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