Dear all, I would like to use a reference model to try to improve my cryo-em refinement geometry. I have an AF3 model that superposes with an RMSD of 1.4Å wrt my structure, and I renumbered the residues so they match with my structure. however, I get the message Reference Model Matching Summary: reference file: renumbered.pdb Model: Reference: Total # of matched residue pairs: 0 Total # of reference model restraints: 0 input file list (truncated from the root) default_model = "RealSpaceRefine_72/rsr71_isolde1_real_space_refined_072.pdb" real_map_files = /cryosparc_P29_J343_010_volume_map_sharp.mrc" default_real_map = cryosparc_P29_J343_010_volume_map_sharp.mrc" restraint_files = eLBOW_46/elbow.P.P_pdb.001.cif" default_restraint = eLBOW_46/elbow.P.P_pdb.001.cif" phil_files = Phenix/.phenix/project_data/real_space_refine_88.eff" default_phil = Phenix/.phenix/project_data/real_space_refine_88.eff" then : reference_model { enabled = True file = "renumbered.pdb" side_chain = False secondary_structure_only = True search_options { chain_max_rmsd = 3.0 Can you please help me with this? Kind regards Valérie