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 65 bond length outliers in this entry (0.97% of 6671 assessed bonds). A summary is provided below.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
B
395
LYS
C-N
16.18
1.56
1.33
1
1
B
396
ASP
N-CA
12.38
1.69
1.46
1
1
A
254
LYS
C-N
12.37
1.50
1.33
1
1
B
254
LYS
C-N
12.34
1.50
1.33
1
1
A
256
PRO
C-N
11.68
1.49
1.33
1
1
B
256
PRO
C-N
11.38
1.49
1.33
1
1
A
256
PRO
N-CA
11.27
1.64
1.47
1
1
B
255
THR
C-N
11.27
1.52
1.34
1
1
B
256
PRO
N-CA
11.21
1.63
1.47
1
1
A
255
THR
C-N
11.09
1.52
1.34
1
1
B
396
ASP
CA-C
10.52
1.30
1.52
1
1
A
254
LYS
CA-C
10.43
1.74
1.52
1
1
B
254
LYS
CA-C
10.31
1.74
1.52
1
1
A
255
THR
CA-C
9.55
1.73
1.52
1
1
B
255
THR
CA-C
9.50
1.72
1.52
1
1
A
256
PRO
CA-C
8.80
1.71
1.52
1
1
A
114
LEU
CA-C
8.60
1.34
1.52
1
1
A
115
ASP
N-CA
8.59
1.29
1.46
1
1
A
255
THR
N-CA
8.58
1.62
1.46
1
1
B
256
PRO
CA-C
8.57
1.71
1.52
1
1
B
115
ASP
N-CA
8.56
1.30
1.46
1
1
B
255
THR
N-CA
8.52
1.62
1.46
1
1
B
396
ASP
C-N
8.50
1.21
1.33
1
1
B
341
LYS
C-N
8.36
1.45
1.33
1
1
B
388
MET
C-N
8.23
1.44
1.33
1
1
B
114
LEU
CA-C
8.11
1.35
1.52
1
1
A
341
LYS
C-N
7.72
1.44
1.33
1
1
A
257
ASP
CA-C
7.69
1.69
1.52
1
1
B
257
ASP
N-CA
7.60
1.60
1.46
1
1
A
257
ASP
N-CA
7.47
1.60
1.46
1
1
B
257
ASP
CA-C
7.22
1.68
1.52
1
1
A
395
LYS
C-N
7.05
1.43
1.33
1
1
B
342
LYS
N-CA
6.77
1.59
1.46
1
1
A
342
LYS
N-CA
5.83
1.57
1.46
1
1
A
396
ASP
CA-C
5.79
1.40
1.52
1
1
B
397
ILE
C-N
5.70
1.41
1.33
1
1
B
392
GLU
CA-C
5.65
1.41
1.52
1
1
A
387
LYS
N-CA
5.63
1.35
1.46
1
1
A
319
GLN
C-N
5.57
1.41
1.33
1
1
A
391
LEU
C-N
5.37
1.40
1.33
1
1
A
396
ASP
N-CA
5.35
1.56
1.46
1
1
A
257
ASP
C-N
5.17
1.40
1.33
1
1
A
388
MET
C-N
5.17
1.40
1.33
1
1
B
389
ASN
N-CA
4.94
1.55
1.46
1
1
B
257
ASP
C-N
4.90
1.40
1.33
1
1
B
395
LYS
N-CA
4.83
1.37
1.46
1
1
A
393
ASN
N-CA
4.79
1.37
1.46
1
1
B
387
LYS
N-CA
4.75
1.37
1.46
1
1
B
208
HIS
C-N
4.65
1.39
1.33
1
1
A
343
GLU
N-CA
4.57
1.37
1.46
1
1
A
397
ILE
N-CA
4.44
1.37
1.46
1
1
B
394
ARG
C-N
4.31
1.27
1.33
1
1
B
319
GLN
C-N
4.31
1.39
1.33
1
1
A
314
GLU
C-N
4.28
1.39
1.33
1
1
A
208
HIS
C-N
4.25
1.39
1.33
1
1
B
106
LYS
CA-C
4.22
1.44
1.52
1
1
B
384
THR
CA-C
4.20
1.44
1.52
1
1
B
320
LYS
N-CA
4.19
1.54
1.46
1
1
A
112
ASP
CA-C
4.16
1.44
1.52
1
1
B
388
MET
N-CA
4.14
1.38
1.46
1
1
A
320
LYS
N-CA
4.12
1.54
1.46
1
1
B
318
PHE
CA-C
4.08
1.44
1.52
1
1
B
105
LYS
CA-C
4.05
1.44
1.52
1
1
A
209
LYS
CA-C
4.04
1.61
1.52
1
1
B
112
ASP
CA-C
4.04
1.44
1.52
1
1

Standard geometry: angle outliers ?

