Table showing results for May 2025

The table shows a selection of parameters. Activate more columns using the drop-down menus below.
peach highlight: initial model; blue highlight: re-refined model

Resolution

• Resolution
• D₉₉
• D_FSC
• D_Model
• D_Model refined

Map vs model

• CC_box
• CC_mask
• EMRinger
• CC_box refined
• CC_mask refined
• EMRinger refined

Geometry

• Bond rmsd
• Angle rmsd
• Cβ devts
• Chirality
• Dihedral rmsd
• Plane rmsd
• Min nonbonded
• Clashscore
• Rota outliers
• Bond rmsd refined
• Angle rmsd refined
• Cβ devts refined
• Chirality refined
• Dihedral rmsd refined
• Plane rmsd refined
• Min nonbonded refined
• Clashscore refined
• Rota outliers refined
• RMSD

Ramachandran

• Rama allowed
• Rama favored
• Rama outliers
• Z-score
• Rama allowed refined
• Rama favored refined
• Rama outliers refined
• Z-score refined

Composition

• # atoms
• # residues
• # chains
• # nucleotides
• # other
• # water
• # H

Other

• Date processed
• Release Date

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Status	PDB code	EMDB code	Date processed	Release Date	Resolution	D99	DFSC	DModel	Bond rmsd	Angle rmsd	Cβ devts	Chirality	Dihedral rmsd	Plane rmsd	Min nonbonded	Clashscore	Rota outliers	Rama allowed	Rama favored	Rama outliers	Z-score	CCbox	CCmask	EMRinger	DModel	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	CCbox	CCmask	EMRinger	# atoms	# residues	# chains	# nucleotides	# other	# water	# H	Logfile
✔	8DKi	27489	2025-05-10	2022-07-05	3.32	3.57	3.28	3.6	0.003	0.64	0.0	0.05	13.79	0.00	2.204	9.78	0.21	4.6	95.4	0.0	-0.62	0.62	0.84	2.61	3.5	0.004	0.64	0.0	0.04	16.01	0.00	2.593	8.98	3.32	7.0	93.0	0.0	-0.20	0.33	0.60	0.86	2.59	4365	552	3	0	0	0	0	logfile
✔	8AC1	15330	2025-05-24	2022-07-05	4.06	4.42	4.14	4.0	0.005	0.65	0.0	0.04	15.16	0.00	1.927	19.97	0.00	8.5	91.5	0.0	-1.14	0.83	0.81	—	4.0	0.004	0.67	0.0	0.04	15.15	0.00	1.926	13.51	0.00	7.1	92.9	0.0	-1.19	0.36	0.83	0.81	—	25188	3141	9	32	3	0	0	logfile
✔	8DKM	27490	2025-05-10	2022-07-05	3.39	3.59	3.10	3.6	0.003	0.67	0.0	0.04	13.47	0.00	2.241	7.23	0.83	6.4	93.6	0.0	-0.94	0.62	0.84	2.67	3.6	0.004	0.60	0.0	0.04	15.48	0.00	2.556	5.17	3.32	6.0	94.0	0.0	-0.10	0.39	0.62	0.87	2.51	4383	553	4	0	1	0	0	logfile
