cryo-EM Re-Refine

Table showing results for November 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	Logfile
✔	8TGG	41235	2024-11-14	2023-07-12	3.6	2.40	3.59	2.2	0.006	0.86	0.0	0.05	18.10	0.01	2.212	22.24	0.49	2.0	97.9	0.1	0.53	0.72	0.72	1.84	2.2	0.004	0.68	0.0	0.04	17.12	0.01	2.593	8.02	6.25	2.4	97.6	0.0	1.55	0.97	0.73	0.73	1.50	5717	758	4	0	2	0	logfile
✔	8K25	36828	2024-11-16	2023-07-12	3.4	3.65	3.55	3.6	0.005	1.14	0.0	0.06	18.39	0.01	2.271	7.89	0.69	7.2	92.8	0.1	-3.18	0.63	0.52	0.39	3.6	0.003	0.69	0.0	0.04	18.44	0.00	2.518	14.29	4.14	6.8	93.2	0.1	-0.76	0.52	0.67	0.60	0.96	9961	1330	8	34	0	0	logfile
✔	8TGH	41236	2024-11-14	2023-07-12	3.5	2.39	3.45	2.2	0.007	0.81	0.0	0.05	17.21	0.01	2.269	16.16	0.98	2.5	97.5	0.0	0.62	0.79	0.82	2.22	2.2	0.003	0.65	0.0	0.04	16.22	0.01	2.617	5.36	3.25	2.9	97.1	0.0	2.35	0.74	0.78	0.79	2.11	5778	767	4	0	2	0	logfile
✔	8TGJ	41238	2024-11-14	2023-07-12	3.5	2.56	3.51	2.9	0.004	0.78	0.0	0.05	18.01	0.01	2.292	25.32	0.66	1.6	98.4	0.0	0.58	0.71	0.72	1.85	2.9	0.005	1.12	1.0	0.04	17.11	0.01	2.384	10.73	5.25	2.5	97.5	0.0	1.44	0.37	0.72	0.72	1.42	5720	761	3	0	1	0	logfile
✔	8TGL	41240	2024-11-14	2023-07-12	3.4	2.34	3.39	3.3	0.005	0.80	0.0	0.04	17.87	0.01	2.218	30.23	0.82	1.7	98.1	0.1	1.90	0.73	0.71	2.60	3.3	0.004	0.78	0.0	0.04	16.39	0.01	2.457	11.91	3.76	2.9	97.1	0.0	1.33	1.30	0.74	0.74	2.73	5734	760	4	0	2	0	logfile
✔	8TGN	41242	2024-11-14	2023-07-12	3.3	2.50	3.28	2.9	0.005	0.97	0.0	0.05	18.68	0.01	2.195	28.85	0.49	1.3	98.5	0.1	0.16	0.71	0.73	1.69	2.9	0.004	0.74	0.0	0.04	17.47	0.01	2.559	11.47	4.25	2.0	98.0	0.0	1.42	0.36	0.72	0.73	1.35	5745	761	4	0	2	0	logfile
✔	8K27	36830	2024-11-20	2023-07-12	3.6	3.70	—	3.6	0.006	1.15	2.0	0.07	21.74	0.01	1.649	5.73	11.13	7.3	92.2	0.5	-3.25	0.83	0.84	2.87	3.6	0.005	0.66	0.0	0.04	20.26	0.00	2.413	5.88	2.60	6.3	93.5	0.1	-1.19	1.25	0.85	0.86	2.97	21183	2396	12	134	0	0	logfile
✔	8PR3	17833	2024-11-19	2023-07-12	3.9	4.21	3.80	4.0	0.006	1.08	0.0	0.05	17.80	0.01	2.278	6.13	0.67	3.0	96.9	0.0	-1.20	0.80	0.83	1.45	4.0	0.003	0.69	0.0	0.04	18.02	0.00	2.484	8.98	2.42	2.5	97.5	0.0	1.40	0.42	0.80	0.84	1.38	17888	2221	9	0	0	0	logfile
✔	8K26	36829	2024-11-16	2023-07-12	3.6	3.91	3.69	3.7	0.006	1.31	1.0	0.07	17.74	0.01	2.221	8.76	0.71	5.7	94.1	0.2	-3.00	0.69	0.54	-0.04	3.7	0.006	1.01	1.0	0.05	17.51	0.00	2.233	23.17	2.56	5.8	94.0	0.2	-0.95	0.67	0.71	0.58	0.55	10549	1336	6	0	0	0	logfile
✔	8PR2	17832	2024-11-17	2023-07-12	3.8	3.87	3.70	3.9	0.005	1.03	0.0	0.05	18.62	0.01	1.770	5.14	0.74	2.5	97.4	0.1	-0.80	0.74	0.81	1.58	3.9	0.004	0.91	1.0	0.04	18.97	0.00	2.375	9.73	3.08	1.7	98.3	0.0	2.55	0.42	0.75	0.83	1.56	14906	1816	6	0	0	0	logfile
