[phenixbb] model vs Wilson b-factor

Pavel Afonine PAfonine at lbl.gov
Wed Apr 21 10:56:47 PDT 2010

Hi Gino,

here are a few points:

- my understanding (please correct me if I'm wrong) is that the accuracy 
of Wilson B estimate drops with the resolution: lower the resolution, 
less accurate is the estimate;

- Wilson B is not a given calculated value - it's just an estimate;

- the total atomic B-factor includes the trace of overall anisotropic 
scale matrix (see Fmodel formula for the total model structure factor: 
Fmodel = scale_overall * exp(-h*U_overall*ht) * (Fcalc + k_sol * 
exp(-B_sol*s^2) * Fmask) ). You can try to disable this and see if this 
was the cause (use "apply_back_trace_of_b_cart=true" keyword for this).

- the things you "tried to resolve this discrepancy" will unlikely to 
change the average B-factor;

- assuming that you used the proper model parameterization and 
refinement strategy given your model and data quality,  I would just 
accept these values as a matter of fact.


> 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?

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