01 January 2013 13 4K Report

I have done homology modelling and then refined the model with MD in gromacs. Then I did clustering of trajectories and selected the average structure of the model. Finally I did energy minimization of the model. But I still have 3 residues in unfavorable regions of the ramachandran plot. All 3 residues are in middle of loops (10-15 residues in length). What is a rational explanation for these outliers ?

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