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 24 bond length outliers in this entry (0.06% of 41860 assessed bonds). A summary is provided below.| Chain | Res | Type | Atoms | |Z| | Observed (Å) | Ideal (Å) | Model ID (Worst) | Models (Total) |
|---|---|---|---|---|---|---|---|---|
|
B
|
191
|
PRO
|
CG-CD
|
25.40
|
0.64
|
1.50
|
1
|
1
|
|
J
|
9
|
MET
|
SD-CE
|
11.34
|
1.51
|
1.79
|
1
|
1
|
|
L
|
192
|
PRO
|
CB-CG
|
10.98
|
0.94
|
1.49
|
1
|
1
|
|
B
|
191
|
PRO
|
N-CD
|
10.48
|
1.62
|
1.47
|
1
|
1
|
|
I
|
273
|
LEU
|
CG-CD1
|
10.19
|
1.18
|
1.52
|
1
|
1
|
|
J
|
10
|
ARG
|
CG-CD
|
7.66
|
1.29
|
1.52
|
1
|
1
|
|
E
|
147
|
MET
|
SD-CE
|
6.48
|
1.63
|
1.79
|
1
|
1
|
|
H
|
120
|
ARG
|
CG-CD
|
6.43
|
1.33
|
1.52
|
1
|
1
|
|
B
|
266
|
LEU
|
CG-CD1
|
6.39
|
1.31
|
1.52
|
1
|
1
|
|
B
|
191
|
PRO
|
N-CA
|
6.39
|
1.37
|
1.47
|
1
|
1
|
|
A
|
380
|
MET
|
CG-SD
|
6.20
|
1.65
|
1.80
|
1
|
1
|
|
B
|
191
|
PRO
|
CB-CG
|
5.99
|
1.79
|
1.49
|
1
|
1
|
|
H
|
128
|
VAL
|
CB-CG1
|
5.89
|
1.33
|
1.52
|
1
|
1
|
|
A
|
570
|
GLU
|
CG-CD
|
5.86
|
1.37
|
1.52
|
1
|
1
|
|
H
|
116
|
GLU
|
CB-CG
|
5.74
|
1.35
|
1.52
|
1
|
1
|
|
B
|
386
|
LEU
|
CG-CD2
|
5.59
|
1.34
|
1.52
|
1
|
1
|
|
E
|
42
|
MET
|
SD-CE
|
5.47
|
1.65
|
1.79
|
1
|
1
|
|
L
|
192
|
PRO
|
N-CD
|
5.25
|
1.40
|
1.47
|
1
|
1
|
|
J
|
188
|
MET
|
SD-CE
|
5.17
|
1.66
|
1.79
|
1
|
1
|
|
L
|
192
|
PRO
|
N-CA
|
4.80
|
1.54
|
1.47
|
1
|
1
|
|
D
|
47
|
MET
|
SD-CE
|
4.72
|
1.67
|
1.79
|
1
|
1
|
|
G
|
257
|
TYR
|
CD1-CE1
|
4.35
|
1.25
|
1.38
|
1
|
1
|
|
K
|
135
|
ARG
|
CB-CG
|
4.22
|
1.39
|
1.52
|
1
|
1
|
|
G
|
257
|
TYR
|
CE2-CZ
|
4.21
|
1.28
|
1.38
|
1
|
1
|
Standard geometry: angle outliers ?
