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
✔	8DR7	27673	2024-02-24	2022-07-20	2.7	3.41	2.84	3.2	0.008	0.60	0.0	0.04	17.41	0.00	1.945	4.68	0.91	1.4	98.6	0.0	1.90	0.85	0.85	2.57	3.2	0.004	0.54	0.0	0.04	17.49	0.00	1.923	5.36	1.34	2.4	97.6	0.0	1.36	1.06	0.79	0.85	2.97	43060	2600	16	50	8	0	21405	logfile
✔	8DQW	27662	2024-02-24	2022-07-20	2.1	2.86	2.16	2.6	0.007	0.55	0.0	0.04	18.05	0.00	1.761	3.31	0.44	1.6	98.4	0.0	2.35	0.77	0.72	3.64	2.7	0.003	0.53	0.0	0.04	17.77	0.00	1.722	3.85	1.11	1.7	98.3	0.0	2.19	2.60	0.82	0.88	3.89	46565	2802	25	36	8	429	22936	logfile
✔	8DR1	27668	2024-02-24	2022-07-20	2.14	2.91	2.21	2.7	0.008	0.57	0.0	0.04	18.10	0.00	1.946	2.66	0.74	1.4	98.6	0.0	1.79	0.80	0.77	4.33	2.7	0.004	0.54	0.0	0.04	17.98	0.00	1.692	3.21	1.25	1.5	98.5	0.0	1.82	0.66	0.78	0.88	4.67	43630	2608	21	64	8	12	21631	logfile
✔	8DQX	27663	2024-02-24	2022-07-20	2.1	2.94	2.16	2.7	0.008	0.68	0.0	0.04	17.32	0.00	1.878	4.91	1.26	2.0	98.0	0.0	1.11	0.79	0.75	4.56	2.7	0.003	0.52	0.0	0.04	17.06	0.00	1.757	4.25	0.95	1.4	98.6	0.0	1.94	0.67	0.80	0.88	4.42	43173	2598	26	27	8	866	21143	logfile
✔	8DRA	27675	2024-02-14	2022-07-20	3.98	4.17	3.98	4.0	0.003	0.77	0.0	0.05	15.74	0.01	2.257	11.58	0.35	5.4	94.6	0.0	-3.01	0.63	0.69	0.62	4.0	0.003	0.74	0.0	0.04	17.24	0.00	2.201	19.57	2.99	5.7	94.2	0.1	-2.44	1.75	0.67	0.74	0.70	9899	1218	3	0	0	0	0	logfile
✔	8DQZ	27666	2024-02-24	2022-07-20	2.92	3.56	3.08	3.3	0.008	0.60	0.0	0.04	16.92	0.00	1.869	5.54	0.30	2.1	97.9	0.0	1.51	0.84	0.85	2.75	3.4	0.003	0.54	0.0	0.04	17.13	0.00	1.810	5.86	0.87	3.1	96.9	0.0	1.35	1.15	0.80	0.86	2.69	42754	2599	15	41	8	0	21302	logfile
✔	8AGU	15424	2024-02-28	2022-07-20	2.7	3.26	2.76	2.7	0.006	0.90	6.0	0.05	21.59	0.01	1.041	6.23	1.81	3.6	96.3	0.1	0.14	0.92	0.88	3.27	2.7	0.005	0.69	5.0	0.04	21.61	0.01	1.922	10.25	2.38	4.3	95.7	0.0	0.57	0.48	0.93	0.91	3.23	149748	9427	68	3568	38	0	0	logfile
✔	8AGX	15427	2024-02-28	2022-07-20	2.4	3.19	2.52	2.5	0.006	0.93	5.0	0.05	21.77	0.01	1.296	4.14	2.04	3.7	96.2	0.1	-0.44	0.92	0.89	3.34	2.6	0.004	0.63	1.0	0.04	21.68	0.00	1.910	8.64	2.02	4.4	95.6	0.0	0.51	0.46	0.94	0.93	3.42	149706	9204	68	3640	41	0	0	logfile
✔	8AGW	15426	2024-02-28	2022-07-20	2.6	3.24	2.70	2.7	0.006	0.90	7.0	0.06	21.72	0.01	1.371	4.13	0.98	3.8	96.1	0.1	-0.36	0.92	0.89	3.19	2.6	0.005	0.61	0.0	0.04	21.64	0.00	1.893	8.41	2.31	4.5	95.5	0.0	0.63	0.46	0.94	0.92	3.22	150269	9285	68	3642	38	0	0	logfile
✔	8AGT	15423	2024-02-29	2022-07-20	2.6	3.22	2.67	2.6	0.006	0.90	6.0	0.05	21.62	0.01	1.011	4.89	1.63	3.6	96.3	0.1	0.14	0.92	0.88	3.20	2.6	0.003	0.60	1.0	0.04	21.63	0.00	1.973	9.10	1.76	4.1	95.8	0.0	0.64	1.16	0.93	0.91	3.03	151341	9428	69	3642	37	0	0	logfile
