Table 4. Comparison of loop closure methods.

	RMSD (Å) for default protocol			RMSD (Å) for CCD protocol			RMSD (Å) for KIC protocol
PDB	loop	IRMSD	LRMSD	loop	IRMSD	LRMSD	loop	IRMSD	LRMSD
1dle	0.09	0.04	0.16	0.25	0.10	0.17	0.11	0.10	0.39
1fc4	0.40	0.08	0.08	0.34	0.09	0.12	0.50	0.11	0.10
1qni	1.99	0.53	0.47	2.85	0.60	0.56	2.21	0.48	0.43
2qpv	0.63	0.19	0.23	0.66	0.20	0.30	0.34	0.11	0.24
3dxv	0.62	0.14	0.13	0.51	0.13	0.12	0.78	0.20	0.18
1u6e	0.13	0.06	0.12	0.17	0.05	0.09	0.09	0.05	0.09
2bwn	1.30	0.30	0.29	1.77	0.40	0.58	1.80	0.36	0.39
1jtp	0.08	0.07	0.30	0.20	0.11	0.21	0.19	0.12	0.42
2hp2	3.43	1.37	1.24	4.56	1.60	1.44	4.68	1.43	1.28
2wya	0.24	0.06	0.06	0.71	0.14	0.12	0.12	0.02	0.03
2obg	0.34	0.26	0.58	0.45	0.33	1.05	0.47	0.36	0.70
2i25	0.11	0.28	2.18	0.22	0.40	3.17	0.11	0.24	2.00
3cgc	2.23	4.74	14.16	3.08	19.38	56.97	2.66	6.63	21.68
3ean	0.06	0.03	0.06	0.06	0.02	0.04	0.07	0.03	0.06
1fec	0.14	0.03	0.04	0.14	0.03	0.02	0.11	0.02	0.03
1zr0	0.17	0.14	0.47	0.10	0.07	0.70	0.06	0.04	0.20

This table demonstrates the rough equality of results from KIC, CCD, and combined loop sampling. The default protocol columns are the same as in Table RMSD; the CCD and KIC columns were generated using either loop modeling type alone. Each column represents one of the RMSD metrics described in the Results. Each of the loop modeling choices is broadly equivalent. Notice that structure 3cgc has in lower RMSDs under the combined protocol than either loop sampling type alone; this is a falsely optimistic interpretation because AnchoredDesign is never correctly predicting 3cgc under any of these protocols. The structures produced for 3cgc are isoenergetic and it is coincidental that the combined protocol happens to have lower RMSDs.