There are 304 bond angle outliers in this entry (3.37% of 9020 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)
B
396
ASP
C-N-CA
20.24
85.27
121.70
1
1
B
395
LYS
C-N-CA
18.98
155.86
121.70
1
1
B
396
ASP
CA-C-N
17.77
80.66
116.20
1
1
B
341
LYS
C-N-CA
14.37
147.57
121.70
1
1
A
256
PRO
C-N-CA
13.75
146.44
121.70
1
1
B
256
PRO
C-N-CA
13.55
146.09
121.70
1
1
A
341
LYS
C-N-CA
12.98
145.07
121.70
1
1
B
392
GLU
C-N-CA
12.87
98.53
121.70
1
1
B
303
PHE
CA-CB-CG
12.39
101.41
113.80
1
1
A
396
ASP
C-N-CA
12.18
99.77
121.70
1
1
B
256
PRO
N-CA-C
12.15
142.48
112.10
1
1
A
256
PRO
N-CA-C
12.07
142.28
112.10
1
1
B
315
TYR
C-N-CA
12.03
143.35
121.70
1
1
A
105
LYS
C-N-CA
11.44
101.11
121.70
1
1
B
395
LYS
CA-C-O
11.34
101.53
120.80
1
1
A
395
LYS
C-N-CA
11.13
141.73
121.70
1
1
B
397
ILE
C-N-CA
10.76
141.06
121.70
1
1
A
392
GLU
C-N-CA
10.41
102.96
121.70
1
1
B
389
ASN
C-N-CA
10.33
103.11
121.70
1
1
B
388
MET
CA-C-O
10.30
103.29
120.80
1
1
B
148
ALA
C-N-CA
10.27
140.18
121.70
1
1
B
257
ASP
N-CA-C
10.26
139.73
111.00
1
1
B
396
ASP
CA-C-O
10.26
138.24
120.80
1
1
A
257
ASP
N-CA-C
10.25
139.71
111.00
1
1
B
197
PHE
CA-CB-CG
9.95
103.85
113.80
1
1
B
394
ARG
C-N-CA
9.93
103.83
121.70
1
1
B
318
PHE
C-CA-CB
9.92
91.25
110.10
1
1
B
388
MET
C-N-CA
9.91
139.54
121.70
1
1
B
316
PHE
CA-CB-CG
9.76
104.04
113.80
1
1
A
391
LEU
C-N-CA
9.62
139.02
121.70
1
1
A
254
LYS
CA-C-N
9.49
135.18
116.20
1
1
B
320
LYS
N-CA-C
9.37
84.75
111.00
1
1
B
257
ASP
CA-C-N
9.33
134.87
116.20
1
1
A
257
ASP
CA-C-N
9.29
134.79
116.20
1
1
B
254
LYS
CA-C-N
9.19
134.57
116.20
1
1
B
394
ARG
C-CA-CB
9.12
92.76
110.10
1
1
B
320
LYS
CA-CB-CG
8.99
96.11
114.10
1
1
A
320
LYS
N-CA-C
8.99
85.84
111.00
1
1
A
257
ASP
O-C-N
8.91
108.74
123.00
1
1
B
319
GLN
C-N-CA
8.83
137.59
121.70
1
1
A
315
TYR
C-CA-CB
8.74
93.49
110.10
1
1
A
82
PHE
CA-CB-CG
8.70
105.10
113.80
1
1
A
98
PHE
CA-CB-CG
8.70
105.10
113.80
1
1
B
315
TYR
C-CA-CB
8.66
93.65
110.10
1
1
B
318
PHE
N-CA-C
8.63
86.84
111.00
1
1
B
257
ASP
O-C-N
8.60
109.24
123.00
1
1
B
69
PHE
CA-CB-CG
8.26
105.54
113.80
1
1
B
397
ILE
CA-C-O
8.23
106.81
120.80
1
1
B
312
ALA
N-CA-C
7.97
133.33
111.00
1
1
A
386
ASP
C-N-CA
7.63
107.96
121.70
1
1
B
96
LYS
C-N-CA
7.63
135.43
121.70
1
1
A
338
ILE
C-N-CA
7.55
108.11
121.70
1
1
B
393
ASN
CA-C-N
7.52
101.16
