I want to refine my structure including a sugar oligomer as the ligand in Phenix GUI.

I first put each subunit into the density and merge them together as the oligomer in Coot. Then I merged the oligomer coordinates to the protein file. Then I run phenix.elbow to get the cif file. Finally, I run phenix.refine. However, the oligomer units were pushed away from each other. I guess I need to modify the cif file to link the oligo units together. Does anyone know how I can I do it?

thanks!