There are 42 bond angle outliers in this entry (0.07% of 57190 assessed bonds). A summary is provided below.| Chain | Res | Type | Atoms | |Z| | Observed (Å) | Ideal (Å) | Model ID (Worst) | Models (Total) |
|---|---|---|---|---|---|---|---|---|
|
L
|
192
|
PRO
|
CB-CG-CD
|
23.09
|
179.97
|
106.10
|
1
|
1
|
|
B
|
191
|
PRO
|
N-CD-CG
|
21.99
|
70.21
|
103.20
|
1
|
1
|
|
L
|
192
|
PRO
|
CA-CB-CG
|
20.80
|
64.97
|
104.50
|
1
|
1
|
|
L
|
192
|
PRO
|
N-CD-CG
|
19.65
|
73.73
|
103.20
|
1
|
1
|
|
B
|
191
|
PRO
|
CA-N-CD
|
14.69
|
91.43
|
112.00
|
1
|
1
|
|
L
|
192
|
PRO
|
CA-N-CD
|
11.99
|
95.21
|
112.00
|
1
|
1
|
|
B
|
191
|
PRO
|
CA-CB-CG
|
11.21
|
83.20
|
104.50
|
1
|
1
|
|
E
|
147
|
MET
|
CG-SD-CE
|
9.90
|
79.13
|
100.90
|
1
|
1
|
|
A
|
511
|
TRP
|
C-N-CA
|
9.84
|
139.41
|
121.70
|
1
|
1
|
|
J
|
10
|
ARG
|
CG-CD-NE
|
9.43
|
132.75
|
112.00
|
1
|
1
|
|
H
|
120
|
ARG
|
CG-CD-NE
|
8.76
|
131.28
|
112.00
|
1
|
1
|
|
B
|
190
|
CYS
|
CA-C-N
|
8.65
|
129.87
|
116.90
|
1
|
1
|
|
B
|
191
|
PRO
|
N-CA-CB
|
7.30
|
94.97
|
103.00
|
1
|
1
|
|
B
|
215
|
PRO
|
CA-N-CD
|
6.96
|
102.25
|
112.00
|
1
|
1
|
|
A
|
570
|
GLU
|
CG-CD-OE1
|
6.39
|
103.70
|
118.40
|
1
|
1
|
|
P
|
29
|
DA
|
O3'-P-OP1
|
6.01
|
89.97
|
108.00
|
1
|
1
|
|
H
|
116
|
GLU
|
CG-CD-OE2
|
5.66
|
131.42
|
118.40
|
1
|
1
|
|
G
|
168
|
LYS
|
C-N-CA
|
5.60
|
131.78
|
121.70
|
1
|
1
|
|
H
|
20
|
TYR
|
C-N-CA
|
5.50
|
131.59
|
121.70
|
1
|
1
|
|
B
|
190
|
CYS
|
CA-C-O
|
5.48
|
111.48
|
120.80
|
1
|
1
|
|
H
|
116
|
GLU
|
CB-CG-CD
|
5.47
|
121.89
|
112.60
|
1
|
1
|
|
K
|
170
|
GLU
|
CA-CB-CG
|
5.39
|
103.32
|
114.10
|
1
|
1
|
|
B
|
427
|
THR
|
C-N-CA
|
5.33
|
131.30
|
121.70
|
1
|
1
|
|
J
|
11
|
GLU
|
CG-CD-OE1
|
5.27
|
106.28
|
118.40
|
1
|
1
|
|
J
|
158
|
THR
|
C-N-CA
|
5.23
|
131.12
|
121.70
|
1
|
1
|
|
B
|
424
|
ARG
|
C-N-CA
|
5.19
|
112.36
|
121.70
|
1
|
1
|
|
A
|
643
|
VAL
|
C-N-CA
|
4.91
|
112.87
|
121.70
|
1
|
1
|
|
J
|
148
|
THR
|
C-N-CA
|
4.82
|
130.37
|
121.70
