[phenixbb] low resolution, high B, low R

gerwald jogl gerwald_jogl at brown.edu
Tue Nov 3 14:01:26 PST 2009

Hi All,

I am working on a 4.2 A structure and feel somewhat uneasy about my 
refinement results.

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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