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