cryo-EM Re-Refine

Table showing results for July 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	Logfile
✘	7SSL	25409	2022-07-11	2021-11-11	3.8	3.94	4.31	3.8	0.009	1.02	0.0	0.08	15.30	0.01	0.524	13.16	1.11	12.6	87.2	0.2	-5.13	0.76	0.73	0.87	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	153348	6626	59	4736	1	0	logfile
✔	6M62	30108	2022-07-11	2020-03-12	3.2	3.35	—	3.3	0.012	1.03	0.0	0.06	18.95	0.01	1.750	17.63	8.91	14.8	84.9	0.2	-4.39	0.73	0.81	2.04	3.3	0.005	0.70	1.0	0.04	18.33	0.01	1.838	12.68	0.63	9.4	90.5	0.1	-1.57	1.11	0.73	0.81	1.79	153289	10320	64	3316	8	0	logfile
✔	6WD2	21621	2022-07-11	2020-03-31	3.6	3.97	4.00	3.8	0.006	0.94	0.0	0.08	13.45	0.01	1.315	11.17	0.44	10.6	87.8	1.6	-4.77	0.83	0.83	0.92	3.8	0.006	0.78	1.0	0.04	15.99	0.01	1.963	24.76	1.17	10.7	89.2	0.1	-2.51	1.49	0.84	0.84	0.76	153282	6417	62	4810	1	0	logfile
✘	5WE6	8815	2022-07-11	2017-07-07	3.4	3.36	3.38	3.3	0.007	1.09	2.0	0.10	16.96	0.01	1.180	1.98	2.48	10.3	87.3	2.4	-4.31	0.77	0.80	2.33	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	153233	6322	97	4801	671	153	logfile
✔	6WD8	21627	2022-07-11	2020-03-31	3.7	4.07	4.18	3.9	0.006	0.96	0.0	0.08	13.51	0.01	1.315	12.67	0.80	11.4	86.9	1.7	-4.88	0.83	0.81	1.18	3.9	0.005	0.77	0.0	0.04	16.54	0.01	2.011	26.97	1.09	11.1	88.8	0.1	-2.64	1.52	0.85	0.82	0.90	153212	6409	62	4810	1	0	logfile
✔	6WD3	21622	2022-07-11	2020-03-31	3.6	3.96	3.97	3.8	0.006	0.95	0.0	0.08	13.44	0.01	1.315	11.61	0.96	12.0	86.3	1.8	-4.89	0.83	0.83	1.34	3.8	0.007	0.82	2.0	0.04	16.06	0.01	1.671	29.20	0.57	11.4	88.4	0.2	-2.74	1.48	0.84	0.84	0.97	153211	6408	62	4811	0	0	logfile
✘	5LZD	4124	2022-07-11	2016-09-29	3.4	3.48	3.51	3.4	0.008	1.22	9.0	0.06	13.59	0.01	1.168	6.19	0.71	7.6	91.0	1.4	-3.90	0.75	0.86	2.27	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	153177	6439	68	4785	152	2	logfile
✔	6WD5	21624	2022-07-11	2020-03-31	3.6	3.95	3.98	3.8	0.006	0.94	0.0	0.08	13.45	0.01	1.312	11.66	0.77	11.6	86.5	2.0	-4.87	0.83	0.83	1.21	3.8	0.007	0.80	2.0	0.04	15.97	0.01	2.029	23.71	0.86	11.4	88.5	0.2	-2.66	0.66	0.84	0.84	0.87	153135	6400	62	4811	0	0	logfile
✔	6WD6	21625	2022-07-10	2020-03-31	3.7	4.07	4.15	3.9	0.006	0.94	0.0	0.08	13.34	0.01	1.316	11.55	0.71	11.1	87.3	1.6	-4.98	0.83	0.82	0.92	3.9	0.008	0.86	4.0	0.04	15.83	0.01	1.765	27.36	0.61	9.7	90.1	0.2	-2.83	0.62	0.84	0.83	0.90	153103	6396	62	4811	0	0	logfile
✔	6WD4	21623	2022-07-10	2020-03-31	3.7	4.02	4.02	3.9	0.006	0.94	0.0	0.08	13.36	0.01	1.313	10.92	0.48	11.3	87.0	1.7	-4.79	0.83	0.83	0.81	3.8	0.007	0.83	1.0	0.04	15.80	0.01	1.998	26.18	1.78	11.3	88.5	0.2	-2.68	0.64	0.84	0.84	0.73	153083	6391	62	4811	0	0	logfile
