[phenixbb] High B-factors after Phenix restrained refinement

Da Duan 2dd13 at queensu.ca
Fri Dec 16 07:54:42 PST 2011

Hi Nat

I was just looking at the average B in the refinement log files from Refmac
and Phenix Refine. Thanks for the clarification on how Refmac and Phenix
calculate the average B. My next question is when depositing the structure,
is it more common to deposit structures with the "residual" B-factors or
B-factors generated by Phenix that includes the TLS and Ucryst
contribution? I also performed sfcheck and the average B generated by the
Wilson plot is ~100 which seems to suggest that the Phenix average B is
probably "more" correct?

Thanks again


On Fri, Dec 16, 2011 at 12:31 AM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13 at queensu.ca> wrote:
> > I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of
> > rigidbody refinement with Phenix Refine I proceeded to restrained
> > refinement. The R/Rfree from the refinement decreased nicely as expected
> but
> > the B average is at ~100 (using Group B factor refinement option). I took
> > the same model and mtz through Refmac and the B average is about ~40. Has
> > anyone experienced this before? I am almost positive it maybe a setting
> > issue in Phenix Refine that i should be looking at to get the B factors
> to
> > refine correctly.
> How are you calculating the average B?  Refmac prints "residual"
> B-factors in the B column of ATOM records - these do not include the
> contribution from TLS and Ucryst (an overall B-factor for the entire
> crystal).  In Phenix, the ATOM records always have the total isotropic
> B-factor, and this will always be higher than the equivalent in
> Refmac.  So it's quite likely that both programs are correct, they're
> just reporting very different things.  (And for what it's worth, a
> mean B-factor of 100 is totally normal at 3.3A resolution.)
> -Nat
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