cryo-EM Re-Refine

Table showing results for all available months

The table shows a selection of parameters. Activate more columns using the drop-down menus below.
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	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
✔	8XQN	38582	2025-01-16	2024-01-05	3.05	2.30	3.12	2.0	0.004	0.62	0.0	0.04	15.73	0.00	2.075	14.89	0.00	3.6	96.4	0.0	1.02	0.76	0.77	2.27	2.0	0.004	0.63	0.04	16.15	0.00	2.532	9.99	3.47	3.5	96.5	0.90	0.31	0.76	0.78	2.17	8976	1135	6	2	logfile
✔	8XQE	38574	2025-06-10	2024-01-05	3.48	2.31	3.68	1.9	0.003	0.75	0.0	0.04	16.12	0.00	2.128	20.23	0.00	6.1	93.9	0.0	-1.58	0.69	0.64	1.27	1.9	0.003	0.74	0.04	17.10	0.00	2.507	14.65	3.63	5.6	94.4	-1.13	0.53	0.71	0.67	0.71	11348	1442	7	0	logfile
✔	8XQE	38574	2025-05-14	2024-01-05	3.48	2.31	3.68	1.9	0.003	0.75	0.0	0.04	16.12	0.00	2.128	20.23	0.00	6.1	93.9	0.0	-1.58	0.69	0.64	1.27	1.8	0.004	0.99	0.04	17.13	0.00	2.201	18.02	4.28	5.5	94.5	-1.21	0.55	0.71	0.67	0.91	11348	1442	7	0	logfile
✔	8XQE	38574	2025-07-29	2024-01-05	3.48	2.31	3.68	1.9	0.003	0.75	0.0	0.04	16.12	0.00	2.128	20.23	0.00	6.1	93.9	0.0	-1.58	0.69	0.64	1.27	1.9	0.003	0.74	0.04	17.10	0.00	2.507	14.65	3.63	5.6	94.4	-1.13	0.53	0.71	0.67	0.71	11348	1442	7	0	logfile
✔	8XPS	38560	2025-01-13	2024-01-04	3.22	3.24	3.25	1.5	0.005	0.85	1.0	0.06	20.48	0.00	2.208	5.24	4.58	9.0	90.6	0.4	-4.49	0.90	0.82	3.01	1.5	0.004	0.91	0.05	15.63	0.01	2.472	9.80	3.12	8.9	91.1	-1.95	1.32	0.92	0.87	2.79	4568	546	7	24	logfile
✔	8XPY	38563	2025-04-27	2024-01-04	3.63	3.53	3.63	1.6	0.004	0.80	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.98	0.05	15.63	0.01	2.346	13.11	3.14	13.8	86.2	-2.44	2.13	0.92	0.84	2.08	4568	546	7	25	logfile
✔	8RM1	19348	2025-01-22	2024-01-04	3.1	2.97	3.03	3.1	0.003	0.66	0.0	0.04	14.78	0.00	2.028	6.11	0.45	5.0	95.0	0.0	-0.52	0.68	0.84	1.75	3.2	0.003	0.59	0.04	15.00	0.00	2.564	4.19	1.46	5.6	94.4	-0.38	0.39	0.67	0.87	1.40	17913	2184	12	18	logfile
✔	8XPY	38563	2025-03-06	2024-01-04	3.63	3.53	3.63	1.6	0.004	0.79	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.91	0.05	15.60	0.00	2.353	12.78	3.56	13.7	86.3	-2.30	2.12	0.92	0.84	2.30	4568	546	7	25	logfile
✔	8XPY	38563	2025-02-11	2024-01-04	3.63	3.53	3.62	1.6	0.004	0.79	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.89	0.05	15.66	0.00	2.343	13.33	3.14	13.8	86.2	-2.24	2.12	0.92	0.84	2.10	4568	546	7	25	logfile
