Hi I am getting the following error during real space refinement of the model and map. Can anybody suggest what it is actually about. It is something about geometry_restraints but I am not able to figure it out where. Can we do something in refinement settings Or change any threshold value to avoid these problems? Input is 80S.pdb ribosome and its corresponding em map. File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1486, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1388, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1269, in check_bonded_distance_cutoff raise RuntimeError(msg) Best regards Firdous