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	Rama allowed	Rama favored	Rama outliers	Z-score	CC_box	CC_mask	EMRinger	D_Model	Bond rmsd	Angle rmsd	Cβ devts	Chirality	Dihedral rmsd	Plane rmsd	Min nonbonded	Clashscore	Rota outliers	Rama allowed	Rama favored	Rama outliers	Z-score	RMSD	CC_box	CC_mask	EMRinger	# atoms	# residues	# chains	# nucleotides	# other	# water	Logfile
✔	7NWT	12635	2023-07-26	2021-03-17	2.66	2.63	—	2.6	0.011	0.84	0.0	0.05	14.14	0.02	1.145	4.87	2.95	2.6	97.4	0.0	-2.35	0.85	0.88	4.38	2.7	0.002	0.65	0.0	0.04	15.17	0.01	1.149	8.11	2.80	3.2	96.8	0.0	0.13	0.28	0.87	0.88	3.51	149932	6355	74	4641	439	2	logfile
✔	5MDV	3489	2023-07-25	2016-11-13	2.97	3.05	2.97	3.0	0.008	1.26	22.0	0.10	16.59	0.02	1.257	3.21	7.74	4.9	94.7	0.4	-1.77	0.79	0.88	3.19	3.0	0.005	0.67	0.0	0.04	15.80	0.01	1.819	7.90	3.99	3.6	96.4	0.0	0.19	0.46	0.81	0.89	2.98	149892	6382	67	4638	442	2	logfile
✔	7SS9	25405	2023-07-25	2021-11-10	3.9	4.09	4.66	4.0	0.010	1.07	0.0	0.09	16.35	0.01	2.130	12.90	1.63	11.7	87.8	0.5	-4.79	0.76	0.73	0.63	4.0	0.005	0.78	0.0	0.04	17.95	0.01	1.998	25.79	1.49	12.4	87.4	0.2	-2.96	0.68	0.77	0.72	0.56	149808	6171	57	4736	0	0	logfile
✔	8AGU	15424	2023-07-25	2022-07-20	2.7	3.26	2.76	2.7	0.006	0.90	6.0	0.05	15.12	0.01	1.041	6.23	1.81	3.6	96.3	0.1	0.14	0.92	0.88	3.27	2.7	0.006	0.68	0.0	0.04	15.52	0.00	1.881	9.66	2.38	4.5	95.4	0.0	0.42	1.17	0.93	0.92	3.26	149748	9427	68	3568	38	0	logfile
✔	8AGX	15427	2023-07-25	2022-07-20	2.4	3.19	2.52	2.5	0.006	0.93	5.0	0.05	15.25	0.01	1.296	4.14	2.04	3.7	96.2	0.1	-0.44	0.92	0.89	3.34	2.6	0.005	0.64	0.0	0.04	15.42	0.00	1.909	8.59	1.84	4.5	95.4	0.0	0.51	0.47	0.94	0.93	3.35	149706	9204	68	3640	41	0	logfile
✔	7MT7	23976	2023-07-25	2021-05-13	2.71	2.43	—	2.8	0.007	0.86	0.0	0.05	14.11	0.01	2.026	2.68	0.17	6.3	93.6	0.1	-4.19	0.87	0.87	3.93	2.8	0.004	0.60	0.0	0.04	14.38	0.01	1.864	6.26	1.79	5.6	94.3	0.1	-0.68	0.44	0.85	0.88	3.08	149696	5629	71	4912	449	0	logfile
✔	6WDi	21637	2023-07-25	2020-03-31	4.0	4.30	4.79	4.1	0.006	0.98	0.0	0.08	13.16	0.01	2.280	9.88	0.49	12.5	85.9	1.6	-4.84	0.77	0.71	—	4.1	0.005	0.81	0.0	0.04	17.46	0.01	1.877	32.96	0.87	12.8	87.1	0.1	-3.23	1.61	0.81	0.75	—	149628	5954	59	4807	0	0	logfile
✔	5MDW	3490	2023-07-25	2016-11-13	3.06	3.16	3.07	3.1	0.009	1.33	26.0	0.11	16.56	0.02	1.464	3.52	7.69	5.6	93.9	0.5	-1.97	0.81	0.89	2.64	3.1	0.007	0.72	0.0	0.04	15.66	0.01	1.807	7.90	0.46	3.9	96.0	0.0	-0.15	1.16	0.83	0.89	2.69	149607	6346	67	4638	440	2	logfile
✔	5L3P	4001	2023-07-25	2016-05-24	3.7	4.66	—	16.0	0.006	0.60	0.0	0.19	12.34	0.02	2.115	7.18	0.00	8.2	89.4	2.4	-1.95	0.44	0.11	0.16	3.9	0.007	1.28	4.0	0.06	18.96	0.01	1.742	61.81	1.02	12.1	87.1	0.8	-2.95	2.41	0.68	0.46	-0.03	149606	6419	58	4704	76	0	logfile
