[phenixbb] Optimizing the Geometry Weight for a 2.76 A structure

Phil Jeffrey pjeffrey at princeton.edu
Fri Apr 2 08:09:55 PDT 2010

More pertinent to this example is the s.d. of the R-free itself, i.e.

sigma(Rfree)/Rfree ~ 1/sqrt(Ntest)

lifted from Kleywegt and Brunger, Structure, 15 August 1996, 4:897–904
(but the original analysis from an earlier paper)

So for 1000 free reflections and an R-free of 24% the sigma is about 
0.75% and exceeds the range of variation that you're seeing, i.e. not a 
significant fluctuation in R-free.

Phil Jeffrey

Pavel Afonine wrote:

> Also, the values 0.2377, 0.2388, 0.2399 ... look all the same to me. If 
> you run 100 identical refinement runs where in each refinement the only 
> difference is the random seed, you will get an ensemble of  refined 
> structures and the Rfree/Rwork spread can be as large as 1-2% or so (it 
> depends on the resolution). This is because the random seed is involved 
> in target weights calculation and therefore a small change in the random 
> seed may slightly change the weights and this may be enough for the 
> refinement to take another route to another "local minimum".

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