✔	7SSD	25407	2022-07-10	2021-11-10	3.3	3.46	3.72	3.4	0.007	0.90	0.0	0.07	14.76	0.01	1.912	9.69	1.08	11.6	87.7	0.7	-5.26	0.75	0.75	1.20	3.4	0.007	0.92	1.0	0.04	17.02	0.01	1.647	23.43	0.32	14.3	85.5	0.2	-3.67	0.98	0.76	0.78	0.89	153049	6597	59	4733	0	0	logfile
✔	5iMQ	6584	2022-07-11	2016-03-06	3.8	3.95	—	3.9	0.012	1.41	0.0	0.07	20.60	0.01	1.006	63.10	4.55	16.6	72.8	10.6	-4.61	0.71	0.65	0.92	3.9	0.006	0.96	2.0	0.04	19.19	0.01	1.732	25.86	1.21	17.1	80.6	2.4	-3.87	0.80	0.82	0.79	0.34	153046	6640	56	4680	1	0	logfile
✘	5LZC	4123	2022-07-10	2016-09-29	4.8	5.11	5.27	4.8	0.007	1.20	10.0	0.06	12.54	0.01	1.153	5.33	0.11	5.7	92.4	1.8	-1.87	0.82	0.82	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	152981	6432	64	4785	5	2	logfile
✔	6WDA	21629	2022-07-10	2020-03-31	3.8	4.14	4.11	3.9	0.006	0.93	0.0	0.08	13.30	0.01	1.314	10.82	0.69	10.6	87.8	1.6	-4.79	0.84	0.82	0.86	3.9	0.008	0.88	2.0	0.04	16.24	0.01	1.801	32.76	1.62	11.9	88.0	0.1	-2.65	1.51	0.86	0.83	0.57	152933	6373	62	4811	0	0	logfile
✔	6WD9	21628	2022-07-10	2020-03-31	3.7	4.05	4.07	3.9	0.006	0.94	0.0	0.08	13.39	0.01	1.313	11.30	0.54	10.7	87.6	1.7	-4.88	0.83	0.82	1.03	3.9	0.006	0.78	2.0	0.04	15.95	0.01	1.991	23.92	1.17	10.8	89.1	0.2	-2.41	0.67	0.84	0.83	0.69	152927	6371	62	4811	0	0	logfile
✔	5U9F	8521	2022-07-10	2016-12-16	3.2	4.48	—	3.3	0.006	0.95	0.0	0.08	13.57	0.01	2.301	12.66	1.02	10.8	88.2	1.0	-5.04	0.87	0.78	1.55	3.4	0.006	0.74	1.0	0.04	15.79	0.01	1.801	26.21	0.96	10.9	89.0	0.1	-2.26	1.46	0.94	0.90	1.08	152819	6576	72	4729	361	0	logfile
✘	7PJW	13462	2022-07-10	2021-08-24	4.0	4.18	3.62	4.0	0.007	0.90	3.0	0.05	16.82	0.01	1.175	23.13	0.46	13.5	86.3	0.2	-4.51	0.71	0.76	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	152719	6657	61	4728	2	0	logfile
✔	5U9G	8522	2022-07-10	2016-12-16	3.2	4.54	—	3.3	0.006	0.92	0.0	0.08	13.52	0.01	2.111	12.41	0.93	10.6	88.5	1.0	-5.08	0.89	0.79	1.20	3.4	0.006	0.73	0.0	0.04	15.50	0.01	1.805	24.37	0.78	9.9	89.9	0.2	-1.89	1.89	0.95	0.91	1.08	152649	6561	70	4729	349	0	logfile
✔	5MMM	3533	2022-07-10	2016-12-11	3.4	3.54	—	3.4	0.008	1.13	0.0	0.05	16.64	0.01	1.757	9.06	9.93	4.9	94.8	0.3	-3.33	0.90	0.86	1.38	3.4	0.006	0.69	2.0	0.04	16.29	0.01	1.109	15.15	0.32	4.6	95.3	0.1	-0.58	0.73	0.89	0.84	1.25	152465	6586	86	4585	955	0	logfile
✘	5ZEP	6921	2022-07-10	2018-02-27	3.4	5.11	—	4.5	0.010	1.18	5.0	0.06	16.72	0.01	1.089	21.21	3.06	8.5	90.3	1.3	-3.96	0.70	0.53	0.11	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	152451	6193	58	4802	262	0	logfile