116.20
1
1
B
392
GLU
CB-CG-CD
7.51
99.83
112.60
1
1
A
388
MET
CG-SD-CE
7.50
84.41
100.90
1
1
B
234
LYS
C-N-CA
7.49
135.18
121.70
1
1
A
197
PHE
CA-CB-CG
7.45
106.35
113.80
1
1
B
313
ASP
CA-CB-CG
7.43
105.17
112.60
1
1
B
320
LYS
C-CA-CB
7.42
124.20
110.10
1
1
B
255
THR
N-CA-C
7.32
131.51
111.00
1
1
A
255
THR
N-CA-C
7.29
131.42
111.00
1
1
A
96
LYS
C-N-CA
7.17
134.61
121.70
1
1
B
394
ARG
CA-C-O
7.17
132.99
120.80
1
1
B
114
LEU
CA-C-N
7.13
101.93
116.20
1
1
A
114
LEU
CA-C-N
7.10
102.00
116.20
1
1
B
98
PHE
CA-CB-CG
7.08
106.72
113.80
1
1
B
311
PRO
N-CA-C
7.01
129.64
112.10
1
1
A
363
TYR
CA-CB-CG
6.96
101.37
113.90
1
1
B
9
PHE
CA-CB-CG
6.86
106.94
113.80
1
1
B
391
LEU
C-N-CA
6.82
133.98
121.70
1
1
B
397
ILE
N-CA-C
6.70
129.77
111.00
1
1
B
395
LYS
CA-C-N
6.70
129.59
116.20
1
1
A
318
PHE
N-CA-C
6.69
92.26
111.00
1
1
A
72
ASN
CA-CB-CG
6.68
105.92
112.60
1
1
B
321
GLY
CA-C-N
6.63
126.84
116.90
1
1
A
311
PRO
N-CA-C
6.61
128.62
112.10
1
1
A
374
PHE
CA-CB-CG
6.58
107.22
113.80
1
1
B
393
ASN
C-N-CA
6.57
109.88
121.70
1
1
A
207
PHE
CA-CB-CG
6.53
107.27
113.80
1
1
A
391
LEU
C-CA-CB
6.51
97.74
110.10
1
1
B
352
TYR
CA-CB-CG
6.45
102.28
113.90
1
1
B
360
PHE
CA-CB-CG
6.43
107.37
113.80
1
1
B
162
TYR
CA-CB-CG
6.42
102.35
113.90
1
1
A
389
ASN
C-N-CA
6.40
110.18
121.70
1
1
A
9
PHE
CA-CB-CG
6.38
107.42
113.80
1
1
B
363
TYR
CA-CB-CG
6.34
102.49
113.90
1
1
A
380
LEU
C-CA-CB
6.31
98.11
110.10
1
1
A
351
PHE
CA-CB-CG
6.29
107.51
113.80
1
1
B
380
LEU
C-CA-CB
6.25
98.22
110.10
1
1
B
147
ASN
CA-CB-CG
6.16
106.44
112.60
1
1
B
338
ILE
C-N-CA
6.13
110.67
121.70
1
1
A
236
PHE
C-CA-CB
6.12
98.47
110.10
1
1
B
48
ARG
C-CA-CB
6.11
98.49
110.10
1
1
B
312
ALA
C-CA-CB
6.11
101.34
110.50
1
1
B
255
THR
CA-C-N
6.07
126.01
116.90
1
1
B
386
ASP
C-N-CA
6.05
110.81
121.70
1
1
A
391
LEU
CA-C-O
6.01
110.58
120.80
1
1
A
254
LYS
O-C-N
6.00
113.39
123.00
1
1
A
255
THR
CA-C-N
5.91
125.77
116.90
1
1
A
235
GLU
C-N-CA
5.90
132.32
121.70
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
104.67
1365

There are 1365 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:254:LYS:C
B:254:LYS:CA
1.59
1
1
A:254:LYS:C
A:254:LYS:CA
1.57
1
1
B:396:ASP:CA
B:396:ASP:N
1.54
1
1
A:122:THR:HG23
C:1:35G:C2
1.51
1
1
B:110:PHE:CZ
D:1:35G:O2'
1.36
1
1
B:111:SER:O
D:1:35G:H4'
1.33
1
1
B:143:LEU:CD2
