[modeller_usage] Adding loops to X-Ray

Hi,
I'm trying to add 3 loops to a crystal structure (loops are missing) without making any changes to the original X-Ray. I base the script on the existing example script 'examples/automodel/loop.py'. 
My script:

##########################################################
from modeller import *
from modeller.automodel import *    # Load the AutoModel class

log.verbose()
env = Environ()

code = '5uv1'

# directories for input atom files
env.io.atom_files_directory = ['.']

# Override the regular LoopModel class to select our own loops
class MyLoop(LoopModel):
    # This routine picks the residues to be refined by loop modeling
    def select_loop_atoms(self):
        # Select gaps for loop modeling
        return Selection(self.residue_range('157:A', '163:A'),
                         self.residue_range('434:A', '439:A'),
                         self.residue_range('507:A', '517:A'))

a = MyLoop(env,
           inimodel='5uv1_fill.B99990001.pdb', #code+'.pdb', # initial model of the target
           sequence=code, # code of the target
           loop_assess_methods=assess.DOPE) # assess loops with DOPE
a.loop.starting_model = 1           # First loop model
a.loop.ending_model   = 4           # Last loop model
a.loop.md_level       = refine.very_fast # Loop model refinement level

a.make()

##########################################################

In the inimodel ('5uv1_fill.B99990001.pdb'), the missing residues have been added and simply appear as a straight line and are only connected to one end. When I try do loop modeling using the above script, the loop atoms hardly move and don't reconnect to the other endpoint. How can I model the loops without making any change to the other atoms.

Thanks,
Dan