|
1
|
1
|
|
G
|
62
|
VAL
|
C-N-CA
|
4.80
|
130.35
|
121.70
|
1
|
1
|
|
J
|
122
|
LEU
|
C-N-CA
|
4.70
|
130.16
|
121.70
|
1
|
1
|
|
B
|
278
|
GLU
|
N-CA-C
|
4.66
|
124.05
|
111.00
|
1
|
1
|
|
B
|
369
|
ARG
|
C-N-CA
|
4.43
|
129.68
|
121.70
|
1
|
1
|
|
K
|
135
|
ARG
|
CA-CB-CG
|
4.41
|
122.93
|
114.10
|
1
|
1
|
|
H
|
120
|
ARG
|
CD-NE-CZ
|
4.33
|
130.46
|
124.40
|
1
|
1
|
|
L
|
258
|
THR
|
C-N-CA
|
4.27
|
129.38
|
121.70
|
1
|
1
|
|
B
|
191
|
PRO
|
CB-CG-CD
|
4.22
|
92.59
|
106.10
|
1
|
1
|
|
G
|
90
|
VAL
|
C-N-CA
|
4.16
|
129.18
|
121.70
|
1
|
1
|
|
B
|
370
|
LYS
|
CA-CB-CG
|
4.15
|
122.41
|
114.10
|
1
|
1
|
|
B
|
257
|
ASP
|
C-N-CA
|
4.15
|
114.23
|
121.70
|
1
|
1
|
|
G
|
127
|
ASP
|
C-N-CA
|
4.10
|
114.33
|
121.70
|
1
|
1
|
|
L
|
249
|
LYS
|
N-CA-C
|
4.09
|
122.44
|
111.00
|
1
|
1
|
|
B
|
190
|
CYS
|
O-C-N
|
4.05
|
116.53
|
123.00
|
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
|
23.71
|
1903
|
There are 1903 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) |
|---|---|---|---|---|
|
B:501:GLN:HB2
|
J:188:MET:HE2
|
1.14
|
1
|
1
|
|
I:273:LEU:HD13
|
K:48:ASN:HA
|
1.13
|
1
|
1
|
|
H:116:GLU:HG2
|
H:120:ARG:HD2
|
1.11
|
1
|
1
|
|
G:249:GLU:HB2
|
G:257:TYR:CE1
|
1.08
|
1
|
1
|
|
B:410:TYR:HB3
|
B:414:PHE:HD2
|
1.08
|
1
|
1
|
|
G:18:ALA:HB2
|
M:2:MET:HE2
|
1.06
|
1
|
1
|
|
B:353:SER:HB2
|
L:273:GLN:HG2
|
1.05
|
1
|
1
|
|
C:140:GLU:OE2
|
C:144:HIS:HD2
|
1.00
|
1
|
1
|
|
L:252:GLY:O
|
L:273:GLN:NE2
|
0.99
|
1
|
1
|
|
B:424:ARG:O
|
I:288:HIS:CE1
|
0.99
|
1
|
1
|
|
C:211:MET:HE2
|
C:240:SER:HB2
|
0.98
|
1
|
1
|
|
J:157:GLU:HA
|
J:160:PRO:HG2
|
0.97
|
1
|
1
|
|
G:237:ARG:HG3
|
G:239:THR:H
|
0.95
|
1
|
1
|
|
E:143:TYR:CZ
|
E:147:MET:HE1
|
0.94
|
1
|
1
|
|
H:116:GLU:HG3
|
H:120:ARG:HH11
|
0.93
|
1
|
1
|
|
G:249:GLU:HB2
|
G:257:TYR:HE1
|
0.93
|
1
|
1
|
|
B:257:ASP:O
|
B:260:GLN:HG3
|
0.93
|
1
|
1
|
|
B:410:TYR:HB3
|
B:414:PHE:CD2
|
0.93
|
1
|
1
|
|
B:543:GLN:H
|
P:37:DG:H5''
|
0.92
|
1
|
1
|
|
G:167:LYS:HZ1
|
