Hi 
 We are trying to refine a protein structure with a (covalently)
 modified residue. The colosest discussion to our problem is:

 
 We ran:

phenix.elbow --residue SSC ourmodel.pdb

 And read the due cif file at phenix refinement. The residue by itself is OK, but we were 

 not able to perform the peptide bond between C and N.
How to complete the .cif file such that it has due restraints for
 the peptide bond with this modified residue?

 Agnes