[phenixbb] Validation question: R-factor (all) and # of unique reflections (all)

Edward A. Berry BerryE at upstate.edu
Tue Jul 5 13:18:03 PDT 2011

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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