cryo-EM Re-Refine

Table showing results for July 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
✔	7UVT	26816	2023-07-06	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	0.70	0.04	17.94	0.01	1.892	21.35	—	0.48	0.77	0.76	—	12409	0	1	386	0	4149	logfile
✔	7XSM	33427	2023-07-06	2022-05-14	4.01	4.70	4.03	4.0	0.002	0.47	0.0	0.03	15.76	0.00	1.969	7.06	0.00	—	0.90	0.75	—	4.0	0.007	0.76	0.04	19.93	0.01	1.773	49.65	—	1.70	0.92	0.82	—	12464	0	1	388	0	4165	logfile
✔	7XSN	33428	2023-07-04	2022-05-14	3.01	4.02	3.04	3.2	0.013	1.06	0.0	0.05	16.67	0.01	2.252	5.79	0.00	—	0.91	0.84	—	3.2	0.006	0.61	0.03	16.36	0.00	2.111	20.82	—	0.30	0.92	0.87	—	8279	0	1	387	0	0	logfile
✔	6o1o	0454	2023-07-07	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	1.77	0.07	13.79	0.00	1.993	31.58	—	1.70	0.78	0.76	—	15193	0	14	66	2757	0	logfile
✔	4UQ8	2676	2023-07-13	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
✔	7YG8	33811	2023-07-04	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	0.63	0.04	15.97	0.00	1.823	18.76	—	0.37	0.91	0.89	—	8440	0	3	395	5	0	logfile
✔	8HD7	34671	2023-07-05	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	0.007	0.80	0.05	16.62	0.01	1.771	17.29	—	2.12	0.91	0.84	—	8983	0	1	419	28	0	logfile
✔	7XD3	33134	2023-07-05	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	17.14	0.01	1.675	17.13	—	1.77	0.87	0.81	—	9062	0	1	423	28	0	logfile
✔	8HD6	34670	2023-07-05	2022-11-03	3.73	4.52	3.73	3.2	0.002	0.54	0.0	0.02	14.51	0.00	1.969	2.97	0.00	—	0.90	0.78	—	3.3	0.008	0.86	0.05	19.11	0.01	1.720	28.98	—	2.31	0.91	0.82	—	8980	0	1	419	25	0	logfile
✔	7ZFW	14704	2023-07-06	2022-04-01	3.8	4.62	3.46	3.0	0.006	0.83	0.0	0.05	17.92	0.03	2.266	2.77	0.00	—	0.32	0.81	—	3.0	0.009	0.90	0.04	20.26	0.01	1.952	38.01	—	2.55	0.33	0.85	—	13188	0	1	615	0	0	logfile
✔	7XSL	33426	2023-07-06	2022-05-14	3.84	4.65	3.83	3.7	0.002	0.47	0.0	0.02	16.20	0.00	1.935	8.02	0.00	—	0.91	0.77	—	3.8	0.006	0.70	0.04	18.31	0.01	1.810	33.53	—	1.02	0.92	0.83	—	12467	0	1	388	0	4168	logfile
✔	7EZ2	31386	2023-07-04	2021-06-01	3.05	2.80	—	3.0	0.005	0.56	0.0	0.03	13.92	0.00	1.809	0.92	0.00	—	0.69	0.81	—	3.0	0.008	0.86	0.05	15.75	0.01	1.755	7.20	—	1.04	0.73	0.89	—	8698	0	3	406	31	0	logfile
✔	7XD5	33136	2023-07-04	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	15.36	0.00	1.949	6.26	—	1.38	0.89	0.90	—	8714	0	3	406	30	0	logfile
✔	7XD4	33135	2023-07-05	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	17.27	0.01	1.748	17.91	—	1.76	0.87	0.78	—	9062	0	1	423	28	0	logfile
✔	7YG9	33812	2023-07-04	2022-07-11	2.68	3.47	2.76	2.8	0.005	0.51	0.0	0.03	15.21	0.00	1.804	13.88	0.00	—	0.86	0.81	—	2.8	0.006	0.61	0.04	15.60	0.00	1.866	18.12	—	0.39	0.92	0.92	—	8630	0	3	404	8	0	logfile
✔	7PTL	13630	2023-07-11	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	0.90	0.04	21.29	0.01	1.737	86.57	—	3.52	0.91	0.92	—	23080	0	1	720	0	7743	logfile
✔	7PTQ	13633	2023-07-08	2021-09-27	4.08	6.47	4.22	4.0	0.005	0.78	0.0	0.04	15.27	0.00	1.983	0.92	0.00	—	0.91	0.80	—	4.0	0.006	0.67	0.04	19.44	0.00	1.852	43.48	—	2.75	0.96	0.94	—	17434	0	1	544	0	5847	logfile
✔	7XD6	33137	2023-07-05	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	0.66	0.04	16.14	0.00	1.883	7.41	—	1.32	0.88	0.89	—	9843	0	3	459	29	0	logfile
✔	6UES	20755	2023-07-03	2019-09-23	3.7	3.94	—	3.2	0.002	0.48	0.0	0.02	17.15	0.00	2.100	7.29	0.00	—	0.87	0.76	—	3.3	0.007	0.87	0.04	21.14	0.01	1.785	36.43	—	1.34	0.88	0.83	—	3842	0	1	119	0	1291	logfile
✔	7R6L	24281	2023-07-04	2021-06-22	2.85	3.04	—	3.0	0.008	0.89	0.0	0.05	16.80	0.01	1.985	4.24	0.00	—	0.67	0.86	—	3.0	0.006	0.73	0.04	16.40	0.01	1.882	7.54	—	0.09	0.62	0.86	—	7857	0	3	366	20	0	logfile