cryo-EM Re-Refine

Table showing results for November 2023

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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	Z-score	CC_box	CC_mask	EMRinger	D_Model	Bond rmsd	Angle rmsd	Chirality	Dihedral rmsd	Plane rmsd	Min nonbonded	Clashscore	Z-score	RMSD	CC_box	CC_mask	EMRinger	# atoms	# residues	# chains	# nucleotides	# other	# H	Logfile
✔	6o1o	0454	2023-11-16	2019-02-21	3.8	4.00	—	3.6	0.008	1.55	0.0	0.07	15.00	0.01	2.295	4.58	0.00	—	0.72	0.70	—	3.6	0.013	1.78	0.07	13.81	0.00	1.989	32.10	—	1.70	0.78	0.76	—	15193	0	14	66	2757	0	logfile
✔	7YGD	33816	2023-11-14	2022-07-11	3.41	4.13	3.42	3.3	0.002	0.49	0.0	0.03	15.33	0.00	2.100	14.25	0.00	—	0.90	0.81	—	3.3	0.007	0.75	0.04	17.32	0.01	1.825	32.10	—	1.50	0.91	0.88	—	8313	0	3	389	6	0	logfile
✔	7XD3	33134	2023-11-14	2022-03-26	4.05	4.16	—	3.8	0.003	0.62	0.0	0.04	16.04	0.00	1.960	1.21	0.00	—	0.85	0.74	—	3.9	0.007	0.80	0.04	17.33	0.01	1.680	17.06	—	1.79	0.87	0.82	—	9062	0	1	423	28	0	logfile
✔	7YGC	33815	2023-11-14	2022-07-11	2.65	3.28	2.77	2.9	0.007	0.50	0.0	0.03	14.78	0.00	1.778	12.79	0.00	—	0.90	0.83	—	2.9	0.004	0.55	0.03	15.37	0.00	1.949	13.78	—	1.47	0.92	0.91	—	8690	0	3	407	6	0	logfile
✔	7YG8	33811	2023-11-14	2022-07-11	2.97	3.59	3.04	3.0	0.002	0.48	0.0	0.03	14.91	0.00	2.042	13.48	0.00	—	0.89	0.82	—	3.0	0.006	0.65	0.04	16.08	0.00	1.846	19.87	—	0.38	0.91	0.89	—	8440	0	3	395	5	0	logfile
✔	7ZFW	14704	2023-11-15	2022-04-01	3.8	4.62	3.46	3.0	0.006	0.83	0.0	0.05	17.97	0.03	2.266	2.77	0.00	—	0.32	0.81	—	3.0	0.008	0.86	0.04	20.23	0.01	1.951	37.51	—	2.54	0.33	0.85	—	13188	0	1	615	0	0	logfile
✔	7YGA	33813	2023-11-14	2022-07-11	2.35	3.08	2.44	2.8	0.008	0.62	0.0	0.04	15.27	0.01	1.779	10.87	0.00	—	0.89	0.87	—	2.8	0.007	0.60	0.04	15.40	0.00	1.828	12.41	—	0.16	0.89	0.88	—	8692	0	3	407	8	0	logfile
✔	7YCG	33738	2023-11-14	2022-07-01	3.18	4.71	3.37	3.5	0.002	0.50	0.0	0.03	14.85	0.00	1.893	15.83	0.00	—	0.94	0.84	—	3.5	0.007	0.67	0.04	15.91	0.00	1.847	33.58	—	0.32	0.95	0.90	—	8661	0	2	404	4	0	logfile
✔	7YGB	33814	2023-11-14	2022-07-11	2.62	3.15	2.70	2.9	0.007	0.52	0.0	0.03	14.47	0.00	2.079	13.50	0.00	—	0.88	0.84	—	2.9	0.007	0.64	0.04	15.02	0.00	1.838	13.89	—	0.88	0.90	0.91	—	8738	0	5	407	54	0	logfile
