[phenixbb] Phenix refine - R free does not decrease

Pavel Afonine pafonine at lbl.gov
Thu Feb 5 19:10:47 PST 2015


Hi Almudena,

knowing that your structure is composed of nucleic acids and resolution 
is around 3A I can envision that refinement may benefit from using 
DNA/RNA specific restraints that we have added just recently and that 
are available in most recent Phenix nightly builds only:

http://www.phenix-online.org/download/nightly_builds.cgi

These molecule-specific restraints include restraints on H-bonds for 
interacting base-pairs and parallelity restraints for stacking bases and 
base-pairs. These restraints help maintaining correct model geometry in 
low-resolution refinements or refinements when R-factors are not quite low.

Now, you say you have 3A resolution data and Rwork= 0.25 and Rfree= 0.32.
Let's see what's in PDB at similar to yours (3A) resolution:

Histogram of Rwork for models in PDB at resolution 2.90-3.10 A:
      0.139 - 0.166      : 20
      0.166 - 0.192      : 221
      0.192 - 0.219      : 611
      0.219 - 0.245      : 684
      0.245 - 0.272      : 288 *<<< your case*
      0.272 - 0.299      : 83
      0.299 - 0.325      : 16
      0.325 - 0.352      : 5
      0.352 - 0.378      : 0
      0.378 - 0.405      : 1
Histogram of Rfree for models in PDB at resolution 2.90-3.10 A:
      0.180 - 0.209      : 31
      0.209 - 0.238      : 205
      0.238 - 0.267      : 592
      0.267 - 0.296      : 733
      0.296 - 0.325      : 285 *<<< your case*
      0.325 - 0.353      : 72
      0.353 - 0.382      : 8
      0.382 - 0.411      : 2
      0.411 - 0.440      : 0
      0.440 - 0.469      : 1
Histogram of Rfree-Rwork for all model in PDB at resolution 2.90-3.10 A:
      0.001 - 0.011      : 32
      0.011 - 0.021      : 85
      0.021 - 0.031      : 224
      0.031 - 0.041      : 353
      0.041 - 0.050      : 412
      0.050 - 0.060      : 375
      0.060 - 0.070      : 221 *<<< your case*
      0.070 - 0.080      : 126
      0.080 - 0.090      : 67
      0.090 - 0.100      : 34

So.. you are not standing too far from a typical structure in PDB at 
this resolution.

If you send me data and model files I will make sure that refinement 
strategy you used is most optimal.

Pavel

On 2/5/15 1:44 AM, 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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