On Tue, Apr 5, 2011 at 1:32 PM, Jason
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. -Nat