Project name: Mod_5574681

Status: done

Started: 2020-11-20 05:51:39
Settings
Chain sequence(s) X: PRGSASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGKMENPSTVQRGLNGEPIFDPFKGFGLTGNAPTDWNEIKGKVPVEVVQSPHSPNLYQSPHSPNLYFVLLVPKVVVEYHQLDKVVKESLEVEATDSFDPTKRLQKDSPMKDSTRESQEKLSLADGGSMSSGGATSTRKALKIEVEKQSGSSDSLLKNDFAKKPLEHKENSGTEVKLAASGEFTKAWKPLLKTDEIEKNRGMGAT
input PDB
Selected Chain(s) X
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with X chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:07:32)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:21:39)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:21:41)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:21:43)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:21:45)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:21:47)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:21:48)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:21:50)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:21:52)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:21:54)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:21:56)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:21:58)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:22:00)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:22:02)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:22:04)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:22:05)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:22:05)
[INFO]       Main:     Simulation completed successfully.                                          (01:22:07)
Show buried residues

Minimal score value
-4.2086
Maximal score value
2.2888
Average score
-0.9546
Total score value
-292.0954

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
16 P X -1.3880
17 R X -2.3920
18 G X -1.8119
19 S X -1.0518
20 A X -0.4781
21 S X -0.1985
22 M X 0.5173
23 S X 0.0000
24 D X -2.0075
25 S X -1.6069
26 E X -2.5809
27 V X -2.5333
28 N X -3.1257
29 Q X -2.9611
30 E X -2.3335
31 A X -1.6851
32 K X -2.6047
33 P X -1.8193
34 E X -2.1824
35 V X -0.7254
36 K X -2.3611
37 P X -1.7617
38 E X -2.2271
39 V X -1.3744
40 K X -2.6499
41 P X -2.4194
42 E X -3.1521
43 T X -2.8738
44 H X -2.6006
45 I X 0.0000
46 N X -1.9370
47 L X 0.0000
48 K X -1.8250
49 V X 0.0000
50 S X -1.4380
51 D X -1.9304
52 G X -1.3697
53 S X -1.1130
54 S X -1.7783
55 E X -1.8585
56 I X -0.0982
57 F X 0.6552
58 F X 0.0000
59 K X -1.9469
60 I X 0.0000
61 K X -2.0283
62 K X 0.0000
63 T X -0.3403
64 T X -0.5066
65 P X -1.0774
66 L X 0.0000
67 R X -1.7643
68 R X -2.2168
69 L X -1.0465
70 M X 0.0000
71 E X -2.7774
72 A X -2.1707
73 F X 0.0000
74 A X 0.0000
75 K X -4.2086
76 R X -3.9315
77 Q X -3.5388
78 G X -3.4242
79 K X -3.6066
80 E X -3.5574
81 M X -1.5261
82 D X 0.0000
83 S X -0.4662
84 L X 0.0000
85 R X 0.0000
86 F X 0.0000
87 L X 0.0000
88 Y X 0.0000
89 D X -0.2049
90 G X 0.0000
91 I X 0.0000
92 R X -1.1113
93 I X 0.0000
94 Q X -1.0151
95 A X 0.0000
96 D X -2.1571
97 Q X 0.0000
98 T X 0.0000
99 P X 0.0000
100 E X -3.5756
101 D X -2.3861
102 L X 0.0000
103 D X -3.0889
104 M X -2.3806
105 E X -2.8990
106 D X -3.1835
107 N X -2.1438
108 D X 0.0000
109 I X -0.5163
110 I X 0.0000
111 E X -1.7801
112 A X 0.0000
113 H X -1.7213
114 R X -1.9755
115 E X -1.3631
116 Q X -0.5775
117 I X 1.1205
118 G X 0.3520
119 G X -0.4602
120 K X -0.8147
121 M X 0.0000
122 E X 0.0000
