[phenixbb] Can not decrease R-free value

Dorothee Liebschner dcliebschner at lbl.gov
Tue May 28 11:46:29 PDT 2019


As pointed out by a phenixbb reader (thanks!), point 3 was misleading:
TLS group cannot be refined with individual *anisotropic* B-factors (due to
technical limitations).


On Fri, May 24, 2019 at 11:38 AM Dorothee Liebschner <dcliebschner at lbl.gov>
wrote:

> Hi,
>
> A high Rfree can indicate that the refinement strategy is not appropriate.
>
> Several suggestions:
> 1) At 2.5 A resolution, you probably don't need reference model
> restraints.
> 2 ) Simulated annealing (SA) is most useful early in refinement, when the
> model is far from convergence. Manually built models, or MR solutions
> involving significant local conformational changes, are common inputs where
> SA can improve over simple gradient-driven refinement. It is generally less
> helpful later in refinement, and/or at high resolution.
> 3) Individual B-factors and TLS are mutually exclusive, so did you define
> different strategies for different areas? If yes, you could try to revisit
> the parameterization.
> 4) It might be also worthwhile to double check the secondary structure
> assignment for secondary structure restraints.
>
> Weight optimization is typically done at the end of refinement. So while
> you are trying to figure out the strategy, you might want to disable it, as
> it is time-consuming.
>
> Best wishes,
>
> Dorothee
>
>
>
> On Thu, May 23, 2019 at 5:54 PM Pham, Hang <Hang.Pham at iaf.inrs.ca> wrote:
>
>> Dear all,
>>
>> I am refining my structures at 2.5 A. The model is well fitting in the
>> electron density. I already add water and ligands.
>> I’m trying these options (XYZ coordinates, real-space, TLS parameters,
>> Individual B-factors, Optimize X-ray/stereochemistry weight, Optimize
>> X-ray/ ADP weight, Reference model restraints, Use secondary structure
>> restraints, Simulated annealing (Cartesian), Automatically correct N/Q/H
>> errors) to refine the structure but the R-free still be high.
>> The reference model is 98% identity with the structure that I’m building.
>> After refining, the R-work always decrease while R-free increase. My last
>> values for R-work is 0.2501 and for  R-free is 0.3246.
>>
>> I’m lost and don’t know what to try more.
>> Can anyone could explain me what happens here ? What others options that
>> I could use to optimize R-free value ?
>>
>> Thank you in advance !
>>
>> Hang Pham
>>
>> ------------------------------------------------------
>> Hang Pham, Ph.D Student,
>> The Doucet Lab
>> Centre Armand-Frappier Santé Biotechnologie
>> Institut National de la Recherche Scientifique (INRS)
>> Université du Québec
>> Réseau International des Instituts Pasteur
>> 531 Boulevard des Prairies
>> Laval (Québec) H7V 1B7  CANADA
>> Téléphone : (450) 687-5010, poste 4210
>> Site web: http://www.profs.inrs.ca/ndoucet/
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
>
> --
> Project Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>


-- 
Project Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190528/72267208/attachment-0001.htm>


More information about the phenixbb mailing list