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Hi all, Many thanks to everyone that replied (publicly and privately) with the helpful advice! My first experience with sugars wasn't so sweet at first, but it all worked out... I think that I've managed to solve the problem. I think the LINKR records were not listed in the correct sequence in the pdb file, and Refmac was getting hung up. Rearranging the LINKR records fixed the problem, and Refmac was able to initiate refinement without any issues (no cif file required). I think when I'd built in the first NAG-NAG-BMA, I did not have LINKR records in the pdb file, but Refmac made its own cif file to account for this - which worked fine for a while (despite the introduction of spurious protein-sugar linkages that I'd not detected at first). Then, when some of the relative protein-sugar or sugar-sugar distances changed, the LINKR records became invalid and Refmac failed. Ultimately, what seemed to worked was: (i) deleting the spurious LINKR records, and (ii) rearranging the LINKR records so that they appeared in the proper sequence (i.e., grouping linkages by chain rather than by linkage type). Thanks again for the assistance! Cheers, Dan