cryo-EM Re-Refine

Table showing results for all available months

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peach highlight: initial model; blue highlight: re-refined model

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Status	PDB code	EMDB code	Date processed	Release Date	Resolution	D₉₉	D_FSC	D_Model	Bond rmsd	Angle rmsd	Chirality	Dihedral rmsd	Plane rmsd	Min nonbonded	Clashscore	Rota outliers	Rama allowed	Rama favored	Z-score	CC_box	CC_mask	EMRinger	D_Model	Bond rmsd	Angle rmsd	Cβ devts	Chirality	Dihedral rmsd	Plane rmsd	Min nonbonded	Clashscore	Rota outliers	Rama allowed	Rama favored	Z-score	RMSD	CC_box	CC_mask	EMRinger	# atoms	# residues	# chains	# other	# water	Logfile
✔	8Y93	39068	2025-02-13	2024-02-06	3.0	3.45	3.17	3.4	0.003	0.60	0.04	11.79	0.00	2.127	7.36	5.15	2.2	97.8	-1.85	0.51	0.68	2.29	3.4	0.003	0.68	0.0	0.04	15.62	0.00	2.298	8.30	3.36	3.3	96.7	1.02	1.08	0.62	0.83	2.14	9055	1130	3	3	0	logfile
✔	8Y93	39068	2024-10-11	2024-02-06	3.0	3.45	3.17	3.4	0.003	0.60	0.04	11.79	0.00	2.127	7.36	5.15	2.2	97.8	-1.85	0.51	0.68	2.29	3.4	0.003	0.66	0.0	0.04	15.49	0.00	2.300	8.02	2.84	3.2	96.8	1.18	1.07	0.61	0.82	1.76	9055	1130	3	3	0	logfile
✔	8VXT	43639	2025-01-19	2024-02-06	4.25	2.73	4.22	2.2	0.003	0.71	0.08	14.08	0.01	2.224	7.78	0.00	3.5	96.5	0.59	0.65	0.63	—	2.0	0.003	0.68	0.0	0.04	14.70	0.00	2.472	10.77	0.00	4.1	95.9	1.35	0.85	0.67	0.67	—	13896	1740	12	6	0	logfile
✔	8Y88	39037	2025-06-27	2024-02-06	3.03	2.43	3.03	2.2	0.002	0.42	0.04	7.75	0.00	2.210	4.18	1.72	3.8	96.2	-3.28	0.75	0.76	3.28	2.1	0.005	0.82	3.0	0.05	12.60	0.01	2.399	5.46	2.97	6.7	93.3	-0.98	0.53	0.77	0.82	2.89	31257	4031	12	27	0	logfile
✔	8Y88	39037	2025-05-29	2024-02-06	3.03	2.43	3.03	2.2	0.002	0.42	0.04	7.75	0.00	2.210	4.18	1.72	3.8	96.2	-3.28	0.75	0.76	3.28	2.1	0.004	0.77	3.0	0.05	12.45	0.00	2.427	5.20	2.79	6.1	93.9	-0.89	0.53	0.77	0.82	2.86	31257	4031	12	27	0	logfile
✔	8Y95	39070	2025-01-16	2024-02-06	3.24	3.62	3.40	3.6	0.003	0.59	0.04	11.30	0.01	1.402	11.16	4.43	5.0	95.0	-1.89	0.50	0.65	1.63	3.6	0.003	0.62	0.0	0.04	14.90	0.00	2.328	10.84	3.27	3.1	96.9	0.73	1.10	0.56	0.78	2.52	9018	1124	4	6	0	logfile
✔	8Y8Z	39064	2025-01-16	2024-02-06	3.29	3.66	3.38	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.003	0.65	0.0	0.04	14.68	0.00	2.316	10.51	3.05	3.0	97.0	0.70	0.82	0.59	0.77	2.28	9082	1130	6	6	4	logfile
✔	8Y8Z	39064	2025-02-13	2024-02-06	3.29	3.66	3.38	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.003	0.65	0.0	0.04	14.68	0.00	2.316	10.51	3.05	3.0	97.0	0.70	0.82	0.59	0.77	2.28	9082	1130	6	6	4	logfile
