[phenixbb] low resolution, high B, low R
gerwald_jogl at brown.edu
Tue Nov 3 14:01:26 PST 2009
I am working on a 4.2 A structure and feel somewhat uneasy about my
First, my R/Rfree at the moment is 0.18/0.25. The refinement is not
complete and weights are not optimized, so the gap may get smaller. It's
just that at 4.2 A, I don't quite expect such low R factors...
There is nothing funny with the data, no messing around, no conversions
- straightforward data set and a basic rigid body,
individual_sites+group_adps, simulated annealing, no tls yet, no ncs. I
am aware that one possible answer is that phenix is just really good...
The other issue is about B factors. Phenix will happily refine B factors
to values of 300 if there is no density in the region and that brings up
the question about how to deal with disordered regions in general. Are
there any current opinions out there about what would constitute
'reasonable' B factors? Conversely, when would a B factor indicate that
it is better to remove the residue from the model instead of leaving it
and calling it disordered. Also, this is after group_adp at 4.2 A -
should I maybe take this as an indication that this is asking too much
from the data and go back to a single adp per chain and tls?
All comments are appreciated. Thanks!
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