Dear Nigel, thank you for the quick reply. I got phenix.pdb_interpretation to run after also supplying the options "disable_uc_volume_vs_n_atoms_check=True" and "proceed_with_excessive_length_bonds=True". It would then later hang on a "Symmetry disulfide" step but at least I got the names of the missing residues. In case it is relevant, they are 4OC, G7M, MA6, UR3, IAS, 1MG, 2MA, 3TD, 6MZ and OMU. phenix.elbow with --final_geometry=... then produced the required cif files. I am however stumped how to proceed from here. When I try to run phenix.combine_focused_maps using any of the cif files as an input argument for the parameter "restraint_files" the same error remains (i.e. the number of unknown symbols remains unchanged at 282): " Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 282 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. " Based on what I saw in the documentation, I am not sure how to work with the "apply_cif_modification" parameter definition when it comes to modified/unusual nucleotides and amino acids. I also ran ReadySet on my 7K00 cif file to generate a combined .ligands.cif restraints file and feed that into phenix.combine_focused_maps, but the outcome was the same as before. An additional problem comes up when I try to supply these restraints, either as individual cif files or as the combined one from ReadySet, to phenix.pdb_interpretation. This fails with the following error: " Sorry: Error processing CIF file: "/home/csteinmetzger/cryo-EM/ecoli_ribosome/wt/ReadySet_14/7k00_add_models_calibrated.ligands.cif" (AssertionError: /usr/software/phenix-1.21.2-5419/modules/cctbx_project/mmtbx/monomer_library/server.py line 371) " The 7K00 model I'm using here has been stripped of all waters, metal ions, small molecule ligands, tRNAs and mRNA in ChimeraX. I was not sure whether that might have done anything to the file to make it problematic. So I downloaded the file freshly from the pdb and supplied it to phenix.combine_focused_maps as is. This results in the following error: " Sorry: The model 7k00.cif does not seem to have complete residues and only RNA or protein (17719 residues and 10141 CA or P atoms) " One thing that does seem to work (at least start without error) is phenix.real_space_refine using my stripped 7K00 model and the .ligands.cif restraints file from ReadySet. I hope we can get phenix.combine_focused_maps to work as well. Christian