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

Edward A. Berry BerryE at upstate.edu
Wed Jul 3 21:03:14 PDT 2013


Yes, running dev-1420, using exactly the same .eff file except for serial number,
the problem is gone.
R-free actually improves in the "end" step, with almost no change
on correcting solvent mask.
Thanks!

start: r_work=0.2315 r_free=0.2704 n_reflections: 87125
start: r_work=0.3154 r_free=0.3389 (reset all scales to undefined)
     bulk-solvent and scaling: r_work=0.2326 r_free=0.2699
     remove outliers:          r_work=0.2326 r_free=0.2699
     correct solvent mask:     r_work=0.2314 r_free=0.2700
final: r_work=0.2314 r_free=0.2700 n_reflections: 87125


Pavel Afonine wrote:
> 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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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>



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