The atom names of F3S (and SF4) have been switched around at least once since it was introduced (or perhaps they weren't standardized before). Using the current library with a cluster from an old file, the restraints will pull it all out of shape- "wonky" as you say. Generate a cluster with modern param (coot get ligad?), superimpose on your input structure, and see if the atom names are the same, if not rename them. And if you explicitly define the links to amino acids, be sure they are revised where necessary to fit the new names. Here is what worked for me when I was refining an old structure in a new phenix about 2 years ago: SF4: FE2 -> FE3 FE3 -> FE2 S2 -> S3 S3 -> S2 F3S: FE1 -> FE4 FE3 -> FE1 FE4 -> FE3 S1 -> S2 S2 -> S4 (S3 -> S3) S4 -> S1 good luck, eab Amy Fernandez via phenixbb wrote on 12/30/2025 9:21 PM:

Hello Phenix BB,

I'm attempting to refine a model with a 3Fe4S cluster into a medium resolution cryoEM map. Every time I run a refinement job, the cluster comes out all wonky, as in the attached image. I found one previous thread on this topic and when I played with the "superpose_ideal_ligand" setting, I got an error stating that the F3S residue is missing atoms. Should I just generate a restraint file? Any advice on how others have handled this welcome.

Best, Amy __________________________________________________ Amy Fernandez Berger Labhttps://berger.med.jhmi.edu/ - The Johns Hopkins University School of Medicine PhD Candidate - Program for Molecular Biophysicshttps://pmb.jhu.edu/

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