cryo-EM Re-Refine

Table showing results for August 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	# H	Logfile
✔	6V39	21030	2023-08-25	2019-11-25	3.04	3.20	—	3.1	0.002	0.49	0.0	0.03	14.66	0.02	1.895	6.19	0.00	2.5	97.4	0.1	-1.02	0.86	0.85	2.53	3.1	0.003	0.62	0.0	0.03	16.06	0.01	1.821	8.08	0.56	4.2	95.7	0.1	0.18	1.17	0.87	0.88	2.71	141897	5458	70	4615	116	273	0	logfile
✘	6YEF	10791	2023-08-25	2020-03-24	3.2	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	141837	5351	60	4639	288	0	0	logfile
✔	8BJQ	16090	2023-08-24	2022-11-05	3.8	4.31	3.77	3.7	0.005	0.69	1.0	0.04	15.16	0.01	1.017	13.25	0.16	4.4	95.4	0.2	-0.16	0.72	0.78	0.75	3.7	0.005	0.73	0.0	0.04	16.68	0.01	0.949	22.48	0.74	6.6	93.3	0.1	-0.70	1.67	0.74	0.85	0.89	141384	8086	64	3580	211	0	0	logfile
✘	6LSR	0963	2023-08-24	2020-01-20	3.13	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	141172	7581	57	3757	246	7	0	logfile
✔	6HD7	0202	2023-08-24	2018-08-17	3.4	3.54	—	3.3	0.002	0.43	0.0	0.03	14.93	0.00	0.345	24.96	0.08	11.1	87.1	1.9	-3.26	0.66	0.65	0.74	3.3	0.007	0.78	0.0	0.04	17.87	0.00	2.034	18.45	0.79	7.7	91.9	0.4	-1.42	1.57	0.76	0.88	1.83	141153	7514	52	3767	234	0	0	logfile
✔	7UPH	26666	2023-08-24	2022-04-15	4.18	5.35	4.33	4.2	0.007	1.00	1.0	0.05	18.96	0.02	1.193	122.79	0.02	12.5	86.5	1.0	-2.90	0.63	0.35	—	4.3	0.007	0.88	1.0	0.04	18.39	0.01	1.165	109.33	0.02	15.7	83.6	0.7	-2.80	1.34	0.87	0.78	—	141080	5442	49	4556	0	0	625	logfile
✔	5ND9	3625	2023-08-24	2017-03-07	3.7	3.83	—	3.7	0.011	1.19	1.0	0.06	15.82	0.01	0.889	8.98	1.12	19.3	80.1	0.6	-5.81	0.76	0.77	1.23	3.9	0.003	0.67	0.0	0.03	15.69	0.01	2.074	16.26	0.80	12.1	87.8	0.0	-2.99	1.33	0.78	0.81	0.84	141051	5461	52	4569	0	0	0	logfile
✔	5ND8	3624	2023-08-24	2017-03-07	3.7	3.81	—	3.7	0.009	1.03	1.0	0.05	14.85	0.01	1.019	7.55	0.73	17.3	82.1	0.6	-5.61	0.77	0.77	1.17	3.7	0.003	0.65	0.0	0.03	15.24	0.00	2.007	16.09	0.86	10.7	89.3	0.1	-2.72	1.30	0.80	0.82	1.16	141043	5462	52	4568	0	0	0	logfile
✔	8B7Y	15905	2023-08-24	2022-10-03	3.0	2.45	2.96	2.8	0.005	0.76	4.0	0.05	15.62	0.01	1.792	5.28	3.80	5.7	93.5	0.8	-1.45	0.77	0.78	2.97	2.8	0.003	0.69	4.0	0.04	15.97	0.01	1.825	13.19	3.20	4.9	94.8	0.2	-0.94	1.55	0.78	0.80	2.79	141008	5315	70	4614	248	28	0	logfile
✔	6Y6X	10709	2023-08-24	2020-02-27	2.8	2.76	—	2.7	0.007	1.01	0.0	0.07	16.90	0.01	1.914	4.55	0.96	7.0	92.7	0.3	-2.80	0.80	0.87	3.06	2.7	0.006	0.70	0.0	0.05	16.85	0.01	1.801	9.88	2.68	6.8	93.1	0.1	-0.38	1.16	0.82	0.91	2.97	140969	6788	60	4049	235	0	0	logfile
