Hi Changyi, I'm not sure if this will answer your question, but it is likely that the cif file you are reading into Refmac is not in the correct format from Hic-Cup. I would suggest reading your coordinate file for the ligand into the Dundee server which will output a cif formats for refinement programs. Scroll down to the Refmac output and save as a .cif, and then read this file into your next round of refinement with Refmac. After this round, Refmac will generate a new cif library containing this ligand. I hope this helps.
Cheers, Paul
