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

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3r_11063/12_2022/6z3r_11063.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3r_11063/12_2022/6z3r_11063.map 2.97
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 1875, in process
    run_clash_guard           = run_clash_guard)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/model/model.py", line 1935, in _setup_restraints_manager
    assume_hydrogens_all_missing = not self.has_hd())
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5844, in geometry_restraints_manager
    log=self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5540, in construct_geometry_restraints_manager
    verbose=True,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/conformation_dependent_library/__init__.py", line 387, in update_restraints
    esd_factor=esd_factor,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/conformation_dependent_library/multi_residue_cdl_class.py", line 321, in apply_updates
    ''' % ''.join(error_atoms))
Sorry: 
  Certain angles in the protein chain (C-N-H or CA-N-H) have not been found
  in the restraints by the Conformational Dependent Library. This usually
  means that the protein backbone is traversing a special position.

  This is unlikely.

  However, to proceed, set cdl=False.

"ATOM    606  N   THR A 279 .*.     N  "
"ATOM    607  CA  THR A 279 .*.     C  "
"ATOM    608  C   THR A 279 .*.     C  "
"ATOM    609  O   THR A 279 .*.     O  "
"ATOM    610  CB  THR A 279 .*.     C  "
"ATOM    611  H   THR A 279 .*.     H  "
"ATOM    614  N   PRO A 280 .*.     N  "
"ATOM    615  CA  PRO A 280 .*.     C  "
"ATOM    616  C   PRO A 280 .*.     C  "
"ATOM    617  O   PRO A 280 .*.     O  "
"ATOM    618  CB  PRO A 280 .*.     C  "
"ATOM    619  H   PRO A 280 .*.     H  "