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!
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