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.

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
9.26
327

There are 327 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:63:LYS:C
I:3:ARG:HD3
1.58
1
1
A:63:LYS:HG3
I:3:ARG:CD
1.52
1
1
A:63:LYS:CG
I:3:ARG:HD2
1.51
1
1
A:60:HIS:CB
I:3:ARG:HH21
1.51
1
1
A:60:HIS:HB3
I:3:ARG:NH2
1.42
1
1
A:61:SER:C
I:3:ARG:HH12
1.31
1
1
A:63:LYS:O
I:3:ARG:HD3
1.24
1
1
A:62:THR:N
I:3:ARG:HH12
1.20
1
1
A:63:LYS:C
I:3:ARG:CD
1.19
1
1
A:63:LYS:CG
I:3:ARG:CD
1.16
1
1
A:60:HIS:C
I:3:ARG:NH2
1.15
1
1
A:63:LYS:O
I:3:ARG:CD
1.15
1
1
A:62:THR:N
I:3:ARG:NH1
1.10
1
1
A:61:SER:C
I:3:ARG:NH1
1.03
1
1
A:12:GLU:HG3
H:18:PHE:CE1
1.03
1
1
A:63:LYS:CB
I:3:ARG:HD2
1.01
1
1
A:61:SER:OG
H:24:LYS:NZ
0.98
1
1
A:63:LYS:HG2
I:3:ARG:HD2
0.97
1
1
C:14:VAL:HG13
C:15:PRO:HD3
0.97
1
1
A:61:SER:N
I:3:ARG:NH2
0.96
1
1
A:63:LYS:CA
I:3:ARG:HD3
0.93
1
1
A:60:HIS:CA
I:3:ARG:NH2
0.93
1
1
A:62:THR:H
I:3:ARG:HH22
0.89
1
1
A:60:HIS:CB
I:3:ARG:NH2
0.89
1
1
A:60:HIS:HB3
I:3:ARG:CZ
0.88
1
1
A:60:HIS:CA
I:3:ARG:HH21
0.87
1
1
A:63:LYS:HG3
I:3:ARG:CG
0.85
1
1
A:60:HIS:C
I:3:ARG:CZ
0.84
1
1
A:61:SER:N
I:3:ARG:HH22
0.84
1
1
A:62:THR:H
I:3:ARG:NH2
0.83
1
1
C:25:VAL:HB
C:26:PRO:HD3
0.82
1
1
D:237:LEU:HB3
D:242:ILE:HD11
0.82
1
1
K:238:GLU:HB3
K:368:LYS:HB2
0.82
1
1
A:63:LYS:HE3
I:3:ARG:O
0.80
1
1
A:60:HIS:HB2
I:3:ARG:HE
0.79
1
1
A:63:LYS:CA
I:3:ARG:CD
0.79
1
1
A:63:LYS:HG2
I:3:ARG:CD
0.79
1
1
J:328:TRP:HB2
J:349:ARG:HA
0.75
1
1
E:237:LEU:HB3
E:366:MET:HE2
0.75
1
1
A:22:TYR:C
L:25:THR:HG21
0.74
1
1
D:210:ASP:HB3
D:211:PRO:HD3
0.74
1
1
A:62:THR:N
I:3:ARG:CZ
0.74
1
1
F:10:GLU:HA
F:20:SER:HA
0.74
1
1
J:199:GLN:HA
J:392:LYS:HG2
0.74
1
1
C:12:ASP:HB2
D:70:LYS:HD3
0.73
1
1
A:22:TYR:C
L:25:THR:CG2
0.73
1
1
J:258:GLU:HB3
J:392:LYS:HB2
0.73
1
1
D:311:THR:HB
D:352:ALA:HB2
0.72
1
1
J:125:LEU:HD23
K:111:LEU:HD13
0.70
1
1
A:62:THR:N
I:3:ARG:HH22
0.70
1
1
A:22:TYR:N
L:25:THR:HG21
0.70
1
1
A:60:HIS:CB
I:3:ARG:CZ
0.69
1
1
J:341:ASP:HA
J:376:ASP:HB2
0.69
1
1
D:94:LEU:HD13
J:102:SER:HB3
0.69
1
1
A:63:LYS:CB
I:3:ARG:CD
0.68
1
1
J:246:THR:HB
J:273:THR:HA
0.68
1
1
A:62:THR:N
I:3:ARG:NH2
0.68
1
1
E:374:ILE:HG12
E:375:PRO:HD2
0.68
1
1
K:105:ASN:HA
K:108:ILE:HD12
0.68
1
1
D:90:GLU:O
D:94:LEU:HG
0.67
1
1
A:60:HIS:NE2
H:17:ASN:HA
0.67
1
1
I:21:TYR:HB3
I:24:ARG:HB2
0.66
1
1
A:60:HIS:CE1
H:17:ASN:HA
0.66
1
1
D:198:ARG:HB3
D:393:MET:HB3
0.66
1
1
A:48:ASP:HA
A:54:ALA:HB2
0.66
1
1
E:243:ARG:HG2
G:28:LEU:HD22
0.66
1
1
K:247:ALA:HB2
K:273:ALA:HB3
0.66
1
1
B:25:MET:HE1
E:13:ALA:HB3
0.65
1
1
A:60:HIS:HB3
I:3:ARG:HH21
0.65
1
1
A:63:LYS:HG2
I:3:ARG:NE
0.65
1
1
J:99:THR:HA
J:103:ASN:HB2
0.65
1
1
C:14:VAL:HG21
D:69:GLN:HB3
0.64
1
1
K:291:PHE:HB3
K:325:LYS:HB3
0.64
1
1
J:34:ARG:HB2
J:35:PRO:HD3
0.64
1
1
A:63:LYS:CD
I:3:ARG:HA
0.63
1
1
C:4:LEU:HD12
D:82:VAL:HA
0.63
1
1
A:60:HIS:CB
I:3:ARG:HE
0.63
1
1
K:179:THR:HB
K:373:ILE:HG13
0.63
1
1
G:24:ARG:O
G:28:LEU:HG
0.62
1
1
J:355:PRO:HA
J:378:VAL:HG13
0.62
1
1
J:104:ILE:HB
J:105:PRO:HD3
0.62
1
1
B:64:ILE:O
B:68:LEU:HG
0.61
1
1
A:63:LYS:CG
I:3:ARG:NE
0.61
1
1
D:341:ASP:HA
D:376:ASP:HB2
0.61
1
1
K:330:HIS:O
K:354:ILE:HA
0.61
1
1
J:243:SER:HA
J:274:VAL:HB
0.61
1
1
J:268:HIS:HB3
J:289:ARG:HG3
0.60
1
1
A:20:SER:HB2
H:26:PRO:HB3
0.60
1
1
A:60:HIS:HB2
I:3:ARG:NE
0.60
1
1
J:316:MET:HG3
J:348:ASN:HB2
0.60
1
1
C:15:PRO:HD2
C:18:PHE:HB3
0.60
1
1
E:236:GLU:HG2
E:246:THR:HG23
0.60
1
1
F:9:LYS:HG3
F:10:GLU:OE1
0.59
1
1
K:302:TRP:HB3
K:315:GLU:HA
0.59
1
1
E:53:LEU:HD12
J:127:SER:HB3
0.59
1
1
F:6:LYS:HB2
F:48:THR:HG21
0.59
1
1
K:245:SER:HB2
K:273:ALA:HB2
0.59
1
1
A:60:HIS:CB
I:3:ARG:NE
0.59
1
1
H:28:GLU:HG3
L:29:SER:HB3
0.59
1
1
D:81:VAL:HG13
D:82:VAL:HG23
0.58
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
2226
2036
164
26