✔	8ABY	15327	2025-05-24	2022-07-05	3.7	4.01	3.81	4.0	0.006	0.63	0.0	0.04	15.03	0.00	2.131	10.11	0.00	4.0	96.0	0.0	-0.33	0.80	0.82	1.54	4.0	0.003	0.60	0.0	0.04	16.63	0.00	2.146	7.42	1.45	3.2	96.8	0.0	0.34	1.20	0.80	0.84	1.13	25719	3166	9	46	3	0	0	logfile
✔	8DKE	27488	2025-05-10	2022-07-05	3.18	3.43	3.12	3.4	0.003	0.74	2.0	0.05	14.40	0.01	2.179	7.36	0.83	6.2	93.8	0.0	-0.95	0.57	0.85	3.68	3.4	0.003	0.59	0.0	0.04	15.59	0.00	2.575	5.29	2.49	6.8	93.2	0.0	0.07	0.26	0.57	0.86	3.34	4369	553	3	0	0	0	0	logfile
✔	7YEA	33768	2025-05-17	2022-07-05	3.82	4.08	3.84	3.9	0.008	0.84	0.0	0.05	13.81	0.01	2.099	22.75	0.00	7.6	92.4	0.0	-1.40	0.81	0.72	1.21	3.9	0.003	0.79	0.0	0.04	15.85	0.00	2.506	11.56	1.87	4.0	96.0	0.0	0.27	1.01	0.81	0.71	0.59	16016	2034	2	0	0	0	0	logfile
✔	8DKC	27487	2025-05-22	2022-07-05	3.5	4.43	3.57	4.1	0.007	1.02	0.0	0.06	14.11	0.01	2.025	31.47	0.04	12.2	87.6	0.2	-2.77	0.82	0.72	0.90	4.1	0.014	1.12	0.0	0.05	16.66	0.01	1.944	21.71	3.17	11.5	88.5	0.0	-2.19	1.04	0.82	0.73	0.55	23282	2950	5	0	0	0	0	logfile
✔	7YE4	33763	2025-05-16	2022-07-05	3.4	3.54	3.37	3.5	0.003	0.68	0.0	0.05	13.68	0.00	2.352	4.16	0.07	6.4	93.6	0.0	-5.13	0.65	0.71	1.84	3.5	0.002	0.61	0.0	0.04	16.06	0.00	2.465	6.30	2.40	6.7	93.3	0.0	-2.22	0.59	0.67	0.77	1.86	13877	1791	6	0	0	0	0	logfile
✔	7YDH	33747	2025-05-12	2022-07-04	3.1	2.35	3.15	2.2	0.006	0.80	0.0	0.05	12.11	0.00	2.153	6.24	0.73	4.3	95.7	0.0	0.01	0.74	0.73	3.58	2.2	0.004	0.65	0.0	0.04	14.48	0.00	2.438	4.64	2.20	3.7	96.2	0.1	0.76	0.42	0.73	0.74	2.54	8764	1116	5	0	0	0	0	logfile
✔	7YDQ	33756	2025-05-10	2022-07-04	4.04	4.32	4.00	4.4	0.006	0.83	0.0	0.04	17.50	0.01	2.262	10.34	0.57	3.2	96.8	0.0	1.21	0.46	0.63	—	4.4	0.003	0.67	0.0	0.04	14.00	0.00	2.572	7.52	0.19	2.4	97.6	0.0	1.38	0.56	0.56	0.68	—	4778	598	2	0	1	0	0	logfile
✔	7YDP	33755	2025-05-11	2022-07-04	3.1	2.36	3.17	2.1	0.005	0.73	0.0	0.05	12.57	0.00	2.123	11.85	0.00	5.2	94.8	0.0	-1.21	0.68	0.65	1.63	2.1	0.004	0.69	0.0	0.04	14.79	0.00	2.512	8.53	1.97	4.7	95.3	0.0	-0.19	0.37	0.68	0.66	1.13	8028	1022	5	0	0	0	0	logfile
✔	7YDM	33753	2025-05-11	2022-07-04	2.89	2.31	2.90	2.1	0.007	0.72	0.0	0.05	13.26	0.01	2.115	3.82	0.00	5.0	95.0	0.0	-0.11	0.79	0.80	3.14	2.1	0.003	0.55	0.0	0.04	16.18	0.00	2.445	2.22	2.04	3.8	96.2	0.0	1.11	1.16	0.80	0.82	1.89	8131	1031	5	0	0	0	0	logfile
