Table 1. Validation scores for all models.

Protein	Model	CCmask	CCbox	CCpeaks	CCvolume	FSC Average	Molprobity Score	Clash Score	Rama. Favored (%)	Rama. Allowed (%)	Rama. Outliers (%)	CaBLAM Outliers	RMSD B Length (Å)	RSMD Angles (°)
Afp1	Foldit	0.9	0.64	0.67	0.89	0.51	0.5	0	98.64	1.36	0	0.69	0.008	0.684
	Microscopist	0.93	0.68	0.72	0.91	0.53	1.52	3.52	94.52	4.11	1.37	2.78	0.008	0.872
	ARP/wARP	0.92	0.68	0.72	0.90	0.53	1.80	7.66	94.37	4.93	0.70	2.14	0.007	0.955
	Phenix	0.85	0.63	0.67	0.81	0.44	1.83	6.17	91.75	8.25	0	0	0.006	0.754
	Buccaneer	0.90	0.61	0.66	0.87	0.51	1.60	2.73	90.51	9.49	0	5.88	0.006	0.918
	Rosetta	0.79	0.51	0.54	0.77	---	1.47	1.32	87.32	11.27	1.41	7.35	0.007	1.007
Afp5	Foldit	0.86	0.72	0.75	0.83	0.54	1.13	1.25	95.92	4.08	0	0.69	0.007	0.738
	Microscopist	0.9	0.77	0.81	0.87	0.55	1.45	1.67	90.48	9.52	0	4.83	0.008	0.896
	ARP/wARP	0.88	0.75	0.79	0.85	0.55	2.06	8.38	87.91	10.23	1.86	8.53	0.08	1.493
	Phenix	0.83	0.69	0.73	0.78	0.42	1.95	4.14	78.45	21.55	0	6.73	0.008	1.225
	Buccaneer	0.84	0.70	0.74	0.80	0.50	1.72	4.82	92.41	7.59	0	3.05	0.009	1.167
	Rosetta	0.69	0.56	0.58	0.65	---	1.59	1.66	84.14	15.17	0.69	9.22	0.006	1.004
Afp7	Foldit	0.86	0.72	0.75	0.84	0.52	0.84	1.2	98.13	1.87	0	0.47	0.004	0.667
	Microscopist	0.87	0.75	0.79	0.85	0.50	1.83	4.81	88.79	11.21	0	8.02	0.006	1.082
	ARP/wARP	0.88	0.75	0.79	0.85	0.53	2.06	8.38	87.91	10.23	1.86	8.53	0.008	1.493
	Phenix	0.8	0.69	0.72	0.74	0.45	2.05	6.18	81.82	17.05	1.14	0	0.008	1.392
	Buccaneer	0.85	0.73	0.76	0.82	0.50	1.88	5.98	90.00	10.00	0	5.71	0.007	1.083
	Rosetta	0.66	0.44	0.47	0.61	---	1.6	2.1	87.02	12.98	0	6.5	0.005	0.863
Afp9	Foldit	0.85	0.75	0.78	0.83	0.47	1.06	2.75	98.21	1.79	0	1.82	0.009	0.829
	Microscopist	0.87	0.79	0.82	0.85	0.46	1.58	2.76	91.07	7.14	1.79	6.36	0.007	1.082
	ARP/wARP	0.86	0.78	0.81	0.84	0.47	2.19	10.27	86.11	13.89	0	11.32	0.007	0.952
	Phenix	0.83	0.73	0.76	0.8	0.41	1.68	2.78	87.18	12.82	0	5	0.006	1.042
	Buccaneer	0.81	0.69	0.72	0.78	0.41	2.00	5.21	80.85	17.02	2.13	6.67	0.009	1.251
	Rosetta	0.81	0.72	0.74	0.79	---	1.69	3.85	91.07	8.93	0	4.55	0.007	1.476

For each of the 4 different proteins, any method that outperformed the other 5 for a particular metric is shaded in green, with any method outperformed by the other 5 shaded red. CC_mask, CC_box, CC_peaks, and CC_volume are correlation coefficients calculated between the model and the map. The differences between these correlation coefficients arise from whether the entire map is used (CC_box), only the map around the atomic centers (CC_mask), the molecular envelope defined by the model (CC_volume), or the strongest peaks in the model and map (CC_peaks) [14]. CaBLAM uses the geometry of Cɑ atoms to evaluate low-resolution structures [35]. Clashscore reports on the number and severity of steric clashes in a model, and Molprobity score combines the Clashscore with other geometric factors to provide an overall evaluation of model quality [35].

AFP, antefeeding prophage; FSC, Fourier shell correlation; Rama., Ramachandran; RMSD, root mean square deviation