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