[phenixbb] problem refining Fe-S cluster

Edward A. Berry BerryE at upstate.edu
Fri Jul 5 07:40:32 PDT 2013

I have a problem refining a structure with iron-sulfur clusters. The irons refine
to low B-factors (~25 in this case, while wilson B and B-average are around 45
and the Sg's ligating the irons are ~30).  The irons have negative difference density
and there is positive density in the center of the cluster (not on the S as it appears;
the S is actually above the plane of the irons and the positive density below).
(see attached map)
It's possible that the cluster is lost in some percent of the molecules, and I
could refine occupancy to get rid of the negative density, but I suspect this is
likely to be because the B-factors are too low. I will try manually setting B
for the Fe's and refining without ADP step, but does anyone have a better suggestion?
This was refined for one macrocycle with

     strategy = *individual_sites individual_sites_real_space rigid_body \
                *individual_adp group_adp tls *occupancies group_anomalous
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