Hi，I would like to ask a question about model refinement.
After building the main chain via Deeptracer, I fixed the model manually. After this I found that there are so many Ramachandran outliers inside the structure ,and I tried to refine it with COOT, It didn’t work very well.
So I’d like to ask for advice on how best to refine the structure.
Thanks
After DeepTracer/Model-Angelo (I find Model-Angelo usually does a better job, although before I used to like DeepTracer) I usually use ISOLDE (the ChimeraX plugin) to do a rough fix (don’t forget to enable secondary structure restraints!) before moving to Coot and other programs for refinement.
Thank you very much for your advice.