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	Cβ devts	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	Rama outliers	Z-score	RMSD	CC_box	CC_mask	EMRinger	# atoms	# residues	# chains	# nucleotides	# other	# water	# H	Logfile
✔	8W0A	43706	2024-11-16	2024-02-13	3.2	3.72	3.22	3.6	0.003	0.59	0.0	0.04	19.61	0.00	1.561	10.62	0.09	8.1	91.9	-1.76	0.72	0.71	1.67	3.6	0.003	0.61	0.0	0.04	19.71	0.00	2.387	9.49	4.35	8.4	91.6	0.0	-1.26	0.46	0.71	0.73	1.06	10216	1272	4	14	0	0	0	logfile
✔	8W0A	43706	2024-08-04	2024-02-13	3.2	3.72	3.22	3.6	0.003	0.59	0.0	0.04	19.61	0.00	1.561	10.62	0.09	8.1	91.9	-1.76	0.72	0.71	1.67	3.6	0.002	0.58	0.0	0.04	19.63	0.00	2.360	9.35	3.98	6.9	93.1	0.0	-1.21	0.46	0.70	0.72	0.75	10216	1272	4	14	0	0	0	logfile
✔	8YBE	39117	2025-01-13	2024-02-13	2.3	2.50	2.34	2.5	0.006	0.89	0.0	0.05	15.84	0.01	2.236	18.77	2.34	0.0	100.0	1.36	0.67	0.82	5.54	2.5	0.005	0.71	0.0	0.04	16.53	0.00	2.598	11.36	1.00	2.2	97.8	0.0	1.31	0.32	0.68	0.83	5.54	3110	370	3	0	2	197	0	logfile
✔	8YBE	39117	2025-02-10	2024-02-13	2.3	2.50	2.34	2.5	0.006	0.89	0.0	0.05	15.84	0.01	2.236	18.77	2.34	0.0	100.0	1.36	0.67	0.82	5.54	2.5	0.005	0.71	0.0	0.04	16.53	0.00	2.598	11.36	1.00	2.2	97.8	0.0	1.31	0.32	0.68	0.83	5.54	3110	370	3	0	2	197	0	logfile
✔	8W0E	43707	2024-10-12	2024-02-13	3.4	3.92	3.68	3.8	0.002	0.54	0.0	0.04	14.57	0.00	1.908	6.90	0.63	5.0	95.0	-0.01	0.77	0.80	1.98	3.8	0.004	0.57	0.0	0.04	16.01	0.00	1.764	5.52	1.54	5.7	94.3	0.0	0.18	0.41	0.77	0.82	1.68	59772	3647	14	50	15	0	29690	logfile
✘	8W0E	43707	2025-01-18	2024-02-13	3.4	3.92	3.68	3.8	0.002	0.54	0.0	0.04	14.57	0.00	1.908	6.90	0.63	5.0	95.0	-0.01	0.77	0.80	1.98	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	59772	3647	14	50	15	0	29690	logfile
✔	8W0E	43707	2024-12-30	2024-02-13	3.4	3.92	3.68	3.8	0.002	0.54	0.0	0.04	14.57	0.00	1.908	6.90	0.63	5.0	95.0	-0.01	0.77	0.80	1.98	3.8	0.004	0.57	0.0	0.04	16.01	0.00	1.764	5.52	1.54	5.7	94.3	0.0	0.18	0.41	0.77	0.82	1.68	59772	3647	14	50	15	0	29690	logfile
✔	8RZ9	19607	2025-04-29	2024-02-12	3.02	2.39	3.08	3.0	0.015	1.26	4.0	0.10	17.55	0.01	1.685	25.25	3.61	6.0	94.0	-1.70	0.76	0.76	0.82	2.1	0.005	1.07	1.0	0.05	18.22	0.00	1.835	19.07	5.84	5.2	94.8	0.0	-0.41	1.38	0.75	0.73	1.10	8571	1067	4	0	4	0	0	logfile
✔	8RZ9	19607	2025-03-13	2024-02-12	3.02	2.39	3.08	3.0	0.010	1.26	4.0	0.10	17.55	0.01	1.685	25.25	3.61	6.0	94.0	-1.70	0.76	0.76	0.82	2.1	0.005	0.73	0.0	0.05	18.11	0.00	1.815	17.90	5.20	5.5	94.5	0.0	-0.47	1.39	0.75	0.73	1.05	8571	1067	4	0	4	0	0	logfile
✔	8RZ9	19607	2025-02-13	2024-02-12	3.02	2.39	3.08	3.0	0.010	1.26	4.0	0.10	17.55	0.01	1.685	25.25	3.61	6.0	94.0	-1.70	0.76	0.76	0.82	2.1	0.005	0.72	0.0	0.05	18.12	0.00	1.816	17.18	5.73	5.2	94.8	0.0	-0.35	1.39	0.75	0.73	1.05	8571	1067	4	0	4	0	0	logfile
