This occurs at the end of refinement. Quite why it's trying to *read* from a string with Fortran-esque overflow formatting while in a writing step I don't know, but the PDB file gets truncated at REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP. The structure is not idyllic, clearly, but I'd like to see the extent of the problem rather than just the first atom. Got to be pretty easy to trap for and map to 999.99 either on the way in or out. Writing refined structure to PDB file: /Users/phil/Structures/reference_models/start_refine_001.pdb n_use = 21264 n_use_u_iso = 21264 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 21264 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 21264 Traceback (most recent call last): File "/usr/local/phenix-1.7.3-928/build/mac-intel-osx/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/command_line.py", line 105, in run refine_object.write_refined_pdb(f_pdb) File "/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/driver.py", line 1379, in write_refined_pdb ignore_hd = not self.neutron_refinement) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 589, in __init__ ignore_hd = ignore_hd) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 504, in __init__ molprobity_scores=True) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model.py", line 1063, in geometry_statistics molprobity_scores = molprobity_scores) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 112, in __init__ self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/validation/clashscore.py", line 182, in analyze_clashes self.pdb_hierarchy = pdb.hierarchy.input(pdb_string=input_str).hierarchy File "/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/hierarchy.py", line 1044, in __init__ source_info=source_info, lines=flex.split_lines(pdb_string)) File "/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/__init__.py", line 582, in input return ext.input(source_info=source_info, lines=lines) ValueError: string, line 5148: ATOM 17 N ILE A 268 -16.878 -22.262 49.415 1.00****** A N ------------------------------------------------------------^ not a floating-point number. Phil Jeffrey Princeton