[phenixbb] model vs Wilson b-factor

[sbiswas2 at ncsu.edu]

Hi,
Although your resolution is low, I was wondering if you have tried adding
hydrogen during refinement, this sometimes makes a difference although
with high resolution data mainly.
Shya





> Hi all,
>
> we've solved a large structure (~20,000 residues/asymm unit), with 4-fold
> ncs and diffraction data to 3.3A.
>
> The Rfree/Rfac is ~28%-24% with OK geometry with no major outliers in the
> Ramachandran plot.
> I would think I'm done (.. after 6 years!).
>
> However, my refined model b-factor (~130A2) is >> Wilson b-factor (~80A2).
> Obviously I'm not too happy with it.
>
> Here is what I tried to resolve this discrepancy:
> --> play with wxu_scale
> --> play with B-factor weight in ncs restraint (4-fold ncs)
> --> play with number of macrocycles
> --> Redefine tls groups
>
> So far nothing really works, except switching from
> individual_adp to group_adp. However, this increases
> my Rfree by almost 3%.
>
> Any ideas?
>
> Thanks in advance,
>
> Gino
> ******************************************************************************
> Gino Cingolani, Ph.D.
> Associate Professor
> Thomas Jefferson University
> Dept. of Biochemistry & Molecular Biology
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> knowledge")
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