Model class without restraints from initial pdb failed. /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hku_34860/12_2023/8hku_34860.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hku_34860/12_2023/8hku_34860.map 2.72 Traceback (most recent call last): File "/net/marbles/raid1/dorothee/rerefine/cryoem/rerefine_script.py", line 952, in get_composition log = null_out()) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/model/model.py", line 244, in __init__ self._ss_annotation = self._model_input.extract_secondary_structure() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/pdb/__init__.py", line 1197, in extract_secondary_structure return secondary_structure.annotation.from_records(records, log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/pdb/secondary_structure.py", line 620, in from_records h = pdb_helix.from_pdb_record(line) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/pdb/secondary_structure.py", line 1934, in from_pdb_record helix_class=cls.helix_class_to_str(int(line[38:40])), File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/pdb/secondary_structure.py", line 1846, in helix_class_to_str return cls._helix_class_array[h_class] IndexError: list index out of range