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	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
✔	9B3D	44135	2024-07-23	2024-03-19	3.41	4.16	3.57	3.8	0.005	0.88	0.0	0.05	15.33	0.01	2.099	1.98	0.00	3.7	96.2	0.1	-3.30	0.79	0.76	1.16	3.8	0.004	0.76	0.0	0.04	15.97	0.00	1.805	13.28	1.45	4.3	95.7	0.1	0.59	0.80	0.80	0.81	1.05	23621	2967	14	12	logfile
✔	9B3D	44135	2024-08-08	2024-03-19	3.41	4.16	3.57	3.8	0.005	0.88	0.0	0.05	15.33	0.01	2.099	1.98	0.00	3.7	96.2	0.1	-3.30	0.79	0.76	1.16	3.8	0.003	0.72	0.0	0.04	15.98	0.00	1.881	9.11	0.82	3.5	96.4	0.1	0.65	0.79	0.80	0.80	1.08	23621	2967	14	12	logfile
✔	9B35	44128	2024-09-26	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.0	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	0.0	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	2024-11-17	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.0	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	2025-01-19	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.0	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
✔	9B35	44128	2024-12-30	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.0	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	2024-07-21	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.0	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	0.73	0.0	0.04	14.33	0.00	2.130	12.59	1.87	10.8	89.1	0.1	-1.05	0.81	0.67	0.82	2.14	14132	1780	8	0	logfile
✔	9B35	44128	2024-08-05	2024-03-18	3.4	3.76	3.53	3.7	0.008	1.24	0.0	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
✔	9B39	44132	2024-07-25	2024-03-18	3.84	4.26	4.00	4.0	0.009	1.54	0.0	0.07	17.94	0.01	2.184	7.62	0.44	15.3	83.2	1.5	-5.60	0.71	0.80	1.55	4.0	0.003	0.92	0.0	0.05	14.48	0.00	2.094	15.75	1.53	13.2	86.3	0.5	-2.21	1.57	0.72	0.80	1.19	27522	3372	22	58	logfile
✔	9B39	44132	2024-08-09	2024-03-18	3.84	4.26	4.00	4.0	0.009	1.54	0.0	0.07	17.94	0.01	2.184	7.62	0.44	15.3	83.2	1.5	-5.60	0.71	0.80	1.55	4.0	0.004	0.93	0.0	0.05	14.51	0.00	2.382	13.44	1.94	13.7	86.0	0.4	-2.15	1.57	0.71	0.80	1.10	27522	3372	22	58	logfile
✔	9B33	44124	2024-11-14	2024-03-18	4.07	4.25	4.00	4.2	0.007	1.56	0.0	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	0.0	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	0.0	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
✔	8YPU	39494	2025-01-24	2024-03-18	2.97	3.16	2.96	3.1	0.006	0.68	3.0	0.05	16.03	0.01	2.065	9.57	0.25	2.7	97.3	0.0	-0.23	0.77	0.86	3.78	3.1	0.004	0.71	1.0	0.04	16.54	0.00	2.532	5.69	2.87	3.1	96.9	0.0	0.12	0.22	0.75	0.88	3.54	22476	2820	4	0	logfile
✔	9B34	44125	2024-12-27	2024-03-18	3.58	3.87	3.58	3.9	0.007	1.47	0.0	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	0.0	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	2024-10-09	2024-03-18	3.58	3.87	3.58	3.9	0.007	1.47	0.0	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	2024-09-23	2024-03-18	3.58	3.87	3.58	3.9	0.007	1.47	0.0	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	2024-08-02	2024-03-18	3.58	3.87	3.58	3.9	0.007	1.47	0.0	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