Hi,
  i wish to model a protein having known pdb structure. After getting a model from modeller and evaluating it I found the Dope scores from template_evaluation.py (-279092.718750)and from model_evaluation.py
(-26497.847656).
  How do I refine the model further so that it becomes comparable with the known pdb structure?
Why do I get a violatins file,Does this mean that my model is incorrect?
  The pdb structure is in form of the protein-NAD adduct, how do I insert NAD in my model. Can I separately model the active site and incorporate a ligand(not biological)in my model?

Thanks and regards,
Deepti