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 no bond length outliers.Standard geometry: angle outliers ?
There are no bond angle outliers.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
|
15.12
|
352
|
|
2
|
12.63
|
294
|
|
3
|
14.69
|
342
|
|
4
|
13.45
|
313
|
|
5
|
14.26
|
332
|
|
6
|
13.88
|
323
|
|
7
|
13.71
|
319
|
|
8
|
12.55
|
292
|
|
9
|
13.96
|
325
|
|
10
|
13.28
|
309
|
There are 3201 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) |
|---|---|---|---|---|
|
I:146:DA:H2''
|
I:147:DT:H5''
|
1.02
|
7
|
7
|
|
J:91:DT:H2'
|
J:92:DT:H71
|
0.98
|
6
|
4
|
|
J:145:DG:H2''
|
J:146:DA:H5'
|
0.96
|
7
|
4
|
|
J:116:DA:H2''
|
J:117:DC:H5''
|
0.96
|
3
|
4
|
|
H:5:GLU:HA
|
I:123:DG:H5'
|
0.92
|
3
|
2
|
|
I:124:DT:H2''
|
I:125:DA:H5''
|
0.92
|
5
|
3
|
|
J:146:DA:H2''
|
J:147:DT:H5''
|
0.92
|
1
|
8
|
|
C:29:ARG:HG2
|
J:113:DT:H5'
|
0.91
|
1
|
4
|
|
J:13:DC:H2''
|
J:14:DT:H5'
|
0.91
|
4
|
4
|
|
I:47:DC:H2''
|
I:48:DT:H72
|
0.89
|
4
|
1
|
|
I:47:DC:H2''
|
I:48:DT:H71
|
0.87
|
9
|
2
|
|
J:69:DC:H2''
|
J:70:DT:H71
|
0.87
|
7
|
6
|
|
I:121:DT:H2''
|
I:122:DG:C8
|
0.87
|
3
|
4
|
|
J:126:DG:H2''
|
J:127:DT:H5''
|
0.86
|
5
|
3
|
|
I:44:DC:H2''
|
I:45:DT:H5'
|
0.86
|
3
|
4
|
|
J:22:DC:H2''
|
J:23:DT:H5'
|
0.83
|
1
|
2
|
|
I:114:DA:H2''
|
I:115:DC:H5''
|
0.83
|
3
|
2
|
|
H:3:ARG:HG3
|
I:123:DG:H4'
|
0.83
|
8
|
2
|
|
I:69:DC:H2''
|
I:70:DT:H71
|
0.83
|
10
|
4
|
|
I:33:DG:H2''
|
I:34:DT:H5''
|
0.83
|
7
|
4
|
|
J:97:DT:H2''
|
J:98:DG:H5''
|
0.82
|
1
|
1
|
|
J:10:DC:H2'
|
J:11:DA:C8
|
0.82
|
5
|
3
|
|
J:47:DC:H2'
|
J:48:DT:H72
|
0.82
|
8
|
2
|
|
J:137:DT:H2''
|
J:138:DG:H5'
|
0.81
|
1
|
2
|
|
A:29:LEU:HD23
|
J:91:DT:H5''
|
0.81
|
6
|
6
|
|
A:4:ARG:HG2
|
J:84:DA:H4'
|
0.81
|
10
|
1
|
|
I:135:DG:H2''
|
I:136:DG:H5''
|
0.81
|
9
|
1
|
|
J:1:DA:H2'
|
J:2:DT:C6
|
0.80
|
5
|
1
|
|
J:55:DA:H2'
|
J:56:DA:C8
|
0.80
|
8
|
3
|
|
D:5:GLU:HA
|
J:123:DG:H5'
|
0.80
|
2
|
2
|
|
H:56:ARG:HD2
|
J:40:DG:H5''
|
0.80
|
5
|
3
|
|
J:57:DA:H2''
|
J:58:DG:C8
|
0.79
|
8
|
7
|
|
H:9:ILE:HD11
|
I:122:DG:H5''
|
0.79
|
9
|
1
|
|
J:72:DG:H2''
|
J:73:DA:H5'
|
0.79
