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	Z-score	RMSD	CC_box	CC_mask	EMRinger	# atoms	# residues	# chains	# other	Logfile
✔	8VD8	43145	2025-01-13	2023-12-14	3.2	2.93	3.17	3.1	0.007	0.81	0.0	0.05	13.73	0.01	2.181	0.80	0.00	1.9	98.1	-0.87	0.66	0.83	3.38	3.1	0.003	0.54	0.0	0.04	16.93	0.00	2.510	3.18	2.27	2.3	97.7	0.76	0.70	0.67	0.84	2.96	47880	5832	24	0	logfile
✔	8VD8	43145	2024-12-27	2023-12-14	3.2	2.93	3.17	3.1	0.007	0.81	0.0	0.05	13.73	0.01	2.181	0.80	0.00	1.9	98.1	-0.87	0.66	0.83	3.38	3.1	0.004	0.60	0.0	0.04	16.83	0.00	2.488	3.85	2.55	2.4	97.6	0.55	0.71	0.66	0.85	2.99	47880	5832	24	0	logfile
✔	8VD8	43145	2024-11-18	2023-12-14	3.2	2.93	3.17	3.1	0.007	0.81	0.0	0.05	13.73	0.01	2.181	0.80	0.00	1.9	98.1	-0.87	0.66	0.83	3.38	3.1	0.004	0.60	0.0	0.04	16.83	0.00	2.488	3.85	2.55	2.4	97.6	0.55	0.71	0.66	0.85	2.99	47880	5832	24	0	logfile
✔	8VD8	43145	2024-10-09	2023-12-14	3.2	2.93	3.17	3.1	0.007	0.81	0.0	0.05	13.73	0.01	2.181	0.80	0.00	1.9	98.1	-0.87	0.66	0.83	3.38	3.1	0.004	0.60	0.0	0.04	16.83	0.00	2.488	3.85	2.55	2.4	97.6	0.55	0.71	0.66	0.85	2.99	47880	5832	24	0	logfile
✔	8VD8	43145	2024-09-23	2023-12-14	3.2	2.93	3.17	3.1	0.007	0.81	0.0	0.05	13.73	0.01	2.181	0.80	0.00	1.9	98.1	-0.87	0.66	0.83	3.38	3.1	0.003	0.56	0.0	0.04	16.76	0.00	2.485	3.46	2.44	2.1	97.9	0.83	0.71	0.67	0.85	3.02	47880	5832	24	0	logfile
✔	8VC2	43130	2024-07-20	2023-12-13	3.98	4.39	3.99	4.4	0.006	0.84	0.0	0.04	14.09	0.01	2.353	2.91	0.31	2.4	97.6	-0.98	0.57	0.71	1.08	4.4	0.003	0.79	0.0	0.04	16.30	0.00	2.244	10.55	4.09	2.0	98.0	2.85	2.89	0.57	0.73	1.08	11796	1516	8	4	logfile
✔	8VC2	43130	2024-12-30	2023-12-13	3.98	4.39	3.99	4.4	0.006	0.84	0.0	0.04	14.09	0.01	2.353	2.91	0.31	2.4	97.6	-0.98	0.57	0.71	1.08	4.4	0.003	0.81	0.0	0.04	16.34	0.00	2.556	9.39	3.46	2.0	98.0	3.06	2.22	0.55	0.72	0.69	11796	1516	8	4	logfile
✔	8VC2	43130	2024-11-16	2023-12-13	3.98	4.39	3.99	4.4	0.006	0.84	0.0	0.04	14.09	0.01	2.353	2.91	0.31	2.4	97.6	-0.98	0.57	0.71	1.08	4.4	0.003	0.81	0.0	0.04	16.34	0.00	2.556	9.39	3.46	2.0	98.0	3.06	2.22	0.55	0.72	0.69	11796	1516	8	4	logfile
✔	8VC2	43130	2024-09-26	2023-12-13	3.98	4.39	3.99	4.4	0.006	0.84	0.0	0.04	14.09	0.01	2.353	2.91	0.31	2.4	97.6	-0.98	0.57	0.71	1.08	4.4	0.003	0.81	0.0	0.04	16.34	0.00	2.556	9.39	3.46	2.0	98.0	3.06	2.22	0.55	0.72	0.69	11796	1516	8	4	logfile
✔	8VC2	43130	2024-10-12	2023-12-13	3.98	4.39	3.99	4.4	0.006	0.84	0.0	0.04	14.09	0.01	2.353	2.91	0.31	2.4	97.6	-0.98	0.57	0.71	1.08	4.4	0.003	0.81	0.0	0.04	16.34	0.00	2.556	9.39	3.46	2.0	98.0	3.06	2.22	0.55	0.72	0.69	11796	1516	8	4	logfile
