cryo-EM Re-Refine

Table showing results for February 2024

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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	# nucleotides	# other	# water	# H	Logfile
✔	7MSW	23970	2024-02-14	2021-05-12	3.76	3.93	3.60	3.8	0.009	0.66	0.0	0.05	10.62	0.00	1.933	0.81	0.00	2.5	97.3	0.2	-0.01	0.79	0.80	1.87	3.8	0.003	0.55	0.0	0.04	14.14	0.00	2.039	6.38	2.03	3.8	96.2	0.0	0.22	0.95	0.79	0.81	1.71	9881	635	1	0	3	0	4959	logfile
✔	7MT3	23975	2024-02-26	2021-05-12	2.8	2.45	—	2.9	0.007	0.80	0.0	0.04	22.33	0.01	1.298	2.40	0.13	7.0	92.9	0.1	-4.52	0.84	0.86	4.06	2.9	0.010	0.77	0.0	0.05	22.42	0.01	0.999	6.20	2.10	7.0	92.9	0.1	-1.39	2.15	0.85	0.87	3.27	147942	5616	68	4835	441	0	0	logfile
✔	7ET2	31296	2024-02-23	2021-05-12	4.2	4.39	—	4.3	0.006	1.04	0.0	0.06	16.25	0.01	2.282	6.60	0.41	4.5	95.5	0.0	-4.80	0.52	0.78	—	4.3	0.003	0.74	0.0	0.04	15.34	0.00	2.088	13.98	0.10	2.8	97.2	0.0	-1.35	0.69	0.45	0.78	—	38880	4812	12	0	0	0	0	logfile
✔	7oiX	12935	2024-02-13	2021-05-12	3.6	3.76	—	3.7	0.007	1.08	0.0	0.06	17.88	0.01	2.133	8.89	0.97	3.5	96.5	0.0	-1.19	0.58	0.74	1.74	3.7	0.003	0.73	0.0	0.04	15.54	0.00	2.293	10.69	3.86	3.8	96.2	0.0	-0.38	1.27	0.63	0.76	1.95	5869	716	5	0	17	0	0	logfile
✔	7MSZ	23972	2024-02-29	2021-05-12	3.1	2.44	—	2.9	0.013	1.14	1.0	0.06	22.78	0.01	1.949	3.55	0.54	9.3	90.6	0.1	-4.96	0.83	0.84	3.69	2.9	0.008	0.77	0.0	0.04	22.64	0.01	1.768	8.31	4.15	8.0	92.0	0.1	-2.16	0.47	0.83	0.85	2.68	152345	6171	72	4836	427	0	0	logfile
✔	7ET1	31294	2024-02-17	2021-05-12	2.6	3.09	2.69	3.0	0.007	1.25	0.0	0.05	17.05	0.01	1.936	9.51	0.19	2.7	97.3	0.0	0.57	0.76	0.87	2.95	3.0	0.005	0.81	0.0	0.04	16.86	0.00	1.583	6.47	1.41	1.8	98.2	0.0	1.22	1.02	0.73	0.90	3.03	10015	1249	5	0	14	1	0	logfile
✔	7oiD	12926	2024-02-22	2021-05-11	3.7	3.36	—	3.3	0.013	1.33	2.0	0.07	20.89	0.01	1.521	9.46	0.07	6.8	93.2	0.0	-2.22	0.73	0.74	2.43	3.3	0.004	0.71	0.0	0.04	21.08	0.00	2.015	14.39	2.79	5.3	94.7	0.0	-0.56	1.18	0.72	0.72	1.69	101125	8217	61	1601	5	0	0	logfile
✔	7oi8	12921	2024-02-21	2021-05-11	3.5	3.27	—	3.2	0.006	0.99	1.0	0.05	19.46	0.01	1.998	7.08	0.03	4.8	95.1	0.0	-1.78	0.75	0.78	2.56	3.2	0.006	0.73	3.0	0.05	20.08	0.01	1.630	12.13	2.42	4.1	95.8	0.0	-0.38	1.17	0.75	0.79	2.08	92769	8181	60	1221	52	0	0	logfile
✔	7oi9	12922	2024-02-21	2021-05-11	3.3	3.23	—	3.2	0.004	0.87	1.0	0.05	18.80	0.01	1.574	6.32	0.06	3.9	96.0	0.0	-1.37	0.72	0.73	2.41	3.2	0.003	0.64	0.0	0.04	19.42	0.00	1.924	11.20	2.71	3.7	96.3	0.0	-0.05	0.50	0.76	0.79	2.18	90599	8105	60	1148	52	0	0	logfile
✔	7oiB	12924	2024-02-20	2021-05-11	3.3	3.27	—	3.2	0.004	0.86	0.0	0.05	18.94	0.01	2.019	6.14	0.03	3.8	96.2	0.0	-1.30	0.76	0.81	2.48	3.2	0.005	0.71	1.0	0.04	19.78	0.01	1.790	12.65	3.35	4.3	95.6	0.0	-0.07	0.48	0.79	0.87	2.38	88360	7838	56	1148	51	0	0	logfile