|
4
|
1
|
|
I:45:DT:H2''
|
I:46:DG:C8
|
0.79
|
1
|
7
|
|
D:86:LYS:HE2
|
K:46:SER:HA
|
0.79
|
8
|
1
|
|
J:72:DG:H2'
|
J:73:DA:C8
|
0.78
|
4
|
4
|
|
J:121:DT:H2''
|
J:122:DG:C8
|
0.78
|
4
|
4
|
|
J:38:DT:H2''
|
J:39:DG:N7
|
0.78
|
5
|
10
|
|
I:47:DC:H2''
|
I:48:DT:C7
|
0.78
|
10
|
5
|
|
J:6:DT:H2''
|
J:7:DA:H5''
|
0.78
|
9
|
1
|
|
K:16:ILE:HD11
|
K:33:LEU:HB2
|
0.78
|
1
|
1
|
|
I:125:DA:H2''
|
I:126:DG:H5''
|
0.78
|
3
|
4
|
|
J:79:DG:H2''
|
J:80:DC:C5
|
0.77
|
6
|
6
|
|
I:88:DG:H4'
|
I:89:DC:H5'
|
0.77
|
5
|
3
|
|
I:38:DT:H2''
|
I:39:DG:N7
|
0.77
|
7
|
10
|
|
J:133:DC:H2''
|
J:134:DA:C8
|
0.77
|
9
|
7
|
|
I:143:DT:H2''
|
I:144:DT:H5'
|
0.77
|
1
|
1
|
|
I:38:DT:H2''
|
I:39:DG:C8
|
0.77
|
10
|
8
|
|
I:36:DT:H2'
|
I:37:DT:C6
|
0.77
|
7
|
5
|
|
J:88:DG:H4'
|
J:89:DC:H5'
|
0.77
|
1
|
4
|
|
I:32:DT:H2''
|
I:33:DG:H5'
|
0.77
|
2
|
1
|
|
J:131:DT:H2''
|
J:132:DG:C8
|
0.76
|
9
|
7
|
|
J:20:DT:H2''
|
J:21:DA:H5'
|
0.76
|
4
|
2
|
|
J:119:DT:H2'
|
J:120:DT:C6
|
0.76
|
6
|
2
|
|
J:38:DT:H2''
|
J:39:DG:C8
|
0.76
|
2
|
10
|
|
J:99:DG:H1'
|
J:100:DA:N7
|
0.76
|
5
|
7
|
|
I:97:DT:H2'
|
I:98:DG:C8
|
0.76
|
9
|
6
|
|
E:6:ARG:HG3
|
J:145:DG:H5'
|
0.76
|
9
|
2
|
|
J:53:DC:H2''
|
J:54:DA:H5'
|
0.75
|
5
|
2
|
|
I:58:DG:H2''
|
I:59:DG:N7
|
0.75
|
8
|
4
|
|
H:73:PRO:HD2
|
H:76:LEU:HB2
|
0.75
|
9
|
5
|
|
J:64:DT:H2'
|
J:65:DT:C6
|
0.75
|
9
|
4
|
|
I:73:DA:H2'
|
I:74:DA:C8
|
0.75
|
4
|
5
|
|
I:128:DA:H2'
|
I:129:DT:C6
|
0.75
|
7
|
4
|
|
F:54:ALA:HA
|
H:54:ASN:HD21
|
0.75
|
2
|
1
|
|
C:51:GLU:HG2
|
K:58:SER:HB2
|
0.75
|
5
|
1
|
|
I:81:DT:H2''
|
I:82:DG:C8
|
0.74
|
5
|
10
|
|
I:67:DA:H2''
|
I:68:DG:C8
|
0.74
|
9
|
7
|
|
J:26:DC:H2''
|
J:27:DA:C8
|
0.74
|
1
|
7
|
|
H:5:GLU:HA
|
I:123:DG:H5''
|
0.74
|
9
|
4
|
|
I:35:DA:H2'
|
I:36:DT:C6
|
0.74
|
3
|
1
|
|
I:130:DC:H2'
|
I:131:DT:H71
|
0.74
|
8
|
3
|
|
E:29:LEU:HB3
|
E:30:PRO:HD3
|
0.73
|
4
|
10
|
|
E:10:VAL:HG21
|
I:83:DA:H3'
|
0.73
|
4
|
3
|
|
I:109:DC:H2''
|
I:110:DA:C8
|
0.73
|
4
|
9
|
|
J:20:DT:H2'
|
J:21:DA:C8
|
0.73
|
9
|
3
|
|
I:88:DG:H2''
|
I:89:DC:C5
|
0.73
|
8
|
5
|
|
J:16:DC:H2''
|
J:17:DA:N7
|
0.73
|
