Re: [phenixbb] phenix.refine_failed

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 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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