Hello! I have an FAD cofactor that appears to be covalently bound to the Asp side chain (~1.6 A away). I was told that I need to refine the structure after indicating the covalent linkage in the pdb.
If I add a line in the pdb "LINK #### ####" and then refine in Refmac5, FAD gets all messed up and shifted out of its density and R factors go up by ~5%. Any suggestions on how to do this refinement would be greatly appreciated! Kateryna