✔	7UNV	26634	2023-07-25	2022-04-11	2.7	3.21	2.68	3.0	0.005	0.62	0.0	0.04	15.01	0.02	1.751	6.95	0.16	6.6	93.0	0.4	-1.44	0.90	0.89	3.23	3.0	0.004	0.71	0.0	0.04	15.77	0.01	1.764	8.46	2.74	7.0	92.7	0.3	-0.81	0.37	0.88	0.93	2.85	149599	6534	85	4605	598	295	logfile
✔	5U4i	8505	2023-07-25	2016-12-04	3.5	3.09	3.83	3.7	0.007	1.17	41.0	0.10	18.54	0.02	1.386	8.56	8.19	6.4	92.7	0.8	-1.32	0.60	0.74	0.22	3.0	0.005	0.80	0.0	0.04	18.66	0.01	1.670	32.60	1.29	7.3	92.6	0.1	-1.91	1.50	0.63	0.74	0.31	149495	6159	61	4715	125	0	logfile
✔	5MDY	3492	2023-07-25	2016-11-13	3.35	3.40	3.43	3.4	0.009	1.39	22.0	0.11	17.07	0.02	1.409	4.38	9.85	6.0	93.5	0.5	-2.09	0.78	0.85	2.23	3.4	0.006	0.77	0.0	0.04	15.91	0.01	1.804	9.44	0.75	5.6	94.4	0.1	-0.59	0.60	0.78	0.85	2.05	149460	6323	68	4638	452	3	logfile
✔	7UNR	26630	2023-07-25	2022-04-11	2.9	3.18	2.93	3.1	0.005	0.64	2.0	0.04	14.92	0.02	1.879	6.56	0.26	7.2	92.4	0.4	-1.63	0.79	0.88	3.11	3.1	0.003	0.63	0.0	0.04	15.66	0.01	1.834	7.03	2.87	6.9	92.8	0.4	-0.99	0.89	0.79	0.89	2.76	149327	6502	82	4606	632	200	logfile
✔	7UNU	26633	2023-07-25	2022-04-11	2.9	3.16	2.89	3.1	0.007	0.70	0.0	0.04	14.92	0.02	1.895	6.14	0.20	8.0	91.6	0.4	-1.70	0.81	0.89	3.42	3.1	0.002	0.67	0.0	0.04	15.85	0.01	1.936	7.18	3.16	6.7	92.9	0.4	-1.00	2.56	0.79	0.89	2.72	149259	6488	86	4606	609	201	logfile
✔	5KPS	8279	2023-07-24	2016-07-05	3.9	5.38	4.05	3.9	0.008	1.11	0.0	0.08	13.49	0.01	1.923	27.29	0.32	12.5	82.8	4.6	-4.23	0.90	0.78	0.50	3.9	0.004	0.76	0.0	0.04	16.32	0.01	1.996	33.51	0.76	10.2	89.0	0.8	-2.31	2.12	0.95	0.90	0.41	149128	6091	58	4734	0	0	logfile
✔	7ST2	25418	2023-07-24	2021-11-11	2.9	3.50	3.04	3.1	0.011	0.89	0.0	0.05	14.79	0.01	2.225	4.06	0.58	9.5	89.9	0.6	-4.70	0.90	0.92	3.02	3.1	0.006	0.69	0.0	0.04	15.29	0.01	2.026	13.86	4.17	9.1	90.6	0.3	-1.71	0.99	0.90	0.93	1.89	149087	6082	58	4735	0	0	logfile
✔	7P7T	13244	2023-07-24	2021-07-20	2.9	3.42	2.91	2.2	0.005	0.40	0.0	0.04	14.00	0.01	1.679	4.44	0.66	2.6	97.4	0.0	0.93	0.89	0.91	3.72	2.1	0.007	0.66	0.0	0.04	14.83	0.00	1.738	10.38	2.10	3.3	96.7	0.0	0.46	0.41	0.89	0.92	3.36	149080	6097	68	4697	307	1	logfile
✔	6WNW	21858	2023-07-24	2020-04-23	3.2	3.94	3.40	3.2	0.007	0.96	0.0	0.08	13.69	0.01	1.975	10.35	0.77	11.5	86.6	2.0	-4.63	0.88	0.82	2.15	3.2	0.005	0.68	0.0	0.04	15.62	0.00	2.025	19.42	0.91	10.1	89.6	0.2	-2.10	1.06	0.91	0.90	1.61	149080	6089	57	4733	0	0	logfile
✔	7SSo	25411	2023-07-24	2021-11-11	3.2	3.61	3.43	3.3	0.010	1.02	0.0	0.08	15.33	0.01	1.353	14.35	0.93	11.4	88.1	0.6	-4.86	0.85	0.86	1.78	3.3	0.004	0.65	0.0	0.04	15.57	0.00	2.042	14.46	0.83	11.1	88.7	0.2	-2.23	0.55	0.85	0.86	1.45	148980	6070	60	4735	0	0	logfile
✔	5KCS	8238	2023-07-24	2016-06-06	3.9	4.07	—	4.0	0.006	0.51	0.0	0.04	12.43	0.02	1.981	9.49	0.19	8.8	88.6	2.6	-3.12	0.61	0.61	0.64	4.0	0.004	0.76	0.0	0.04	15.46	0.01	1.967	16.63	1.04	9.0	90.4	0.7	-1.78	1.92	0.71	0.80	0.83	148945	6656	59	4641	1	0	logfile