[phenixbb] Question about structure quality

Nathaniel Echols nechols at lbl.gov
Tue Apr 5 13:47:02 PDT 2011

On Tue, Apr 5, 2011 at 1:32 PM, Jason <phenix.upitt at gmail.com> wrote:

> I have a refined structure with phenix.
> The resolution=3.8 angstrom. Molprobity analysis shows following. Can
> anyone tell me if the structure is acceptable or I need to do something to
> improve it before going to publication? Thanks.
> Poor rotamers20.95%Goal: <1%Ramachandran outliers6.15%Goal: <0.2%Ramachandran
> favored 80.13%Goal: >98%Cβ deviations >0.25Å23Goal: 0Residues with bad
> bonds:0.00%Goal: 0% Residues with bad angles:0.75%

What's the clashscore?  RMS(bonds), RMS(angles), R-work, R-free?

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.

The rotamer outliers are difficult to avoid without a reference model,
unfortunately; I'd like to fix this, but it's going to take time.  The
c-beta deviations and bad angles should be fixed; this may require
optimizing the X-ray/stereochemistry weight during refinement.  However,
they may result from sidechains sticking out of the density, which often
results in local distortions.

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