cryo-EM Re-Refine

Table showing results for March 2025

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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	# other	# water	# H	Logfile
✔	3JC2	3245	2025-03-05	2015-11-15	3.6	3.58	3.95	3.7	0.012	1.63	2.0	0.08	14.90	0.01	1.175	18.51	7.32	11.5	84.5	4.0	-4.52	0.22	0.59	1.48	3.6	0.004	0.87	0.0	0.04	16.96	0.00	2.512	12.68	2.93	8.5	90.9	0.6	-1.43	3.29	0.24	0.53	1.22	3911	482	4	32	0	0	logfile
✔	5FNA	3241	2025-03-06	2015-11-11	4.8	4.43	—	4.2	0.013	1.51	0.0	0.08	12.32	0.01	2.219	36.54	0.00	6.0	94.0	0.0	-1.83	0.48	0.71	—	4.2	0.003	0.74	0.0	0.04	13.16	0.00	2.636	9.16	0.00	7.2	92.8	0.0	-0.43	2.64	0.49	0.78	—	5328	680	8	0	0	0	logfile
✔	5FN5	3240	2025-03-14	2015-11-10	4.3	4.62	—	4.3	0.012	1.85	28.0	0.11	18.82	0.01	2.074	13.59	14.00	11.4	84.3	4.3	-1.91	0.65	0.62	—	4.3	0.004	0.85	0.0	0.04	14.02	0.01	2.341	17.80	0.00	8.1	91.1	0.7	-0.78	1.03	0.69	0.79	—	9645	1227	4	0	0	0	logfile
✔	3JBS	6478	2025-03-05	2015-10-13	2.9	3.04	—	3.2	0.010	1.32	0.0	0.06	8.67	0.01	2.510	0.00	0.00	2.9	97.1	0.0	0.51	0.21	0.76	4.15	3.0	0.003	0.67	0.0	0.04	18.15	0.00	2.651	4.14	4.61	1.2	98.8	0.0	0.57	1.84	0.21	0.82	3.36	1401	175	1	0	0	0	logfile
✘	5A7U	3079	2025-03-05	2015-07-10	4.8	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	455	27	2	1	0	231	logfile
✔	5A6F	3063	2025-03-13	2015-06-25	4.2	5.75	—	5.0	0.012	1.50	0.0	0.05	12.32	0.01	2.112	10.08	3.74	12.2	87.6	0.2	-4.94	0.56	0.74	—	4.6	0.003	0.57	0.0	0.04	11.03	0.00	2.323	6.94	0.00	6.2	93.8	0.0	-0.87	1.44	0.58	0.75	—	8881	540	2	43	0	4330	logfile
✘	3J9S	6272	2025-03-14	2015-02-19	2.6	3.83	—	3.5	0.020	1.80	0.0	0.12	18.55	0.01	0.216	25.10	6.86	1.3	98.0	0.8	1.97	0.68	0.76	3.15	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	9813	1191	6	15	315	0	logfile
✔	3J9E	6240	2025-03-05	2015-01-10	3.3	2.66	—	3.3	0.032	3.28	0.0	0.09	21.31	0.02	1.223	20.81	24.26	9.8	87.3	2.9	-3.41	0.77	0.88	3.26	3.3	0.003	0.74	0.0	0.04	17.90	0.00	2.518	8.27	3.89	7.9	91.1	1.0	0.90	1.59	0.73	0.85	3.34	4098	520	1	0	0	0	logfile
✔	3J9D	6239	2025-03-11	2015-01-09	3.3	2.70	—	3.4	0.027	2.04	0.0	0.08	20.57	0.01	2.034	23.66	24.92	8.2	89.6	2.2	-3.64	0.81	0.89	2.90	3.3	0.022	0.83	0.0	0.04	18.14	0.00	2.320	13.97	6.46	7.7	91.8	0.5	-1.50	2.36	0.75	0.84	2.71	6086	746	2	1	0	0	logfile
✔	3J89	6123	2025-03-13	2014-10-07	3.6	2.21	—	3.5	0.022	1.64	0.0	0.10	11.97	0.01	2.578	2.11	0.00	3.5	96.5	0.0	-0.96	0.83	0.81	0.77	3.2	0.003	0.49	0.0	0.03	20.41	0.00	2.203	4.65	4.26	0.4	99.6	0.0	3.43	1.37	0.81	0.79	0.07	9025	551	19	0	0	4598	logfile
✔	3KTT	5148	2025-03-05	2009-11-25	4.0	2.33	—	4.5	0.020	2.86	20.0	0.20	15.20	0.01	1.652	179.94	7.82	6.3	89.4	4.3	-0.59	0.27	0.28	—	2.1	0.004	1.07	0.0	0.05	17.36	0.00	2.473	20.06	2.69	9.0	89.8	1.2	-1.87	1.70	0.30	0.39	—	3855	513	1	0	0	0	logfile
✘	3A5X	1641	2025-03-05	2009-08-13	4.0	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	-4.41	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—	3616	494	1	0	0	0	logfile
✔	1oED	1044	2025-03-06	2003-03-24	4.0	3.94	—	10.4	0.014	2.29	3.0	0.10	17.23	0.01	1.183	224.94	19.76	5.2	92.7	2.1	-3.67	0.39	0.18	—	9.1	0.008	1.41	1.0	0.05	16.16	0.01	1.749	28.75	3.12	2.3	97.7	0.0	1.42	2.69	0.61	0.41	—	4926	636	5	0	0	0	logfile