Table 1.

Accuracy of models before and after refinement using high-resolution cryo-EM maps and hybrid density maps of 5, 6, and 8 Å resolutions

Case a	#Amino acids b	Res. (Å) c	AF2 pLDDT d	AF2TM e	Refined models f
					High	5 Å	6 Å	8 Å
7LV9-23530-B	97	4.5	55.37	0.39	0.42	0.23	0.34	0.34
T1047S1D1-7BGL-12183-A	211	2.2	75.74	0.53	0.71	0.50	0.51	0.49 g
T1047S2D3-7BGL-12183-A	116	2.2	75.17	0.71	0.76	0.51 g	0.55 g	0.51 g
7KZZ-23093-B	281	3.42	89.76	0.76	0.81	0.80	0.70	0.66
7KU7-23035-A	269	3.4	88.56	0.76	0.79	0.79	0.78	0.71
7LCI-23274-R	393	2.9	81.15	0.82	0.95	0.94	0.94	0.64
7M7B-23709-A	209	2.95	77.60	0.83	0.91	0.81	0.81	0.81
7MLZ-23914-A	196	3.71	83.09	0.84	0.90	0.88	0.87	0.61
7MJS-23883-H	132	3.03	89.57	0.88	0.98	0.92	0.88	0.63 g
7BRM-30160-A	257	3.6	87.52	0.89	0.89	0.94	0.90 g	0.84
7LX5-23566-B	196	3.44	82.93	0.89	0.93	0.93	0.92	0.64
7EDA-31062-A	334	2.78	89.02	0.90	0.92	0.93	0.86	0.66 g
7L6U-23208-A	311	3.3	89.74	0.90	0.96	0.95	0.95	0.93

^aProtein IDs (PDB ID_EMDB ID_Chain ID). For the two chains involved in CASP challenges, CASP target IDs are indicated.

^bThe number of amino acids in the protein.

^cThe resolution of cryo-EM maps.

^dThe average pLDDT scores of AlphaFold2 models.

^eThe accuracy is indicated as TM scores for models obtained from AlphaFold2.

^fTM scores for models refined using Phenix (Terwilliger et al., 2022), the cryo-EM maps (High) and the hybrid density maps at 5, 6, and 8 Å, respectively.

^gThe Phenix resolution parameter was tuned 2–3 Å lower than the nominal resolution of the density map to ensure completion of the refinement protocol (see text).