[phenixbb] divergence of R and Rfree at the last step of refinement

Pavel Afonine pafonine at lbl.gov
Wed Jul 3 13:53:07 PDT 2013


Hi Ed,

please try latest build - this keeps changing from build to build. If 
this doesn't fix it then please send me the files off list and I will 
investigate.

Pavel

On 7/3/13 1:40 PM, Edward A. Berry wrote:
> I'm refining a structure with phenix-dev-1414 version,
> and R-free decreases until the last step where R-work drops
> sharply and R-free increases. Am I doing something wrong?
>
>  R-factors, x-ray target values and norm of gradient of x-ray target
>  stage     r-work r-free  xray_target_w  xray_target_t
>    0    :  0.3068 0.3347   4.111964e+00   4.184576e+00
>    1_bss:  0.2296 0.2735   3.919523e+00   4.036648e+00
> 1_weight:  0.2296 0.2735   3.919523e+00   4.036648e+00
> 1_xyzrec:  0.2377 0.2725   3.938818e+00   4.036514e+00
>    1_adp:  0.2311 0.2707   3.918953e+00   4.031556e+00
>    1_occ:  0.2311 0.2707   3.918944e+00   4.031541e+00
>      end:  0.2187 0.2795   3.907777e+00   4.050961e+00
> //////////////////////////////////////////////////////////////////
>
> Looking in the log file, it seems that this happens at the stage of
> correcting the solvent mask:
> ============================= updating all scales 
> =============================
>
> start: r_work=0.3152 r_free=0.3389 (reset all scales to undefined)
>     bulk-solvent and scaling: r_work=0.2324 r_free=0.2703
>     remove outliers:          r_work=0.2324 r_free=0.2703
> *-> correct solvent mask:     r_work=0.2187 r_free=0.2795 <--***
> final: r_work=0.2187 r_free=0.2795
>
> overall anisotropic scale matrix:
>       V0: 2.5130,-0.3626,1.3424,-0.7174,-0.0625,-2.3276
>       V1: -0.0348,-0.0556,-0.0105,-0.0091,0.0085,0.0052
>
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