We are currently trying to build a model that has a nonstandard ligand that is covalently bonded to two peptide chains.  We've placed the ligand and linked it using Coot, but phenix.refine keeps removing the links.  We generated the restraints using Elbow and wrote the .edits file using phenix.link_edits, but phenix.refine is still removing the links.  We also tried turning on automatic ligand linking in phenix.refine, but that didn't work either.  Any advice?