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
