Dear Nasir,

Ramachandran Plot as you are aware provides us with information regarding the conformation of protein residues and their corresponding phi psi torsion angles. Now the outlier residues are the ones which do not have a stable phi:psi angle value and thus they are predicted to be conformationaly unstable.

The basic reason why this happens is the nature of the template and the identity ratio between the template and the query. You can check the number of outliers prior o simulation and post simulation. If the number of outlier increases after simulation, you might want to look at the force field that you are using.

Hope this helps, Best Sayak

Dear Sayak,

thanks for your answering and good suggestions.

Sayak i am searching for the reason behind the outlier region as Is there structural problems such as repulsion, but trivial to discuss? Is there special structure to make it have physiological role?

Unfortunately Nasir, outliers in structures are just bad conformations of amino acids. However, if you are working with unstructured or disordered proteins then you might have large number of outliers since that is the instrinsic property of such proteins - "disordered state"

Regarding whether amino acids which are in outlier region have specific physiological roles - I am not sure since there are no such report to my knowledge.