Statistics: Model class (with restraints) from pdb  failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txj_26159/12_2022/7txj_26159.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txj_26159/12_2022/7txj_26159.map 3.9
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-dev-4807/modules/cctbx_project/mmtbx/model/model.py", line 1828, in process
    allow_missing_symmetry = True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/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-dev-4807/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5777, in __init__
    restraints_loading_flags=restraints_loading_flags)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3358, in __init__
    self.counts.raise_duplicate_atom_labels_if_necessary()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 342, in raise_duplicate_atom_labels_if_necessary
    if (len(msg) != 0): raise Sorry(msg.rstrip())
Sorry: number of groups of duplicate atom labels: 3259
  total number of affected atoms:          6518
  group "ATOM    .*.  P    DT 1   1 .*.     P  "
        "ATOM    .*.  P    DT 1   1 .*.     P  "
  group "ATOM    .*.  OP1  DT 1   1 .*.     O  "
        "ATOM    .*.  OP1  DT 1   1 .*.     O  "
  group "ATOM    .*.  OP2  DT 1   1 .*.     O  "
        "ATOM    .*.  OP2  DT 1   1 .*.     O  "
  group "ATOM    .*.  O5'  DT 1   1 .*.     O  "
        "ATOM    .*.  O5'  DT 1   1 .*.     O  "
  group "ATOM    .*.  C5'  DT 1   1 .*.     C  "
        "ATOM    .*.  C5'  DT 1   1 .*.     C  "
  group "ATOM    .*.  C4'  DT 1   1 .*.     C  "
        "ATOM    .*.  C4'  DT 1   1 .*.     C  "
  group "ATOM    .*.  O4'  DT 1   1 .*.     O  "
        "ATOM    .*.  O4'  DT 1   1 .*.     O  "
  group "ATOM    .*.  C3'  DT 1   1 .*.     C  "
        "ATOM    .*.  C3'  DT 1   1 .*.     C  "
  group "ATOM    .*.  O3'  DT 1   1 .*.     O  "
        "ATOM    .*.  O3'  DT 1   1 .*.     O  "
  group "ATOM    .*.  C2'  DT 1   1 .*.     C  "
        "ATOM    .*.  C2'  DT 1   1 .*.     C  "
  ... 3249 remaining groups not shown