[phenixbb] R value difference in model vs data vs refinement

Nathaniel Echols nechols at lbl.gov
Thu Mar 22 11:46:15 PDT 2012

One other thought on this: which R-factors reported by model_vs_data
did you use?  This will calculate R-factors with and without outlier
removal; the latter is equivalent to phenix.refine with default
settings, but it is maybe not the obvious one to use.  A few
reflections with extreme values could account for the difference you


On Mon, Mar 19, 2012 at 11:20 AM, Christian Roth
<christian.roth at bbz.uni-leipzig.de> wrote:
> Dear all,
> I refined a structure in phenix quite good resolution (1.4 Ang.)
> After the last refinement
> I created the "table 1" to extract all data. Interestingly I got a warning due
> to small changes in the R values
> R/Rfree after Refinement. 15,46/18,16
> Phenix modelvs.data gives me
> R/Rfree 15,34/18,07
> Interestingly this is nearly exactly the value which I got after the first OHS
> scattering optimization from phenix
> R/Rfree  15,43/18,03
> The differences are of course very small and negeligible, but  I wonder why it
> happens. Esspecially taking into account that it was refined with phenix and in
> this case I would expect that both values match exactly.
> Thank you very much in advance
> Best Regards
> Christian
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