnit name=extract_asu/>
<RecomputeDensityMap name=recompute_dens/>
<FitBfactors adp_strategy=individual name=fit_bs/>
<TagPoseWithRefinementStats name=tag_i tag=input/>
<TagPoseWithRefinementStats name=tag_c tag=cycle/>
<TagPoseWithRefinementStats name=tag_f tag=final/>
<SetCrystWeight bb=1 cartesian=1 chi=1 name=set_cryst_wt_cart scorefxn=xtal scorefxn_ref=xtal weight_scale=0.5/>
<SetCrystWeight bb=1 bondangle=1 chi=1 jump=ALL name=set_cryst_wt_tors scorefxn=xtal scorefxn_ref=xtal weight_scale=0.5/>
<SymMinMover bb=1 bondangle=1 chi=1 jump=ALL max_iter=100 name=min_tors_xtal scorefxn=xtal tolerance=0.0001 type=lbfgs_armijo_rescored/>
<SymMinMover bb=1 cartesian=1 chi=1 max_iter=100 name=min_cart_xtal scorefxn=xtal tolerance=0.0001 type=lbfgs_armijo_rescored/>
<SymMinMover bb=1 bondangle=1 chi=1 jump=ALL max_iter=25 name=min_dens scorefxn=dens tolerance=0.00001 type=lbfgs_armijo/>
<SymPackRotamersMover name=screpack_soft scorefxn=dens_soft task_operations=extra,restrict,keep_curr/>
<SymPackRotamersMover name=screpack scorefxn=dens task_operations=extra,restrict,keep_curr/>
<ParsedProtocol name=stage1cycle>
<Add mover=recompute_dens/>
<Add mover=screpack_soft/>
<Add mover=set_cryst_wt_tors/>
<Add mover=min_tors_xtal/>
<Add mover=fit_bs/>
<Add mover=tag_c/>
</ParsedProtocol>
<ParsedProtocol name=stage2cycle>
<Add mover=recompute_dens/>
<Add mover=screpack/>
<Add mover=min_dens/>
<Add mover=set_cryst_wt_tors/>
<Add mover=min_tors_xtal/>
<Add mover=fit_bs/>
<Add mover=tag_c/>
</ParsedProtocol>
<ParsedProtocol name=stage3cycle>
<Add mover=recompute_dens/>
<Add mover=screpack/>
<Add mover=set_cryst_wt_cart/>
<Add mover=min_cart_xtal/>
<Add mover=fit_bs/>
<Add mover=tag_c/>
</ParsedProtocol>
</MOVERS>
<PROTOCOLS>
<Add mover=setup_opts/>
<Add mover=setup_symm/>
<Add mover=tag_i/>
<Add mover=stage1cycle/>
<Add mover=stage1cycle/>
<Add mover=stage1cycle/>
<Add mover=stage2cycle/>
<Add mover=stage2cycle/>
<Add mover=stage2cycle/>
<Add mover=stage2cycle/>
<Add mover=stage2cycle/>
<Add mover=stage3cycle/>
<Add mover=stage3cycle/>
<Add mover=tag_f/>
<Add mover=extract_asu/>
</PROTOCOLS>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/rama/Rama09_noEH_kernel25_it08.dat
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 748 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1424 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 2105 bb-independent torsions.
