Two benchmark sets were used. The first set consisted of 28 CASP10 refinement targets. The second set consisted of 103 CASP11-13 refinement targets. We note that five CASP12 targets were excluded because of a lack of experimental structures. The first set was used to examine the effect of parameters for MD simulation procedures such as simulation temperature and the type of bias restraints. The second set was utilized as a test set to compare the performances between refinement protocols.