D:1:35G:O6
1.33
1
1
B:396:ASP:N
B:397:ILE:N
1.29
1
1
B:143:LEU:HD21
D:1:35G:O6
1.27
1
1
A:122:THR:HG21
C:1:35G:C6
1.26
1
1
A:115:ASP:OD2
C:1:35G:C1'
1.26
1
1
A:115:ASP:OD2
C:1:35G:H1'
1.19
1
1
A:122:THR:CG2
C:1:35G:N1
1.18
1
1
A:115:ASP:CG
C:1:35G:N3
1.17
1
1
A:115:ASP:OD2
C:1:35G:N3
1.17
1
1
A:122:THR:CG2
C:1:35G:C2
1.14
1
1
B:188:MET:HG2
B:214:ILE:HD11
1.13
1
1
B:396:ASP:N
B:397:ILE:H
1.13
1
1
B:128:ILE:HG21
B:163:LEU:HD13
1.13
1
1
A:342:LYS:H
A:342:LYS:HD2
1.13
1
1
B:88:ILE:N
D:1:35G:O2P
1.12
1
1
A:232:LYS:HB2
A:260:GLU:HG2
1.12
1
1
A:181:ILE:HG23
A:367:ILE:HD11
1.11
1
1
A:340:ASN:HD21
A:343:GLU:HB2
1.10
1
1
B:289:CYS:HA
B:320:LYS:HE2
1.10
1
1
A:338:ILE:HG22
A:372:THR:HG23
1.09
1
1
A:126:MET:HE1
A:156:GLU:HA
1.08
1
1
B:230:MET:HA
B:230:MET:HE2
1.08
1
1
A:395:LYS:HB2
B:391:LEU:HD23
1.07
1
1
B:240:TRP:HB2
B:243:ARG:HD2
1.07
1
1
B:257:ASP:HB2
B:301:ASN:HA
1.07
1
1
A:64:THR:HG23
A:67:SER:H
1.06
1
1
B:286:ASP:HA
B:291:ILE:HD11
1.06
1
1
B:181:ILE:HD13
B:363:TYR:HB3
1.05
1
1
A:115:ASP:HB2
C:1:35G:O4'
1.03
1
1
A:115:ASP:OD1
C:1:35G:N3
1.03
1
1
A:339:VAL:HG11
A:342:LYS:HA
1.02
1
1
B:340:ASN:HD21
B:343:GLU:HB2
1.02
1
1
A:122:THR:HG21
A:143:LEU:HD23
1.02
1
1
B:392:GLU:HG3
B:398:ALA:HB3
1.02
1
1
A:195:LYS:HD2
A:209:LYS:HG2
1.01
1
1
A:294:LEU:HD11
A:307:MET:HE1
1.01
1
1
A:395:LYS:HG2
A:398:ALA:HB2
1.00
1
1
A:257:ASP:HB2
A:301:ASN:HA
1.00
1
1
A:288:TRP:HE3
A:320:LYS:HA
0.99
1
1
A:289:CYS:HA
A:320:LYS:HE2
0.99
1
1
B:87:GLY:HA2
B:111:SER:HB3
0.99
1
1
B:319:GLN:HG2
B:330:ILE:H
0.98
1
1
B:110:PHE:CE1
D:1:35G:O2'
0.97
1
1
A:288:TRP:CE3
A:320:LYS:HA
0.97
1
1
B:321:GLY:HA3
B:328:TRP:CE3
0.96
1
1
A:294:LEU:HA
A:315:TYR:CE1
0.96
1
1
A:395:LYS:HG2
B:391:LEU:HB2
0.96
1
1
B:200:LEU:HD12
B:385:TYR:HD1
0.95
1
1
B:58:THR:HG21
B:61:LEU:HD11
0.95
1
1
A:82:PHE:HZ
A:114:LEU:HB2
0.95
1
1
A:388:MET:HA
A:391:LEU:CD1
0.95
1
1
A:118:THR:HG23
A:120:TYR:H
0.95
1
1
A:87:GLY:HA2
A:111:SER:HB3
0.94
1
1
B:225:VAL:HG12
B:267:ILE:HG12
0.94
1
1
A:297:TYR:CD1
A:314:GLU:HB2
0.94
1
1
B:291:ILE:HB
B:318:PHE:CE1
0.94
1
1
A:175:THR:HG23
B:175:THR:HG21
0.94
1
1
B:392:GLU:HG3
B:398:ALA:CB
0.94
1
1
A:339:VAL:CG1
A:342:LYS:HA
0.93
1
1
A:187:GLN:HA
A:187:GLN:HE21
0.93
1
1
A:267:ILE:CD1
A:279:VAL:HG22
0.92
1
1
A:319:GLN:HB3
A:330:ILE:HB
0.92
1
1
A:388:MET:HA
