Backbone degrees of freedom (dofs) that were free to move in simulations. For each model system we include the main evidence that was used for choosing a specific set of degrees of freedom.

1pdb-id used: 1k3e[66] ; protein total length is 146 residues.2Simulations with local energy minimization are denoted by [M], see Methods.3Gaussian Network Models analysis on iGNM server http://ignm.ccbb.pitt.edu/[22], using default cutoff parameter of 10 ? for building the harmonic potential.4pdb-ids used: 1urp[83], 2dri[84] ; protein total length is 271 residues.5pdb-ids used: 2ezm[74], 1l5e[73]; protein total length is 101 residues.