Table 2. Assembly-construction results of the benchmark data set.

The EMDB IDs of the density maps and the number of subunits of the complexes are given. PDB structures or models obtained by modelling were used as target structures. The fifth column shows the Situs score of docking the PDB structure into the density map. The sixth column gives the r.m.s.d.s of the models and the seventh column shows the IS-score of interfaces in the model structures evaluated with respect to the PDB structures. The eighth and ninth columns present the results of docking the model structures into the density maps: the Situs score and the correlation calculated by Chimera, respectively.

EMDB ID	Predicted structure	Target structures	Template set	PDB structure, Situs result (Å)	Model, r.m.s.d. (Å)	Model, IS-score	Model, Situs result (Å)	Model, correlation
1494	Trimer	3crf B, 2co1 AB	Default set + 2cnz AB	1.16	4.92	0.80–0.83	1.36	0.79
1980	Trimer	2zhc A	Default set + 3iku HJ	6.16	3.83	0.14–0.21	4.17	0.59
1980	Tetramer	2zhc A	Default set + 3iku HJ	6.16	4.16	0.12–0.20	7.38	0.51
2055	Pentamer	4aod A model	Default set	2.22	2.16	0.33–0.38	1.95	0.89
2427	Trimer	4lsp G, 3se9 H model, 3se9 L model	Default set + 3ngb GH	1.78	4.64	0.14–0.33	2.01	0.84
5140	Octamer	3iyf A model	Default set + 3kfk CD	2.35	7.35	0.24–0.37	2.95	0.78
5505	Hexamer	1e9r A model	Default set	3.04	2.44	0.67–0.71	1.07	0.84
5672	Hexamer	3dvl A model	Default set	1.53	1.86	0.41–0.51	4.50	0.96