There are 26 unique backbone outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
A
56
HIS
1
B
8
PRO
1
C
14
VAL
1
D
83
ASN
1
D
103
ASN
1
D
200
ASP
1
D
271
GLY
1
D
350
CYS
1
E
56
ASN
1
E
147
GLY
1
E
326
CYS
1
E
329
GLY
1
E
359
TRP
1
G
8
PRO
1
G
169
PRO
1
G
170
SER
1
J
81
VAL
1
J
85
TYR
1
J
200
ASP
1
J
262
GLY
1
J
292
ALA
1
J
350
CYS
1
K
56
ASN
1
K
147
GLY
1
K
185
LEU
1
K
326
CYS
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
1982
1571
219
192

There are 192 unique sidechain outliers. Detailed list of outliers are tabulated below. The output is limited to 100 rows.

Chain Res Type Models (Total)
A
2
GLU
1
A
3
SER
1
A
15
SER
1
A
21
SER
1
A
23
SER
1
A
29
SER
1
A
38
THR
1
A
49
GLU
1
A
52
SER
1
A
53
GLU
1
A
61
SER
1
B
10
CYS
1
B
13
GLU
1
B
14
ASP
1
B
18
LYS
1
B
34
GLN
1
B
45
ASN
1
B
47
LEU
1
B
58
HIS
1
B
86
SER
1
B
140
SER
1
B
146
GLU
1
B
158
GLN
1
B
166
ASP
1
C
4
LEU
1
C
8
LYS
1
C
14
VAL
1
C
20
SER
1
D
21
THR
1
D
31
GLN
1
D
53
THR
1
D
63
LEU
1
D
65
LYS
1
D
72
GLN
1
D
77
ASP
1
D
78
ASN
1
D
83
ASN
1
D
86
SER
1
D
87
SER
1
D
89
LEU
1
D
92
HIS
1
D
99
THR
1
D
106
THR
1
D
124
LYS
1
D
125
LEU
1
D
153
GLU
1
D
156
GLU
1
D
163
GLU
1
D
164
THR
1
D
174
SER
1
D
175
SER
1
D
213
LYS
1
D
223
THR
1
D
245
LEU
1
D
259
ASP
1
D
291
THR
1
D
319
SER
1
D
330
THR
1
D
335
LYS
1
D
336
GLN
1
D
366
THR
1
D
371
LYS
1
D
374
THR
1
D
376
ASP
1
D
386
SER
1
D
397
ILE
1
D
400
PHE
1
E
9
THR
1
E
18
THR
1
E
28
GLN
1
E
60
SER
1
E
80
ILE
1
E
89
THR
1
E
124
GLU
1
E
129
THR
1
E
139
ASP
1
E
170
GLU
1
E
172
ASP
1
E
174
SER
1
E
182
GLN
1
E
185
LEU
1
E
188
SER
1
E
208
THR
1
E
210
THR
1
E
241
ASN
1
E
243
ARG
1
E
257
GLU
1
E
284
ASP
1
E
287
SER
1
E
301
THR
1
E
304
ASN
1
E
310
GLU
1
E
319
SER
1
E
346
THR
1
E
351
ASP
1
E
358
THR
1
E
377
ASN
1
E
380
THR
1
F
1
LYS
1
F
13
THR
1