✔	8XPY	38563	2025-01-13	2024-01-04	3.63	3.53	3.62	1.6	0.004	0.79	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.89	0.05	15.66	0.00	2.343	13.33	3.14	13.8	86.2	-2.24	2.12	0.92	0.84	2.10	4568	546	7	25	logfile
✔	8RM1	19348	2025-05-19	2024-01-04	3.1	2.97	3.03	3.1	0.003	0.66	0.0	0.04	14.78	0.00	2.195	6.11	0.45	5.0	95.0	0.0	-0.52	0.68	0.84	1.75	3.2	0.003	0.63	0.04	14.97	0.00	2.558	4.03	1.11	5.9	94.1	-0.66	0.38	0.68	0.87	1.24	17913	2184	12	18	logfile
✔	8RM1	19348	2025-06-16	2024-01-04	3.1	2.97	3.03	3.1	0.003	0.66	0.0	0.04	14.78	0.00	2.195	6.11	0.45	5.0	95.0	0.0	-0.52	0.68	0.84	1.75	3.2	0.003	0.63	0.04	14.93	0.00	2.548	4.03	1.36	5.7	94.3	-0.58	0.38	0.66	0.87	1.31	17913	2184	12	18	logfile
✔	8RM1	19348	2024-11-19	2024-01-04	3.1	2.97	3.03	3.1	0.003	0.66	0.0	0.04	14.78	0.00	2.028	6.11	0.45	5.0	95.0	0.0	-0.52	0.68	0.84	1.75	3.2	0.004	0.65	0.05	15.01	0.00	2.513	4.42	1.16	5.9	94.1	-0.69	0.40	0.68	0.87	1.34	17913	2184	12	18	logfile
✔	8XPY	38563	2024-12-27	2024-01-04	3.63	3.53	3.62	1.6	0.004	0.79	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.89	0.05	15.32	0.00	2.454	10.89	2.72	12.4	87.6	-2.28	2.13	0.91	0.83	2.01	4568	546	7	25	logfile
✔	8XPY	38563	2024-11-14	2024-01-04	3.63	3.53	3.62	1.6	0.004	0.79	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.89	0.05	15.32	0.00	2.454	10.89	2.72	12.4	87.6	-2.28	2.13	0.91	0.83	2.01	4568	546	7	25	logfile
✔	8XPY	38563	2024-10-09	2024-01-04	3.63	3.53	3.62	1.6	0.004	0.79	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.89	0.05	15.32	0.00	2.454	10.89	2.72	12.4	87.6	-2.28	2.13	0.91	0.83	2.01	4568	546	7	25	logfile
✔	8XPY	38563	2025-07-23	2024-01-04	3.63	3.53	3.63	1.6	0.004	0.80	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.98	0.05	15.63	0.01	2.346	13.11	3.14	13.8	86.2	-2.44	2.13	0.92	0.84	2.08	4568	546	7	25	logfile
✔	8XPY	38563	2025-06-05	2024-01-04	3.63	3.53	3.63	1.6	0.004	0.80	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.98	0.05	15.63	0.01	2.346	13.11	3.14	13.8	86.2	-2.44	2.13	0.92	0.84	2.08	4568	546	7	25	logfile
✔	8XPY	38563	2025-05-10	2024-01-04	3.63	3.53	3.63	1.6	0.004	0.80	0.0	0.05	29.42	0.00	2.217	10.44	4.39	10.1	89.9	0.0	-4.21	0.90	0.79	2.54	1.5	0.004	0.96	0.05	15.48	0.00	2.382	12.44	2.30	13.3	86.7	-2.46	2.12	0.92	0.83	2.20	4568	546	7	25	logfile
✔	8RM0	19347	2025-05-18	2024-01-04	3.8	2.58	3.83	2.3	0.004	0.76	0.0	0.05	13.70	0.01	2.251	5.19	0.19	3.4	96.6	0.0	-0.81	0.76	0.76	2.77	2.2	0.003	0.79	0.05	16.33	0.00	2.534	5.87	3.96	5.1	94.9	-0.72	0.70	0.77	0.77	2.76	16311	2088	18	48	logfile