Hi, I believe I have reported this bug before, but it is not fixed in the phenix.reduce and phenix.ready_set yet. The problem is the hydrogens added by reduce when there is a glycan. Here is the error message. Number of atoms with unknown nonbonded energy type symbols: 12 "ATOM 8332 HD22 ASN B 99 .*. H " "ATOM 11820 HD22 ASN B 320 .*. H " "ATOM 12615 HD22 ASN B 371 .*. H " "ATOM 14058 HO4 NAG B3320 .*. H " "ATOM 14086 HO4 NAG B3321 .*. H " "ATOM 14136 HO4 NAG B3371 .*. H " "ATOM 22458 HD22 ASN D 99 .*. H " "ATOM 25955 HD22 ASN D 320 .*. H " "ATOM 26750 HD22 ASN D 371 .*. H " "ATOM 28256 HO4 NAG D3320 .*. H " ... (remaining 2 not shown) ... Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 12 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. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). The hydrogen left on the N atom of the ASN is correct, but should be named as HD21 as defined in the ccp4 cif library. And the HO4 for the NAG glycan is just wrong. I have to delete all these hydrogens to get phenix.refine going. -- Jianghai