[phenixbb] phenix.refine_failed

[Xue-Yuan Pei]

  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
>