9
|
8
|
|
I:58:DG:H4'
|
I:59:DG:H5'
|
0.73
|
5
|
1
|
|
J:102:DC:H2''
|
J:103:DA:C8
|
0.73
|
7
|
2
|
|
J:10:DC:H2''
|
J:11:DA:C8
|
0.72
|
7
|
2
|
|
B:2:ASP:HB3
|
B:5:GLN:HB2
|
0.72
|
3
|
1
|
|
J:69:DC:H2''
|
J:70:DT:C7
|
0.72
|
8
|
5
|
|
J:119:DT:H2''
|
J:120:DT:H5'
|
0.72
|
4
|
2
|
|
I:67:DA:H2''
|
I:68:DG:N7
|
0.72
|
4
|
8
|
|
J:134:DA:H2''
|
J:135:DG:C8
|
0.72
|
10
|
8
|
|
J:90:DC:H2''
|
J:91:DT:C7
|
0.72
|
2
|
1
|
|
I:139:DG:H2'
|
I:140:DA:C8
|
0.72
|
6
|
4
|
|
J:136:DG:H2'
|
J:137:DT:H71
|
0.72
|
5
|
1
|
|
I:125:DA:C2'
|
I:126:DG:H5''
|
0.72
|
3
|
3
|
|
E:6:ARG:HG3
|
J:145:DG:H5''
|
0.72
|
7
|
4
|
|
H:68:VAL:HG13
|
H:72:LEU:HD12
|
0.72
|
7
|
5
|
|
J:18:DG:H2'
|
J:19:DA:C8
|
0.72
|
9
|
1
|
|
J:67:DA:H1'
|
J:68:DG:N7
|
0.72
|
3
|
2
|
|
J:58:DG:H1'
|
J:59:DG:N7
|
0.72
|
5
|
2
|
|
J:82:DG:H2''
|
J:83:DA:H5''
|
0.72
|
8
|
1
|
|
J:8:DT:H2'
|
J:9:DC:C6
|
0.72
|
10
|
4
|
|
D:5:GLU:HA
|
J:123:DG:H5''
|
0.72
|
7
|
6
|
|
I:6:DT:H2'
|
I:7:DA:C8
|
0.72
|
10
|
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
|
835
|
802
|
27
|
6
|
|
2
|
835
|
798
|
34
|
3
|
|
3
|
835
|
798
|
28
|
9
|
|
4
|
835
|
803
|
26
|
6
|
|
5
|
835
|
800
|
31
|
4
|
|
6
|
835
|
802
|
29
|
4
|
|
7
|
835
|
804
|
29
|
2
|
|
8
|
835
|
793
|
35
|
7
|
|
9
|
835
|
797
|
33
|
5
|
|
10
|
835
|
801
|
28
|
6
|
| Chain | Res | Type | Models (Total) |
|---|---|---|---|
|
C
|
105
|
LYS
|
10
|
|
D
|
73
|
PRO
|
6
|
|
G
|
106
|
LYS
|
6
|
|
C
|
106
|
LYS
|
5
|
|
H
|
73
|
PRO
|
5
|
|
H
|
74
|
GLY
|
5
|
|
K
|
45
|
ALA
|
4
|
|
A
|
45
|
ASP
|
2
|
|
C
|
104
|
PRO
|
2
|
|
D
|
2
|
LYS
|
2
|
|
A
|
7
|
PRO
|
1
|
|
A
|
98
|
ARG
|
1
|
|
E
|
7
|
PRO
|
1
|
|
F
|
74
|
THR
|
1
|
|
K
|
56
|
VAL
|
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
|
719
|
641
|
43
|
35
|
|
2
|
719
|
648
|
41
|
30
|
|
3
|
719
|
636
|
54
|
29
|
|
4
|
719
|
625
|
49
|
45
|
|
5
|
719
|
648
|
37
|
34
|
|
6
|
719
|
640
|
46
|
33
|
|
7
|
719
|
641
|
47
|
31
|
|
8
|
719
|
630
|
53
|
36
|
|
9
|
719
|
646
|
42
|
31
|
|
10
|
719
|
643
|
50
|
26
|
| Chain | Res | Type | Models (Total) |
|---|---|---|---|
|
G
|
85
|
SER
|
10
|