✔	8DR6	27672	2024-02-24	2022-07-20	2.39	3.20	2.47	3.0	0.002	0.52	0.0	0.04	17.90	0.00	1.996	3.30	0.95	1.3	98.7	0.0	2.01	0.85	0.85	3.82	3.0	0.003	0.53	0.0	0.04	18.00	0.00	1.779	3.80	1.17	1.7	98.3	0.0	1.94	0.58	0.77	0.86	3.76	43630	2608	20	63	9	12	21632	logfile
✔	8DR5	27671	2024-02-24	2022-07-20	2.76	3.39	2.90	3.2	0.007	0.56	0.0	0.04	17.22	0.00	1.939	4.82	0.82	2.0	98.0	0.0	1.42	0.84	0.84	2.91	3.2	0.003	0.54	0.0	0.04	17.52	0.00	1.880	5.63	1.15	2.6	97.4	0.0	1.38	1.39	0.79	0.85	2.87	45375	2749	17	50	8	0	22595	logfile
✔	7YJN	33875	2024-02-14	2022-07-20	3.4	3.63	3.43	3.6	0.019	1.74	21.0	0.13	15.89	0.01	1.776	26.04	8.37	11.1	87.0	1.9	-2.39	0.70	0.83	2.69	3.6	0.003	0.66	0.0	0.04	16.17	0.00	2.200	7.15	3.48	5.7	94.1	0.2	0.22	0.51	0.69	0.84	2.05	8528	1095	6	0	1	0	0	logfile
✔	8DR0	27667	2024-02-24	2022-07-20	2.42	3.22	2.49	3.0	0.008	0.56	0.0	0.04	17.94	0.00	2.058	3.70	1.04	1.4	98.6	0.0	2.09	0.87	0.85	3.77	3.0	0.003	0.52	0.0	0.04	17.94	0.00	1.919	4.56	0.91	1.9	98.1	0.0	1.83	1.78	0.80	0.86	3.73	42882	2608	15	41	8	0	21368	logfile
✔	8AG5	15416	2024-02-16	2022-07-19	3.47	2.11	—	1.9	0.003	0.49	0.0	0.04	17.82	0.00	2.194	6.46	0.26	3.8	96.2	0.0	0.35	0.75	0.75	3.20	1.9	0.002	0.49	0.0	0.04	17.78	0.00	2.206	6.76	2.55	3.8	96.2	0.0	0.65	0.24	0.76	0.78	2.88	13762	1703	4	0	0	0	0	logfile
✔	7YJ1	33868	2024-02-14	2022-07-19	3.1	3.27	3.03	3.2	0.006	0.84	0.0	0.05	18.00	0.00	1.486	11.68	9.53	7.4	91.9	0.7	-3.00	0.72	0.88	2.84	3.2	0.002	0.57	0.0	0.04	16.93	0.00	2.176	4.42	2.05	4.2	95.8	0.0	-0.46	0.34	0.70	0.88	2.24	9140	1154	6	0	1	0	0	logfile
✔	8AG3	15414	2024-02-13	2022-07-19	3.47	2.17	3.26	2.0	0.002	0.60	0.0	0.04	17.16	0.01	2.143	8.90	0.00	6.6	93.4	0.0	-1.45	0.61	0.73	3.03	1.8	0.003	0.63	0.0	0.05	17.40	0.01	2.085	9.47	4.22	8.2	91.8	0.0	-1.12	0.32	0.62	0.77	2.98	2632	322	2	0	0	0	0	logfile
✔	8DQK	27655	2024-02-13	2022-07-19	4.0	4.35	4.38	3.9	0.003	0.72	0.0	0.05	12.56	0.01	2.134	12.28	0.00	2.6	97.2	0.1	0.14	0.55	0.56	—	4.1	0.004	0.69	0.0	0.04	15.44	0.00	2.107	19.61	3.97	4.4	95.4	0.1	0.29	1.71	0.60	0.70	—	5891	733	1	0	0	0	0	logfile
✔	8DQL	27656	2024-02-13	2022-07-19	3.0	2.95	2.90	2.9	0.002	0.47	0.0	0.04	14.89	0.00	2.309	5.10	0.00	3.6	96.4	0.0	2.01	0.74	0.81	1.75	2.9	0.003	0.58	0.0	0.04	16.65	0.00	2.302	5.25	2.74	4.5	95.5	0.0	1.70	3.33	0.75	0.84	1.98	6402	771	3	0	0	0	0	logfile
✔	7YJ4	33871	2024-02-14	2022-07-19	3.19	3.39	3.21	3.4	0.004	0.67	0.0	0.05	14.73	0.01	2.175	9.63	1.55	5.5	94.4	0.1	-0.72	0.60	0.73	1.95	3.4	0.003	0.65	0.0	0.04	16.06	0.00	2.141	11.36	2.06	5.1	94.9	0.0	-0.35	0.67	0.63	0.79	2.19	8985	1154	7	0	0	0	0	logfile