[modeller_usage] exposed core in generated structures

Hello all-

I have a series of models that I'm looking to analyze. It seems that in many cases, the models that have been created have surface pockets/holes exposing a small portion of the hydrophobic core that are unexpected (given the template structures) and which I believe to be artifacts to the modeling process. The alignments are good, and I've been unable to come up with a way to get rid of these holes. Any suggestions are more than welcome. I also have images that I can email if what I wrote above isn't decriptive enough.