where r i and r i o are Cartesian coordinates of Cα atoms of the i-th residue for a conformation and the reference model, respectively. k 0 is the force constant and b flat is the flat-bottom width of the flat-bottom harmonic restraint. We used here k 0 = 0.025 kcal/mol/Å 2 and b flat = 4 Å. Such potentials were successful in allowing some structure transitions within "restraint-free" regions; and this allowed remarkable structural improvements in some cases. Here we tested additional variants of restraints. First, we tested flat-bottom harmonic restraints applied to distances between Cα atoms (Eq. 2)