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	Rama outliers	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	# other	Logfile
✔	9B33	44124	2025-02-11	2024-03-18	4.07	4.25	4.00	4.2	0.007	1.56	0.08	13.12	0.01	2.141	8.98	0.49	23.2	75.3	1.5	-6.09	0.63	0.62	—	4.1	0.004	1.02	0.0	0.06	12.59	0.01	1.977	22.31	0.00	22.6	76.4	1.1	-4.71	1.20	0.68	0.68	—	3619	474	4	4	logfile
✔	9B33	44124	2025-03-05	2024-03-18	4.07	4.25	3.97	4.2	0.007	1.56	0.08	13.12	0.01	2.141	8.98	0.49	23.2	75.3	1.5	-6.09	0.63	0.62	—	4.1	0.006	1.09	0.0	0.06	12.75	0.01	1.914	24.55	0.00	23.2	76.0	0.9	-4.94	1.23	0.70	0.71	—	3619	474	4	4	logfile
✔	9B33	44124	2025-04-26	2024-03-18	4.07	4.25	3.97	4.2	0.007	1.56	0.08	13.12	0.01	2.141	8.98	0.49	23.2	75.3	1.5	-6.09	0.63	0.62	—	4.1	0.006	1.09	0.0	0.06	12.75	0.01	1.914	24.55	0.00	23.2	76.0	0.9	-4.94	1.23	0.70	0.71	—	3619	474	4	4	logfile
✔	9B33	44124	2025-05-09	2024-03-18	4.07	4.25	3.97	4.2	0.007	1.56	0.08	13.12	0.01	2.141	8.98	0.49	23.2	75.3	1.5	-6.09	0.63	0.62	—	4.1	0.004	1.03	0.0	0.06	12.53	0.01	1.987	20.49	0.00	22.3	76.4	1.3	-4.67	1.20	0.68	0.68	—	3619	474	4	4	logfile
✔	9B33	44124	2024-08-02	2024-03-18	4.07	4.25	4.00	4.2	0.007	1.56	0.08	13.12	0.01	2.141	8.98	0.49	23.2	75.3	1.5	-6.09	0.63	0.62	—	4.1	0.004	1.00	0.0	0.05	12.87	0.01	2.033	18.94	0.00	22.1	77.0	0.9	-4.65	1.21	0.69	0.69	—	3619	474	4	4	logfile
✔	9B33	44124	2024-09-23	2024-03-18	4.07	4.25	4.00	4.2	0.007	1.56	0.08	13.12	0.01	2.141	8.98	0.49	23.2	75.3	1.5	-6.09	0.63	0.62	—	4.1	0.004	1.00	0.0	0.05	12.87	0.01	2.033	18.94	0.00	22.1	77.0	0.9	-4.65	1.21	0.69	0.69	—	3619	474	4	4	logfile
✔	9B33	44124	2024-10-09	2024-03-18	4.07	4.25	4.00	4.2	0.007	1.56	0.08	13.12	0.01	2.141	8.98	0.49	23.2	75.3	1.5	-6.09	0.63	0.62	—	4.1	0.004	1.00	0.0	0.05	12.87	0.01	2.033	18.94	0.00	22.1	77.0	0.9	-4.65	1.21	0.69	0.69	—	3619	474	4	4	logfile
✔	9B33	44124	2024-12-27	2024-03-18	4.07	4.25	4.00	4.2	0.007	1.56	0.08	13.12	0.01	2.141	8.98	0.49	23.2	75.3	1.5	-6.09	0.63	0.62	—	4.1	0.004	1.00	0.0	0.05	12.87	0.01	2.033	18.94	0.00	22.1	77.0	0.9	-4.65	1.21	0.69	0.69	—	3619	474	4	4	logfile
✘	9B38	44131	2024-08-08	2024-03-18	3.36	3.64	3.42	3.6	0.008	1.30	0.08	20.14	0.01	2.270	4.66	0.76	9.0	90.6	0.4	-5.67	0.71	0.77	2.51	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	22670	2720	26	74	logfile
✘	9B38	44131	2024-09-29	2024-03-18	3.36	3.64	3.42	3.6	0.008	1.30	0.08	20.14	0.01	2.270	4.66	0.76	9.0	90.6	0.4	-5.67	0.71	0.77	2.51	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	22670	2720	26	74	logfile
