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[modeller_usage] one question,please answer


Dear all,
I have one question about evaluation of my built model by DOPE score. After building model, I refined the side chains of residues with SCWRL3 program.The total Dope score of initial model was better than the refined model;but the structure of two disallowed regions of my initial model  (with DOPE score higher than -0.03) were become better. 
In evaluation of stereochemical features of built models by PROCHECK, the side chains , as we expected, became better . but the amount of bad contacts became more.
Could you tell me please which model is better? (initial model or refined model)
One note : Before refining by SCWRL3 ,I have refined the loops of my model with modeller;But it did not built a better model.
Thanks for your attention.
Best regards,