[phenixbb] Can not decrease R-free value

Dorothee Liebschner dcliebschner at lbl.gov
Fri May 24 11:38:23 PDT 2019


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,


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/
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