Hello Smith,
In the X-ray statistics by resolution bin of the Phenix.refine result, there is a column "%complete". For my refinement data, I find the better the resolution (from lower resolution to the higher resolution), the lower the completeness (for example for 40-6 A, %complete is 98, for 3.1-3.0 A, %complete is 60%, for 2.2-2.1 A, %complete is 6%).
Will you please tell me what does this "%complete" mean? why it decreases in the better diffraction bin?
Completeness is how many reflections you have compared to theoretically possible. So the higher completeness the better. Ideally (and it's not that uncommon these days) you should have 100% complete data set in d_min-inf resolution. Anything below say 80 in any resolution bin is bad, and numbers you quote 6-60% mean something is wrong withe the dataset.
For the Ramachandran restrain in the Phenix.refine, there was a recommendation that for good resolution (I forget how much exactly, maybe 2.5 A), do not use Ramachandran restrain.
True.
But for a crystal data with resolution better than 1.5 A, in the X-ray statistics by resolution bin of the Phenix.refine result, there are more rows with resolution poorer than the defined 2.5 A (for example 40-6 A,6-3 A), although the crystal has a resolution better than 1.5 A (for example 1.4 A), can I use Ramachandran restrain in the Phenix.refine in this situation?
If I use Ramachandran restrain in the Phenix.refine, I find the R-work and R-free level goes up, can we say the strategy of Ramachandran restrain in my refinement was not appropriate?
A situation when using Ramachandran restraints may be useful starts at approximately 3A resolution and lower. Also note, Ramachandran restraints may only be used to prevent Ramachandran plot outliers, not fix them. And if you use these restraints to fix Ramachandran plot outliers (for example, when there are too many so that manual fixing is not practical), then make sure all fixed outliers make sense. Pavel