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "extra" of type ExtraRotamersGeneric
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict" of type RestrictToRepacking
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "keep_curr" of type IncludeCurrent
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
protocols.jd2.parser.ScoreFunctionLoader: defined score function "xtal" with weights "talaris2013"
setting xtal weight cart_bonded to 0.5
setting xtal weight pro_close to 0
symmetrizing xtal
defined score function "dens_soft" with weights "soft_rep"
setting dens_soft weight fa_elec to 0.7
setting dens_soft weight cart_bonded to 0.5
setting dens_soft weight pro_close to 0
setting dens_soft weight elec_dens_fast to 20
symmetrizing dens_soft
defined score function "dens" with weights "talaris2013"
setting dens weight cart_bonded to 0.5
setting dens weight pro_close to 0
setting dens weight elec_dens_fast to 20
symmetrizing dens
protocols.jd2.DockDesignParser: Defined mover named "setup_opts" of type SetRefinementOptions
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group JUMPGROUP1: [master 1] 3:0 2:0 4:0 5:0 6:0 7:0 8:0 9:0
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=10 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group JUMPGROUP2: [master 10] 14:0 12:0 16:0 18:0 20:0 22:0 24:0 26:0
core.conformation.symmetry.SymmData: symmetry name: phasermodel_in_P_21_21_21
core.conformation.symmetry.SymmData: number of subunits: 9
core.conformation.symmetry.SymmData: number of interfaces: 1
core.conformation.symmetry.SymmData: score subunit number: VRT_0_0_0_0
core.conformation.symmetry.SymmData: anchor the subunits at residue: 1
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_0_0_0_0
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -16.4505 4.65753 -61.8953
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_0_0_0_0_base
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -17.4505 3.65753 -62.8953
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_0_1_0_0
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 72.6955 4.65753 -61.8953
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_0_1_0_0_base
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 71.6955 3.65753 -62.8953
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_0_n1_0_0
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -105.596 4.65753 -61.8953
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_0_n1_0_0_base
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -106.596 3.65753 -62.8953
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_1_n1_0_0
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: -28.1225 -4.65753 21.8187
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_1_n1_0_0_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: -27.1225 -3.65753 20.8187
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_1_n1_0_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: -28.1225 -4.65753 -145.609
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_1_n1_0_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: -27.1225 -3.65753 -146.609
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_0_0_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 16.4505 85.983 -21.8187
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_0_0_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 17.4505 84.983 -20.8187
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_0_n1_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 16.4505 -76.668 -21.8187
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_0_n1_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 17.4505 -77.668 -20.8187
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_n1_0_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -72.6955 85.983 -21.8187
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_n1_0_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -71.6955 84.983 -20.8187
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_n1_n1_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -72.6955 -76.668 -21.8187
