[phenixbb] phenix.refine_failed

Xue-Yuan Pei xyp20 at mole.bio.cam.ac.uk
Mon Dec 12 07:29:06 PST 2011


my data was processed upto 3.3A with I/sigma of 2.
Xue


On Mon, 12 Dec 2011, Nathaniel Echols wrote:

> 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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