[modeller_usage] high model clashscore

Dear Modeller Caretaker,When performing homology modeling with default parameters ("model-default.py") and subsequent analysis with Molprobity (http://molprobity.biochem.duke.edu/) I obtain models with much more high clashscore than the template has, and model optimization does not help much.Then, Kinemage (http://kinemage.biochem.duke.edu) shows a lot of "bad" van der Waals contacts.What should I do to obtain model of higher quality (I mean to reduce clashscore and number of "bad" contacts)? Thanks in advance,Anton.