[phenixbb] Refinement differences?

[Pavel Afonine]

Hi Mark,

to me statistics from both refinement runs look essentially the same in 
a sense that if you run say 100 refinement jobs each one starting with 
slightly perturbed structure (shake in coordinates with rmsd~0.3-0.5A, 
shake in B-factor) you will get ensemble of essentially the same but 
still slightly different refined models. Variation in R-factors my be 
~0.5-2% between models in the ensemble. Geometry may vary slightly as 
well. With this in mind I would say different numbers you get are within 
the spread and I doubt the differences are really significant.

The strangest thing to me is that you still get ~9% or rotamer outliers: 
2155 is supposed to be much better in eliminating rotamer outliers 
(although it is still limited to without H included).

I agree with Eckhard: we made a lot of changed recently, such as re-do 
NCS how NCS works, using CDL (conformation dependent library for 
restraints), etc..

Of course there may be other reasons for differences between these two 
runs but this is all I can tell given amount of information provided!

All the best,
Pavel


On 2/9/16 13:54, Mark A Saper wrote:
> Hi,
> I used Phenix, build 2037 to refine a a new structure.  I reran the 
> refinement (with the identical parameters) in build 2155 (v1.10.1) and 
> obtained different statistics and slightly worse geometry.  Any idea why?
>
> In *2037*:
>                  start         final
>   ---------------------------------------
>   R-work:           0.2488        0.2244
>   R-free:           0.3003        0.2851
>   RMS(angles):      1.67           0.80
>   RMS(bonds):       0.020          0.004
>
>                Ramachandran outliers: 1.2% (Goal: < 0.2%)
>                   Ramachandran favored:  94.5% (Goal: > 98%)
>                       Rotamer outliers:   8.7% (Goal: 1%)
>                        C-beta outliers:   0    (Goal: 0)
>                             Clashscore:   3.14
>                          Overall score:   2.19
>
> *2155*
>
>                    start         final
> ---------------------------------------
>   R-work:           0.2488  0.2331
>   R-free:           0.3003  0.2856
>   RMS(angles):      1.77 0.72
>   RMS(bonds):       0.020  0.004
>
>                  Ramachandran outliers:   1.4% (Goal: < 0.2%)
>                   Ramachandran favored:  93.4% (Goal: > 98%)
>                       Rotamer outliers:   9.4% (Goal: 1%)
>                        C-beta outliers:   0    (Goal: 0)
>                             Clashscore:   4.10
>                          Overall score:   2.36
> _________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry, University of Michigan
> Ann Arbor MI  48109-1055 U.S.A.
> saper at umich.edu <mailto:saper at umich.edu>     phone (734) 764-3353     
> fax (734) 764-3323
>
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160210/3c3b4590/attachment.htm>