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	Chirality	Dihedral rmsd	Plane rmsd	Min nonbonded	Clashscore	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	# chains	# nucleotides	# other	# H	Logfile
✔	7XSK	33425	2023-11-15	2022-05-14	3.53	4.49	3.42	3.4	0.001	0.44	0.02	15.94	0.00	1.970	6.98	—	0.90	0.76	—	3.4	0.006	0.67	0.04	18.57	0.01	1.759	30.56	—	1.87	0.91	0.83	—	12467	1	388	0	4168	logfile
✔	7XD4	33135	2023-11-14	2022-03-26	3.89	4.13	—	3.8	0.003	0.59	0.03	15.73	0.00	1.880	1.73	—	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	1	423	28	0	logfile
✔	7EZ2	31386	2023-11-14	2021-06-01	3.05	2.80	—	3.0	0.005	0.56	0.03	13.94	0.00	1.809	0.92	—	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	3	406	31	0	logfile
✔	8HD7	34671	2023-11-14	2022-11-03	3.52	3.99	3.58	3.3	0.003	0.60	0.03	14.67	0.00	1.927	2.96	—	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	1	419	28	0	logfile
✔	7EZ0	31385	2023-11-14	2021-06-01	3.14	3.26	—	3.2	0.003	0.56	0.03	14.43	0.00	1.804	2.25	—	0.74	0.79	—	3.2	0.006	0.68	0.04	15.56	0.00	1.860	8.26	—	1.91	0.76	0.85	—	8306	1	387	27	0	logfile
✔	8i7N	35223	2023-11-14	2023-02-01	2.98	3.12	2.92	3.0	0.006	0.66	0.04	14.75	0.00	1.982	2.00	—	0.82	0.83	—	3.0	0.008	0.72	0.04	15.20	0.01	1.929	5.19	—	0.94	0.88	0.92	—	8979	1	418	29	0	logfile
✔	7XD5	33136	2023-11-14	2022-03-26	2.84	3.32	2.81	3.1	0.003	0.58	0.03	13.91	0.00	1.864	0.61	—	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	3	406	30	0	logfile
✔	7R6L	24281	2023-11-14	2021-06-22	2.85	3.04	—	3.0	0.008	0.89	0.05	16.80	0.01	1.985	4.24	—	0.67	0.86	—	3.0	0.007	0.74	0.04	16.42	0.01	1.881	7.63	—	0.08	0.63	0.86	—	7857	3	366	20	0	logfile
✔	7YG9	33812	2023-11-14	2022-07-11	2.68	3.47	2.76	2.8	0.005	0.51	0.03	15.25	0.00	1.804	13.88	—	0.86	0.81	—	2.8	0.006	0.61	0.04	15.66	0.00	1.870	18.05	—	0.39	0.92	0.92	—	8630	3	404	8	0	logfile
✔	7XSL	33426	2023-11-15	2022-05-14	3.84	4.65	3.83	3.7	0.002	0.47	0.02	16.20	0.00	1.935	8.02	—	0.91	0.77	—	3.8	0.007	0.70	0.04	18.25	0.01	1.810	33.93	—	1.01	0.92	0.83	—	12467	1	388	0	4168	logfile
✔	7YCi	33740	2023-11-14	2022-07-01	2.98	4.31	3.09	3.2	0.002	0.48	0.02	14.96	0.00	1.521	15.79	—	0.93	0.84	—	3.3	0.005	0.62	0.03	16.16	0.00	1.852	24.59	—	0.93	0.95	0.90	—	8474	2	395	4	0	logfile
✔	7ZJ5	14741	2023-11-15	2022-04-08	4.55	5.91	5.09	4.4	0.002	0.65	0.04	14.68	0.00	2.256	0.50	—	0.92	0.85	—	4.5	0.008	0.84	0.04	17.52	0.01	1.638	62.68	—	3.95	0.94	0.90	—	12014	1	374	1	4030	logfile
✔	7XSN	33428	2023-11-14	2022-05-14	3.01	4.02	3.04	3.2	0.013	1.06	0.05	16.67	0.01	2.252	5.79	—	0.91	0.84	—	3.2	0.006	0.62	0.03	16.39	0.00	2.117	21.47	—	0.29	0.92	0.87	—	8279	1	387	0	0	logfile
✔	7YGC	33815	2023-11-14	2022-07-11	2.65	3.28	2.77	2.9	0.007	0.50	0.03	14.78	0.00	1.778	12.79	—	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	3	407	6	0	logfile
✔	6UET	20756	2023-11-13	2019-09-23	4.1	4.91	—	5.1	0.010	1.61	0.07	15.67	0.02	1.977	4.88	—	0.62	0.73	—	5.0	0.007	0.95	0.05	22.51	0.01	1.786	49.59	—	0.78	0.66	0.80	—	3869	1	119	1	1291	logfile
✔	7XSM	33427	2023-11-15	2022-05-14	4.01	4.70	4.03	4.0	0.002	0.47	0.03	15.76	0.00	1.969	7.06	—	0.90	0.75	—	4.0	0.007	0.77	0.04	20.06	0.01	1.776	49.17	—	1.71	0.92	0.82	—	12464	1	388	0	4165	logfile
✔	6UES	20755	2023-11-13	2019-09-23	3.7	3.94	—	3.2	0.002	0.48	0.02	17.15	0.00	2.100	7.29	—	0.87	0.76	—	3.3	0.007	0.89	0.04	21.28	0.01	1.783	38.25	—	1.34	0.88	0.83	—	3842	1	119	0	1291	logfile
✔	8HD6	34670	2023-11-14	2022-11-03	3.73	4.52	3.73	3.2	0.002	0.54	0.02	14.51	0.00	1.969	2.97	—	0.90	0.78	—	3.3	0.006	0.73	0.04	18.64	0.01	1.772	23.51	—	2.31	0.91	0.82	—	8980	1	419	25	0	logfile
✔	6X64	22069	2023-11-16	2020-05-27	3.7	4.01	—	3.7	0.008	1.34	0.05	9.32	0.01	2.584	0.78	—	0.68	0.84	—	3.7	0.009	1.23	0.05	5.42	0.00	2.111	10.35	—	2.35	0.69	0.86	—	15840	36	0	3168	0	logfile
✔	6oEH	20020	2023-11-21	2019-03-27	3.8	3.93	—	3.7	0.010	1.38	0.07	11.62	0.01	2.381	2.81	—	0.38	0.77	—	3.7	0.007	1.05	0.04	5.09	0.00	2.203	12.28	—	0.52	0.40	0.80	—	32900	14	0	6580	0	logfile