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low sequence identity

Dear Modeller support,
I am modeling at low sequence identity and I believe to have the following 
problem: The homologous scaffold (comprising a core of beta strands) of my 
target, after a fisrt round of modeling, displays a (suspiciously) low RMSD 
with respect to the template, and a LOT of bad contacts involving the 
hydrophobic core. Consequently I think that in my target secondary structure 
motifs should be arranged more spaciously. How can I accomplish this in terms 
of additional modeling restraints, or chopping up the alignment and modeling 
in pieces, or whatever will work?