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 53 bond length outliers in this entry (0.73% of 7273 assessed bonds). A summary is provided below.| Chain | Res | Type | Atoms | |Z| | Observed (Å) | Ideal (Å) | Model ID (Worst) | Models (Total) |
|---|---|---|---|---|---|---|---|---|
|
C
|
477
|
TPO
|
OG1-P
|
9.78
|
1.52
|
1.72
|
1
|
1
|
|
C
|
467
|
SEP
|
O2P-P
|
4.83
|
1.51
|
1.61
|
1
|
1
|
|
C
|
478
|
SEP
|
O3P-P
|
4.82
|
1.51
|
1.61
|
1
|
1
|
|
C
|
493
|
SEP
|
O2P-P
|
4.81
|
1.51
|
1.61
|
1
|
1
|
|
C
|
463
|
SEP
|
O3P-P
|
4.80
|
1.51
|
1.61
|
1
|
1
|
|
C
|
478
|
SEP
|
O1P-P
|
4.79
|
1.51
|
1.61
|
1
|
1
|
|
C
|
463
|
SEP
|
O1P-P
|
4.79
|
1.51
|
1.61
|
1
|
1
|
|
C
|
467
|
SEP
|
O3P-P
|
4.79
|
1.51
|
1.61
|
1
|
1
|
|
C
|
467
|
SEP
|
O1P-P
|
4.79
|
1.51
|
1.61
|
1
|
1
|
|
C
|
493
|
SEP
|
O3P-P
|
4.79
|
1.51
|
1.61
|
1
|
1
|
|
C
|
493
|
SEP
|
O1P-P
|
4.79
|
1.51
|
1.61
|
1
|
1
|
|
C
|
463
|
SEP
|
O2P-P
|
4.78
|
1.51
|
1.61
|
1
|
1
|
|
C
|
478
|
SEP
|
O2P-P
|
4.76
|
1.51
|
1.61
|
1
|
1
|
|
C
|
493
|
SEP
|
OG-P
|
4.42
|
1.52
|
1.61
|
1
|
1
|
|
C
|
467
|
SEP
|
OG-P
|
4.42
|
1.52
|
1.61
|
1
|
1
|
|
C
|
463
|
SEP
|
OG-P
|
4.41
|
1.52
|
1.61
|
1
|
1
|
|
C
|
478
|
SEP
|
OG-P
|
4.40
|
1.52
|
1.61
|
1
|
1
|
|
C
|
476
|
HIS
|
CE1-NE2
|
4.37
|
1.36
|
1.32
|
1
|
1
|
|
A
|
295
|
HIS
|
CE1-NE2
|
4.36
|
1.36
|
1.32
|
1
|
1
|
|
B
|
32
|
HIS
|
CE1-NE2
|
4.35
|
1.36
|
1.32
|
1
|
1
|
|
A
|
353
|
HIS
|
CD2-NE2
|
4.33
|
1.33
|
1.37
|
1
|
1
|
|
A
|
353
|
HIS
|
CE1-NE2
|
4.33
|
1.36
|
1.32
|
1
|
1
|
|
C
|
197
|
HIS
|
CD2-NE2
|
4.33
|
1.33
|
1.37
|
1
|
1
|
|
C
|
281
|
HIS
|
CD2-NE2
|
4.32
|
1.33
|
1.37
|
1
|
1
|
|
C
|
117
|
HIS
|
CD2-NE2
|
4.32
|
1.33
|
1.37
|
1
|
1
|
|
B
|
25
|
HIS
|
CE1-NE2
|
4.32
|
1.36
|
1.32
|
1
|
1
|
|
C
|
88
|
HIS
|
CE1-NE2
|
4.32
|
1.36
|
1.32
|
1
|
1
|
|
C
|
476
|
HIS
|
CD2-NE2
|
4.30
|
1.33
|
1.37
|
1
|
1
|
|
C
|
114
|
HIS
|
CE1-NE2
|
4.30
|
1.36
|
1.32
|
1
|
1
|
|
A
|
198
|
HIS
|
CE1-NE2
|
4.30
|
1.36
|
1.32
|
1
|
1
|
|
A
|
30
|
HIS
|
CD2-NE2
|
4.29
|
1.33
|
1.37
|
1
|
1
|
|
C
|
197
|
HIS
|
CE1-NE2
|
4.29
|
1.36
|
1.32
|
1
|
1
|
|
A
|
295
|
HIS
|
CD2-NE2
|
4.28
|
1.33
|
1.37
|
1
|
1
|
|
C
|
416
|
HIS
|
CD2-NE2
|
4.28
|
1.33
|
1.37
|
1
|
1
|
|
A
|
30
|
HIS
|
CE1-NE2
|
4.27
|
1.36
|
1.32
|
1
|
1
|
|
C
|
117
|
HIS
|
CE1-NE2
|
4.27
|
1.36
|
1.32
|
1
|
1
|
|
C
|
88
|
HIS
|
CD2-NE2
|
4.26
|
1.33
|
1.37
|
1
|
1
|
|
A
|
159