✔	7oi0	12916	2024-02-20	2021-05-11	2.76	2.96	2.85	2.8	0.014	1.08	0.0	0.06	24.49	0.01	1.912	23.66	0.23	10.2	89.8	0.0	-2.50	0.80	0.75	2.74	2.8	0.009	0.88	0.0	0.05	23.95	0.01	2.013	18.20	2.45	8.4	91.6	0.0	-0.99	0.37	0.83	0.80	2.41	29255	1037	17	963	0	374	0	logfile
✔	7oHY	12913	2024-02-17	2021-05-11	3.9	4.70	3.99	3.1	0.002	0.44	0.0	0.03	22.64	0.00	1.780	5.59	0.61	4.2	95.8	0.0	1.53	0.82	0.72	0.73	3.2	0.007	0.68	0.0	0.04	23.53	0.00	1.714	24.22	2.34	8.6	91.4	0.1	-0.81	1.74	0.85	0.80	1.12	125318	4067	28	1837	2	0	53608	logfile
✔	7oiF	12928	2024-02-24	2021-05-11	3.0	4.31	3.02	2.9	0.018	1.18	1.0	0.08	22.84	0.02	1.454	7.90	0.21	3.7	96.1	0.2	-3.85	0.87	0.80	2.41	3.0	0.005	0.79	0.0	0.04	22.97	0.01	1.728	18.29	2.69	4.5	95.5	0.0	-0.49	0.60	0.93	0.90	2.02	145152	5738	70	4651	418	0	0	logfile
✔	7oii	12930	2024-02-24	2021-05-11	3.0	3.56	2.91	2.7	0.017	1.20	0.0	0.07	22.80	0.03	1.514	7.87	0.23	3.6	96.2	0.2	-3.84	0.85	0.83	3.42	2.8	0.006	0.80	0.0	0.04	22.96	0.01	1.257	14.47	3.39	4.0	96.0	0.0	-0.20	1.21	0.90	0.90	2.97	145171	5754	69	4648	424	0	0	logfile
✔	7oHT	12908	2024-02-19	2021-05-11	4.7	6.83	4.99	3.5	0.002	0.48	0.0	0.04	22.77	0.00	1.855	6.77	1.28	5.3	94.6	0.1	0.83	0.81	0.61	—	3.4	0.003	0.57	0.0	0.03	22.76	0.00	1.820	18.58	0.00	8.5	91.3	0.1	-0.69	1.74	0.86	0.78	—	135365	5154	30	1618	3	0	59714	logfile
✔	7oHU	12909	2024-02-17	2021-05-11	3.7	4.68	3.77	3.4	0.008	0.53	1.0	0.03	22.49	0.00	1.811	5.44	0.45	3.5	96.5	0.0	1.01	0.83	0.76	1.33	3.4	0.009	0.66	1.0	0.04	22.97	0.00	1.757	17.30	1.99	7.6	92.4	0.0	-0.63	1.31	0.85	0.81	1.56	127652	4202	29	1840	2	0	54773	logfile
✔	7oiG	12929	2024-02-24	2021-05-11	3.2	3.93	3.16	3.0	0.011	1.03	0.0	0.06	22.86	0.02	1.449	8.53	0.21	3.6	96.2	0.1	-3.86	0.88	0.85	2.63	3.0	0.005	0.72	0.0	0.04	23.03	0.01	1.122	15.06	3.65	3.8	96.2	0.0	-0.05	1.62	0.91	0.90	2.27	145136	5738	68	4651	402	0	0	logfile
✔	7oHP	12904	2024-02-23	2021-05-11	3.9	5.25	4.02	3.0	0.005	0.54	0.0	0.03	22.32	0.00	1.733	6.18	1.01	4.3	95.5	0.2	1.17	0.80	0.64	0.37	3.1	0.005	0.68	0.0	0.04	23.08	0.00	1.793	24.53	2.62	8.6	91.4	0.0	-1.16	1.73	0.83	0.74	0.43	143939	5290	35	1781	1	0	63394	logfile
✔	7oiM	12932	2024-02-22	2021-05-11	4.0	4.68	3.92	3.7	0.006	1.32	7.0	0.07	14.13	0.01	2.069	5.16	0.05	8.1	91.7	0.2	-3.63	0.81	0.66	—	3.8	0.003	0.76	0.0	0.04	15.30	0.00	2.023	13.57	1.26	7.3	92.7	0.0	-0.35	0.66	0.90	0.81	—	35597	4426	1	0	6	0	0	logfile
✔	7oi7	12920	2024-02-20	2021-05-11	3.5	3.35	—	3.3	0.006	0.95	1.0	0.05	18.54	0.01	2.041	6.91	0.10	4.3	95.7	0.0	-1.48	0.73	0.75	2.42	3.3	0.007	0.73	0.0	0.04	19.35	0.01	1.852	12.90	3.26	4.9	95.1	0.0	-0.27	0.51	0.74	0.77	2.13	89747	8101	60	1110	52	0	0	logfile