[phenixbb] refinement question
PAfonine at lbl.gov
Fri Jun 26 12:30:48 PDT 2009
I would add a couple of comments too:
> I am wondering why the ncs refinement gives me a better Rfree (21.0%)
Because by using NCS you added some "observations", therefore you
improved the data-to-parameters ratio, which in turn reduced degree of
The fact that the R-factor dropped (and not increased) probably suggests
that you selected NCS groups correctly.
> the ncs refinement gives me a better Rfree (21.0%)
> than without ncs (21.7%).
Here is another stream of thought...
The target for restrained coordinate (and similarly for B-factor)
refinement looks like this (in phenix.refine):
T_total = wxc_scale * wxc * T_xray + wc * T_geometry
where the relative target weight wxc is determined as wxc ~ ratio of
Brünger, A.T., Karplus, M. & Petsko, G.A. (1989). Acta Cryst. A45,
50-61. "Crystallographic refinement by simulated annealing: application
Brünger, A.T. (1992). Nature (London), 355, 472-474. "The free R value:
a novel statistical quantity for assessing the accuracy of crystal
Adams, P.D., Pannu, N.S., Read, R.J. & Brünger, A.T. (1997). Proc. Natl.
Acad. Sci. 94, 5018-5023. "Cross-validated maximum likelihood enhances
crystallographic simulated annealing refinement"
Before wxc scale is computed, the structure is subject of a short
molecular dynamics run - this is where the random component comes into
Now, having said this, we know that if you run, for example, 100
identical phenix.refine runs, where the only difference between each run
is the random seed, you will get 100 slightly different refinement
results. The spread in R-factors depends on resolution, and if I
remember correctly, for a structure at ~2A resolution I was getting
delta_R~ from 0.1 to 2%. It can be higher at lower resolution, and
smaller at higher resolution.
The NCS term goes into T_geometry, which in turn means that it changes
(somehow) the weight. This may explain the difference in R-factors and,
I would say, the one less then 1% I would consider insignificant (unless
it is highly systematic and consistent observation, and unless it is not
made weight independent).
To make it less arbitrary I would suggest to run two refinement jobs
using "optimize_wxc=true optimize_wxu=true", one with NCS and the other
one without using NCS. I'm sure I suggested this a month or two ago.
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