On Tue, Apr 5, 2011 at 1:57 PM, Pavel Afonine
- Often using Ramachandran restraints fixes the problem right away, so I would probably do it first, and then walk through the list of outliers that you had before refinement run with Ramachandran restraints, and see *how* these outliers were fixed. Nat's suggestion should work too but might require more up-front work.
It will "fix" the problem only to the extent that the Ramachandran statistics/plot look better - this does not automatically mean that the structure is more accurate. When you are refining against one of the primary validation criteria, more up-front work is essential. (The restraints will also not automatically fix every problem, so if you blindly turn them on without any rebuilding, the result will likely be worse than if you correct as many residues as possible yourself.) -Nat