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 rotamers | 20.95% | Goal: <1% |
| Ramachandran outliers | 6.15% | Goal: <0.2% |
| Ramachandran favored |
80.13% | Goal: >98% |
| Cβ deviations >0.25Å | 23 | Goal: 0 |
| Residues 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