[phenixbb] ncs

Nathaniel Echols NEchols at lbl.gov
Tue May 5 08:49:42 PDT 2009

On May 4, 2009, at 6:48 PM, Maia Cherney wrote:
> The resolution is 2.15 A. The NCS was always on during the refinement
> until we got low R factors (19.2% and 21.2%). Then the NCS was turned
> off for the final refinement and the R factors increased, which is
> strange as they should be going down when you apply less restraints.

This isn't necessarily true - regardless of which program you use to  
refine, R-work isn't actually the refinement target, and minimization  
algorithms aren't foolproof either.  When you remove the restraints  
you are effectively decreasing the observation:parameter ratio, which  
increases the risk of overfitting.  If nothing else I would expect the  
gap between Rwork and Rfree to increase, but I've also seen both  
increase when NCS restraints were removed.

It may be possible that the NCS restraints are biasing your test set,  
leading to the suspiciously low Rfree-Rwork gap, but I thought this  
only applied when the NCS approached crystallographic symmetry, and  
there's no such thing as fivefold crystallographic symmetry.   
Hopefully someone else on the list can clarify this.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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