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