[modeller_usage] Homology modelling a loop

Hello, I need to model a missing loop for my protein. I used the sequence of missing loop and aligned with its homologous sequence. Then I modeled my loop from the alignment. Now the problem is my modeled loop is very far away from the place where it needs to be ( due to the template i used). So how can I stitch my loop into the protein. Also, is there a way to homology model the loop such that its position is within the protein. I am attaching my script and alignment files. Sincerely, Anjela Manandhar Graduate Student Biochemistry Program Graduate Center, City University of New York 365 Fifth Avenue, NY-10016, USA