I recently submitted a sequence for modelling (job id 2.3) together with a template (obtained by X-ray crystallography). However, the structural alignment between the first ranked model (C-score -1.94 tm-score 0.48±0.15) and the template shows poor alignment. On the other hand, the second ranked model, that have a better C-score (C-score -1.53), seems a bit more comparable to the template. What should I do? Considering the C-score and structural alignment with the template, could I pick the second model as the most accurate one? Moreover, when I Run I-tasser without any template, the first ranked model seems more accurate than the previous one (c-score -0.94 tm-score 0.60±0.14). Should I prefer the model predicted using the template or should I choose the model with the best overall score?
Thank You in advance