>On ssessing the stereochemical
> quality of the model, I found that it had 28 outliers residues (phi, psi), that
> were lying in disallowed regions of Ramachandran plot. Most of these residues
> are functionally important and hence can not be ignored. Will it be fine to
> select each of these residues and model them using loop modelling?
I am not the greatest expert in the area, but, maybe, I could try to help you with somethings.
You said you are working with a tetrameric model. It must be a very large model. The first point I think you should pay attention is: How large is it? Which percentage 28 residues represents? Of course 28 residues are not irrelevant, but I think you should put it on the right scale. In a 280 residues model it could mean your model is not good. On the hand, in a 2800 residues (we are talking about a tetrameric model), it just represent 1%. Any way, the suggestion you have already received in the first answer is one manner to correct "mismodelled" residues. But don't forget the begining, your template. Even, making more models.
Another point is that residues in disallowed regions generally means mismodelled residues, but them can also be related with important functions and these "wrong" angles are indicative of functionally important positions (there are a few papers discussing it, but I am not really updated). Check the template. Do these residues have "allowed" angles? And in other homologous structures?
I hope my email help more than confuse you.
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