I predicted the tertiary structure of a protein with Swiss-Model and Phyre2. Then, I refined the structure using ModRefiner. When I got a Ramachandran plot of the structure some outliers were present, like in the picture above:
The residues in the general plot are GLN; LYS; SER; GLN; and the ones in the pre-proline plot is GLN.
What is the better explanation for this outliers and how can I solve them?
I appreciate any help!