|
HIS
|
CD2-NE2
|
4.26
|
1.33
|
1.37
|
1
|
1
|
|
B
|
9
|
HIS
|
CE1-NE2
|
4.26
|
1.36
|
1.32
|
1
|
1
|
|
B
|
9
|
HIS
|
CD2-NE2
|
4.26
|
1.33
|
1.37
|
1
|
1
|
|
B
|
32
|
HIS
|
CD2-NE2
|
4.26
|
1.33
|
1.37
|
1
|
1
|
|
C
|
281
|
HIS
|
CE1-NE2
|
4.25
|
1.36
|
1.32
|
1
|
1
|
|
A
|
219
|
HIS
|
CE1-NE2
|
4.25
|
1.36
|
1.32
|
1
|
1
|
|
A
|
219
|
HIS
|
CD2-NE2
|
4.24
|
1.33
|
1.37
|
1
|
1
|
|
A
|
210
|
HIS
|
CE1-NE2
|
4.24
|
1.36
|
1.32
|
1
|
1
|
|
B
|
25
|
HIS
|
CD2-NE2
|
4.23
|
1.33
|
1.37
|
1
|
1
|
|
A
|
210
|
HIS
|
CD2-NE2
|
4.23
|
1.33
|
1.37
|
1
|
1
|
|
A
|
111
|
HIS
|
CE1-NE2
|
4.23
|
1.36
|
1.32
|
1
|
1
|
|
C
|
416
|
HIS
|
CE1-NE2
|
4.23
|
1.36
|
1.32
|
1
|
1
|
|
A
|
111
|
HIS
|
CD2-NE2
|
4.23
|
1.33
|
1.37
|
1
|
1
|
|
C
|
114
|
HIS
|
CD2-NE2
|
4.22
|
1.33
|
1.37
|
1
|
1
|
|
A
|
198
|
HIS
|
CD2-NE2
|
4.21
|
1.33
|
1.37
|
1
|
1
|
|
A
|
159
|
HIS
|
CE1-NE2
|
4.21
|
1.36
|
1.32
|
1
|
1
|
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
|
3.85
|
55
|
There are 55 clashes. The table below contains the detailed list of all clashes based on a MolProbity analysis. Bad clashes are >= 0.4 Angstrom.
| Atom 1 | Atom 2 | Clash(Å) | Model ID (Worst) | Models (Total) |
|---|---|---|---|---|
|
A:327:LEU:O
|
A:328:VAL:HG13
|
0.84
|
1
|
1
|
|
C:459:ARG:O
|
C:460:LYS:C
|
0.75
|
1
|
1
|
|
A:337:ASP:O
|
A:338:LEU:CB
|
0.71
|
1
|
1
|
|
A:42:LEU:C
|
A:42:LEU:HD13
|
0.65
|
1
|
1
|
|
A:337:ASP:O
|
A:338:LEU:CG
|
0.65
|
1
|
1
|
|
C:165:TYR:C
|
C:165:TYR:CD1
|
0.63
|
1
|
1
|
|
A:337:ASP:O
|
A:338:LEU:HB2
|
0.62
|
1
|
1
|
|
C:62:TYR:N
|
C:63:PRO:HD2
|
0.59
|
1
|
1
|
|
A:204:ASP:C
|
A:204:ASP:OD1
|
0.57
|
1
|
1
|
|
C:71:ALA:N
|
C:72:PRO:CD
|
0.57
|
1
|
1
|
|
A:339:ALA:O
|
A:340:SER:HB3
|
0.56
|
1
|
1
|
|
C:165:TYR:CD1
|
C:166:THR:N
|
0.56
|
1
|
1
|
|
C:469:SER:O
|
C:470:TYR:CB
|
0.55
|
1
|
1
|
|
A:203:LEU:N
|
A:203:LEU:HD12
|
0.55
|
1
|
1
|
|
A:202:SER:C
|
A:203:LEU:HD12
|
0.54
|
1
|
1
|
|
C:305:LEU:N
|
C:306:PRO:CD
|
0.53
|
1
|
1
|
|
C:391:PHE:O
|
C:392:GLY:C
|
0.53
|
1
|
1
|
|
C:339:VAL:N
|
C:340:PRO:CD
|
0.53
|
1
|
1
|
|
A:337:ASP:O
|
A:338:LEU:HG
|
0.52
|
1
|
1
|
|
A:15:ASN:OD1
|
A:16:GLY:N
|
0.50
|
1
|
1
|
|
A:87:PHE:HA
|
A:88:PRO:C
|
0.50
|
1
|
1
|
|
A:5:GLY:O
|
A:6:THR:HB
|
0.47
|
1
|
1
|
|
A:76:ARG:O
|
C:366:THR:HG23
|
0.47
|
1
|
1
|
|
C:62:TYR:N
|
C:63:PRO:CD
|
0.47
|
1
|
1
|
|
A:66:GLU:CD
|
A:66:GLU:N
|
0.47
|
1
|
1
|
|
A:42:LEU:HD13
|