✔	8Y8Z	39064	2025-03-13	2024-02-06	3.29	3.66	3.37	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.003	0.66	0.0	0.04	14.69	0.00	2.290	9.29	3.15	2.4	97.6	0.81	0.82	0.60	0.77	2.28	9082	1130	6	6	4	logfile
✔	8Y8Z	39064	2025-04-30	2024-02-06	3.29	3.66	3.37	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.003	0.66	0.0	0.04	14.69	0.00	2.290	9.29	3.15	2.4	97.6	0.81	0.82	0.60	0.77	2.28	9082	1130	6	6	4	logfile
✔	8Y8Z	39064	2025-05-12	2024-02-06	3.29	3.66	3.37	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.003	0.65	0.0	0.04	14.68	0.00	2.316	10.51	3.05	3.0	97.0	0.70	0.82	0.59	0.77	2.28	9082	1130	6	6	4	logfile
✔	8Y8Z	39064	2025-06-07	2024-02-06	3.29	3.66	3.37	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.003	0.66	0.0	0.04	14.69	0.00	2.290	9.29	3.15	2.4	97.6	0.81	0.82	0.60	0.77	2.28	9082	1130	6	6	4	logfile
✔	8Y8Z	39064	2025-07-27	2024-02-06	3.29	3.66	3.37	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.003	0.66	0.0	0.04	14.69	0.00	2.290	9.29	3.15	2.4	97.6	0.81	0.82	0.60	0.77	2.28	9082	1130	6	6	4	logfile
✔	8Y8Z	39064	2024-10-11	2024-02-06	3.29	3.66	3.38	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.004	0.70	0.0	0.04	14.91	0.00	2.243	10.12	3.47	3.5	96.5	0.63	0.84	0.59	0.78	2.34	9082	1130	6	6	4	logfile
✔	8Y8Z	39064	2024-11-15	2024-02-06	3.29	3.66	3.38	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.004	0.70	0.0	0.04	14.91	0.00	2.243	10.12	3.47	3.5	96.5	0.63	0.84	0.59	0.78	2.34	9082	1130	6	6	4	logfile
✔	8Y8Z	39064	2024-12-28	2024-02-06	3.29	3.66	3.38	3.6	0.007	0.63	0.04	11.55	0.00	1.761	8.07	6.41	2.6	97.4	-2.01	0.49	0.64	2.05	3.6	0.004	0.70	0.0	0.04	14.91	0.00	2.243	10.12	3.47	3.5	96.5	0.63	0.84	0.59	0.78	2.34	9082	1130	6	6	4	logfile
✔	8Y89	39038	2025-05-28	2024-02-06	3.32	2.55	3.35	2.2	0.002	0.44	0.04	7.94	0.00	2.210	4.81	1.78	4.4	95.6	-2.29	0.73	0.73	2.36	2.2	0.006	0.75	0.0	0.05	12.15	0.00	2.374	5.94	2.69	6.4	93.6	-1.10	0.96	0.76	0.80	2.43	30645	3956	19	36	0	logfile
✔	8Y89	39038	2025-06-26	2024-02-06	3.32	2.55	3.35	2.2	0.002	0.44	0.04	7.94	0.00	2.210	4.81	1.78	4.4	95.6	-2.29	0.73	0.73	2.36	2.1	0.003	0.62	0.0	0.04	12.19	0.00	2.276	5.69	2.66	5.4	94.6	-0.95	0.97	0.76	0.79	2.42	30645	3956	19	36	0	logfile
✔	8VXT	43639	2025-05-16	2024-02-06	4.25	2.73	4.20	2.2	0.003	0.71	0.08	14.08	0.01	2.224	7.78	0.00	3.5	96.5	0.59	0.65	0.63	—	2.0	0.003	0.68	0.0	0.04	14.70	0.00	2.472	10.77	0.00	4.1	95.9	1.35	0.85	0.67	0.67	—	13896	1740	12	6	0	logfile
✔	8VXT	43639	2025-06-12	2024-02-06	4.25	2.73	4.20	2.2	0.003	0.71	0.08	14.08	0.01	2.224	7.78	0.00	3.5	96.5	0.59	0.65	0.63	—	2.0	0.003	0.68	0.0	0.04	14.79	0.00	2.376	11.42	0.00	3.9	96.1	1.50	0.86	0.67	0.67	—	13896	1740	12	6	0	logfile