Statistics: Model class (with restraints) from pdb failed. /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/01_2022/7ppo_13583.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppo_13583/01_2022/7ppo_13583.map 2.91 Traceback (most recent call last): File "/net/marbles/raid1/dorothee/rerefine/cryoem/rerefine_script.py", line 345, in get_statistics model.process(make_restraints=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/cctbx_project/mmtbx/model/model.py", line 1709, in process allow_missing_symmetry = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/cctbx_project/mmtbx/utils/__init__.py", line 287, in process_pdb_files allow_missing_symmetry = allow_missing_symmetry) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/cctbx_project/mmtbx/utils/__init__.py", line 358, in _process_pdb_file substitute_non_crystallographic_unit_cell_if_necessary=allow_missing_symmetry) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5745, in __init__ restraints_loading_flags=restraints_loading_flags) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3552, in __init__ log=log, File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2778, in __init__ conf_altloc=conformer.altloc, mm=mm) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 950, in assign_from_monomer_mapping ' new symbol: "%s" (%s)' % (symbol, source)])) Sorry: Conflicting scattering type symbols: initial symbol: "H" (from pdb element column) new symbol: "O" (with residue name 86N) atom: "HETATM 3634 OXT 86N A 860 .*. H "