[phenixbb] Peptides bonds in cyclic peptides

Hi, I've been trying to refine a structure of a protein with a cyclic peptide bound to it. Adding LINK/CONECT to the pdb file works in coot but the bonds are not present after refinement in phenix. I tried creating a param file (I followed recommendations for making ASN/NAG bonds posted here a while ago, but changed the names of connected residues) and included it in refinement, but the bond was not formed and the amino and carboxy groups of respective amino acids were far apart. I also got a message after refinement that a cif file was not specified. What's the solution? Thanks, Chris