Hello, I am trying to refine PDB 1YEW using the default phenix settings. $phenix.refine 1yew.pdb 1yew.mtz yields: ''' Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 6 Please edit the PDB 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. ''' $ phenix.ready_set 1YEW_H.pdb yields: ''' Sorry: Atoms in the input are supposed to be bound CU1(CUA) - CU2(CUA) = 2.58 Fix the input file and retry ''' I assume this means that the Cu atoms in CUA are at an inappropriate distance. Is there an easy way to find out what the appropriate distance is? Can I fix this in coot? Thanks, Bradley