[phenixbb] Sugar refine in phenix

Hi everyone, This is a basic question. I would like to refine the sugar ends of my protein. The sugar polymers are made of NAG and BMA and whenever I use phenix.ready_set and subsequently phenix.refine it results in a structure of disconnnected sugar monomers. Indeed the cif file generated by phenix.ready_set does'nt give any geometry constraints for connecting the monomers. How do create a cif file that tells phenix.refine how to refine the sugars? Thanks, Jan