[phenixbb] refinement in low resolution

Pavel Afonine PAfonine at lbl.gov
Thu Dec 17 12:39:11 PST 2009


> I did tight the restrain and R/Rfree drops to 37/41 % with rms for the 
> monomer is around 0.12.

this looks reasonable...

> Also I did surprise to see the ranges of R factor while doing 
> simulated annealing but final R-factor
> goes high to 37/41 % ?
> Is it anything wrong with convergence?
>    step=   50 temperature= 2284.4 rmsd=0.6256 r_work=0.3061 r_free=0.3564
>    step=   75 temperature= 2174.4 rmsd=0.7957 r_work=0.2978 r_free=0.3483
>    step=  100 temperature= 2064.4 rmsd=0.8910 r_work=0.2978 r_free=0.3681
>    step=  125 temperature= 1954.4 rmsd=0.9354 r_work=0.2977 r_free=0.3710
>    step=  150 temperature= 1844.4 rmsd=0.9684 r_work=0.2953 r_free=0.3793
>    step=  175 temperature= 1734.4 rmsd=0.9924 r_work=0.2928 r_free=0.3819

Are you running torsion angle SA? I guess the numbers above indicate the 
overfitting. Can you try the same run with more tight geometry 
restraints (smaller value of wxc_scale parameter) - try several 
different values (smaller than the default one, 0.5 and choose the one 
that gives more reasonable Rfree-Rwork gap)?

If you have NCS - use it.

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