On Ramachandran Plot analysis if there are as many as 8% amino acids in unfavorable regions, what does it mean? What is the minimum percentage of amino acids in a favorable region for a protein so as to qualify Ramachandran plot analysis?
There is no minimum percentage. Any set of phi and psi angles can be plotted on the Ramachandran plot. Ramachandran outliers (and there are >1 definition of an outlier) maybe an indication that the model is poorly built, it may suggest that there are strained bonds for a legitimate reason.