I have modelled a structure with a template having 24% identity as per the pdb blast result .. and my template had formylated glycine which I also wanted in my model so i modelled the structure using model-ligand.py script.. The verify 3D score of that model is coming as 60% only .. can anybody tell me how can i improve the score .. I modeled some 50 structures and then for the best one I went for loop modeling and then loop refining using modeler only but I am not able to increase the score .. can anybody tell how can i improve the scores and structure too..