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

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q06_20544/12_2022/6q06_20544.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q06_20544/12_2022/6q06_20544.map 2.7
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 5458, in construct_geometry_restraints_manager
    log=log,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/monomer_library/linking_mixins.py", line 857, in process_nonbonded_for_links
    links[key][-1]+=bond_i_seqs[0]
IndexError: list index out of range