[phenixbb] Problem in reducing R-factor
pafonine at lbl.gov
Fri Oct 11 08:27:17 PDT 2013
> I am solving a crystal structure at 1.3Å.
I would expect Rwork~0.15-0.17, Rfree~0.17-0.19 at this resolution
(numbers obtained using phenix.r_factor_statistics).
> Completeness of the data-set (...) at this resolution are 99.5%
Completeness reported as single number (as opposed to completeness
reported vs resolution) isn't really very informative..
> Structure has two molecules per asymmetric unit. I used TLS parameters and NCS restraints.
Resolution limit for using NCS is roughly about 2A. So turning OFF NCS
is clearly a good idea. However, effect of using torsion NCS should
vanish at this resolution. So I am particularly interested to know if
turning NCS off helps or shows any effect at all.
> Rwork and Rfree are 18.09 and 19.62 respectively.
If it is really 1.3A resolution then R-factors could be better.
> I tried with reducing WXC_scale
If you choose to do it manually then at this resolution you should
rather try increasing this value, as the target is
T = wxc_scale * wxc * Tdata + wc * Trestraints .
If none of the above helps please send me data and model files and I
will try suggesting optimal refinement strategy.
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