A:43:VAL:N
|
0.46
|
1
|
1
|
|
C:469:SER:O
|
C:470:TYR:HB2
|
0.46
|
1
|
1
|
|
C:62:TYR:HB3
|
C:63:PRO:HD3
|
0.46
|
1
|
1
|
|
A:339:ALA:O
|
A:340:SER:CB
|
0.46
|
1
|
1
|
|
A:328:VAL:HG11
|
A:342:ASP:HB3
|
0.45
|
1
|
1
|
|
C:321:ALA:O
|
C:322:ASN:C
|
0.45
|
1
|
1
|
|
A:25:ARG:NH1
|
C:477:TPO:HG21
|
0.45
|
1
|
1
|
|
A:13:SER:HB2
|
A:14:PRO:CD
|
0.44
|
1
|
1
|
|
A:13:SER:OG
|
A:15:ASN:OD1
|
0.44
|
1
|
1
|
|
C:123:ASP:C
|
C:123:ASP:OD1
|
0.44
|
1
|
1
|
|
C:369:GLY:O
|
C:370:ARG:CB
|
0.44
|
1
|
1
|
|
A:61:PHE:C
|
A:61:PHE:CD1
|
0.44
|
1
|
1
|
|
A:50:GLU:HG2
|
A:51:ARG:N
|
0.44
|
1
|
1
|
|
A:150:CYS:O
|
A:151:ALA:HB2
|
0.43
|
1
|
1
|
|
A:203:LEU:CD1
|
A:203:LEU:N
|
0.43
|
1
|
1
|
|
A:327:LEU:C
|
A:328:VAL:HG22
|
0.43
|
1
|
1
|
|
C:264:TYR:O
|
C:268:THR:HG23
|
0.42
|
1
|
1
|
|
C:47:SER:O
|
C:48:THR:C
|
0.42
|
1
|
1
|
|
C:1:ASP:C
|
C:1:ASP:OD1
|
0.42
|
1
|
1
|
|
A:42:LEU:C
|
A:42:LEU:CD1
|
0.42
|
1
|
1
|
|
A:61:PHE:CZ
|
A:317:ILE:HD11
|
0.41
|
1
|
1
|
|
C:388:MET:N
|
C:389:PRO:CD
|
0.41
|
1
|
1
|
|
A:327:LEU:O
|
A:328:VAL:CG1
|
0.41
|
1
|
1
|
|
A:59:CYS:SG
|
A:142:VAL:HG13
|
0.41
|
1
|
1
|
|
C:388:MET:HB2
|
C:389:PRO:HD3
|
0.41
|
1
|
1
|
|
A:13:SER:HB2
|
A:14:PRO:HD2
|
0.41
|
1
|
1
|
|
C:490:LEU:CB
|
C:491:PRO:HA
|
0.41
|
1
|
1
|
|
A:38:ASP:N
|
A:38:ASP:OD1
|
0.41
|
1
|
1
|
|
A:48:LEU:N
|
A:48:LEU:HD22
|
0.41
|
1
|
1
|
|
C:487:GLY:O
|
C:488:LEU:C
|
0.41
|
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
|
859
|
791
|
53
|
15
|
| Chain | Res | Type | Models (Total) |
|---|---|---|---|
|
A
|
6
|
THR
|
1
|
|
A
|
328
|
VAL
|
1
|
|
A
|
333
|
GLY
|
1
|
|
A
|
338
|
LEU
|
1
|
|
A
|
340
|
SER
|
1
|
|
C
|
149
|
THR
|
1
|
|
C
|
322
|
ASN
|
1
|
|
C
|
331
|
GLY
|
1
|
|
C
|
366
|
THR
|
1
|
|
C
|
370
|
ARG
|
1
|
|
C
|
392
|
GLY
|
1
|
|
C
|
459
|
ARG
|
1
|
|
C
|
460
|
LYS
|
1
|
|
C
|
482
|
VAL
|
1
|
|
C
|
486
|
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
|
761
|
696
|
46
|
19
|
| Chain | Res | Type | Models (Total) |
|---|---|---|---|
|
A
|
6
|
THR
|
1
|
|
A
|
30
|
HIS
|
1
|
|
A
|
40
|
VAL
|
1
|
|
A
|
50
|
GLU
|
1
|
|
A
|
66
|
GLU
|
1
|
|
A
|
81
|
VAL
|
1
|
|
A
|
142
|
VAL
|
1
|
|
A
|
155
|
GLU
|
1
|
|
A
|
204
|
ASP
|
1
|
|
A
|
224
|
THR
|
1
|
|
A
|
227
|
THR
|
1
|
|
A
|
327
|
LEU
|
1
|
|
A
|
328
|
VAL
|
1
|
|
A
|
329
|
VAL
|
1
|
|
A
|
335
|
LEU
|
1
|
|
C
|
373
|
THR
|
1
|
|
C
|
455
|
LEU
|
1
|
|
C
|
469
|
SER
|
1
|
|
C
|
490
|
LEU
|
1
|