Brian (and PDB staff listening in),
  Restraint files downloaded from the pdb are autogenerated, you
unfortunately can't even deposit cif files alongside your coordinates
and diffraction data. And autogeneration does not work well for metal
clusters. Based on connectivity/atom names, the "ox" and "red" forms of
the P-cluster are identified as the same compound. The correct treatment
should be to have a constraint file with both geometries and the same
ligand-ID, but that's not possible to implement. Your best bet is to
create the restraints by hand using one of the high-res structures as a
guide, and give the ox and red different names during your refinement.
The name will be changed during deposition. It's a pain, I've gone
through it a couple of times. If you want, I can send you cif files we
used in the past off-list.

HTH,

Jens

On Thu, 2015-07-23 at 16:21 -0600, Brian Eilers wrote:
> Hello,
> 
> 
> 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