A:391:LEU:HD12
0.92
1
1
B:313:ASP:HB2
B:315:TYR:CE2
0.92
1
1
A:181:ILE:HG23
A:367:ILE:CD1
0.92
1
1
B:95:THR:CB
B:97:LYS:HG2
0.92
1
1
A:111:SER:O
C:1:35G:H4'
0.92
1
1
A:122:THR:HG21
C:1:35G:N1
0.91
1
1
B:294:LEU:HB3
B:295:PRO:HD3
0.91
1
1
A:122:THR:CG2
C:1:35G:C6
0.91
1
1
A:319:GLN:HG2
A:330:ILE:H
0.91
1
1
B:297:TYR:CD2
B:314:GLU:HB2
0.91
1
1
B:235:GLU:HB2
B:257:ASP:CA
0.90
1
1
B:319:GLN:HB2
B:322:PRO:HG3
0.90
1
1
A:95:THR:HB
A:97:LYS:HG2
0.90
1
1
A:95:THR:CB
A:97:LYS:HG2
0.89
1
1
B:339:VAL:HG11
B:342:LYS:HA
0.89
1
1
A:371:LEU:HD13
A:375:LEU:HD23
0.89
1
1
A:294:LEU:HB3
A:295:PRO:HD3
0.89
1
1
A:128:ILE:CD1
A:163:LEU:HD13
0.89
1
1
B:111:SER:O
D:1:35G:C4'
0.89
1
1
A:321:GLY:HA3
A:328:TRP:CE3
0.88
1
1
B:319:GLN:HG2
B:330:ILE:N
0.88
1
1
A:291:ILE:HD13
A:318:PHE:CE1
0.88
1
1
B:159:PHE:CE2
B:163:LEU:HD11
0.88
1
1
A:9:PHE:CG
B:161:LYS:HD2
0.88
1
1
B:339:VAL:CG1
B:342:LYS:HA
0.88
1
1
A:340:ASN:ND2
A:343:GLU:HB2
0.88
1
1
A:98:PHE:CD1
A:128:ILE:HG22
0.87
1
1
A:228:LEU:HD22
A:261:VAL:HG13
0.87
1
1
A:82:PHE:CZ
A:114:LEU:HB2
0.87
1
1
B:87:GLY:CA
B:111:SER:HB3
0.87
1
1
A:395:LYS:CG
B:391:LEU:HB2
0.87
1
1
B:304:ILE:HG12
B:336:LEU:HD12
0.87
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
794
716
42
36

There are 36 unique backbone outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
A
21
SER
1
A
102
PRO
1
A
144
ASN
1
A
234
LYS
1
A
241
PRO
1
A
258
GLY
1
A
261
VAL
1
A
262
ASN
1
A
301
ASN
1
A
302
GLY
1
A
309
ASN
1
A
312
ALA
1
A
313
ASP
1
A
318
PHE
1
A
320
LYS
1
A
324
ASP
1
A
340
ASN
1
A
342
LYS
1
A
353
ASN
1
A
396
ASP
1
B
144
ASN
1
B
148
ALA
1
B
234
LYS
1
B
235
GLU
1
B
238
ASP
1
B
242
ILE
1
B
258
GLY
1
B
261
VAL
1
B
262
ASN
1
B
313
ASP
1
B
320
LYS
1
B
340
ASN
1
B
341
LYS
1
B
342
LYS
1
B
353
ASN
1
B
396
ASP
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
724
620
72
32

There are 32 unique sidechain outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
A
22
MET
1
A
28
LYS
1
A
50
ARG
1
A
56
VAL
1
A
187
GLN
1
A
209
LYS
1
A
222
ARG
1
A
235
GLU
1
A
251
LYS
1
A
254
LYS
1
A
260
GLU
1
A
315
TYR
1
A
320
LYS
1
A
342
LYS
1
A
388
MET
1
A
399
GLN
1
B
107
ASN
1
B
200
LEU
1
B
233
GLU
1
B
242
ILE
1
B
251
LYS
1
B
254
LYS
1
B
267
ILE
1
B
274
LYS
1
B
315
TYR
1
B
320
LYS
1
B
336
LEU
1
B
390
LYS
1
B
391
LEU
1
B
395
LYS
1
B
397
ILE
1
B
399
GLN
1