core.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_n1_n1_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -71.6955 -77.668 -20.8187
core.conformation.symmetry.SymmData: Dof for jump: 1
core.conformation.symmetry.SymmData: x 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: x_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: Dof for jump: 10
core.conformation.symmetry.SymmData: x 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: x_angle 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y_angle 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z_angle 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: Jump JUMP_0_0_0_0_to_com VRT_0_0_0_0 VRT_0_0_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_0_0_0_0_to_subunit VRT_0_0_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_0_1_0_0 VRT_0_0_0_0 VRT_0_1_0_0
core.conformation.symmetry.SymmData: Jump JUMP_0_1_0_0_to_com VRT_0_1_0_0 VRT_0_1_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_0_1_0_0_to_subunit VRT_0_1_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_0_n1_0_0 VRT_0_0_0_0 VRT_0_n1_0_0
core.conformation.symmetry.SymmData: Jump JUMP_0_n1_0_0_to_com VRT_0_n1_0_0 VRT_0_n1_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_0_n1_0_0_to_subunit VRT_0_n1_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_0 VRT_0_0_0_0 VRT_1_n1_0_0
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_0_to_com VRT_1_n1_0_0 VRT_1_n1_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_0_to_subunit VRT_1_n1_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_n1 VRT_0_0_0_0 VRT_1_n1_0_n1
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_n1_to_com VRT_1_n1_0_n1 VRT_1_n1_0_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_n1_to_subunit VRT_1_n1_0_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_0_0_n1 VRT_0_0_0_0 VRT_3_0_0_n1
core.conformation.symmetry.SymmData: Jump JUMP_3_0_0_n1_to_com VRT_3_0_0_n1 VRT_3_0_0_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_3_0_0_n1_to_subunit VRT_3_0_0_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_n1 VRT_0_0_0_0 VRT_3_0_n1_n1
core.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_n1_to_com VRT_3_0_n1_n1 VRT_3_0_n1_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_n1_to_subunit VRT_3_0_n1_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_0_n1 VRT_0_0_0_0 VRT_3_n1_0_n1
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_0_n1_to_com VRT_3_n1_0_n1 VRT_3_n1_0_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_0_n1_to_subunit VRT_3_n1_0_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_n1_n1 VRT_0_0_0_0 VRT_3_n1_n1_n1
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_n1_n1_to_com VRT_3_n1_n1_n1 VRT_3_n1_n1_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_n1_n1_to_subunit VRT_3_n1_n1_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Include subunit:
core.conformation.symmetry.SymmData: Output subunit:
core.conformation.symmetry.SymmData: SlideType: RANDOM
core.conformation.symmetry.SymmData: SlideCriteriaType: CEN_DOCK_SCORE
core.conformation.symmetry.SymmData: SlideCriteriaVal: AUTOMATIC
core.conformation.symmetry.SymmData: SlideOrder: none
protocols.jd2.DockDesignParser: Defined mover named "setup_symm" of type SetupForSymmetry
protocols.jd2.DockDesignParser: Defined mover named "extract_asu" of type ExtractAsymmetricUnit
protocols.jd2.DockDesignParser: Defined mover named "recompute_dens" of type RecomputeDensityMap
protocols.jd2.DockDesignParser: Defined mover named "fit_bs" of type FitBfactors
protocols.jd2.DockDesignParser: Defined mover named "tag_i" of type TagPoseWithRefinementStats
protocols.jd2.DockDesignParser: Defined mover named "tag_c" of type TagPoseWithRefinementStats
protocols.jd2.DockDesignParser: Defined mover named "tag_f" of type TagPoseWithRefinementStats
protocols.jd2.DockDesignParser: Defined mover named "set_cryst_wt_cart" of type SetCrystWeight
protocols.jd2.DockDesignParser: Defined mover named "set_cryst_wt_tors" of type SetCrystWeight
protocols.simple_moves.MinMover: Options chi, bb: 1, 1
protocols.jd2.DockDesignParser: Defined mover named "min_tors_xtal" of type SymMinMover
