[phenixbb] Question about structure quality

Pavel Afonine pafonine at lbl.gov
Tue Apr 5 13:57:12 PDT 2011

Hi Jason,

> The Ramachandran statistics are poor; I've seen worse published, but 
> it would be wise to fix these.  I'm assuming you don't have a 
> high-resolution structure that you can use as a reference model - this 
> is usually the best option.  Otherwise, adding Ramachandran restraints 
> will probably help a lot, but you should first fix all outliers 
> manually in Coot (also applying real-space refinement with Coot's 
> Ramachandran restraints turned on), as the default potential is very 
> tight and can pull residues the wrong way if they're starting from a 
> very bad position.

- 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.

- Run refinement with weights optimization (optimize_wxc=true);

- Use NCS if available;

- Secondary structure restraints should definitely help, but:
   -- you need to have secondary structure well defined in your input 
model if you want phenix.refine to pick it up automatically (and 
correctly), or alternatively
   -- define it manually in a parameter file and supply to phenix.refine.


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