[phenixbb] phenix.refine_failed

[Nathaniel Echols]

Were you trying to perform grouped ADP refinement? What is the
resolution of your structure?

-Nat

On Mon, Dec 12, 2011 at 7:00 AM, Xue-Yuan Pei <xyp20 at mole.bio.cam.ac.uk> wrote:
>  Dear Phenix Experts:
>  My phenix.refine has developped the following error (see below). I tried
>  to check my PDB format, there is not B-factor error. so what could be
>  wrong that stoped my phenix.refine without PDB  and .def files in
>  the output?
>  Many thanks for your advice.
>  Xue yuan Pei, Ph.D
>  Department of Biochemistry
>  University of Cambridge
>  Cambridge CB2 1GA
>  U.K
>
>> Error messages:
>> Traceback (most recent call last):
>>   File
>> "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/command_line/refine.py",
>> line 11, in <module>
>>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>>   File
>>
>> "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py",
>> line 105, in run
>>     refine_object.write_refined_pdb(f_pdb)
>>   File
>> "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/refinement/driver.py",
>> line 1284, in write_refined_pdb
>>     ignore_hd = not self.neutron_refinement)
>>   File
>>
>> "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py",
>> line 534, in __init__
>>     ignore_hd = ignore_hd)
>>   File
>>
>> "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py",
>> line 449, in __init__
>>     molprobity_scores=True)
>>   File "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model.py",
>> line 1063, in geometry_statistics
>>     molprobity_scores    = molprobity_scores)
>>   File
>>
>> "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py",
>> line 112, in __init__
>>     self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy)
>>   File
>>
>> "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/validation/clashscore.py",
>> line 167, in analyze_clashes
>>     stdin_lines=tmp_r.as_pdb_string())
>>   File
>> "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/iotbx/pdb/hierarchy.py",
>> line 527, in as_pdb_string
>>     siguij=siguij)
>> RuntimeError: atom B-factor does not fit into F6.2 format:
>>   "ATOM      1  N   GLY A   1 "
>>   B-factor: 111147.29
>
>
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