Hello, I am trying to model an O-glycosylation modification at a threonine, but this seems to be problematic when I try to refine the model in refmac. The run fails, and the log says that a new ligand was found (the sugar). It offers a lib.cif file to add to the library and try the refinement again. I looked at this file and it looked fine (i.e. it wrote out the correct bond that is made between the sugar and threonine). However, when I tried to refine again with the lib.cif file, the run failed again and gave the same message. Thanks for any advice!
