[phenixbb] model vs Wilson b-factor
rdey at usc.edu
Wed Apr 21 11:19:45 PDT 2010
I recently refined a structure at 3.7 A resolution using PHENIX and I got the following result.
R/R(free) rmsd in bond/angle B(ave) Outliers in
0.2436/0.2822 0.011/0.920 260.12 1.23%
With different trials I found the B(ave) to vary between 230 to 280. Is this B(ave) is ok for pdb submission? What options I should try to reduce B(ave). Is there any chart showing acceptable range of B(ave) at different resolutions?
----- Original Message -----
From: Pavel Afonine <PAfonine at lbl.gov>
Date: Wednesday, April 21, 2010 11:00 am
Subject: Re: [phenixbb] model vs Wilson b-factor
To: Gino.Cingolani at jefferson.edu, PHENIX user mailing list <phenixbb at phenix-online.org>
> 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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