[phenixbb] differences in refinement stats between phenix-dev-2219 and -1.9-1692

Ezequiel Noguera back_noguera at yahoo.com.ar
Tue Dec 15 13:56:25 PST 2015

Hi Pavelphenix.reduce doesn't work well in my hands. I used "automatically add H's" in the phenix GUI instead. The other steps were exactly as you outlined (no water update). Thank you.
PS: phenix.reduce reads my file, but it output a pdb file with the added H's with "0" in the second column (and "new" in the last column)

    El Martes, 15 de diciembre, 2015 20:35:32, Pavel Afonine <pafonine at lbl.gov> escribió:

  Hi Ezequiel,
 version: dev-2247: Final: r_work = 0.1753 r_free = 0.2040
 version: dev-2247: Final: r_work = 0.1663 r_free = 0.2017
 look the same in a sense that if you 100 refinements each one starting with a slightly perturbed model you will get 100 slightly different refined models with both, Rwork and Rfree, varying withing about 1% at this resolution. Having said that I can postulate that r_work = 0.1753 is the same as r_work = 0.1663, and r_free = 0.2040 is the same as r_free = 0.2017.
 For some discussion see pages 75-77 here:
 "Improved target weight optimization in phenix.refine" here:
 Now, before I proceed commenting, question: did you follow exactly the steps 1)-2)-3) that I outlined in my previous email? Otherwise it does not make much sense to compare results obtained using different refinement settings.
 On 12/15/15 12:00, Ezequiel Noguera wrote:
      Thank you very much, Pavel. I don't save H's when I modify the model in coot (the input PDB file that I sent you was the output from coot). I did the refinement again, now in version 2247, without NCS. I got the same results, higher R factors and RMS deviations for the newer version. I got better results when I used "update waters" (both in Rfactors and RMS). Below, I list the statistics for refinement without updating waters. Significant differences remain. Could it be any difference in settings of default parameters between  versions?
  version: dev-2247
  Start: r_work = 0.1687 r_free = 0.2011 bonds = 0.046 angles = 1.321
 Final: r_work = 0.1753 r_free = 0.2040 bonds = 0.030 angles = 0.593
  version: 1.9-1692
  Start: r_work = 0.1651 r_free = 0.2018 bonds = 0.013 angles = 1.409
 Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011 angles = 1.321

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