|
K
|
1
|
LEU
|
10
|
|
D
|
61
|
SER
|
9
|
|
E
|
44
|
THR
|
9
|
|
H
|
61
|
SER
|
9
|
|
A
|
44
|
THR
|
8
|
|
B
|
51
|
THR
|
8
|
|
E
|
51
|
SER
|
8
|
|
K
|
10
|
SER
|
8
|
|
C
|
63
|
THR
|
7
|
|
C
|
88
|
THR
|
7
|
|
E
|
22
|
THR
|
7
|
|
F
|
74
|
THR
|
7
|
|
G
|
63
|
THR
|
7
|
|
K
|
57
|
SER
|
7
|
|
K
|
68
|
SER
|
7
|
|
A
|
40
|
GLN
|
6
|
|
A
|
51
|
SER
|
6
|
|
B
|
74
|
THR
|
6
|
|
C
|
85
|
SER
|
6
|
|
E
|
50
|
SER
|
5
|
|
G
|
5
|
SER
|
5
|
|
K
|
29
|
CYS
|
5
|
|
A
|
22
|
THR
|
4
|
|
A
|
50
|
SER
|
4
|
|
C
|
3
|
SER
|
4
|
|
D
|
22
|
THR
|
4
|
|
F
|
51
|
THR
|
4
|
|
G
|
3
|
SER
|
4
|
|
H
|
93
|
SER
|
4
|
|
K
|
41
|
THR
|
4
|
|
D
|
57
|
SER
|
3
|
|
D
|
86
|
LYS
|
3
|
|
D
|
92
|
THR
|
3
|
|
E
|
23
|
GLU
|
3
|
|
G
|
76
|
ASN
|
3
|
|
H
|
57
|
SER
|
3
|
|
K
|
4
|
ASP
|
3
|
|
K
|
30
|
ASN
|
3
|
|
K
|
46
|
SER
|
3
|
|
K
|
47
|
LEU
|
3
|
|
A
|
4
|
ARG
|
2
|
|
A
|
32
|
GLN
|
2
|
|
A
|
41
|
ASP
|
2
|
|
B
|
52
|
GLU
|
2
|
|
C
|
5
|
SER
|
2
|
|
C
|
51
|
GLU
|
2
|
|
C
|
59
|
ASP
|
2
|
|
D
|
37
|
ASN
|
2
|
|
E
|
21
|
SER
|
2
|
|
E
|
27
|
ARG
|
2
|
|
E
|
41
|
ASP
|
2
|
|
E
|
45
|
ASP
|
2
|
|
G
|
6
|
ASN
|
2
|
|
G
|
59
|
ASP
|
2
|
|
H
|
21
|
ASP
|
2
|
|
K
|
34
|
CYS
|
2
|
|
K
|
52
|
CYS
|
2
|
|
K
|
55
|
ARG
|
2
|
|
K
|
75
|
TRP
|
2
|
|
K
|
89
|
ARG
|
2
|
|
A
|
23
|
GLU
|
1
|
|
A
|
28
|
LYS
|
1
|
|
A
|
37
|
GLU
|
1
|
|
A
|
79
|
LYS
|
1
|
|
B
|
12
|
ILE
|
1
|
|
B
|
46
|
ASP
|
1
|
|
B
|
48
|
VAL
|
1
|
|
B
|
49
|
THR
|
1
|
|
C
|
7
|
ARG
|
1
|
|
C
|
25
|
ASN
|
1
|
|
C
|
29
|
ARG
|
1
|
|
C
|
42
|
MET
|
1
|
|
C
|
45
|
LEU
|
1
|
|
C
|
58
|
ARG
|
1
|
|
C
|
76
|
ASN
|
1
|
|
C
|
82
|
LYS
|
1
|
|
C
|
87
|
VAL
|
1
|
|
C
|
94
|
VAL
|
1
|
|
D
|
5
|
GLU
|
1
|
|
D
|
6
|
SER
|
1
|
|
D
|
14
|
VAL
|
1
|
|
D
|
21
|
ASP
|
1
|
|
D
|
26
|
SER
|
1
|
|
D
|
48
|
SER
|
1
|
|
D
|
56
|
ARG
|
1
|
|
D
|
58
|
THR
|
1
|
|
D
|
83
|
GLU
|
1
|
|
D
|
93
|
SER
|
1
|
|
E
|
4
|
ARG
|
1
|
|
E
|
48
|
PHE
|
1
|
|
E
|
49
|
GLN
|
1
|
|
E
|
69
|
GLU
|
1
|
|
E
|
79
|
LYS
|
1
|
|
F
|
8
|
THR
|
1
|
|
F
|
24
|
ILE
|
1
|
|
F
|
36
|
LEU
|
1
|
|
F
|
52
|
GLU
|
1
|
|
F
|
75
|
LEU
|
1
|
|
G
|
12
|
PHE
|
1
|