Statistics: Model class (with restraints) from pdb failed. /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dr2_7988/05_2022/6dr2_7988.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dr2_7988/05_2022/6dr2_7988.map 4.33 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-4597/modules/cctbx_project/mmtbx/model/model.py", line 1815, in process run_clash_guard = run_clash_guard) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/cctbx_project/mmtbx/model/model.py", line 1875, in _setup_restraints_manager assume_hydrogens_all_missing = not self.has_hd()) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5813, in geometry_restraints_manager log=self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5511, in construct_geometry_restraints_manager verbose=True, File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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-4597/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 20135 N ASP A1435 .*. N " "ATOM 20136 CA ASP A1435 .*. C " "ATOM 20137 C ASP A1435 .*. C " "ATOM 20138 O ASP A1435 .*. O " "ATOM 20139 CB ASP A1435 .*. C " "ATOM 20140 H ASP A1435 .*. H " "ATOM 20144 N PRO A1436 .*. N " "ATOM 20145 CA PRO A1436 .*. C " "ATOM 20146 C PRO A1436 .*. C " "ATOM 20147 O PRO A1436 .*. O " "ATOM 20148 CB PRO A1436 .*. C " "ATOM 20149 H PRO A1436 .*. H "