Thank you Nat, Pavel, Actually, the NCS approaches a 3-fold crystallographic symmetry axis with 3 types of protein molecules plus 2 restraint groups for DNA molecules. The result is the same with "optimize_wxc=true optimize_wxu=true" options, Rfree is going up without NCS by ~1.5%. Rwork is practically the same. Should I increase the test set (now it's 5%)? or should I leave NCS=true for the final pdb? Maia Nathaniel Echols wrote:
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.
-Nat
------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
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