Table 1.

Energetics, kinetics, and structures from Markov state models of refinement landscapes

Target	Initial model*	Initial state* (MD†)	Native state* (MD†)	ΔΔG (native − initial),‡ kcal/mol	MFPT§/slowest transition, μs	Number of transitions¶
TR816	2.53/51.8/22.0	2.79/50.0/24.6	0.80/86.8/52.8	−2.46 (±0.02)	1.7/3.7 (5.1#)	5
TR837	2.95/43.8/21.1	3.93/36.0/16.7	0.88/80.2/55.1	−2.60 (±0.06)	43.4/33.1	7
TR854	2.27/60.4/28.2	2.69/66.8/31.8	1.04/80.0/45.7	−1.59 (±0.02)	1.5/1.0	3
TR782	1.93/65.2/37.1	1.99/66.8/36.2	0.94/86.4/55.4	−0.65 (±0.06)	39.6/31.0	5
TR872	5.59/56.8/38.1	2.98/67.9/43.1	1.97/79.8/55.8	−0.83 (±0.02)	2.9/2.2	2
TR921	3.51/48.4/27.1	3.32/54.2/30.4	0.90/87.3/57.8	−0.85 (±0.06)	637.9/623.0	15
TR769	1.74/59.8/33.0	1.47/65.5/35.2	1.14/72.4/41.2	−1.10 (±0.01)	0.8/0.5	2
TR894	2.23/54.2/23.6	2.49/54.2/24.8	0.85/95.4/54.2	−1.71 (±0.04)	6.0/3.9	5

^*Structure similarity between structures in Cα RMSD, GDT-HA, and GDC-SC.

^†Ensemble-averaged structures based on conformations for a given state sampled in the MD simulations.

^‡Free energy difference between the native and the initial state with SEs evaluated from 20 MSM iterations with 95% trajectory subsets.

^§Mean first passage time between initial and native state.

^¶Between initial and native states.

^#Alternate transition path.