Estimating MSM mean first passage time. We estimated timescales among our discrete states using the mfpt function from the deeptime package. The mean first passage time (MFPT) is defined as the expected time (reported in units of number of simulation frames) to reach one state when starting in another. To calculate the mean first passage time, we provided the function with a transition probability matrix for our metastable states as well as the lag time used to construct the MSM. We obtained these coarse-grained transition probability matrices using the pcca function from deeptime. Figure . Concatenated trajectory data projected onto a 2D TICA landscape. We concatenate six 100 ns parallel trajectories each of benzene, butylbenzene and hexylbenzene bound to their native crystal structures (4w52, 4w57, 4w59, respectively) to form a concatenated trajectory (18 trajectories, total 1.8 µs). In this concatenated trajectory, we select the pairwise distances between all C α -C α and C β -C β atoms in the F-helix as features. Using TICA to resolve coordinates along the slowest motions of the system, we show the trajectory projected onto the top two tICs. We map where the crystal structures for 4w52 (purple star), 4w57 (cyan star) and 4w59 (green star) fall on this landscape. The arrangement of the crystal structures suggest that traversing along the first TICA component captures the discrete changes in the F-helix.