[modeller_usage] I have problem my protien has some area seems to be extra

My template is single ... The generated output models (i created 10 moedls with modeller) the model with best energy has some area leaning out of the structure which seems to be not included in the protien ....(When Viewed with Swiss pdb Viewer)

How could i made it fit to the alignment with template. i m attaching that output file with it. its a sequence of a Baffalo family (Nili ravi); Thanx!