Hi,
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
Ramachandran
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?
Thanks...
Raja
----- Original Message -----
From: Pavel Afonine
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.
Pavel.
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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