Refinement with the combined restraints was overall the best choice among the tested types of restraints (Figure ). Refinement with different types of restraints was tested at two simulation temperatures, 298.15 K and 360 K. Regardless of the simulation temperature, the combined restraints generally worked well for improving both global and local structure features. Comparing performances between the Cartesian restraints and the distance restraints, the Cartesian restraints showed better performance in terms of improving global structure similarity (based on RMSD and GDT-HA scores ), whereas the distance restraints did as good or slightly better for local structure refinement (based on lDDT and SphereGrinder 58 scores) (Figure and Figure ). Some examples of refinement with different restraints are illustrated in Figure . Refinement of TR663 (PDB ID: 4EXR) was successful regardless of the restraint type, but it was most successful with the distance restraints (Figure ). With the distance restraints, collective motions of larger structure elements such as secondary structure elements became possible as they are linked by restraints. As a result, orientation error of a helix and β-sheet curvature were improved, while keeping their local structures. These improvements led to significant improvements in both global and local structure qualities. With Cartesian restraints, it was also possible to improve these regions, but the refinement was not as extensive as with the distance restraints because the sampling necessary to achieve the improvements required too much deviation from the initial model in terms of RMSD. Therefore, the Cartesian restraints limited the ability to reach the lower energy states closer to the native (Figure ).