Hi Ezequiel,

version: dev-2247: Final: r_work = 0.1753 r_free = 0.2040
vs
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:
http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf
and
"Improved target weight optimization in phenix.refine" here:
http://phenix-online.org/newsletter/CCN_2011_07.pdf

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.

Pavel

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