✔	8K1V	36805	2024-11-14	2023-07-11	3.48	3.80	3.32	3.9	0.001	0.31	0.0	0.03	13.71	0.00	2.283	2.43	0.00	0.6	99.4	0.0	5.96	0.54	0.76	1.54	3.9	0.003	0.56	0.0	0.04	14.71	0.00	2.480	4.01	2.94	1.7	98.3	0.0	4.79	0.74	0.53	0.79	2.49	4059	484	6	0	11	2	logfile
✔	8PQL	17822	2024-11-17	2023-07-11	3.76	2.60	—	2.1	0.003	0.70	0.0	0.04	17.44	0.01	1.986	7.89	0.54	9.3	90.7	0.0	-0.67	0.78	0.73	1.62	2.1	0.003	0.65	0.0	0.04	17.62	0.00	2.275	7.47	4.60	8.4	91.6	0.0	-0.32	0.29	0.78	0.74	1.53	13553	1837	10	0	4	0	logfile
✔	8K1Z	36806	2024-11-14	2023-07-11	3.41	3.55	3.06	3.6	0.002	0.42	0.0	0.03	13.66	0.00	2.241	4.01	0.00	1.1	98.9	0.0	5.04	0.60	0.77	1.90	3.6	0.003	0.62	0.0	0.04	15.42	0.00	2.510	4.98	3.19	2.1	97.9	0.0	4.85	1.33	0.62	0.82	1.41	4059	484	6	0	11	2	logfile
✔	8K1L	36794	2024-11-16	2023-07-11	3.44	3.80	3.50	3.7	0.004	1.17	0.0	0.05	16.42	0.01	2.067	19.32	0.37	5.9	94.1	0.0	-1.16	0.65	0.85	1.91	3.7	0.003	0.64	0.0	0.04	16.86	0.00	2.537	9.91	3.02	6.1	93.8	0.2	0.12	0.37	0.66	0.85	1.80	10026	1271	3	0	1	0	logfile
✔	8K20	36808	2024-11-15	2023-07-11	3.7	4.39	3.57	3.7	0.003	0.60	0.0	0.04	14.08	0.00	2.100	14.06	0.00	2.8	97.2	0.0	0.88	0.82	0.64	0.83	3.8	0.003	0.65	0.0	0.04	15.94	0.00	2.047	12.99	1.84	3.9	96.1	0.0	0.29	0.96	0.83	0.67	0.74	9356	1209	7	0	1	0	logfile
✔	8K1J	36793	2024-11-14	2023-07-11	3.0	3.30	3.06	3.4	0.001	0.34	0.0	0.03	13.84	0.00	2.296	2.67	0.00	0.4	99.6	0.0	5.90	0.58	0.77	0.99	3.3	0.003	0.52	0.0	0.04	14.88	0.00	2.513	2.55	2.21	2.1	97.9	0.0	4.72	0.60	0.62	0.83	1.10	4069	484	6	0	11	12	logfile
✔	8K1o	36797	2024-11-14	2023-07-11	2.9	3.14	2.87	3.2	0.007	1.00	0.0	0.05	17.98	0.01	1.945	3.29	0.42	6.0	94.0	0.0	-1.93	0.62	0.85	3.48	3.2	0.003	0.57	0.0	0.04	16.88	0.00	1.999	2.47	1.55	4.3	95.7	0.0	0.55	0.96	0.65	0.88	2.78	7163	937	6	0	6	0	logfile
✔	8K1P	36798	2024-11-14	2023-07-11	3.4	3.64	3.33	3.6	0.007	0.86	0.0	0.05	16.58	0.01	2.062	5.37	0.14	7.6	92.4	0.0	-1.68	0.73	0.88	2.91	3.6	0.003	0.58	0.0	0.04	16.26	0.00	1.993	3.72	0.71	5.8	94.2	0.0	-0.07	0.38	0.67	0.88	2.69	7139	934	6	0	7	0	logfile
✔	8K1N	36796	2024-11-14	2023-07-11	3.0	3.28	2.95	3.3	0.008	1.24	6.0	0.07	15.25	0.01	2.218	9.86	0.70	8.5	91.5	0.0	-1.83	0.59	0.82	2.51	3.3	0.004	0.65	0.0	0.04	16.77	0.00	2.409	8.08	3.34	5.7	94.3	0.0	-0.10	1.75	0.63	0.86	2.18	7175	952	4	0	2	0	logfile
✔	8K1S	36800	2024-11-20	2023-07-11	2.83	3.20	2.99	3.2	0.004	0.61	0.0	0.04	10.43	0.00	2.272	6.20	0.76	2.4	97.6	0.0	1.13	0.59	0.75	2.70	3.2	0.004	0.74	0.0	0.05	15.94	0.00	2.437	8.59	2.94	4.4	95.6	0.0	1.85	1.38	0.58	0.81	2.33	21000	2695	24	0	12	0	logfile