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	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
✔	8i7N	35223	2023-07-05	2023-02-01	2.98	3.12	2.92	3.0	0.007	0.66	0.04	14.75	0.00	1.982	2.00	—	0.82	0.83	—	3.0	0.008	0.74	0.04	15.18	0.01	1.932	5.19	—	0.94	0.87	0.91	—	8979	1	418	29	0	logfile
✔	7URi	26713	2023-07-03	2022-04-22	2.6	2.67	2.95	2.6	0.009	1.37	0.12	25.77	0.01	2.201	7.31	—	0.05	0.34	—	2.6	0.008	1.44	0.07	23.84	0.01	2.072	23.68	—	2.06	0.08	0.38	—	1905	1	90	0	0	logfile
✔	8HD6	34670	2023-07-05	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	0.008	0.86	0.05	19.11	0.01	1.720	28.98	—	2.31	0.91	0.82	—	8980	1	419	25	0	logfile
✔	7R6M	24282	2023-07-04	2021-06-22	3.68	3.27	—	3.4	0.006	0.94	0.04	17.86	0.01	2.005	4.72	—	0.53	0.72	—	3.4	0.007	0.85	0.04	18.31	0.01	1.758	16.73	—	0.19	0.53	0.72	—	7755	3	362	13	0	logfile
✔	6X64	22069	2023-07-08	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
✔	6UET	20756	2023-07-03	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	22.46	0.01	1.737	49.85	—	0.79	0.66	0.81	—	3869	1	119	1	1291	logfile
✔	6oDJ	20021	2023-07-12	2019-03-26	3.5	3.75	—	3.7	0.009	1.50	0.07	11.32	0.01	2.438	2.03	—	0.81	0.81	—	3.7	0.012	1.73	0.06	7.96	0.00	2.090	10.56	—	0.60	0.82	0.83	—	25415	17	0	5083	0	logfile
✔	7SAM	24952	2023-07-03	2021-09-22	4.3	6.95	4.38	4.2	0.001	0.39	0.02	13.28	0.00	1.952	2.96	—	0.84	0.51	—	4.3	0.007	0.88	0.04	22.84	0.01	1.820	82.61	—	5.78	0.96	0.87	—	5399	1	169	0	1802	logfile
✔	7UR5	26705	2023-07-03	2022-04-21	2.6	2.89	2.82	2.9	0.008	1.48	0.11	25.09	0.01	2.204	2.44	—	0.05	0.58	—	2.9	0.005	0.83	0.04	20.54	0.01	2.027	14.87	—	1.86	0.08	0.65	—	5709	3	270	0	0	logfile
✔	7XSL	33426	2023-07-06	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	0.006	0.70	0.04	18.31	0.01	1.810	33.53	—	1.02	0.92	0.83	—	12467	1	388	0	4168	logfile
✔	7URM	26714	2023-07-03	2022-04-22	3.0	3.11	3.56	2.9	0.009	1.41	0.11	23.67	0.01	2.440	0.70	—	0.14	0.53	—	3.0	0.007	1.16	0.05	22.87	0.01	1.983	29.94	—	1.70	0.15	0.54	—	1905	1	90	0	0	logfile
✔	6oEH	20020	2023-07-15	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
✔	6UES	20755	2023-07-03	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	0.87	0.04	21.14	0.01	1.785	36.43	—	1.34	0.88	0.83	—	3842	1	119	0	1291	logfile
✔	5G2Y	3332	2023-07-06	2016-04-16	4.5	4.38	—	3.8	0.001	0.22	0.01	11.90	0.00	2.269	2.32	—	0.58	0.28	—	3.7	0.007	1.02	0.05	23.60	0.01	1.933	73.59	—	2.96	0.89	0.78	—	13494	1	630	0	0	logfile
✔	6oEF	20020	2023-07-20	2019-03-27	3.8	3.98	—	3.8	0.007	1.67	0.07	11.76	0.01	2.376	3.96	—	0.47	0.78	—	3.8	0.006	1.21	0.05	6.00	0.00	2.197	8.15	—	0.58	0.49	0.80	—	51240	14	0	10248	0	logfile
✔	6o1o	0454	2023-07-07	2019-02-21	3.8	4.00	—	3.6	0.008	1.55	0.07	15.00	0.01	2.295	4.58	—	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	14	66	2757	0	logfile
✔	6LHV	0900	2023-07-07	2019-12-10	4.59	4.86	—	4.4	0.010	1.38	0.05	5.37	0.00	1.654	9.63	—	0.70	0.59	—	4.4	0.010	1.38	0.05	6.64	0.00	2.051	53.25	—	3.58	0.84	0.81	—	8456	3	0	1707	0	logfile
✔	7EZ0	31385	2023-07-04	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	0.005	0.67	0.04	15.53	0.00	1.862	8.10	—	1.91	0.76	0.86	—	8306	1	387	27	0	logfile
✔	7YGD	33816	2023-07-04	2022-07-11	3.41	4.13	3.42	3.3	0.002	0.49	0.03	15.33	0.00	2.100	14.25	—	0.90	0.81	—	3.3	0.007	0.75	0.04	17.38	0.01	1.823	32.82	—	1.50	0.91	0.89	—	8313	3	389	6	0	logfile
✔	7ZFW	14704	2023-07-06	2022-04-01	3.8	4.62	3.46	3.0	0.006	0.83	0.05	17.92	0.03	2.266	2.77	—	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	1	615	0	0	logfile