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? thanks, margot