Hello all!

I am using Modeller to construct a homology model of my query sequence (250AAs) from two template proteins (A: major protein of 225 AAs and B: minor protein of 25 AAs). The overall identity of the query and template is very high (~85%). There is a loop of 20-25 amino acid, which is constructed using the template B. 

To my surprise, in the final model, the constructed loop of about 20 amino acid is very weird and is folding back into the protein (sandwiched between secondary structure) resulting in numerous clashes. I feel this is unusual. Could anyone suggest me the reason for this and the probable solution as well?

Best,