Bootstrap uncertainty analysis. In order to assess the uncertainty of our constructed models, a bootstrap analysis was performed for the MSM implied timescales (Figure ), VAMP-2 scores for 5, 10, 50, 75 and 100 microstates (Figure ), and macrostate populations (Figure ). In the bootstrap analysis, 5 independent models were constructed and analyzed using ∼50% randomly-excluded trajectories totaling ∼50% of the aggregate length. In each bootstrap, we enforced the inclusion of equal numbers of trajectories started from folded and unfolded conformations. In all figures, error bars reflect computed standard deviations across the bootstraps.