Is it possible to do a loop refinment of a model by giving the residue
range plus the template (which will hold the desired spatial location)?
If you already know the "desired spatial location" then what are you
trying to refine?
The orientation of the loop in my model its different to my template’s.
Modeller does not use the template orientation for loops (many loops
correspond to insertions anyway). The starting conformation for a loop
is random and is influenced only by the termini positions. See the loop
modeling paper or https://salilab.org/modeller/10.1/manual/node499.html
If you want to manually set the starting conformation for the loop,
override the build_ini_loop() method: