[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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