[phenixbb] Phenix refine - R free does not decrease

Almudena Ponce Salvatierra maps.farma at gmail.com
Thu Feb 5 01:44:35 PST 2015

Dear all,

I am refining my structure (data at 3 A), with a model that is complete.
However the Rs values are: R work= 0.25 and Rfree= 0.32. I have read
"Improved target weight optimization in phenix.refine" (In the
computational crystallographic newsletter 2011) and what I understand is
that just by marking the boxes "improve xray/stereochemistry weight" and
"improve xray/adp weight" it should work... giving me the best possible

I'm refining individual coordinates, occupancies, b-factors (isotropic for
all atoms), TLS, and using secondary structure restraints, automatic ligand
linking and experimental phases restraints. Also, I chose this strategy
because I have finished building the structure and according to some of the
suggestions in "towards automated crystallographic structure refinement
with phenix.refine".

I am actually quite confused and don't know what to think... is it a matter
of the weights? is it only that this is as good as it gets?

Any suggestions and comments are welcome.

Thanks a lot in advance,


Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
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