[phenixbb] High B-factors after Phenix restrained refinement

Steiner, Roberto roberto.steiner at kcl.ac.uk
Fri Dec 16 08:11:33 PST 2011

Hi Da

Even if you deposit a structure refined with Refmac the PDB now expects the total B values being present. Have a look at

What you call "more" correct does not really make much sense to me if I understand you properly. If you follow the link given above (or use TLSANL directly from the CCP4) and get 'total Bs' from Refmac  I am sure they will be more or less the same and the Bs from phenix.refine.


On 16 Dec 2011, at 15:54, Da Duan wrote:

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<mailto:nechols at lbl.gov>> wrote:
On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13 at queensu.ca<mailto: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.)

phenixbb mailing list
phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>


Roberto Steiner, PhD
Randall Division of Cell and Molecular Biophysics Group Leader
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.steiner at kcl.ac.uk<mailto:roberto.steiner at kcl.ac.uk>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20111216/413185a4/attachment.htm>

More information about the phenixbb mailing list