In the denominator of the R-factor equation, Sum(|Fobs|) could be replaced by Nref*<Fobs>. Then if <Fobs> is the same for free and working reflections, which it should be to a good approximation, it could easily be shown that the overall R factor is the average of the free and working R-factor, weighted by the number of reflections in each. Thus if 5% of reflections ar free, Rall = .05*Rfree + .95*Rwork Although the meaning of this is quite different from the Rall you would get by doing a final refinement against all reflections. Young-Jin Cho wrote:
Hi everyone, While I am trying to deposit, I am faced with several things that I am not sure: FYI. I am in the <Refinement Statistics> section (Auto Dep Input Tool) in the PDB bank. Most values are came from pdb file that was made from phenix.refine but it asks me "R-factor (all)" that satisfy the limits established by high & low resolution cut off and "number of unique reflections (all)". My simple question is if phenix has those kind of information, if so where I can find them.
Another question is if I changed water (deletion or changed occupancy) based on 'precheck', should I run phenix.refine again to get R/Rfree values in correct? I am not sure if these are captured by PDB automatically or not. (seemingly they do like that at this point but not 100% sure yet.)
With many thanks~
Young-Jin
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