✔	7YDY	33760	2025-05-28	2022-07-04	4.75	4.05	4.52	4.0	0.002	0.47	0.0	0.04	10.39	0.00	2.253	5.17	0.44	3.1	96.9	0.0	-3.89	0.68	0.53	—	3.9	0.004	0.80	0.0	0.05	12.10	0.00	2.323	13.33	0.03	7.2	92.8	0.0	-2.22	2.11	0.71	0.70	—	28760	3638	14	0	36	0	0	logfile
✔	7YDi	33748	2025-05-13	2022-07-04	3.98	3.84	3.72	3.8	0.003	0.70	0.0	0.05	14.60	0.00	1.938	5.91	0.67	3.8	96.2	0.0	-0.82	0.64	0.62	0.76	3.8	0.005	1.01	2.0	0.05	16.33	0.00	2.382	9.67	3.33	4.3	95.7	0.0	-0.30	2.19	0.71	0.73	1.28	9675	1229	5	0	5	0	0	logfile
✔	7YDJ	33749	2025-05-12	2022-07-04	3.03	2.35	3.05	2.1	0.006	0.73	0.0	0.05	12.73	0.00	2.184	6.74	0.10	6.2	93.8	0.0	-0.66	0.75	0.75	2.66	2.1	0.003	0.62	0.0	0.04	14.87	0.00	2.605	4.00	1.36	4.3	95.7	0.0	0.63	0.36	0.75	0.75	2.39	8751	1111	5	0	0	0	0	logfile
✔	7YD1	33745	2025-05-09	2022-07-02	2.99	2.38	9.70	2.2	0.002	0.49	0.0	0.04	9.00	0.00	2.215	6.14	5.46	10.0	90.0	0.0	-4.06	0.75	0.74	3.20	2.2	0.006	0.83	0.0	0.05	13.61	0.01	2.527	10.44	2.73	10.7	89.3	0.0	-1.95	0.61	0.77	0.79	2.61	3305	428	3	0	0	0	0	logfile
✔	8DK5	27483	2025-05-17	2022-07-02	2.71	3.29	2.87	3.2	0.011	1.11	3.0	0.07	27.41	0.01	2.088	9.15	0.39	4.6	95.3	0.2	-0.97	0.74	0.79	3.50	3.2	0.004	0.62	0.0	0.04	27.47	0.00	2.402	6.67	2.64	4.2	95.8	0.0	1.27	1.59	0.72	0.81	3.30	15618	1210	12	298	0	0	0	logfile
✔	7YCZ	33743	2025-05-29	2022-07-02	3.24	2.49	3.19	2.2	0.002	0.54	0.0	0.04	9.01	0.00	2.214	6.11	4.91	5.5	94.5	0.0	-4.43	0.74	0.74	2.72	2.2	0.004	0.75	0.0	0.05	14.02	0.00	2.351	9.45	4.52	7.4	92.6	0.0	-1.65	0.74	0.78	0.80	2.65	32113	4171	9	0	0	0	0	logfile
✔	7YCY	33742	2025-05-27	2022-07-02	3.74	2.71	3.68	2.1	0.002	0.53	0.0	0.04	8.83	0.00	2.242	5.97	4.56	6.3	93.7	0.0	-4.39	0.72	0.71	2.15	2.1	0.003	0.71	0.0	0.04	13.73	0.00	2.444	9.96	3.61	7.6	92.4	0.0	-2.04	0.79	0.72	0.73	1.92	29175	3773	9	0	0	0	0	logfile
✔	7YD0	33744	2025-05-28	2022-07-02	3.58	2.60	3.55	2.1	0.002	0.59	0.0	0.04	9.45	0.00	2.223	7.06	5.95	6.5	93.4	0.1	-4.80	0.71	0.70	2.21	2.2	0.003	0.72	0.0	0.05	14.05	0.00	2.176	10.98	4.21	8.4	91.6	0.0	-2.24	1.29	0.72	0.73	1.81	30413	3944	7	0	0	0	0	logfile

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