Hi Bryan,

should prosthetic groups be attached to proteins by those LINK or CONNECT records as found in typical PDB files?

phenix.refine ignores LINK and CONECT records completely (many reasons). You can use the geometry_restraint.edits to define custom bonds and angles (see phenix.refine documentation), or define cif links and modifications by hand.

e-LBOW seems for _ligands_ only.

Do you have a concrete problem with elbow? Ralf