Hi all, hope this message finds you well. As in a previous topic from 2018, I’m having problems refining a covalent-bounded ligand. The link shall be made between a carbon atom that is double bonded to an oxigen “SMILES C1=CC=C(C=C1)C=O” and the SG group of a Cys residue. I generated a CIF dictionary through AceDRG in COOT and CCP4i2. But after trying different approaches during refinement, (Automatic Linking parameters, Atom selection, acceptor & donnor, ligand bond cut off and so) the result keeps being a non bounded enzyme-ligand complex (“Not linked: pdbres="LIG A 401”). I readed in the phenixbb that this was solved by changing the nature of the ligand ( http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html), but is not the way I would like to follow. Any suggestions or ideas would be greatly appreciated, thanks a lot for your time. Stay safe. -- “I’ve learned to think like a virus; no neurons, a lot of sex, and a lot of errors.” John J. Holland Biól. Sergio Aguirre Sampieri