The conformational substates of the metastable form of Motor S and their transition network were obtained in the form of a Markov state model (MSM), through analysis of the thirteen classical MD trajectories. Representative conformations of the four resulting substates are depicted in Fig , along with circles indicating their steady state probabilities estimated from the MSM transition matrix. The ESI furthermore provides Cartesian coordinates of ten sample conformations for each Markov state. The transition time constants, i.e. inverse rate constants, are shown with black arrows representing the associated transitions between substates. Orange arrows represent photoisomerization. As noted in Sections 3.1 and 3.3, the transition to the stable form is always preceded by a flip of the stator pucker to that of the target stable form. The MSM groups the conformations with this pucker into a single substate, called metastable substate 1 (MS1), and an additional red arrow goes from MS1 to the stable form in Fig 7 . The 10ns time constant for this transition is estimated from the simulation time spent in MS1 for all 13 trajectories, divided by the number of THI transitions observed. The large arrow from the metastable form as a whole to the stable form is labeled with rate constant computed by WESTPA simulation (Section 3.3.4). The states and labelled arrows in Fig a complete kinetic model of the whole motor rotation process, which is analyzed quantitatively in Section 3.3.3.