As mentioned in the title, is there any way to ignore/skip loop modeling in MODELLER9v21? My script is as follows:

==========[script]============

env = environ()
a = automodel(env, alnfile='HM_1KTZ-202_het.ali',
              knowns='202_het', sequence='TGFbeta1_HM_1KTZ',
              assess_methods=(assess.DOPE,
                              #soap_protein_od.Scorer(),
                              assess.GA341))
a.starting_model = 1
a.ending_model = 3
a.make()

==========[script]============

My template has a missing loop (13 amino acids long) but MODELLER automatically links before/after the loop region for the modeled structures, which looked quite unreasonable.