Our aim in CASP12 was to improve our Template‐Based Modeling (TBM) methods through better model selection, accuracy self‐estimate (ASE) scores and refinement. To meet this aim, we developed two new automated methods, which we used to score, rank, and improve upon the provided server models. Firstly, the ModFOLD6_rank method, for improved global Quality Assessment (QA), model ranking and the detection of local errors. Secondly, the ReFOLD method for fixing errors through iterative QA guided refinement. For our automated predictions we developed the IntFOLD4‐TS protocol, which integrates the ModFOLD6_rank method for scoring the multiple‐template models that were generated using a number of alternative sequence‐structure alignments. Overall, our selection of top models and ASE scores using ModFOLD6_rank was an improvement on our previous approaches. In addition, it was worthwhile attempting to repair the detected errors in the top selected models using ReFOLD, which gave us an overall gain in performance. According to the assessors' formula, the IntFOLD4 server ranked 3rd/5th (average Z‐score > 0.0/–2.0) on the server only targets, and our manual predictions (McGuffin group) ranked 1st/2nd (average Z‐score > −2.0/0.0) compared to all other groups.