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
|
7.99
|
29
|
There are 29 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:160:ALA:HA
|
A:163:MET:HE2
|
0.77
|
1
|
1
|
|
A:101:VAL:HA
|
A:163:MET:HE1
|
0.74
|
1
|
1
|
|
A:157:THR:HG21
|
A:175:ARG:HH11
|
0.68
|
1
|
1
|
|
A:42:PHE:O
|
A:46:THR:OG1
|
0.62
|
1
|
1
|
|
A:9:GLU:OE2
|
A:79:TYR:OH
|
0.58
|
1
|
1
|
|
A:118:MET:HE1
|
A:182:TRP:HZ3
|
0.55
|
1
|
1
|
|
A:102:ASP:O
|
A:159:LYS:NZ
|
0.54
|
1
|
1
|
|
A:45:ILE:HG23
|
A:92:LEU:HD22
|
0.54
|
1
|
1
|
|
A:164:ARG:O
|
A:167:VAL:HG22
|
0.53
|
1
|
1
|
|
A:156:PHE:HB3
|
A:171:PHE:CZ
|
0.52
|
1
|
1
|
|
A:82:ARG:NE
|
C:2:HOH:O
|
0.52
|
1
|
1
|
|
A:163:MET:HE3
|
A:167:VAL:HG21
|
0.52
|
1
|
1
|
|
B:1:RET:H8
|
B:1:RET:H171
|
0.52
|
1
|
1
|
|
A:20:MET:HE1
|
A:213:VAL:HA
|
0.49
|
1
|
1
|
|
A:77:PRO:HG2
|
A:201:LEU:HD22
|
0.49
|
1
|
1
|
|
A:153:PHE:CE2
|
A:179:VAL:HG21
|
0.47
|
1
|
1
|
|
A:194:GLU:N
|
A:194:GLU:OE1
|
0.45
|
1
|
1
|
|
A:43:TYR:CE1
|
A:224:LEU:HD13
|
0.45
|
1
|
1
|
|
B:1:RET:H7
|
B:1:RET:H181
|
0.45
|
1
|
1
|
|
A:86:TRP:O
|
A:90:THR:OG1
|
0.45
|
1
|
1
|
|
A:153:PHE:CD2
|
A:179:VAL:HG21
|
0.44
|
1
|
1
|
|
A:131:TYR:O
|
A:134:ARG:HB2
|
0.44
|
1
|
1
|
|
A:66:LEU:HD23
|
A:79:TYR:CD2
|
0.44
|
1
|
1
|
|
A:166:GLU:CD
|
A:166:GLU:H
|
0.43
|
1
|
1
|
|
A:20:MET:CE
|
A:213:VAL:HA
|
0.43
|
1
|
1
|
|
A:56:MET:HG3
|
A:85:ASP:HB2
|
0.43
|
1
|
1
|
|
A:19:LEU:HA
|
A:19:LEU:HD12
|
0.41
|
1
|
1
|
|
A:174:LEU:O
|
A:178:THR:OG1
|
0.41
|
1
|
1
|
|
A:163:MET:HE3
|
A:167:VAL:CG2
|
0.40
|
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
|
228
|
220
|
8
|
0
|
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
|
181
|
145
|
13
|
23
|
| Chain | Res | Type | Models (Total) |
|---|---|---|---|
|
A
|
7
|
ARG
|
1
|
|
A
|
11
|
ILE
|
1
|
|
A
|
19
|
LEU
|
1
|
|
A
|
28
|
LEU
|
1
|
|
A
|
46
|
THR
|
1
|
|
A
|
61
|
LEU
|
1
|
|
A
|
66
|
LEU
|
1
|
|
A
|
68
|
MET
|
1
|
|
A
|
100
|
LEU
|
1
|
|
A
|
101
|
VAL
|
1
|
|
A
|
111
|
LEU
|
1
|
|
A
|
119
|
ILE
|
1
|
|
A
|
128
|
THR
|
1
|
|
A
|
132
|
SER
|
1
|
|
A
|
153
|
PHE
|
1
|
|
A
|
157
|
THR
|
1
|
|
A
|
159
|
LYS
|
1
|
|
A
|
164
|
ARG
|
1
|
|
A
|
166
|
GLU
|
1
|
|
A
|
187
|
VAL
|
1
|
|
A
|
199
|
VAL
|
1
|
|
A
|
211
|
LEU
|
1
|
|
A
|
223
|
LEU
|
1
|