cryo-EM Re-Refine

Table showing results for February 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	Cβ devts	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	2023-02-20	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	0.0	0.04	17.94	0.01	1.892	21.35	—	0.48	0.77	0.76	—	12409	0	1	386	0	4149	logfile
✔	7XSN	33428	2023-02-18	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	0.0	0.03	16.36	0.00	2.111	20.82	—	0.30	0.92	0.87	—	8279	0	1	387	0	0	logfile
✔	7PTL	13630	2023-02-24	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	0.0	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	2023-02-22	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	0.0	0.04	19.44	0.00	1.852	43.48	—	2.75	0.96	0.94	—	17434	0	1	544	0	5847	logfile
✔	7R6L	24281	2023-02-18	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	0.0	0.04	16.40	0.01	1.882	7.54	—	0.09	0.62	0.86	—	7857	0	3	366	20	0	logfile
✔	7XSM	33427	2023-02-20	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	0.0	0.04	19.93	0.01	1.773	49.65	—	1.70	0.92	0.82	—	12464	0	1	388	0	4165	logfile
✔	6LHW	0901	2023-02-21	2019-12-10	4.84	5.29	—	4.6	0.008	1.37	1.0	0.05	5.28	0.00	1.530	14.43	0.00	—	0.64	0.56	—	4.6	0.008	1.29	0.0	0.04	6.56	0.00	2.027	44.00	—	3.20	0.83	0.64	—	7644	0	3	0	1541	0	logfile
✔	7XSK	33425	2023-02-20	2022-05-14	3.53	4.49	3.42	3.4	0.001	0.44	0.0	0.02	15.94	0.00	1.970	6.98	0.00	—	0.90	0.76	—	3.4	0.007	0.68	0.0	0.04	18.66	0.01	1.750	33.29	—	1.90	0.91	0.83	—	12467	0	1	388	0	4168	logfile
✔	7XSL	33426	2023-02-20	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	0.0	0.04	18.31	0.01	1.810	33.53	—	1.02	0.92	0.83	—	12467	0	1	388	0	4168	logfile
✔	7SAM	24952	2023-02-17	2021-09-22	4.3	6.95	4.38	4.2	0.001	0.39	0.0	0.02	13.28	0.00	1.952	2.96	0.00	—	0.84	0.51	—	4.3	0.007	0.88	0.0	0.04	22.84	0.01	1.820	82.61	—	5.78	0.96	0.87	—	5399	0	1	169	0	1802	logfile
✔	6X64	22069	2023-02-21	2020-05-27	3.7	4.01	—	3.7	0.008	1.34	0.0	0.05	9.32	0.01	2.584	0.78	0.00	—	0.68	0.84	—	3.7	0.009	1.23	0.0	0.05	5.42	0.00	2.111	10.35	—	2.35	0.69	0.86	—	15840	0	36	0	3168	0	logfile
✔	6X5i	22051	2023-02-18	2020-05-26	4.3	4.27	—	4.0	0.060	2.79	210.0	0.16	29.93	0.00	2.206	29.57	0.00	—	0.70	0.70	—	4.0	0.011	1.53	210.0	0.13	24.62	0.00	1.571	57.36	—	3.30	0.69	0.74	—	4480	70	70	0	280	0	logfile
✔	6oDJ	20021	2023-02-25	2019-03-26	3.5	3.75	—	3.7	0.009	1.50	0.0	0.07	11.32	0.01	2.438	2.03	0.00	—	0.81	0.81	—	3.7	0.012	1.73	0.0	0.06	7.96	0.00	2.090	10.56	—	0.60	0.82	0.83	—	25415	0	17	0	5083	0	logfile
✔	6UES	20755	2023-02-17	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	0.0	0.04	21.14	0.01	1.785	36.43	—	1.34	0.88	0.83	—	3842	0	1	119	0	1291	logfile
✔	6LHV	0900	2023-02-21	2019-12-10	4.59	4.86	—	4.4	0.010	1.38	0.0	0.05	5.37	0.00	1.654	9.63	0.00	—	0.70	0.59	—	4.4	0.010	1.38	0.0	0.05	6.64	0.00	2.051	53.25	—	3.58	0.84	0.81	—	8456	0	3	0	1707	0	logfile
✔	7R6M	24282	2023-02-18	2021-06-22	3.68	3.27	—	3.4	0.006	0.94	0.0	0.04	17.86	0.01	2.005	4.72	0.00	—	0.53	0.72	—	3.4	0.007	0.85	0.0	0.04	18.31	0.01	1.758	16.73	—	0.19	0.53	0.72	—	7755	0	3	362	13	0	logfile
✔	6PoM	20416	2023-02-17	2019-07-04	4.9	5.01	—	5.0	0.003	0.64	0.0	0.03	17.29	0.00	2.075	3.10	0.00	—	0.61	0.64	—	5.0	0.010	1.28	0.0	0.06	21.46	0.01	1.930	61.80	—	1.76	0.75	0.80	—	4937	0	2	230	0	0	logfile
✔	5G2Y	3332	2023-02-20	2016-04-16	4.5	4.38	—	3.8	0.001	0.22	0.0	0.01	11.90	0.00	2.269	2.32	0.00	—	0.58	0.28	—	3.7	0.007	1.02	0.0	0.05	23.60	0.01	1.933	73.59	—	2.96	0.89	0.78	—	13494	0	1	630	0	0	logfile
✔	4UQ8	2676	2023-02-26	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	0.0	0.41	5.47	0.00	2.110	23.19	—	2.11	0.61	0.83	—	28647	33	54	0	5686	0	logfile
✔	7T6E	25714	2023-02-17	2021-12-13	3.1	3.11	—	3.1	0.129	5.90	240.0	0.23	23.20	0.02	2.041	30.29	0.00	—	0.60	0.87	—	3.1	0.122	5.61	240.0	0.36	21.80	0.02	2.082	31.46	—	0.19	0.66	0.90	—	3480	0	60	0	300	0	logfile