C validating tutorial
One approach that works well to fix this type of problem is to first mutate the offending residue to an alanine, and then run real-space refinement.
These steps allow the C-beta position to be properly refined, without being trapped by the other misfit sidechain atoms (similar to the backrub in Ki NG).
Find the list of rotamer outliers, and click on Leu 27 from the A chain, which will center on this residue in the Coot window.Change your point of view (maybe center on C-gamma) and Click "Undo" and "Redo" a few times until you are comfortable with how this change is carried out.Similarly, you can correct many of the other sidechain outliers in the GUI list.It is a dynamic mechanism of validating and testing the actual product. LAKSHAY SHARMA AND I’M FULL STACK TEST AUTOMATION ENGINEER.