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
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