Statistics: Creating restraints_manager failed. /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cev_45520/09_2024/9cev_45520.cif /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cev_45520/09_2024/9cev_45520.map 3.26 Traceback (most recent call last): File "/net/marbles/raid1/dorothee/rerefine/cryoem/rerefine_script.py", line 391, in get_statistics checked_model.process(make_restraints=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/model/model.py", line 1990, in process allow_missing_symmetry = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/utils/__init__.py", line 286, in process_pdb_files allow_missing_symmetry = allow_missing_symmetry) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/utils/__init__.py", line 371, in _process_pdb_file raise Sorry(msg) Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 13 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary.