PDB-IHM

System for Archiving Integrative Structures

4. Model quality ?

For models with atomic structures, MolProbity analysis is performed. For models with coarse-grained or multi-scale structures, excluded volume analysis is performed.

4.1b. MolProbity Analysis ?

Excluded volume satisfaction for the models in the entry are listed below. The Analysed column shows the number of particle-partice or particle-atom pairs for which excluded volume was analysed.

Standard geometry: bond outliers ?

There are 472 bond length outliers in this entry (1.32% of 35889 assessed bonds). A summary is provided below. The output is limited to 100 rows.

Chain	Res	Type	Atoms	\|Z\|	Observed (Å)	Ideal (Å)	Model ID (Worst)	Models (Total)
A	1074	U	O4'-C1'	119.31	3.80	1.41	1	1
A	1075	G	N7-C5	67.69	2.74	1.39	1	1
A	13	U	C2'-O2'	60.60	2.63	1.42	1	1
A	1074	U	C4-C5	56.79	2.57	1.43	1	1
A	13	U	C4-C5	56.64	2.56	1.43	1	1
A	12	A	C2'-C1'	55.94	2.65	1.53	1	1
A	13	U	C4'-O4'	55.84	2.57	1.45	1	1
A	11	G	C5-C6	52.32	2.47	1.42	1	1
A	1074	U	C3'-C2'	51.43	2.55	1.53	1	1
A	13	U	C5-C6	46.47	0.41	1.34	1	1
A	13	U	C2'-C1'	45.23	2.43	1.53	1	1
A	1076	A	C6-N1	42.22	2.20	1.35	1	1
A	11	G	C6-N1	40.72	0.58	1.39	1	1
A	1075	G	C8-N7	40.08	0.50	1.30	1	1
A	1074	U	C4'-C3'	38.92	2.30	1.52	1	1
A	1074	U	O3'-P	38.40	2.18	1.61	1	1
A	1074	U	N1-C2	37.52	2.13	1.38	1	1
A	12	A	O4'-C1'	35.41	0.70	1.41	1	1
A	12	A	C8-N7	31.59	0.68	1.31	1	1
A	1076	A	N9-C8	30.76	1.99	1.37	1	1
A	13	U	C2-O2	30.39	0.61	1.22	1	1
A	1074	U	C1'-N1	29.83	2.07	1.48	1	1
A	13	U	C4'-C3'	29.30	2.11	1.52	1	1
A	1076	A	N7-C5	28.82	1.96	1.39	1	1
A	11	G	C6-O6	26.94	1.78	1.24	1	1
A	1075	G	O4'-C1'	25.25	1.03	1.41	1	1
A	12	A	C3'-C2'	24.77	1.03	1.53	1	1
A	12	A	C2-N3	24.72	1.83	1.33	1	1
A	11	G	C2-N2	24.59	1.83	1.34	1	1
A	1075	G	C4'-O4'	24.47	1.82	1.45	1	1
A	1074	U	C3'-O3'	24.26	1.90	1.42	1	1
A	1075	G	C5-C4	24.02	0.90	1.38	1	1
A	12	A	C3'-O3'	24.00	0.94	1.42	1	1
A	1074	U	C2'-C1'	23.06	1.07	1.53	1	1
A	916	U	C2-O2	21.69	1.65	1.22	1	1
A	11	G	C5-C4	21.50	0.95	1.38	1	1
A	1074	U	N3-C4	19.99	1.78	1.38	1	1
A	13	U	N3-C4	19.98	0.98	1.38	1	1
A	12	A	N3-C4	19.89	1.74	1.34	1	1
A	1075	G	C6-N1	19.65	1.00	1.39	1	1
A	1075	G	C2'-O2'	19.64	1.71	1.42	1	1
A	1075	G	N9-C8	19.50	0.98	1.37	1	1
A	1075	G	N1-C2	18.91	1.75	1.37	1	1
A	1076	A	C2-N3	18.69	1.70	1.33	1	1
A	12	A	C6-N6	18.43	1.70	1.33	1	1
A	13	U	C4-O4	18.02	1.59	1.23	1	1
A	1075	G	C1'-N9	16.38	1.23	1.48	1	1
A	1074	U	C4'-O4'	16.32	1.12	1.45	1	1
A	1075	G	C2'-C1'	15.98	1.77	1.53	1	1
A	12	A	N9-C8	14.49	1.08	1.37	1	1
A	1075	G	O3'-P	14.21	1.39	1.61	1	1
A	14	C	C4'-O4'	14.20	1.66	1.45	1	1
A	1075	G	C5-C6	13.68	1.69	1.42	1	1
A	12	A	C6-N1	13.58	1.62	1.35	1	1
A	12	A	O3'-P	13.57	1.81	1.61	1	1
A	12	A	C4'-O4'	12.97	1.71	1.45	1	1
A	12	A	N1-C2	12.76	1.08	1.34	1	1
A	1075	G	C2-N2	12.52	1.59	1.34	1	1
A	1075	G	N9-C4	12.52	1.63	1.38	1	1
A	13	U	P-O2P	11.86	1.25	1.49	1	1
A	13	U	C1'-N1	11.75	1.71	1.48	1	1
A	12	A	C5-C6	11.30	1.18	1.41	1	1
A	13	U	O3'-P	11.18	1.77	1.61	1	1
A	917	U	O5'-C5'	10.79	1.26	1.42	1	1
A	1074	U	N1-C6	10.70	1.16	1.38	1	1
A	13	U	O4'-C1'	10.64	1.62	1.41	1	1
A	13	U	C5'-C4'	10.38	1.71	1.51	1	1
A	1076	A	C5-C6	10.26	1.61	1.41	1	1
A	1074	U	O5'-C5'	9.70	1.23	1.43	1	1
A	755	A	P-OP2	9.56	1.29	1.49	1	1
A	14	C	P-OP1	9.34	1.30	1.49	1	1
A	1074	U	C4-O4	9.12	1.05	1.23	1	1
A	228	G	C4'-O4'	9.12	1.59	1.45	1	1
A	12	A	O5'-C5'	8.94	1.25	1.43	1	1
A	1076	A	C6-N6	8.89	1.16	1.33	1	1
A	1524	U	O3'-P	8.83	1.47	1.61	1	1
A	1524	U	C4'-O4'	8.79	1.59	1.45	1	1
A	12	A	N9-C4	8.54	1.54	1.37	1	1
A	1076	A	C5-C4	8.48	1.21	1.38	1	1
A	13	U	P-O5'	8.36	1.76	1.59	1	1
A	228	G	P-O5'	8.35	1.72	1.59	1	1
A	572	C	C4'-C3'	8.17	1.65	1.53	1	1
A	14	C	C3'-O3'	8.12	1.30	1.42	1	1
A	1074	U	C2-O2	7.86	1.06	1.22	1	1
A	1075	G	C3'-C2'	7.69	1.64	1.52	1	1
A	239	A	C4'-O4'	7.67	1.57	1.45	1	1
A	1061	U	O3'-P	7.48	1.49	1.61	1	1
A	427	A	P-OP2	7.47	1.34	1.49	1	1
A	324	C	O3'-P	7.46	1.50	1.61	1	1
A	1075	G	P-O5'	7.38	1.48	1.59	1	1
A	14	C	P-OP2	7.24	1.63	1.49	1	1
A	239	A	O3'-P	6.93	1.50	1.61	1	1
A	1074	U	C5'-C4'	6.93	1.37	1.51	1	1
A	368	C	C4'-O4'	6.93	1.56	1.45	1	1
A	14	C	P-O5'	6.92	1.70	1.59	1	1
A	1061	U	C4'-O4'	6.82	1.56	1.45	1	1
A	956	U	C2'-O2'	6.74	1.51	1.41	1	1
A	1045	U	O3'-P	6.72	1.51	1.61	1	1
A	1114	U	C4'-O4'	6.69	1.55	1.45	1	1
A	1097	A	C2'-O2'	6.65	1.51	1.41	1	1

Standard geometry: angle outliers ?

There are 294 bond angle outliers in this entry (0.53% of 55586 assessed bonds). A summary is provided below. The output is limited to 100 rows.

Chain	Res	Type	Atoms	\|Z\|	Observed (Å)	Ideal (Å)	Model ID (Worst)	Models (Total)
A	1074	U	C3'-O3'-P	28.28	77.79	120.20	1	1
A	12	A	O4'-C1'-C2'	23.53	60.35	107.40	1	1
A	12	A	C4'-O4'-C1'	22.48	154.97	110.00	1	1
A	1074	U	O4'-C1'-N1	18.79	52.12	108.50	1	1
A	1074	U	C1'-N1-C2	17.77	64.40	117.70	1	1
A	1075	G	N7-C5-C4	15.89	63.12	110.80	1	1
A	13	U	O2-C2-N3	15.81	74.77	122.20	1	1
A	12	A	O4'-C1'-N9	14.59	137.69	108.50	1	1
A	1074	U	O4-C4-C5	14.55	82.24	125.90	1	1
A	1075	G	C5-C4-N3	14.35	85.55	128.60	1	1
A	12	A	C2'-C1'-N9	13.98	84.45	112.40	1	1
A	13	U	C3'-O3'-P	13.87	99.40	120.20	1	1
A	13	U	N1-C2-O2	13.21	162.43	122.80	1	1
A	1075	G	C6-C5-C4	12.47	156.20	118.80	1	1
A	1075	G	C4'-O4'-C1'	12.29	122.19	109.90	1	1
A	12	A	C4'-C3'-O3'	11.78	136.06	112.50	1	1
A	13	U	O4-C4-C5	11.62	91.04	125.90	1	1
A	12	A	C8-N7-C5	11.55	138.55	103.90	1	1
A	1075	G	C3'-C2'-O2'	11.48	93.48	110.70	1	1
A	12	A	O3'-C3'-C2'	11.39	91.02	113.80	1	1
A	13	U	O2'-C2'-C1'	11.20	74.59	108.20	1	1
A	1074	U	C1'-N1-C6	10.97	154.11	121.20	1	1
A	1074	U	C4'-C3'-O3'	10.96	79.62	112.50	1	1
A	13	U	N3-C4-C5	10.80	82.20	114.60	1	1
A	1076	A	N7-C5-C6	10.52	100.74	132.30	1	1
A	1074	U	O3'-P-O5'	10.29	119.44	104.00	1	1
A	1075	G	C8-N9-C4	10.16	136.89	106.40	1	1
A	13	U	P-O5'-C5'	10.16	90.43	120.90	1	1
A	11	G	C5-C6-O6	10.01	98.57	128.60	1	1
A	324	C	C3'-O3'-P	9.93	135.10	120.20	1	1
A	11	G	N7-C5-C4	9.91	140.53	110.80	1	1
A	1524	U	C3'-O3'-P	9.89	135.03	120.20	1	1
A	12	A	N7-C5-C6	9.72	161.45	132.30	1	1
A	13	U	C4'-C3'-O3'	9.58	83.76	112.50	1	1
A	12	A	C3'-O3'-P	9.52	134.48	120.20	1	1
A	1076	A	C2'-C1'-N9	9.41	97.89	112.00	1	1
A	11	G	C6-C5-C4	9.33	90.81	118.80	1	1
A	1074	U	C2'-C1'-N1	9.24	140.12	112.40	1	1
A	1076	A	O4'-C1'-N9	9.00	121.99	108.50	1	1
A	1074	U	O3'-P-O1P	8.99	81.04	108.00	1	1
A	12	A	N7-C5-C4	8.95	83.85	110.70	1	1
A	11	G	C8-N7-C5	8.93	77.51	104.30	1	1
A	12	A	O3'-P-O5'	8.81	117.21	104.00	1	1
A	12	A	O2'-C2'-C1'	8.80	90.61	108.20	1	1
A	11	G	O6-C6-N1	8.79	146.28	119.90	1	1
A	1074	U	C5'-C4'-O4'	8.77	83.18	109.50	1	1
A	1075	G	O2'-C2'-C1'	8.51	121.17	108.40	1	1
A	1075	G	C5-C6-N1	8.48	86.06	111.50	1	1
A	572	C	C3'-O3'-P	8.28	132.62	120.20	1	1
A	964	A	O3'-C3'-C2'	8.21	121.81	109.50	1	1
A	1075	G	C1'-N9-C4	8.10	102.21	126.50	1	1
A	1045	U	C3'-O3'-P	7.98	132.17	120.20	1	1
A	1061	U	C3'-O3'-P	7.92	132.07	120.20	1	1
A	13	U	C3'-C2'-O2'	7.90	133.50	109.80	1	1
A	239	A	C3'-O3'-P	7.86	131.99	120.20	1	1
A	1074	U	C4'-O4'-C1'	7.85	86.45	110.00	1	1
A	1075	G	C5'-C4'-O4'	7.85	121.57	109.80	1	1
A	56	A	C3'-O3'-P	7.83	131.95	120.20	1	1
A	12	A	C1'-N9-C8	7.82	104.25	127.70	1	1
A	572	C	O4'-C4'-C3'	7.74	98.36	106.10	1	1
A	1097	A	C3'-O3'-P	7.42	131.33	120.20	1	1
A	1222	C	C3'-O3'-P	7.41	131.31	120.20	1	1
A	956	U	C3'-O3'-P	7.31	131.17	120.20	1	1
A	916	U	N1-C2-O2	7.13	101.41	122.80	1	1
A	11	G	N9-C4-C5	7.10	84.11	105.40	1	1
A	909	A	C3'-O3'-P	7.08	130.82	120.20	1	1
A	1076	A	C5-C6-N1	7.07	96.50	117.70	1	1
A	1075	G	O4'-C1'-N9	7.06	119.10	108.50	1	1
A	1075	G	N7-C5-C6	7.05	109.25	130.40	1	1
A	978	U	C3'-O3'-P	7.01	130.72	120.20	1	1
A	1075	G	N9-C4-N3	7.00	147.01	126.00	1	1
A	12	A	C3'-C2'-O2'	6.96	123.72	109.80	1	1
A	1074	U	N3-C4-C5	6.80	94.20	114.60	1	1
A	362	A	C3'-O3'-P	6.70	130.25	120.20	1	1
A	368	C	C3'-O3'-P	6.66	130.20	120.20	1	1
A	1075	G	O4'-C4'-C3'	6.64	97.36	104.00	1	1
A	1076	A	C5-C6-N6	6.60	143.51	123.70	1	1
A	368	C	O3'-C3'-C2'	6.51	119.26	109.50	1	1
A	1075	G	N9-C4-C5	6.49	124.88	105.40	1	1
A	1177	G	O3'-C3'-C2'	6.46	119.19	109.50	1	1
A	11	G	N7-C5-C6	6.42	111.15	130.40	1	1
A	12	A	N6-C6-N1	6.40	99.41	118.60	1	1
A	13	U	C1'-N1-C2	6.34	98.68	117.70	1	1
A	1135	G	C3'-O3'-P	6.32	129.68	120.20	1	1
A	1074	U	C4'-C3'-C2'	6.26	121.08	102.30	1	1
A	368	C	C3'-C2'-O2'	6.25	105.23	114.60	1	1
A	572	C	O3'-C3'-C2'	6.17	118.75	109.50	1	1
A	1075	G	O1P-P-O2P	6.14	138.03	119.60	1	1
A	116	A	C4'-C3'-O3'	6.10	103.85	113.00	1	1
A	1343	G	O3'-C3'-C2'	6.09	118.64	109.50	1	1
A	47	A	C3'-O3'-P	5.97	129.15	120.20	1	1
A	13	U	O2P-P-O5'	5.97	92.80	110.70	1	1
A	47	A	O2'-C2'-C1'	5.91	102.93	111.80	1	1
A	325	A	O3'-C3'-C2'	5.88	118.33	109.50	1	1
A	480	G	C3'-C2'-O2'	5.85	105.82	114.60	1	1
A	1281	A	O3'-C3'-C2'	5.78	118.17	109.50	1	1
A	1049	G	C3'-O3'-P	5.77	128.86	120.20	1	1
A	480	G	C3'-O3'-P	5.75	128.82	120.20	1	1
A	1177	G	C4'-O4'-C1'	5.69	104.01	109.70	1	1
A	1358	A	O3'-C3'-C2'	5.64	117.97	109.50	1	1

Too-close contacts ?

The following all-atom clashscore is based on a MolProbity analysis. All-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The table below contains clashscores for all atomic models in this entry.

Model ID	Clash score	Number of clashes
1	21.89	1082

There are 1082 clashes. The table below contains the detailed list of all clashes based on a MolProbity analysis. Bad clashes are >= 0.4 Angstrom. The output is limited to 100 rows.

Atom 1	Atom 2	Clash(Å)	Model ID (Worst)	Models (Total)
A:11:G:C2	A:11:G:C6	1.64	1	1
A:1075:G:C1'	A:1075:G:C2'	1.61	1	1
A:12:A:C6	A:12:A:N6	1.59	1	1
A:12:A:C4	A:12:A:N3	1.54	1	1
A:1076:A:C2	A:1076:A:N3	1.53	1	1
A:13:U:C1'	A:13:U:N1	1.52	1	1
A:1074:U:C4	A:1074:U:N3	1.49	1	1
A:916:U:C2	A:916:U:O2	1.48	1	1
A:11:G:C2	A:11:G:N2	1.46	1	1
A:12:A:C2	A:12:A:N3	1.45	1	1
A:1075:G:C2'	A:1075:G:O2'	1.38	1	1
A:12:A:C4'	A:12:A:O4'	1.38	1	1
A:11:G:C6	A:11:G:O6	1.36	1	1
A:1076:A:C5	A:1076:A:N7	1.34	1	1
A:1075:G:C2	A:1075:G:N1	1.32	1	1
A:1076:A:C8	A:1076:A:N9	1.29	1	1
A:13:U:C3'	A:13:U:C4'	1.29	1	1
A:1075:G:C4'	A:1075:G:O4'	1.27	1	1
A:14:C:C4'	A:14:C:O4'	1.25	1	1
A:1074:U:C3'	A:1074:U:O3'	1.19	1	1
A:1074:U:C1'	A:1074:U:C2	1.19	1	1
A:1074:U:C2	A:1074:U:N1	1.17	1	1
A:1074:U:C1'	A:1074:U:N1	1.16	1	1
A:1076:A:C5	A:1076:A:C8	1.16	1	1
A:12:A:H1'	A:12:A:O4'	1.14	1	1
A:13:U:C1'	A:13:U:C2	1.11	1	1
A:1076:A:C6	A:1076:A:N1	1.09	1	1
A:1074:U:C3'	A:1074:U:C4'	1.08	1	1
A:12:A:C1'	A:12:A:C4'	1.03	1	1
A:11:G:C5	A:11:G:C6	1.02	1	1
A:12:A:C1'	A:12:A:O4'	1.00	1	1
A:1074:U:H1'	A:1074:U:O2	1.00	1	1
A:1074:U:O3'	A:1075:G:P	1.00	1	1
A:1076:A:C2	A:1076:A:C4	0.97	1	1
A:13:U:C1'	A:13:U:C2'	0.96	1	1
A:1074:U:C1'	A:1074:U:O2	0.95	1	1
A:1074:U:C3'	A:1075:G:P	0.93	1	1
A:1074:U:C4	A:1074:U:C5	0.92	1	1
A:13:U:C4	A:13:U:C5	0.91	1	1
A:695:C:H2'	A:696:G:H5''	0.89	1	1
A:239:A:H4'	A:240:U:H5'	0.89	1	1
A:12:A:N9	A:12:A:O4'	0.89	1	1
A:1207:U:H4'	A:1209:A:H1'	0.88	1	1
A:13:U:H2'	A:14:C:O4'	0.88	1	1
A:1076:A:C4	A:1076:A:C8	0.88	1	1
A:1082:U:H3	A:1095:G:H22	0.87	1	1
A:660:G:H22	A:737:G:H1	0.85	1	1
A:11:G:C4	A:11:G:C6	0.84	1	1
A:1319:G:H2'	A:1320:A:C8	0.84	1	1
A:1074:U:C2'	A:1074:U:C3'	0.83	1	1
A:12:A:C2	A:12:A:C4	0.82	1	1
A:61:A:H2'	A:61:A:N3	0.82	1	1
A:836:C:H2'	A:838:U:H5''	0.80	1	1
A:74:A:H2'	A:75:G:C8	0.80	1	1
A:1215:A:H2'	A:1216:G:C8	0.79	1	1
B:210:ARG:HE	B:229:PRO:HB2	0.79	1	1
A:1075:G:C2'	A:1075:G:N9	0.78	1	1
A:1304:U:H2'	A:1305:G:H8	0.78	1	1
A:235:U:H4'	A:235:U:OP1	0.78	1	1
A:11:G:C6	A:11:G:N1	0.78	1	1
A:1304:U:H2'	A:1305:G:C8	0.76	1	1
A:1214:C:H2'	A:1215:A:C8	0.75	1	1
A:942:A:H2'	A:943:G:C8	0.75	1	1
A:497:C:H2'	A:498:A:H8	0.75	1	1
A:1097:A:H4'	A:1098:A:O5'	0.75	1	1
A:1121:U:H2'	A:1122:U:H5''	0.75	1	1
A:433:U:H2'	A:434:U:O4'	0.74	1	1
A:1214:C:H2'	A:1215:A:H8	0.74	1	1
A:83:C:H2'	A:84:U:H4'	0.74	1	1
A:12:A:C1'	A:12:A:C2'	0.74	1	1
A:1001:A:H2'	A:1002:G:O4'	0.74	1	1
A:1075:G:C1'	A:1075:G:C3'	0.74	1	1
A:760:C:H3'	A:761:G:H21	0.74	1	1
A:808:G:H2'	A:808:G:N3	0.73	1	1
A:1074:U:C2	A:1074:U:C4	0.73	1	1
A:996:A:H2'	A:997:C:C6	0.73	1	1
A:386:U:H2'	A:387:G:C8	0.72	1	1
A:469:U:H2'	A:470:G:H8	0.72	1	1
A:1322:U:H2'	A:1323:C:C6	0.72	1	1
A:1073:G:N2	A:1075:G:H3'	0.72	1	1
A:1247:A:H2'	A:1248:A:C8	0.72	1	1
A:918:G:H2'	A:919:A:C8	0.72	1	1
A:13:U:C4'	A:13:U:O3'	0.72	1	1
A:669:A:H2'	A:670:G:C8	0.72	1	1
A:1204:C:H2'	A:1205:C:O4'	0.72	1	1
A:12:A:C2'	A:12:A:O4'	0.72	1	1
A:1232:A:H4'	A:1300:G:H4'	0.71	1	1
A:497:C:H2'	A:498:A:C8	0.71	1	1
A:264:U:H2'	A:265:C:C6	0.71	1	1
A:514:C:H2'	A:526:G:C8	0.70	1	1
A:1075:G:C1'	A:1075:G:C4'	0.70	1	1
A:1022:G:H2'	A:1023:C:C6	0.70	1	1
A:963:C:H3'	A:964:A:H5'	0.70	1	1
A:1056:U:H2'	A:1057:G:H8	0.70	1	1
A:1076:A:N7	A:1077:A:H1'	0.70	1	1
A:266:A:H2'	A:267:C:C6	0.69	1	1
A:13:U:C2'	A:14:C:O4'	0.69	1	1
A:1067:C:H2'	A:1068:G:H8	0.69	1	1
A:1076:A:C8	A:1077:A:O4'	0.69	1	1
A:1326:U:H2'	A:1327:G:H5'	0.69	1	1

Torsion angles: Protein backbone ?

In the following table, Ramachandran outliers are listed. The Analysed column shows the number of residues for which the backbone conformation was analysed.

Model ID	Analysed	Favored	Allowed	Outliers
1	250	246	3	1

There are 1 unique backbone outliers. Detailed list of outliers are tabulated below.

Chain	Res	Type	Models (Total)
B	114	THR	1

Torsion angles : Protein sidechains ?

In the following table, sidechain rotameric outliers are listed. The Analysed column shows the number of residues for which the sidechain conformation was analysed.

Model ID	Analysed	Favored	Allowed	Outliers
1	216	194	14	8

There are 8 unique sidechain outliers. Detailed list of outliers are tabulated below.

Chain	Res	Type	Models (Total)
B	1	GLN	1
B	5	ASN	1
B	21	LYS	1
B	65	LEU	1
B	75	ASP	1
B	139	LYS	1
B	189	LYS	1
B	215	ASN	1