✔	7XD5	33136	2023-11-14	2022-03-26	2.84	3.32	2.81	3.1	0.003	0.58	0.0	0.03	13.91	0.00	1.864	0.61	0.00	—	0.88	0.86	—	3.1	0.004	0.64	0.04	15.34	0.00	1.950	6.11	—	1.39	0.89	0.90	—	8714	0	3	406	30	0	logfile
✔	4UQ8	2676	2023-11-20	2014-06-21	4.95	5.05	4.64	4.9	0.012	2.07	23.0	1.38	6.71	0.01	1.032	64.12	25.00	—	0.57	0.75	—	4.9	0.013	2.54	0.41	5.47	0.00	2.110	23.19	—	2.11	0.61	0.83	—	28647	33	54	0	5686	0	logfile
✔	7EZ2	31386	2023-11-14	2021-06-01	3.05	2.80	—	3.0	0.005	0.56	0.0	0.03	13.94	0.00	1.809	0.92	0.00	—	0.69	0.81	—	3.0	0.007	0.85	0.05	15.80	0.01	1.484	7.35	—	1.04	0.73	0.89	—	8698	0	3	406	31	0	logfile
✔	7PTL	13630	2023-11-18	2021-09-27	4.9	10.06	4.95	—	0.005	1.01	0.0	0.06	16.11	0.01	2.401	0.61	0.00	—	0.88	0.79	—	—	0.007	0.89	0.04	21.14	0.01	1.735	83.10	—	3.49	0.92	0.92	—	23080	0	1	720	0	7743	logfile
✔	7XD6	33137	2023-11-14	2022-03-26	2.84	3.25	2.83	3.0	0.005	0.74	0.0	0.04	15.28	0.00	1.975	1.30	0.00	—	0.88	0.86	—	3.0	0.005	0.67	0.04	16.16	0.00	1.876	7.55	—	1.32	0.88	0.89	—	9843	0	3	459	29	0	logfile
✔	7XD7	33138	2023-11-14	2022-03-26	3.02	3.40	—	3.1	0.003	0.61	0.0	0.04	14.03	0.00	1.736	0.77	0.00	—	0.90	0.86	—	3.1	0.007	0.67	0.04	15.11	0.00	1.866	7.88	—	2.19	0.92	0.92	—	8693	0	1	405	30	0	logfile
✔	7UVT	26816	2023-11-15	2022-05-02	3.9	4.17	4.00	4.1	0.001	0.41	0.0	0.02	16.13	0.00	1.897	6.61	0.00	—	0.76	0.74	—	4.1	0.006	0.72	0.04	18.00	0.01	1.911	21.68	—	0.46	0.77	0.77	—	12409	0	1	386	0	4149	logfile
✔	8HD7	34671	2023-11-14	2022-11-03	3.52	3.99	3.58	3.3	0.003	0.60	0.0	0.03	14.67	0.00	1.927	2.96	0.00	—	0.89	0.77	—	3.3	0.008	0.83	0.05	16.67	0.01	1.800	17.97	—	2.13	0.90	0.82	—	8983	0	1	419	28	0	logfile
✔	7XD4	33135	2023-11-14	2022-03-26	3.89	4.13	—	3.8	0.003	0.59	0.0	0.03	15.73	0.00	1.880	1.73	0.00	—	0.85	0.73	—	3.8	0.007	0.78	0.04	17.52	0.01	1.755	18.36	—	1.84	0.87	0.78	—	9062	0	1	423	28	0	logfile
✔	7URM	26714	2023-11-13	2022-04-22	3.0	3.11	3.56	2.9	0.009	1.41	0.0	0.11	23.67	0.01	2.440	0.70	0.00	—	0.14	0.53	—	3.0	0.007	1.16	0.05	22.80	0.01	1.988	29.25	—	1.68	0.15	0.54	—	1905	0	1	90	0	0	logfile
✔	7URi	26713	2023-11-13	2022-04-22	2.6	2.67	2.95	2.6	0.009	1.37	0.0	0.12	25.77	0.01	2.201	7.31	0.00	—	0.05	0.34	—	2.6	0.008	1.44	0.07	24.06	0.01	2.073	23.33	—	2.06	0.08	0.38	—	1905	0	1	90	0	0	logfile