I have modeled an analog of a protein using MODELLER version 9.18. After modeling, one of the two loops of the protein showed relatively high energy in the DOPE energy profile (Fig attached). So, this loop region of the protein was refined using MODELLER.
For validation I have used ERRAT along with other programs. In the ERRAT plot the overall quality factor of the model was 96.0784. But the plot showed there were some residues (within the refined region) which attained zero (0) value (Fig attached).
Can anyone help me to interpret this result? Is it acceptable or should I not use loop refinement for my protein?