[phenixbb] questions related to Phenix refinement

Pavel Afonine pafonine at lbl.gov
Sat Jan 17 20:36:30 PST 2015

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.


> 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.


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