[phenixbb] Reproducibility of R-factors

Pavel Afonine pafonine at lbl.gov
Tue Sep 14 12:17:01 PDT 2010

  Hi Mike,

if you send me the input files (model and data) then I might be able to 
find out why you observe this difference.

Some possible sources of difference are discussed in the paper that Jeff 
mentioned in previous email:

Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, 
Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD:
phenix.model_vs_data: a high-level tool for the calculation of 
crystallographic model and data statistics. J. Appl. Cryst. 2010, 43, 


On 9/14/10 12:02 PM, miket at chem.ucla.edu wrote:
> Hi All,
> I recently used phenix.model_vs_data to evaluate a structure that was refined using Refmac. The R_work and R_free calculated by refmac are 0.18 and 0.20, while model_vs_data calculates them as 0.20 and 0.22. Should I be concerned about this discrepancy? Is it typical for different programs to calculate different values for R-factors using the same data, and if so what is the source of this difference? Seems to me like there shouldn't be much of a difference (at least not 2%). Maybe I'm wrong.
> Any insight/advice would be appreciated.
> Thanks,
> Mike Thompson

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