Analysis of the MSM construction by the bootstrap method.

From the Model 1 trajectory set (379 trajectories), 300 trajectories (~80%) were sampled with replacement, and 5 datasets (Sets 1–5) were created. For each dataset, we constructed the MSM models and classified them into the macrostates, as described in the Methods section. The microstates of MSM are plotted on the PC1-PC3 plane. The sizes of the circles are proportional to the populations of the clusters, and the centers of the clusters are color-coded according to their macrostates, as in Fig 5a. The results gave similar distributions of the macrostates, showing the robustness of the MSM constructed in this study.

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