“…Other order parameter pairs to characterize 2D motions include the RMSD to/from the final and/or initial structure(s) [23,59,61,62], essential variables from PCA or NMA [8,23,43,65,69,70], and fractions of native contacts relative to the initial and final structures [16,59]. Lou and Cukier [71], Brokaw and Chu [72], and Pontiggia et al [73] all measure NMP-CORE separation with the distance between residues 55 and 169, but each, respectively, monitor LID-CORE variation differently: LID-CORE mass-center distance [71], C α distance between residues 127 and 194 [72], and LID-CORE angle [73]. Progress along one dimension (e.g., plotting the potential of mean force) was captured using domain mass-center distances [24,58,69,74], RMSD to and/or from crystal structures [15,61,67,75], and indices or distances along a computed reaction coordinate pathway [24,47,48,66,76,77].…”