[phenixbb] phenix.refine_failed
Nathaniel Echols
nechols at lbl.gov
Mon Dec 12 07:10:10 PST 2011
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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