I am trying to refine a protein structure that has a Fe(8)-S(7) cluster bound to it.  I have been using a cif file that has the ligand 1CL downloaded from the Protein Data Bank. This cluster is in the oxidized form and should be that way in my structure as well, but when I use refmac in CCP4i (6.4.0) it ends up refining the cluster to the reduced form.  The maps have positive density where the cluster should be, indicating that the cluster should be in the oxidized form.  It seems like refmac wants to idealize the bonds in the cluster instead of using the map as a guide for where the Fe and S atoms should go. Is there a way in refmac to ease the restraints on the cluster so that it refines with the data, and not make idealized bonds?

Thanks,

Brian

Brian Eilers

Research Associate

Dept Chemistry and Biochemistry

Montana State University