protocols.simple_moves.MinMover: Options chi, bb: 1, 1
protocols.jd2.DockDesignParser: Defined mover named "min_cart_xtal" of type SymMinMover
protocols.simple_moves.MinMover: Options chi, bb: 1, 1
protocols.jd2.DockDesignParser: Defined mover named "min_dens" of type SymMinMover
protocols.RosettaScripts.util: Object screpack_soft reading the following task_operations: Adding the following task operations
extra restrict keep_curr
protocols.jd2.DockDesignParser: Defined mover named "screpack_soft" of type SymPackRotamersMover
protocols.RosettaScripts.util: Object screpack reading the following task_operations: Adding the following task operations
extra restrict keep_curr
protocols.jd2.DockDesignParser: Defined mover named "screpack" of type SymPackRotamersMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
added mover "recompute_dens" with filter "true_filter"
added mover "screpack_soft" with filter "true_filter"
added mover "set_cryst_wt_tors" with filter "true_filter"
added mover "min_tors_xtal" with filter "true_filter"
added mover "fit_bs" with filter "true_filter"
added mover "tag_c" with filter "true_filter"
protocols.jd2.DockDesignParser: Defined mover named "stage1cycle" of type ParsedProtocol
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
added mover "recompute_dens" with filter "true_filter"
added mover "screpack" with filter "true_filter"
added mover "min_dens" with filter "true_filter"
added mover "set_cryst_wt_tors" with filter "true_filter"
added mover "min_tors_xtal" with filter "true_filter"
added mover "fit_bs" with filter "true_filter"
added mover "tag_c" with filter "true_filter"
protocols.jd2.DockDesignParser: Defined mover named "stage2cycle" of type ParsedProtocol
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
added mover "recompute_dens" with filter "true_filter"
added mover "screpack" with filter "true_filter"
added mover "set_cryst_wt_cart" with filter "true_filter"
added mover "min_cart_xtal" with filter "true_filter"
added mover "fit_bs" with filter "true_filter"
added mover "tag_c" with filter "true_filter"
protocols.jd2.DockDesignParser: Defined mover named "stage3cycle" of type ParsedProtocol
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
added mover "setup_opts" with filter "true_filter"
added mover "setup_symm" with filter "true_filter"
added mover "tag_i" with filter "true_filter"
added mover "stage1cycle" with filter "true_filter"
added mover "stage1cycle" with filter "true_filter"
added mover "stage1cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage3cycle" with filter "true_filter"
added mover "stage3cycle" with filter "true_filter"
added mover "tag_f" with filter "true_filter"
added mover "extract_asu" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy phasermodel_in.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetRefinementOptions - setup_opts=======================
{
protocols.cryst.cryst_movers: Setting options:
protocols.cryst.cryst_movers: prime_and_switch:1
protocols.rosetta_scripts.ParsedProtocol:
}
=======================END MOVER SetRefinementOptions - setup_opts=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
{
protocols.rosetta_scripts.ParsedProtocol:
}
=======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForSymmetry - setup_symm=======================
{
core.conformation.symmetry.util: =================== SYM FOLD TREE, jump notation: =symfixed= *indep* #symdof# jump[=follows] ========================
VRT_0_0_0_0(13609)
|----#j73#--->VRT_0_0_0_0_base(13610)----#j64#----->1:Sub1B(1-146)
| |146----*j1*---->147:Sub1B(147-378)
| |1------*j2*---->379:Sub1A(379-524)524----*j3*---->525:Sub1A(525-756)
| |1------*j4*---->757:Sub1C(757-902)902----*j5*---->903:Sub1C(903-1134)
| \1------*j6*---->1135:Sub1D(1135-1280)1280----*j7*---->1281:Sub1D(1281-1512)
|----=j74=--->VRT_0_1_0_0(13613)---j75=73--->VRT_0_1_0_0_base(13614)---j65=64--->3025:Sub3B(3025-3170)
| |3170----j15=1--->3171:Sub3B(3171-3402)
| |3025----j16=2--->3403:Sub3A(3403-3548)3548----j17=3--->3549:Sub3A(3549-3780)
