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[ccp4bb]: Link-statement

Dear all,
I have a problem when refining a protein-structure in refmac with ccp4-4.2.1. I have a covalently attached peptide-moiety bound to my protein. I was trying to connect the two residues, which are connected, by putting "MAKE LINK" or  "LINK" in the header of my pdb and specifying the two residues. But after the refinement it removed the "MAKE LINK" or "LINK"-statement in the header and did not connect the two parts. I am suspecting I am not using the right keyword or doing something else stupidly wrong.  I have also tried to specify the atoms in the two residues which I want to connect, but still have the same problem. 
I would appreciate any advice what I am doing wrong and what I have to do to succeed in linking the two parts.
Thanks very much,
Florian Schmitzberger
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
CB2 1GA Cambridge
Tel: +44 1223 766029