cryo-EM Re-Refine

Table showing results for May 2022

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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
✔	5TAZ	8390	2022-05-14	2016-09-10	4.3	4.46	4.85	4.3	0.004	0.86	4.0	0.05	9.92	0.01	1.373	4.90	0.58	10.2	89.6	0.2	-5.04	0.74	0.73	—	4.3	0.008	0.92	2.0	0.04	12.16	0.01	0.886	20.48	0.00	12.5	87.3	0.2	-2.18	0.83	0.75	0.77	—	121276	13500	12	0	3712	0	0	logfile
✔	6GEJ	4395	2022-05-17	2018-04-26	3.6	3.77	—	3.7	0.003	0.62	0.0	0.04	18.57	0.00	1.491	9.16	3.93	4.6	95.4	0.0	-2.70	0.82	0.77	0.98	3.7	0.005	0.84	0.0	0.04	20.68	0.01	0.891	11.32	0.40	4.8	95.2	0.0	-0.31	0.84	0.84	0.80	1.01	43702	4683	29	308	151	0	0	logfile
✔	7ACR	11718	2022-05-23	2020-09-11	3.44	3.72	3.11	2.6	0.003	0.69	21.0	0.04	15.49	0.02	0.444	14.10	1.77	5.3	94.3	0.4	-1.02	0.87	0.78	1.12	2.5	0.006	0.81	0.0	0.04	17.40	0.01	0.908	23.52	0.81	9.0	90.9	0.1	-2.06	1.64	0.89	0.85	1.23	151668	5858	66	4920	214	0	0	logfile
✔	6T59	10380	2022-05-18	2019-10-15	3.11	3.19	3.02	7.3	0.011	0.83	0.0	0.05	17.10	0.00	1.148	10.88	0.76	8.9	91.0	0.1	-5.04	0.22	0.01	0.07	3.1	0.006	0.97	0.0	0.05	19.44	0.01	0.922	26.27	0.78	9.6	90.4	0.0	-2.67	2.07	0.59	0.59	0.42	143047	7383	64	3890	225	0	0	logfile
✔	6Q97	4476	2022-05-25	2018-12-17	3.9	3.69	—	20.0	0.011	1.20	0.0	0.16	18.93	0.02	1.320	7.03	0.38	10.1	89.8	0.1	-5.34	0.15	0.01	0.22	3.6	0.008	1.00	0.0	0.05	20.31	0.01	0.925	23.65	0.12	10.6	89.4	0.0	-3.47	2.14	0.26	0.21	0.31	156609	6124	72	5051	441	2	0	logfile
✔	6PJ6	20353	2022-05-24	2019-06-27	2.2	2.48	—	2.5	0.011	1.07	14.0	0.06	15.16	0.02	1.227	5.32	2.25	5.6	94.4	0.1	-2.65	0.62	0.85	4.58	2.5	0.006	0.72	0.0	0.04	15.73	0.01	0.931	7.61	2.47	5.6	94.3	0.0	-0.99	1.30	0.63	0.86	4.35	154542	3356	67	3016	187	3897	59624	logfile
✔	7ACJ	11717	2022-05-23	2020-09-11	3.2	3.44	3.22	3.1	0.003	0.64	19.0	0.03	15.46	0.02	0.852	13.36	0.61	5.1	94.7	0.2	-0.99	0.85	0.81	1.87	3.1	0.006	0.77	0.0	0.04	17.01	0.01	0.953	17.63	0.69	8.4	91.6	0.1	-1.46	1.23	0.88	0.87	1.96	151803	5864	64	4920	310	0	0	logfile
✔	7LVK	23539	2022-05-23	2021-02-25	2.2	2.31	—	2.4	0.009	0.93	8.0	0.06	14.61	0.02	1.324	2.50	0.81	5.1	94.8	0.2	-2.34	0.64	0.86	5.37	2.4	0.006	0.72	0.0	0.04	15.08	0.01	0.971	5.80	2.00	4.7	95.2	0.1	-0.37	0.97	0.67	0.88	5.15	151436	3222	63	3015	182	2716	58704	logfile
✔	5WE4	8814	2022-05-25	2017-07-07	3.1	3.04	3.02	3.0	0.008	1.16	3.0	0.10	17.51	0.02	1.575	3.80	3.52	9.8	87.9	2.3	-4.03	0.78	0.81	2.62	3.0	0.009	0.94	0.0	0.05	17.15	0.01	0.977	12.76	0.99	9.2	90.2	0.6	-2.13	3.97	0.83	0.82	2.48	155067	6324	117	4802	1620	996	0	logfile
✔	5GAD	8000	2022-05-17	2015-11-24	3.7	4.17	—	3.9	0.009	1.11	1.0	0.05	15.93	0.01	1.737	9.28	10.34	3.5	96.5	0.1	-3.19	0.77	0.79	1.52	3.9	0.007	0.67	0.0	0.03	15.21	0.01	0.987	18.22	0.58	3.8	96.1	0.1	-0.19	1.60	0.81	0.88	1.37	98006	4087	49	3049	507	0	0	logfile