L:404:ARG:HH22
|
0.92
|
1
|
1
|
|
D:56:ASP:HB3
|
D:61:MET:HE2
|
0.92
|
1
|
1
|
|
K:149:THR:HG21
|
K:182:LYS:HD3
|
0.91
|
1
|
1
|
|
H:116:GLU:CG
|
H:120:ARG:HD2
|
0.91
|
1
|
1
|
|
C:140:GLU:OE2
|
C:144:HIS:CD2
|
0.90
|
1
|
1
|
|
B:336:LEU:HD21
|
B:358:LEU:HD12
|
0.89
|
1
|
1
|
|
B:422:ASP:H
|
B:427:THR:HG22
|
0.89
|
1
|
1
|
|
B:501:GLN:OE1
|
K:194:PHE:HB3
|
0.88
|
1
|
1
|
|
A:568:LEU:HD11
|
A:606:PHE:HB3
|
0.88
|
1
|
1
|
|
H:116:GLU:CG
|
H:120:ARG:HH11
|
0.88
|
1
|
1
|
|
C:132:ASP:O
|
C:136:GLU:HG2
|
0.88
|
1
|
1
|
|
G:113:MET:HG2
|
G:114:ASP:H
|
0.88
|
1
|
1
|
|
A:584:THR:HA
|
K:185:ARG:HD3
|
0.87
|
1
|
1
|
|
H:116:GLU:HG3
|
H:120:ARG:NH1
|
0.86
|
1
|
1
|
|
A:570:GLU:OE1
|
K:170:GLU:HG2
|
0.86
|
1
|
1
|
|
B:273:ILE:HD12
|
B:276:THR:HB
|
0.86
|
1
|
1
|
|
I:288:HIS:CE1
|
I:289:TYR:O
|
0.86
|
1
|
1
|
|
K:136:VAL:HG13
|
K:154:LEU:HD12
|
0.85
|
1
|
1
|
|
J:35:GLY:O
|
J:150:LEU:HD12
|
0.85
|
1
|
1
|
|
D:246:GLN:HE21
|
E:251:TYR:HB3
|
0.84
|
1
|
1
|
|
G:167:LYS:NZ
|
L:404:ARG:HH22
|
0.84
|
1
|
1
|
|
B:657:MET:HE3
|
B:689:LYS:HB3
|
0.84
|
1
|
1
|
|
N:37:ILE:HB
|
N:80:GLU:H
|
0.84
|
1
|
1
|
|
G:168:LYS:HB2
|
G:169:ASN:HA
|
0.84
|
1
|
1
|
|
B:503:ALA:O
|
J:185:ARG:NH1
|
0.84
|
1
|
1
|
|
B:280:ARG:HH12
|
B:387:GLU:HG2
|
0.84
|
1
|
1
|
|
J:9:MET:HE3
|
K:135:ARG:HB3
|
0.84
|
1
|
1
|
|
J:151:ALA:HB1
|
J:153:THR:H
|
0.83
|
1
|
1
|
|
J:69:MET:HG2
|
J:76:PRO:HB3
|
0.82
|
1
|
1
|
|
I:273:LEU:HD13
|
K:48:ASN:CA
|
0.82
|
1
|
1
|
|
D:64:GLN:N
|
D:64:GLN:OE1
|
0.82
|
1
|
1
|
|
I:271:GLY:HA2
|
K:51:PRO:HD3
|
0.82
|
1
|
1
|
|
B:288:LEU:HD13
|
B:324:ARG:HB3
|
0.82
|
1
|
1
|
|
B:360:GLY:H
|
L:253:VAL:H
|
0.81
|
1
|
1
|
|
N:36:ILE:HG12
|
N:80:GLU:HG2
|
0.81
|
1
|
1
|
|
B:302:ASP:HB2
|
B:380:ARG:HE
|
0.81
|
1
|
1
|
|
B:176:ASN:OD1
|
B:177:LEU:N
|
0.81
|
1
|
1
|
|
O:3:DT:O2
|
P:65:DG:N2
|
0.81
|
1
|
1
|
|
B:292:LEU:HD22
|
B:374:PHE:CD1
|
0.81
|
1
|
1
|
|
B:414:PHE:HE1
|
B:437:CYS:HB2
|
0.81
|
1
|
1
|
|
A:360:ARG:HH12
|
A:433:GLN:HB3
|
0.80
