[phenixbb] Can not decrease R-free value

Pham, Hang Hang.Pham at iaf.inrs.ca
Thu May 23 17:51:57 PDT 2019

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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