Statistics: Creating restraints_manager  failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9o_31498/12_2023/7f9o_31498.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9o_31498/12_2023/7f9o_31498.map 4.5
Traceback (most recent call last):
  File "/net/marbles/raid1/dorothee/rerefine/cryoem/rerefine_script.py", line 402, in get_statistics
    checked_model.process(make_restraints=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/model/model.py", line 1885, in process
    allow_missing_symmetry = True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/utils/__init__.py", line 372, in _process_pdb_file
    raise Sorry(msg)
Sorry: Fatal problems interpreting model file:
  Number of atoms with unknown nonbonded energy type symbols: 1659
    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.