[phenixbb] Phenix refine - R free does not decrease

Andreas Förster docandreas at gmail.com
Thu Feb 5 02:06:34 PST 2015

Dear Almudena,

I promise not to make a habit of advertising other programs on the 
Phenix mailing list, but just once I would like to encourage you (and 
the community) to try all the tools at your disposal.

Different refinement programs have different strength and weaknesses. 
Secondary-structure restraints in Phenix are great for low-resolution 
data, but so is jelly-body refinement in Refmac.  A dodgy 3.2 Å 
structure I'm currently working on was improved dramatically by 
Buster-TNT.  The Ramachandran plot tightened, and R free plunged by four 
percentage points.


On 05/02/2015 10:44, Almudena Ponce Salvatierra wrote:
> 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
> Rfree.
> 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,
> Best,
> Almudena
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
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