I have the following doubts and questions:
Do I need to refine all of these three loops?
No, only if you think it'll be useful.
and should there be an order
in which to refine each of these loops ( i mean, starting from N-terminus
of the larger loop, etc)?
Usually it's best to refine all three simultaneously.
Do small loops (1-5 residues) need to be refined only by the modeller
script 'model-loop-tiny.py'? If yes, please explain, why? Or the regular
'loop.py' script is fine?