[phenixbb] real space refinement of 3Fe4S cluster

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/