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FreeR flags are a bit of a pain - there is the number you should select, then how to compensate for non-crystallographic symmetry and putative twinning.

Vilmos has written a useful Rfree assignment tool which covers possible twinning problems. It selects FreeR flags for the highest Laue symmetry consistent with the crystal class (eg P6/mmm for a trigonal crystal) then extends that set to cover the actual Laue group - eg P3 so that all symmetry eqivs - ( h k l and -h -k -l fand -h-k, h, l and ... ) for example would have the same value.

Sometimes that also helps with NCS which can line up along crystal axes, but it doesnt cover every scenario.. In general if you have NCS your Free R values tend to be lower than expected..

Eleanor

On 10 July 2018 at 21:49, Paul Adams <[log in to unmask]> wrote:

I’ll also add for completeness, that (in Phenix at least) by default a total of 2000 reflections will be selected at most - meaning if you have a lot of reflections the total percentage selected will be substantially less than 10% or even 5%.

> On Jul 10, 2018, at 7:44 AM, Pavel Afonine <[log in to unmask]> wrote:
>
> It's important to remember that free-R reflections are not only used to calculate Rfree, but also are used in calculation of m and D scales in 2mFo-DFc and mFo-DFc maps, as well as in likelihood-based refinement targets. The fact is that you need to have a sufficient amount of free-R reflections in each relatively thin resolution bin. Some authors estimate this number as at lest 50 reflections per bin. In Phenix binning is defined such that each sufficiently thin bin gets no less than 150 reflections. Bernhard pointed out about "precision or significance of Rfee". Also, I would add that too few free-R reflections can affect refinement progress (not only robustness of Rfree value) (I've done relevant tests to convince myself more than a decade ago)! Thus I favor having 10% just to be on a safer side.
>
> Pavel
>
>
> On Tue, Jul 10, 2018 at 1:02 AM, 张士军 <[log in to unmask]> wrote:
> Dear all
>
> I am confusing the choose of free R-flags recently. Rfactor means calculatted from reflection not used in refinement,so what's big the difference between different percentage of R-flags,like it's about 5% in ccp4 -refmac, while it is 10% in phenix-refinement,what's the difference between them and how they affect the Rwork and Rfree values when do refinement. Thanks a lot !
>
> best regards
>
> shijun
>
>
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Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

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