✔	6i0Y	0322	2022-05-16	2018-10-26	3.2	4.80	—	4.7	0.010	1.49	8.0	0.07	15.55	0.01	0.682	13.08	11.41	16.0	77.5	6.5	-5.00	0.59	0.58	0.26	4.7	0.005	0.83	0.0	0.04	16.07	0.01	0.990	21.89	1.57	13.8	84.2	2.0	-2.85	1.60	0.59	0.70	0.58	93619	3551	48	3049	144	439	0	logfile
✔	5UYP	8619	2022-05-24	2017-02-24	3.9	4.42	4.29	3.6	0.007	1.07	0.0	0.09	13.92	0.01	1.318	13.13	1.57	14.3	82.6	3.1	-5.15	0.87	0.79	0.53	3.6	0.006	0.84	0.0	0.04	17.28	0.01	0.996	36.52	1.14	14.6	85.2	0.2	-3.39	0.80	0.87	0.83	0.41	153780	6476	63	4811	1	0	0	logfile
✔	7NSH	12567	2022-05-13	2021-03-07	3.2	3.39	3.12	3.3	0.003	0.53	0.0	0.05	15.69	0.00	1.187	7.82	0.02	4.2	95.8	0.1	0.71	0.80	0.84	2.70	3.3	0.004	0.69	0.0	0.04	17.05	0.01	0.999	10.50	0.25	5.0	94.9	0.0	0.45	1.20	0.79	0.89	2.66	112448	9643	79	1611	229	2	0	logfile
✔	6VQT	21356	2022-05-13	2020-02-05	3.03	4.54	3.09	4.1	0.009	1.15	0.0	0.06	16.32	0.01	1.733	10.43	4.94	2.7	97.3	0.0	1.39	0.78	0.80	1.43	4.1	0.003	0.72	0.0	0.04	16.44	0.00	0.999	9.77	0.43	2.9	97.1	0.0	2.46	1.06	0.77	0.84	1.36	9144	1168	4	0	6	0	0	logfile
✔	5GAG	8003	2022-05-16	2015-11-26	3.8	3.95	—	3.8	0.007	1.04	1.0	0.05	15.71	0.00	1.789	8.25	9.03	3.0	96.9	0.1	-3.35	0.79	0.90	1.98	3.8	0.006	0.68	0.0	0.04	15.28	0.01	1.000	16.28	0.83	4.3	95.6	0.1	-0.56	0.70	0.78	0.88	1.97	94030	3598	46	3049	473	0	0	logfile
✔	5LMo	4074	2022-05-12	2016-08-01	4.3	4.71	4.30	4.3	0.009	1.47	50.0	0.12	20.86	0.01	0.865	18.52	20.40	10.6	85.8	3.6	-2.76	0.80	0.69	—	4.3	0.005	0.76	0.0	0.04	16.86	0.01	1.006	33.78	0.00	8.7	90.8	0.5	-1.87	2.17	0.87	0.84	—	54110	2622	29	1533	110	0	0	logfile
✔	6FTJ	4317	2022-05-23	2018-02-22	4.7	4.88	—	4.7	0.011	1.39	18.0	0.10	19.94	0.01	0.475	12.17	11.77	9.8	87.8	2.4	-4.05	0.63	0.62	—	4.7	0.005	0.85	0.0	0.04	18.31	0.01	1.011	33.68	0.03	9.7	89.9	0.5	-1.97	1.12	0.67	0.71	—	152111	8263	73	3938	461	0	0	logfile
✔	5o5J	3748	2022-05-18	2017-06-02	3.45	3.51	—	3.4	0.008	1.20	0.0	0.05	17.48	0.01	1.740	9.43	11.65	5.4	94.5	0.1	-3.62	0.65	0.87	1.42	3.4	0.008	0.76	0.0	0.04	16.67	0.01	1.011	13.99	0.50	4.2	95.7	0.1	0.28	0.66	0.64	0.84	1.54	52163	2406	28	1536	219	0	0	logfile
✔	5o9G	3765	2022-05-14	2017-06-19	4.8	5.07	4.71	10.4	0.003	0.48	0.0	0.03	22.47	0.00	2.194	7.47	0.36	9.1	90.8	0.1	-4.25	0.51	0.13	—	4.8	0.003	0.71	0.0	0.04	23.98	0.00	1.014	17.73	0.00	5.5	94.4	0.1	-1.08	2.79	0.83	0.69	—	19681	1610	11	324	2	0	0	logfile
✔	6GEN	4396	2022-05-17	2018-04-27	3.6	4.67	—	4.5	0.004	0.75	0.0	0.04	20.46	0.01	2.109	5.91	8.77	3.9	96.0	0.0	-4.51	0.78	0.58	-0.18	4.4	0.003	0.76	0.0	0.04	21.34	0.00	1.014	16.32	0.38	4.7	95.3	0.0	-0.45	2.07	0.84	0.74	0.08	44481	4683	29	346	151	0	0	logfile