✔	8VC2	43130	2025-01-18	2023-12-13	3.98	4.39	3.99	4.4	0.006	0.84	0.0	0.04	14.09	0.01	2.353	2.91	0.31	2.4	97.6	-0.98	0.57	0.71	1.08	4.4	0.003	0.75	0.0	0.04	16.56	0.00	2.563	9.59	5.27	1.7	98.3	3.01	2.22	0.56	0.72	0.88	11796	1516	8	4	logfile
✔	8VC2	43130	2024-02-15	2023-12-13	3.98	4.39	3.99	4.4	0.006	0.84	0.0	0.04	14.09	0.01	2.353	2.91	0.31	2.4	97.6	-0.98	0.57	0.71	1.08	4.4	0.004	0.96	1.0	0.04	16.35	0.01	2.236	10.63	4.64	2.7	97.3	1.52	2.23	0.56	0.73	1.08	11796	1516	8	4	logfile
✔	8VC2	43130	2024-06-27	2023-12-13	3.98	4.39	3.99	4.4	0.006	0.84	0.0	0.04	14.09	0.01	2.353	2.91	0.31	2.4	97.6	-0.98	0.57	0.71	1.08	4.4	0.004	0.96	1.0	0.04	16.35	0.01	2.236	10.63	4.64	2.7	97.3	1.52	2.23	0.56	0.73	1.08	11796	1516	8	4	logfile
✔	8VC2	43130	2024-08-05	2023-12-13	3.98	4.39	3.99	4.4	0.006	0.84	0.0	0.04	14.09	0.01	2.353	2.91	0.31	2.4	97.6	-0.98	0.57	0.71	1.08	4.4	0.003	0.79	0.0	0.04	16.41	0.00	2.596	9.47	4.40	2.1	97.9	2.87	2.21	0.56	0.73	0.88	11796	1516	8	4	logfile
✔	8XFE	38302	2024-11-19	2023-12-13	2.98	3.64	3.04	3.4	0.009	0.97	0.0	0.06	10.56	0.01	2.240	4.39	0.49	5.9	94.1	-5.62	0.84	0.79	4.15	3.4	0.003	0.74	0.0	0.04	14.61	0.00	2.488	7.00	1.73	3.3	96.7	-0.47	0.79	0.84	0.83	2.92	20339	2625	5	0	logfile
✔	8XFE	38302	2025-01-23	2023-12-13	2.98	3.64	3.04	3.4	0.009	0.97	0.0	0.06	10.56	0.01	2.240	4.39	0.49	5.9	94.1	-5.62	0.84	0.79	4.15	3.4	0.003	0.73	0.0	0.04	14.60	0.00	2.473	6.60	1.92	3.1	96.9	-0.31	1.02	0.84	0.83	2.84	20339	2625	5	0	logfile
✔	8VC1	43129	2024-10-13	2023-12-13	2.85	3.23	2.92	3.2	0.012	1.46	0.0	0.06	17.03	0.01	2.196	4.03	0.30	2.1	97.9	-1.02	0.59	0.82	3.63	3.3	0.003	0.54	0.0	0.04	16.19	0.00	2.631	7.98	1.11	1.7	98.3	4.02	0.43	0.57	0.82	1.93	13128	1564	8	32	logfile
✔	8RGH	19133	2024-12-29	2023-12-13	3.9	4.34	3.89	4.0	0.012	1.88	4.0	0.10	14.04	0.02	2.504	0.53	0.00	4.7	95.3	-1.05	0.82	0.66	1.27	4.0	0.004	0.75	0.0	0.04	15.97	0.00	2.318	13.89	1.47	4.3	95.7	0.50	0.92	0.84	0.70	1.13	9682	1287	6	0	logfile
✔	8VC1	43129	2024-12-30	2023-12-13	2.85	3.23	2.92	3.2	0.012	1.46	0.0	0.06	17.03	0.01	2.196	4.03	0.30	2.1	97.9	-1.02	0.59	0.82	3.63	3.3	0.003	0.54	0.0	0.04	16.19	0.00	2.631	7.98	1.11	1.7	98.3	4.02	0.43	0.57	0.82	1.93	13128	1564	8	32	logfile
✔	8VC1	43129	2024-02-15	2023-12-13	2.85	3.23	2.92	3.2	0.012	1.46	0.0	0.06	17.03	0.01	2.196	4.03	0.30	2.1	97.9	-1.02	0.59	0.82	3.63	3.2	0.003	0.51	0.0	0.03	16.24	0.00	2.232	8.98	1.34	1.4	98.6	4.06	0.45	0.56	0.80	2.26	13128	1564	8	32	logfile