Table 1. Comparison between the (α_h, β_h, γ_h) Sampled by TOPRNA Bulge Simulations, the (α_h, β_h, γ_h) Conformations Observed in the PDB, and Conformations Predicted by the Rigid-Body Model²⁹.

bulge	fraction of total (αh, βh, γh) sampled by TOPRNA (rigid-body)a	fraction of TOPRNA (αh, βh, γh) overlap with rigid-bodyb	fraction of rigid-body (αh, βh, γh) overlap with TOPRNAc	fraction of PDB conformations sampled by TOPRNA (rigid-body)d
1-nt	0.075 (0.053)	0.61	1.0	1.0 (1.0)
2-nt	0.11 (0.097)	0.72	0.95	0.99 (0.79)
3-nt	0.15 (0.20)	0.81	0.80	1.0 (0.99)
4-nt	0.20 (0.38)	0.81	0.53	1.0 (0.93)

^aDue to rounding (α_h, β_h, γ_h) to a 10° vs 5° grid, the rigid-body fractions differ slightly from that reported in ref (29).

^bThe fraction of TOPRNA sampled conformations that are found within the ref (29) idealized-helix topologically allowed space.

^cThe fraction of ref (29) idealized-helix topologically allowed conformations sampled by TOPRNA, excluding ref (29) conformations that were added to the rigid-body-rotation-derived allowable conformations as estimates of error padding or “intrinsic helical degrees of freedom”.

^dComparisons were done to a total of 1853, 705, 347, and 30 PDB structures of 1-, 2-, 3-, and 4-nt bulge systems, respectively.