|
1
|
1
|
|
B:136:SER:HB3
|
B:389:THR:HB
|
0.80
|
1
|
1
|
|
B:346:VAL:HG23
|
L:220:ASN:HD21
|
0.80
|
1
|
1
|
|
G:67:LYS:HB2
|
K:9:ARG:HD2
|
0.80
|
1
|
1
|
|
I:198:PRO:HB2
|
I:254:MET:SD
|
0.80
|
1
|
1
|
|
I:169:MET:HA
|
I:169:MET:HE2
|
0.80
|
1
|
1
|
|
C:81:THR:OG1
|
C:89:GLN:NE2
|
0.80
|
1
|
1
|
|
B:424:ARG:HE
|
B:426:PRO:HG2
|
0.79
|
1
|
1
|
|
I:39:LEU:HD12
|
P:53:DT:H2'
|
0.79
|
1
|
1
|
|
D:263:MET:HE2
|
D:297:ILE:HG13
|
0.79
|
1
|
1
|
|
G:76:ILE:HG21
|
K:45:ARG:HB3
|
0.79
|
1
|
1
|
|
B:497:ARG:NH2
|
B:707:ASN:OD1
|
0.79
|
1
|
1
|
|
D:263:MET:CE
|
D:297:ILE:HG13
|
0.79
|
1
|
1
|
|
B:543:GLN:HA
|
B:546:GLU:HB2
|
0.79
|
1
|
1
|
|
J:36:ASP:HB2
|
J:69:MET:HE1
|
0.79
|
1
|
1
|
|
B:426:PRO:HA
|
I:290:ILE:HD11
|
0.78
|
1
|
1
|
|
B:138:THR:HB
|
B:155:CYS:HB3
|
0.78
|
1
|
1
|
|
C:211:MET:HE2
|
C:240:SER:CB
|
0.78
|
1
|
1
|
|
H:16:GLU:HG3
|
H:17:MET:HE2
|
0.78
|
1
|
1
|
|
A:569:LYS:HG3
|
K:184:ARG:HH21
|
0.78
|
1
|
1
|
|
N:109:MET:HA
|
N:109:MET:HE2
|
0.78
|
1
|
1
|
|
O:39:DG:H2''
|
O:40:DC:H5''
|
0.77
|
1
|
1
|
|
B:359:SER:HB2
|
L:253:VAL:C
|
0.77
|
1
|
1
|
|
B:284:GLU:OE2
|
B:378:ARG:NH2
|
0.77
|
1
|
1
|
|
A:380:MET:SD
|
A:381:TRP:CD1
|
0.76
|
1
|
1
|
|
L:253:VAL:HG13
|
L:278:ASP:HB2
|
0.76
|
1
|
1
|
|
B:416:ILE:HG22
|
B:435:PHE:HD1
|
0.76
|
1
|
1
|
|
G:32:ARG:HG2
|
M:83:VAL:HB
|
0.76
|
1
|
1
|
|
G:228:ARG:HE
|
K:176:PRO:HD2
|
0.76
|
1
|
1
|
|
B:292:LEU:HD22
|
B:374:PHE:HD1
|
0.76
|
1
|
1
|
|
I:913:LYS:HA
|
P:66:DT:H2''
|
0.76
|
1
|
1
|
|
A:577:LYS:HD3
|
A:604:THR:HG21
|
0.75
|
1
|
1
|
|
B:354:PRO:HA
|
B:415:THR:HA
|
0.75
|
1
|
1
|
|
G:91:VAL:HG11
|
G:138:LEU:H
|
0.75
|
1
|
1
|
|
J:155:ASP:O
|
K:148:LYS:NZ
|
0.75
|
1
|
1
|
|
D:340:GLY:HA3
|
E:146:ARG:HH12
|
0.75
|
1
|
1
|
|
B:386:LEU:HA
|
I:103:ARG:HE
|
0.75
|
1
|
1
|
|
H:63:ILE:HG23
|
H:119:ARG:HH21
|
0.75
|
1
|
1
|
|
G:18:ALA:HA
|
M:2:MET:H
|
0.75
|
1
|
1
|
|
B:424:ARG:HH22
|
L:228:LYS:HZ2
|
0.75
|
1
|
1
|
|
E:6:ASP:HB2
|
E:155:GLN:HB2
|
0.74
|
