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

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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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It is giving the error when formatting a new pdb file for writing out the refinement results. For some reason the b-factor refinement is unstable. Could you send me (directly, not the list) the inputs for debugging? I'll need the pdb file, the reflection file (usually mtz), the .eff file from the run that crashed, and any .cif files in case you have ligands. Ralf 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:

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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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