| |3025----j18=4--->3781:Sub3C(3781-3926)3926----j19=5--->3927:Sub3C(3927-4158)
| \3025----j20=6--->4159:Sub3D(4159-4304)4304----j21=7--->4305:Sub3D(4305-4536)
|----=j76=--->VRT_0_n1_0_0(13611)---j77=73--->VRT_0_n1_0_0_base(13612)---j66=64--->1513:Sub2B(1513-1658)
| |1658----j8=1---->1659:Sub2B(1659-1890)
| |1513----j9=2---->1891:Sub2A(1891-2036)2036----j10=3--->2037:Sub2A(2037-2268)
| |1513----j11=4--->2269:Sub2C(2269-2414)2414----j12=5--->2415:Sub2C(2415-2646)
| \1513----j13=6--->2647:Sub2D(2647-2792)2792----j14=7--->2793:Sub2D(2793-3024)
|----=j78=--->VRT_1_n1_0_0(13615)---j79=73--->VRT_1_n1_0_0_base(13616)---j67=64--->4537:Sub4B(4537-4682)
| |4682----j22=1--->4683:Sub4B(4683-4914)
| |4537----j23=2--->4915:Sub4A(4915-5060)5060----j24=3--->5061:Sub4A(5061-5292)
| |4537----j25=4--->5293:Sub4C(5293-5438)5438----j26=5--->5439:Sub4C(5439-5670)
| \4537----j27=6--->5671:Sub4D(5671-5816)5816----j28=7--->5817:Sub4D(5817-6048)
|----=j80=--->VRT_1_n1_0_n1(13617)---j81=73--->VRT_1_n1_0_n1_base(13618)---j68=64--->6049:Sub5B(6049-6194)
| |6194----j29=1--->6195:Sub5B(6195-6426)
| |6049----j30=2--->6427:Sub5A(6427-6572)6572----j31=3--->6573:Sub5A(6573-6804)
| |6049----j32=4--->6805:Sub5C(6805-6950)6950----j33=5--->6951:Sub5C(6951-7182)
| \6049----j34=6--->7183:Sub5D(7183-7328)7328----j35=7--->7329:Sub5D(7329-7560)
|----=j82=--->VRT_3_0_0_n1(13619)---j83=73--->VRT_3_0_0_n1_base(13620)---j69=64--->7561:Sub6B(7561-7706)
| |7706----j36=1--->7707:Sub6B(7707-7938)
| |7561----j37=2--->7939:Sub6A(7939-8084)8084----j38=3--->8085:Sub6A(8085-8316)
| |7561----j39=4--->8317:Sub6C(8317-8462)8462----j40=5--->8463:Sub6C(8463-8694)
| \7561----j41=6--->8695:Sub6D(8695-8840)8840----j42=7--->8841:Sub6D(8841-9072)
|----=j84=--->VRT_3_0_n1_n1(13621)---j85=73--->VRT_3_0_n1_n1_base(13622)---j70=64--->9073:Sub7B(9073-9218)
| |9218----j43=1--->9219:Sub7B(9219-9450)
| |9073----j44=2--->9451:Sub7A(9451-9596)9596----j45=3--->9597:Sub7A(9597-9828)
| |9073----j46=4--->9829:Sub7C(9829-9974)9974----j47=5--->9975:Sub7C(9975-10206)
| \9073----j48=6--->10207:Sub7D(10207-10352)10352----j49=7--->10353:Sub7D(10353-10584)
|----=j86=--->VRT_3_n1_0_n1(13623)---j87=73--->VRT_3_n1_0_n1_base(13624)---j71=64--->10585:Sub8B(10585-10730)
| |10730----j50=1--->10731:Sub8B(10731-10962)
| |10585----j51=2--->10963:Sub8A(10963-11108)11108----j52=3--->11109:Sub8A(11109-11340)
| |10585----j53=4--->11341:Sub8C(11341-11486)11486----j54=5--->11487:Sub8C(11487-11718)
| \10585----j55=6--->11719:Sub8D(11719-11864)11864----j56=7--->11865:Sub8D(11865-12096)
\----=j88=--->VRT_3_n1_n1_n1(13625)---j89=73--->VRT_3_n1_n1_n1_base(13626)---j72=64--->12097:Sub9B(12097-12242)
|12242----j57=1--->12243:Sub9B(12243-12474)
|12097----j58=2--->12475:Sub9A(12475-12620)12620----j59=3--->12621:Sub9A(12621-12852)
|12097----j60=4--->12853:Sub9C(12853-12998)12998----j61=5--->12999:Sub9C(12999-13230)
\12097----j62=6--->13231:Sub9D(13231-13376)13376----j63=7--->13377:Sub9D(13377-13608)
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
protocols.rosetta_scripts.ParsedProtocol:
}
=======================END MOVER SetupForSymmetry - setup_symm=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
{
protocols.rosetta_scripts.ParsedProtocol:
}
=======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER TagPoseWithRefinementStats - tag_i=======================
{
-------------- next part --------------
Output directory:
/home/gebauer/tmp/rosetta_6
=========================== Importing data and flags ==========================
----------Setting up input files for Rosetta----------
----------Loading model and data----------
=========================== ROSETTA X-ray refinement ==========================
|-starting model--------------------------------------------------------------|
| target_work(ml) = 7.62563 r_work = 0.4769 r_free = 0.4887 |
|-----------------------------------------------------------------------------|
Validation statistics (starting model):
Ramachandran outliers = 0.27 %
favored = 95.25 %
Rotamer outliers = 9.45 %
C-beta deviations = 20
Clashscore = 14.46
Molprobity score = 2.74
Generating 5 models on 4 processors...