✔	8RZ9	19607	2025-01-15	2024-02-12	3.02	2.39	3.08	3.0	0.010	1.26	4.0	0.10	17.55	0.01	1.685	25.25	3.61	6.0	94.0	-1.70	0.76	0.76	0.82	2.1	0.005	0.72	0.0	0.05	18.12	0.00	1.816	17.18	5.73	5.2	94.8	0.0	-0.35	1.39	0.75	0.73	1.05	8571	1067	4	0	4	0	0	logfile
✔	8RZ9	19607	2024-12-28	2024-02-12	3.02	2.39	3.08	3.0	0.010	1.26	4.0	0.10	17.55	0.01	1.685	25.25	3.61	6.0	94.0	-1.70	0.76	0.76	0.82	3.0	0.004	0.71	0.0	0.05	18.10	0.00	1.856	15.75	5.20	4.7	95.3	0.0	-0.30	1.39	0.74	0.72	0.99	8571	1067	4	0	4	0	0	logfile
✔	8RZ9	19607	2025-05-12	2024-02-12	3.02	2.39	3.08	3.0	0.015	1.26	4.0	0.10	17.55	0.01	1.685	25.25	3.61	6.0	94.0	-1.70	0.76	0.76	0.82	2.1	0.005	1.07	1.0	0.05	18.16	0.00	1.823	19.07	5.73	5.2	94.8	0.0	-0.43	1.38	0.75	0.73	1.10	8571	1067	4	0	4	0	0	logfile
✔	8VZo	43684	2024-11-14	2024-02-12	2.49	2.66	2.50	2.7	0.013	1.82	1.0	0.10	14.97	0.03	2.347	6.25	3.67	4.0	96.0	-2.36	0.56	0.81	3.92	2.6	0.005	0.64	0.0	0.05	15.30	0.01	2.597	5.00	1.54	2.6	97.4	0.0	1.92	0.50	0.67	0.89	4.03	4796	615	4	0	1	0	0	logfile
✔	8VZo	43684	2024-12-27	2024-02-12	2.49	2.66	2.50	2.7	0.013	1.82	1.0	0.10	14.97	0.03	2.347	6.25	3.67	4.0	96.0	-2.36	0.56	0.81	3.92	2.6	0.005	0.64	0.0	0.05	15.30	0.01	2.597	5.00	1.54	2.6	97.4	0.0	1.92	0.50	0.67	0.89	4.03	4796	615	4	0	1	0	0	logfile
✔	8VZo	43684	2024-09-23	2024-02-12	2.49	2.66	2.50	2.7	0.013	1.82	1.0	0.10	14.97	0.03	2.347	6.25	3.67	4.0	96.0	-2.36	0.56	0.81	3.92	2.6	0.005	0.64	0.0	0.05	15.30	0.01	2.597	5.00	1.54	2.6	97.4	0.0	1.92	0.50	0.67	0.89	4.03	4796	615	4	0	1	0	0	logfile
✔	8VZo	43684	2024-10-09	2024-02-12	2.49	2.66	2.50	2.7	0.013	1.82	1.0	0.10	14.97	0.03	2.347	6.25	3.67	4.0	96.0	-2.36	0.56	0.81	3.92	2.6	0.005	0.64	0.0	0.05	15.30	0.01	2.597	5.00	1.54	2.6	97.4	0.0	1.92	0.50	0.67	0.89	4.03	4796	615	4	0	1	0	0	logfile
✔	8VZo	43684	2025-03-06	2024-02-12	2.49	2.66	2.50	2.7	0.013	1.82	1.0	0.10	14.97	0.03	2.347	6.25	3.67	4.0	96.0	-2.36	0.56	0.81	3.92	2.6	0.003	0.58	0.0	0.04	15.19	0.00	2.609	4.69	2.12	2.0	98.0	0.0	2.24	0.51	0.67	0.88	3.83	4796	615	4	0	1	0	0	logfile
✔	8VZo	43684	2025-04-27	2024-02-12	2.49	2.66	2.50	2.7	0.013	1.82	1.0	0.10	14.97	0.03	2.347	6.25	3.67	4.0	96.0	-2.36	0.56	0.81	3.92	2.6	0.003	0.58	0.0	0.04	15.19	0.00	2.609	4.69	2.12	2.0	98.0	0.0	2.24	0.51	0.67	0.88	3.83	4796	615	4	0	1	0	0	logfile
✔	8VZo	43684	2025-05-10	2024-02-12	2.49	2.66	2.50	2.7	0.013	1.82	1.0	0.10	14.97	0.03	2.347	6.25	3.67	4.0	96.0	-2.36	0.56	0.81	3.92	2.6	0.003	0.57	0.0	0.04	15.16	0.00	2.615	4.69	1.74	2.1	97.9	0.0	2.40	0.51	0.67	0.88	3.65	4796	615	4	0	1	0	0	logfile