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
|
4722
|
4111
|
558
|
53
|
| Chain | Res | Type | Models (Total) |
|---|---|---|---|
|
A
|
71
|
HIS
|
1
|
|
A
|
110
|
PRO
|
1
|
|
A
|
145
|
LYS
|
1
|
|
A
|
150
|
ASP
|
1
|
|
A
|
199
|
LEU
|
1
|
|
B
|
354
|
PRO
|
1
|
|
B
|
355
|
PRO
|
1
|
|
B
|
426
|
PRO
|
1
|
|
B
|
428
|
ILE
|
1
|
|
C
|
32
|
PRO
|
1
|
|
D
|
16
|
GLU
|
1
|
|
D
|
36
|
VAL
|
1
|
|
D
|
37
|
PHE
|
1
|
|
D
|
68
|
PRO
|
1
|
|
D
|
264
|
ALA
|
1
|
|
E
|
82
|
PHE
|
1
|
|
E
|
92
|
ASN
|
1
|
|
G
|
8
|
LEU
|
1
|
|
G
|
13
|
ALA
|
1
|
|
G
|
18
|
ALA
|
1
|
|
G
|
20
|
LEU
|
1
|
|
G
|
21
|
PRO
|
1
|
|
G
|
43
|
LEU
|
1
|
|
G
|
61
|
ASN
|
1
|
|
G
|
91
|
VAL
|
1
|
|
G
|
97
|
VAL
|
1
|
|
G
|
118
|
MET
|
1
|
|
G
|
128
|
ASN
|
1
|
|
G
|
129
|
CYS
|
1
|
|
G
|
170
|
PRO
|
1
|
|
G
|
237
|
ARG
|
1
|
|
G
|
240
|
ILE
|
1
|
|
G
|
241
|
VAL
|
1
|
|
H
|
55
|
ILE
|
1
|
|
I
|
913
|
LYS
|
1
|
|
J
|
10
|
ARG
|
1
|
|
J
|
149
|
ALA
|
1
|
|
J
|
151
|
ALA
|
1
|
|
J
|
152
|
ILE
|
1
|
|
J
|
153
|
THR
|
1
|
|
J
|
155
|
ASP
|
1
|
|
J
|
159
|
LEU
|
1
|
|
L
|
190
|
ARG
|
1
|
|
L
|
218
|
ILE
|
1
|
|
L
|
237
|
GLY
|
1
|
|
L
|
243
|
VAL
|
1
|
|
L
|
245
|
ILE
|
1
|
|
L
|
251
|
GLY
|
1
|
|
L
|
259
|
ASN
|
1
|
|
L
|
270
|
ASN
|
1
|
|
L
|
312
|
GLN
|
1
|
|
N
|
43
|
ALA
|
1
|
|
N
|
131
|
SER
|
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
|
4194
|
3176
|
993
|
25
|
| Chain | Res | Type | Models (Total) |
|---|---|---|---|
|
A
|
38
|
VAL
|
1
|
|
A
|
65
|
MET
|
1
|
|
A
|
187
|
HIS
|
1
|
|
A
|
398
|
ASP
|
1
|
|
B
|
42
|
MET
|
1
|
|
B
|
136
|
SER
|
1
|
|
B
|
257
|
ASP
|
1
|
|
B
|
266
|
LEU
|
1
|
|
B
|
444
|
ILE
|
1
|
|
B
|
501
|
GLN
|
1
|
|
B
|
546
|
GLU
|
1
|
|
B
|
708
|
LEU
|
1
|
|
C
|
41
|
ARG
|
1
|
|
C
|
359
|
MET
|
1
|
|
C
|
424
|
MET
|
1
|
|
D
|
295
|
CYS
|
1
|
|
D
|
315
|
LEU
|
1
|
|
G
|
48
|
TYR
|
1
|
|
G
|
59
|
MET
|
1
|
|
G
|
100
|
PHE
|
1
|
|
H
|
30
|
SER
|
1
|
|
I
|
247
|
ILE
|
1
|
|
J
|
69
|
MET
|
1
|
|
J
|
123
|
TRP
|
1
|
|
L
|
299
|
CYS
|
1
|