Hi Amy, first step, to help you we need to reproduce the problem on our end. For that, we need all input files, as well as the *.eff and *.log files. Also, please send us the refined model and describe what’s not right with it more precisely than just “comes out all wonky.” We will take it from there! All the best! Pavel On 12/30/25 18:21, Amy Fernandez via phenixbb wrote:
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