DEBUG dumping error message
ERROR: Rosetta exited with status 1
stderr output:
show_stack(1): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/boost_adaptbx/boost/python.py(25) import_ext
show_stack(2): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/scitbx/math/ext.py(6) <module>
show_stack(3): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/scitbx/math/__init__.py(2) <module>
show_stack(4): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/cctbx/maptbx/__init__.py(17) <module>
show_stack(5): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/cctbx/miller/__init__.py(10) <module>
show_stack(6): /usr/local/science/phenix4rosetta/phenix-dev-1523/cctbx_project/mmtbx/utils/__init__.py(2) <module>
show_stack(7): /usr/local/science/phenix4rosetta/phenix-dev-1523/phenix/phenix/rosetta/xray_target.py(3) <module>
libc backtrace (106 frames, most recent call last):
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x401e31]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fad8d97c76d]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x401c7e]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(utility::pointer::owning_ptr<protocols::moves::Mover>)+0x35) [0x7fad8f0239b5]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(utility::pointer::owning_ptr<protocols::moves::Mover>)+0xbdb) [0x7fad8f04abcb]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x27e) [0x7fad8efd075e]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> > const*, std::vector<std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> >, std::allocator<std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> > > > >)+0x30) [0x7fad8efcfda0]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover_filter_pair(core::pose::Pose&, std::pair<std::pair<utility::pointer::owning_ptr<protocols::moves::Mover>, std::string>, utility::pointer::owning_ptr<protocols::filters::Filter> > const&)+0x126) [0x7fad8efcf916]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libprotocols.6.so(protocols::cryst::TagPoseWithRefinementStatsMover::apply(core::pose::Pose&)+0x27) [0x7fad8797d9c7]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libcore.3.so(core::scoring::cryst::PhenixInterface::getScore(core::pose::Pose const&)+0x1a6) [0x7fad8a3a0686]
/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/build/src/release/linux/3.5/64/x86/gcc/4.6/python/libcore.3.so(core::scoring::cryst::PhenixInterface::initialize_target_evaluator(core::pose::Pose const&, std::string)+0x5bc) [0x7fad8a39cf4c]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_Import+0xbd) [0x7fad8508b4dd]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_CallFunction+0x7e) [0x7fad84fcc8fe]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x4c82b) [0x7fad84fcc82b]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x324) [0x7fad8508ac04]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a700) [0x7fad8508a700]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x324) [0x7fad8508ac04]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a700) [0x7fad8508a700]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x109e1a) [0x7fad85089e1a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x25a4) [0x7fad8506d154]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47) [0x7fad8506a5c7]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7fad84fcc753]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x21c) [0x7fad8508aafc]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x108f79) [0x7fad85088f79]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2) [0x7fad85088ce2]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7fad85071f82]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x57f8) [0x7fad850703a8]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x855) [0x7fad85071e45]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x59dd) [0x7fad8507058d]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0xe886f) [0x7fad8506886f]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1da) [0x7fad8508aaba]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a412) [0x7fad8508a412]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(+0x10a1a5) [0x7fad8508a1a5]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x98) [0x7fad8508c028]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/base/lib/libpython2.7.so.1.0(_PyImport_GetDynLoadFunc+0x12d) [0x7fad850a56dd]
/lib/x86_64-linux-gnu/libdl.so.2(dlopen+0x31) [0x7fad8483cfc1]
/lib/x86_64-linux-gnu/libdl.so.2(+0x152f) [0x7fad8483d52f]
/lib64/ld-linux-x86-64.so.2(+0xf176) [0x7fad8feb9176]
/lib/x86_64-linux-gnu/libdl.so.2(+0xf26) [0x7fad8483cf26]
/lib64/ld-linux-x86-64.so.2(+0x1331a) [0x7fad8febd31a]
/lib64/ld-linux-x86-64.so.2(+0xf176) [0x7fad8feb9176]
/lib64/ld-linux-x86-64.so.2(+0x13ada) [0x7fad8febdada]
/lib64/ld-linux-x86-64.so.2(+0xf3df) [0x7fad8feb93df]
/lib64/ld-linux-x86-64.so.2(+0xf306) [0x7fad8feb9306]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(+0x17f799) [0x7fad77433799]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(boost::math::detail::erf_inv_initializer<long double, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> >::init::do_init()+0x12) [0x7fad7751ab92]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(+0x259c7a) [0x7fad7750dc7a]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/scitbx_math_ext.so(long double boost::math::detail::erf_inv_imp<long double, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> >(long double const&, long double const&, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> const&, mpl_::int_<64> const*)+0x3a7) [0x7fad77514747]
/lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7fad8d9914a0]
/usr/local/science/phenix4rosetta/phenix-dev-1523/build/intel-linux-2.6-x86_64/lib/boost_python_meta_ext.so(init_module_boost_python_meta_ext()+0) [0x7fad7db89250]
Segmentation fault (Python and libc call stacks above)
This crash may be due to a problem in any imported
Python module, including modules which are not part
of the cctbx project. To disable the traps leading
to this message, define these environment variables
(e.g. assign the value 1):
BOOST_ADAPTBX_FPE_DEFAULT
BOOST_ADAPTBX_SIGNALS_DEFAULT
This will NOT solve the problem, just mask it, but
may allow you to proceed in case it is not critical.
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