Statistics: Creating restraints_manager  failed.

/net/cci-nas-00/data/ceres_data/8qn6_18508/08_2025/8qn6_18508.cif /net/cci-nas-00/data/ceres_data/8qn6_18508/08_2025/8qn6_18508.map 2.4
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/CERES/rerefine_script.py", line 391, in get_statistics
    checked_model.process(make_restraints=True)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/model/model.py", line 2039, in process
    self._processed_pdb_file, _ = processed_pdb_files_srv.process_pdb_files(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/utils/__init__.py", line 279, in process_pdb_files
    return self._process_pdb_file(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/utils/__init__.py", line 344, in _process_pdb_file
    processed_pdb_file = monomer_library.pdb_interpretation.process(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 6026, in __init__
    self.all_chain_proxies = build_all_chain_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 3525, in __init__
    self.counts.raise_duplicate_atom_labels_if_necessary()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/pdb/hierarchy.py", line 366, in raise_duplicate_atom_labels_if_necessary
    if (len(msg) != 0): raise Sorry(msg.rstrip())
Sorry: number of groups of duplicate atom labels: 2910
  total number of affected atoms:          5820
  group "ATOM    .*.  N   ASP F   1 .*.     N  "
        "ATOM    .*.  N   ASP F   1 .*.     N  "
  group "ATOM    .*.  CA  ASP F   1 .*.     C  "
        "ATOM    .*.  CA  ASP F   1 .*.     C  "
  group "ATOM    .*.  C   ASP F   1 .*.     C  "
        "ATOM    .*.  C   ASP F   1 .*.     C  "
  group "ATOM    .*.  O   ASP F   1 .*.     O  "
        "ATOM    .*.  O   ASP F   1 .*.     O  "
  group "ATOM    .*.  CB  ASP F   1 .*.     C  "
        "ATOM    .*.  CB  ASP F   1 .*.     C  "
  group "ATOM    .*.  CG  ASP F   1 .*.     C  "
        "ATOM    .*.  CG  ASP F   1 .*.     C  "
  group "ATOM    .*.  OD1 ASP F   1 .*.     O  "
        "ATOM    .*.  OD1 ASP F   1 .*.     O  "
  group "ATOM    .*.  OD2 ASP F   1 .*.     O  "
        "ATOM    .*.  OD2 ASP F   1 .*.     O  "
  group "ATOM    .*.  N   ALA F   2 .*.     N  "
        "ATOM    .*.  N   ALA F   2 .*.     N  "
  group "ATOM    .*.  CA  ALA F   2 .*.     C  "
        "ATOM    .*.  CA  ALA F   2 .*.     C  "
  ... 2900 remaining groups not shown