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

Edward A. Berry BerryE at upstate.edu
Wed Jul 3 13:40:50 PDT 2013

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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