Table 1. Benchmark of SWM compared to previous Rosetta FARFAR over different classes of RNA structure motifs.

Category	Motif properties			Best of five cluster centers
				RMSD (Å)*		FNWC†,*
	No. of motifs	Length*	Strands*	SWM	FARFAR	SWM	FARFAR
Single helix or multiple helices with crystallographic context provided
Trans-helix loop	15	6	1	0.83	3.29	1.00	0.77
Apical loop	4	4.5	1	1.14	2.96	1.00	1.00
Two-way junction	14	7.5	2	0.74	1.15	1.00	1.00
Multi-helix junction	5	11	3	1.91	1.93	0.80	0.33
Tertiary contact	10	8.5	2	1.25	1.78	0.83	0.50
Multiple helices without crystallographic context provided
Two-way junction	15	7	2	1.59	1.40	1.00	0.55
Multi-helix junction	5	10	3	2.60	3.45	0.40	0.20
Tertiary contact	8	8.5	2	2.89	2.13	0.36	0.20
Non-helix embedded	5	10	4	2.81	4.30	0.80	0.71
Overall	82	7	2	1.49	1.93	0.96	0.67

*Median values reported. Mean values given in tables S3 and S4.

†Fraction of non–Watson-Crick pairs from experimental structure observed in computational model.