[phenixbb] problem refining Fe-S cluster

Pavel Afonine pafonine at lbl.gov
Fri Jul 5 08:03:30 PDT 2013

Hi Ed,

it looks like occupancies and B-factors need to be refined and refined 
until convergence. Also, if you apply any distance restraints for 
clusters (restrain Fe-S distances) make sure these restraints are 
correct. I've seen many cases like this and typically refining 
occupancy/b-factors and making sure restraints are correct solves the 
problem. I've never seen fixing specific parameters help and I can't 
understand logic for doing this.

If you get stuck with this you can send me files off list and I'll have 
a look.


On 7/5/13 7:40 AM, Edward A. Berry wrote:
> 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
> thanks,
> eab

More information about the phenixbb mailing list