Figure : Implied timescales of binding mode transitions. The implied timescales shown here were calculated from an MSM utilizing all of our MD simulations of toluene in T4 lysozyme L99A. The black line denotes when the lagtime is equal to the implied timescale; timescales below this line (gray) have already relaxed and cannot be estimated accurately; shown here are the 10 slowest implied timescales. Overall, this shows that the slowest timescale in this system (in this case the out-ofplane flip of the ring ) has an implied timescale of roughly 100 ns.