[phenixbb] Refinement differences?

[Eckhard Hofmann]

Dear Mark,
there were chances to the geometry restraints which most likely would 
affect your refinement.
Do you have NCS in your refinement? This has been overhauled completely, 
and is currently not very verbose.
Generally I would not be very concerned about the exact values, given 
changes in the program. And it looks to me that you are not yet at the 
final point of refinement anyway.
What is your resolution?
All the best,
Eckhard



Am 09.02.2016 um 22:54 schrieb Mark A Saper:
> 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
>
>
>
>
>
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-- 
Eckhard Hofmann <eckhard.hofmann at bph.ruhr-uni-bochum.de>
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/318
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762
ORCID: 0000-0003-4874-372X