Hi all,
I have a refined structure with phenix. The resolution=3.2 Ĺ. After refinement, the R-work=0.2186, R-free=0.2864, Bonds=0.010, Angles=1.515.

Ramachandran outliers: 4.8%, Ramachandran favored: 80.8%.

Rotamer outliers: 14.5%, c-beta outliers: 2

clashscore: 16.28, overall score: 3.32

To fix the Ramanchandran outliers, in coot, by changing the phi-psi of the outliers, I could manage to move most of them to the allowed positions. But, after another refinement in phenix, those outliers come back.

I am wondering whether any of you have any suggestions for me on how to fix these outliers.

Also, I read in a previous post that “all outliers could be first fixed 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”.

I am wondering whether any of you have done this before in coot, and can you please tell me specifically how this is done. Thank you so much!

Best,

Wei