✔	8YPT	39493	2025-05-22	2024-03-18	3.05	3.26	3.06	3.3	0.003	0.59	0.05	15.68	0.00	2.167	7.27	0.80	1.9	98.1	0.0	0.24	0.68	0.84	3.33	3.3	0.003	0.52	0.0	0.04	16.21	0.00	2.536	4.47	3.23	2.4	97.6	0.0	0.32	1.21	0.72	0.87	3.52	23068	2894	5	0	logfile
✔	8YPT	39493	2025-01-25	2024-03-18	3.05	3.26	3.06	3.3	0.003	0.59	0.05	15.68	0.00	2.167	7.27	0.80	1.9	98.1	0.0	0.24	0.68	0.84	3.33	3.3	0.003	0.52	0.0	0.04	16.21	0.00	2.536	4.47	3.23	2.4	97.6	0.0	0.32	1.21	0.72	0.87	3.52	23068	2894	5	0	logfile
✔	9B35	44128	2025-01-19	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.06	10.75	0.01	2.030	5.09	0.65	11.7	87.4	0.9	-5.51	0.68	0.81	3.08	3.7	0.005	0.78	0.0	0.04	14.50	0.01	2.468	10.33	1.94	11.3	88.6	0.2	-0.93	0.81	0.67	0.82	1.98	14132	1780	8	0	logfile
✔	9B34	44125	2024-10-09	2024-03-18	3.58	3.87	3.58	3.9	0.007	1.47	0.08	12.86	0.01	2.121	8.00	0.49	23.6	74.5	1.9	-5.95	0.68	0.68	1.73	3.8	0.006	1.49	1.0	0.06	16.83	0.01	2.041	20.49	6.17	23.0	76.0	1.1	-4.29	2.01	0.72	0.73	0.92	3619	474	4	4	logfile
✔	9B34	44125	2024-11-14	2024-03-18	3.58	3.87	3.58	3.9	0.007	1.47	0.08	12.86	0.01	2.121	8.00	0.49	23.6	74.5	1.9	-5.95	0.68	0.68	1.73	3.8	0.006	1.49	1.0	0.06	16.83	0.01	2.041	20.49	6.17	23.0	76.0	1.1	-4.29	2.01	0.72	0.73	0.92	3619	474	4	4	logfile
✔	9B34	44125	2025-05-09	2024-03-18	3.58	3.87	3.56	3.9	0.007	1.47	0.08	12.86	0.01	2.121	8.00	0.49	23.6	74.5	1.9	-5.95	0.68	0.68	1.73	3.8	0.004	1.04	0.0	0.05	16.71	0.01	2.058	17.26	4.20	23.2	75.7	1.1	-4.30	1.62	0.71	0.72	0.92	3619	474	4	4	logfile
✔	9B35	44128	2024-08-05	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.06	10.75	0.01	2.244	5.09	0.65	11.7	87.4	0.9	-5.51	0.68	0.81	3.08	3.7	0.003	0.75	0.0	0.04	14.39	0.00	2.479	9.58	1.68	10.4	89.5	0.1	-0.70	1.58	0.67	0.81	1.91	14132	1780	8	0	logfile
✔	9B35	44128	2024-09-26	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.06	10.75	0.01	2.030	5.09	0.65	11.7	87.4	0.9	-5.51	0.68	0.81	3.08	3.7	0.003	0.75	0.0	0.04	14.52	0.00	2.455	9.58	1.74	10.8	89.1	0.1	-0.74	1.59	0.67	0.81	1.89	14132	1780	8	0	logfile
✔	9B35	44128	2024-10-13	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.06	10.75	0.01	2.030	5.09	0.65	11.7	87.4	0.9	-5.51	0.68	0.81	3.08	3.7	0.003	0.75	0.0	0.04	14.52	0.00	2.455	9.58	1.74	10.8	89.1	0.1	-0.74	1.59	0.67	0.81	1.89	14132	1780	8	0	logfile
✔	9B34	44125	2025-04-26	2024-03-18	3.58	3.87	3.56	3.9	0.007	1.47	0.08	12.86	0.01	2.121	8.00	0.49	23.6	74.5	1.9	-5.95	0.68	0.68	1.73	3.8	0.004	1.01	0.0	0.05	16.39	0.01	2.023	16.56	2.47	22.6	76.6	0.9	-4.32	2.02	0.71	0.73	1.13	3619	474	4	4	logfile