✔	5NGM	3640	2023-08-24	2017-03-18	2.9	3.05	—	3.0	0.006	0.86	0.0	0.05	17.23	0.01	0.270	7.58	0.81	8.3	91.7	0.0	-4.79	0.70	0.72	2.80	3.0	0.005	0.63	0.0	0.04	17.58	0.00	1.847	11.83	4.43	6.7	93.3	0.0	-1.89	0.66	0.78	0.85	2.33	140965	5610	57	4559	205	0	0	logfile
✔	7UG6	26485	2023-08-24	2022-03-24	2.9	2.56	3.01	2.9	0.010	0.89	0.0	0.05	16.41	0.01	2.043	9.51	0.01	4.6	95.4	0.0	-1.03	0.77	0.86	4.01	2.9	0.006	0.66	0.0	0.04	17.11	0.00	2.002	12.03	2.23	4.1	95.9	0.0	0.16	0.32	0.77	0.87	3.21	140950	8738	53	3338	1	0	0	logfile
✔	5Li0	4050	2023-08-24	2016-07-13	3.8	3.91	—	3.8	0.014	1.18	1.0	0.05	14.64	0.01	1.920	5.40	0.20	14.9	84.7	0.5	-5.64	0.75	0.79	1.99	3.8	0.006	0.75	0.0	0.04	15.26	0.00	1.344	14.34	0.77	11.1	88.8	0.1	-2.61	0.71	0.75	0.81	1.15	140825	5396	58	4575	41	162	0	logfile
✔	6HA1	0176	2023-08-24	2018-08-07	3.1	3.55	—	3.3	0.007	1.09	0.0	0.07	17.11	0.01	1.892	7.10	0.90	8.8	90.7	0.6	-3.85	0.78	0.79	2.71	3.3	0.005	0.69	0.0	0.04	17.19	0.01	2.031	16.80	1.06	8.9	90.9	0.2	-1.54	0.62	0.83	0.87	2.00	140824	5299	52	4622	1	0	0	logfile
✔	6ENF	3898	2023-08-24	2017-10-04	3.2	3.22	—	3.2	0.003	0.75	1.0	0.04	13.88	0.01	1.244	4.82	0.53	8.0	91.7	0.3	-4.83	0.75	0.78	2.02	3.2	0.002	0.59	0.0	0.03	15.29	0.00	2.074	10.66	0.51	7.7	92.2	0.2	-1.82	1.26	0.80	0.84	1.84	140797	5531	53	4546	0	0	0	logfile
✔	7QV1	14157	2023-08-24	2022-01-19	3.5	3.50	—	3.2	0.002	0.51	0.0	0.03	15.47	0.00	1.575	5.96	0.41	5.1	94.8	0.1	-2.06	0.73	0.82	1.19	3.2	0.005	0.72	0.0	0.04	16.98	0.01	1.988	17.18	0.98	8.2	91.7	0.1	-1.43	3.30	0.75	0.86	1.20	140774	5254	53	4635	24	0	0	logfile
✔	6S0X	10076	2023-08-24	2019-06-18	2.425	2.50	—	2.5	0.021	2.13	0.0	0.11	21.61	0.01	0.917	12.73	19.66	9.7	90.2	0.1	-4.36	0.60	0.63	2.41	2.5	0.006	1.01	0.0	0.06	20.43	0.01	1.508	19.66	6.55	8.9	91.0	0.0	-2.03	0.70	0.65	0.65	2.44	140672	5589	53	4559	1	0	0	logfile
✔	6VWL	21420	2023-08-23	2020-02-20	3.1	3.37	—	3.0	0.005	0.62	0.0	0.04	13.89	0.00	1.922	7.24	1.40	4.2	95.7	0.0	-2.42	0.82	0.85	2.58	3.0	0.003	0.56	0.0	0.03	15.33	0.00	1.910	12.94	0.39	5.1	94.9	0.0	-0.57	0.53	0.83	0.87	2.05	140603	5383	58	4593	34	0	0	logfile
✘	6LSS	0964	2023-08-24	2020-01-20	3.23	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	140545	7369	67	3750	250	16	0	logfile
✘	7UMH	26601	2023-08-24	2022-04-07	2.6	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	140516	12747	124	0	798	461	0	logfile