123 N X -1.2047
124 P X 0.0000
125 S X -0.7301
126 T X 0.0000
127 V X -0.6442
128 Q X -1.9279
129 R X -1.2968
130 G X -0.8646
131 L X -0.0177
132 N X -1.3018
133 G X -1.4162
134 E X -1.1526
135 P X -0.9360
136 I X 0.0000
137 F X 0.0000
138 D X -0.6558
139 P X -0.1951
140 F X 0.3923
141 K X -0.1819
142 G X -0.2347
143 F X 1.6980
144 G X 1.1938
145 L X 1.5920
146 T X 0.3003
147 G X -0.7948
148 N X -1.3707
149 A X -1.2553
150 P X -1.1479
151 T X -1.2614
152 D X -2.2738
153 W X -1.3829
154 N X -1.8761
155 E X -1.9710
156 I X 0.0000
157 K X -1.7961
158 G X -1.4989
159 K X -0.7114
160 V X 0.1837
161 P X 0.0528
162 V X 0.4551
163 E X -0.3352
164 V X 1.4198
165 V X 1.2702
166 Q X -0.4199
167 S X -0.4911
168 P X -0.7603
169 H X -0.6509
170 S X -0.4576
171 P X 0.0000
172 N X -0.0360
173 L X 1.1633
174 Y X 0.0000
175 Q X 0.0000
176 S X 0.0000
177 P X 0.0000
178 H X -0.7703
179 S X -0.6174
180 P X -0.4742
181 N X -0.6339
182 L X 0.8931
183 Y X 0.0000
184 F X 2.2888
185 V X 1.4347
186 L X 0.0000
187 L X 0.0000
188 V X 0.0000
189 P X 0.0000
190 K X -1.6137
191 V X 0.0000
192 V X 0.0000
193 V X -0.3950
194 E X -1.6563
195 Y X -0.6424
196 H X -1.3772
197 Q X -2.2678
198 L X 0.0000
199 D X -3.1398
200 K X -1.7178
201 V X 0.3261
202 V X 0.7950
203 K X -0.7268
204 E X -0.4284
205 S X -0.1243
206 L X 0.4495
207 E X -0.2979
208 V X 0.0000
209 E X -1.7202
210 A X -1.7459
211 T X -1.2376
212 D X -1.8179
213 S X -0.5396
214 F X 0.1476
215 D X -1.8412
216 P X -1.6588
217 T X -1.8073
218 K X -2.4096
219 R X -1.6410
220 L X 0.3347
221 Q X -0.5734
222 K X -1.4576
223 D X -2.1865
224 S X -1.9621
225 P X -1.0819
226 M X -0.5929
227 K X -1.5471
228 D X 0.0000
229 S X -1.3637
230 T X -1.4256
231 R X -2.4158
232 E X -2.3442
233 S X -1.7207
234 Q X -2.2275
235 E X -2.0015
236 K X -1.2833
237 L X -0.0310
238 S X 0.0000
239 L X 0.5411
240 A X -0.3945
241 D X 0.0000
242 G X -0.8388
243 G X -0.8294
244 S X -0.3755
245 M X 0.6426
246 S X -0.0280
247 S X -0.5118
248 G X -0.7038
249 G X -0.7715
250 A X -0.5365
251 T X -0.6900
252 S X -0.8866
253 T X -1.0026
254 R X -2.3812
255 K X -1.5084
256 A X -0.1124
257 L X 1.2648
258 K X 0.1025
259 I X 0.9649
260 E X -0.2648
261 V X 0.4886
262 E X -0.9372
263 K X -2.1359
264 Q X -1.8954
265 S X -1.5151
266 G X -1.2425
267 S X -1.0636
268 S X -1.1539
269 D X -1.7254
270 S X -1.0493
271 L X -0.3822
272 L X -0.0058
273 K X -0.3464
274 N X -0.7657
275 D X 0.0000
276 F X 0.3275
277 A X 0.2239
278 K X 0.0000
279 K X -1.6676
280 P X -1.0498
281 L X 0.0467
282 E X -0.9859
283 H X -2.2111
284 K X -2.7771
285 E X -3.5209
286 N X -2.8081
287 S X -1.6580
288 G X -1.2533
289 T X -1.1496
290 E X -1.7763
291 V X 0.6428
292 K X 0.1558
293 L X 1.0901
294 A X 0.0000
295 A X -0.2884
296 S X -0.4836
297 G X -0.5966
298 E X -0.3078
299 F X 0.5566
300 T X -0.4475
301 K X -1.2897
302 A X -0.3241
303 W X -0.0994
304 K X -1.0693
305 P X -0.7753
306 L X -0.4545
307 L X -1.1623
308 K X -1.9753
309 T X -1.9411
310 D X -3.2716
311 E X -3.5452
312 I X 0.0000
313 E X -3.5317
314 K X -4.1250
315 N X -3.8612
316 R X -3.4397
317 G X -2.8047
318 M X 0.0000
319 G X -1.3994
320 A X -0.6420
321 T X -0.9198
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.9546 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A3D Score
model_8 -0.9546 View CSV PDB
model_4 -1.0377 View CSV PDB
model_9 -1.0393 View CSV PDB
model_6 -1.0603 View CSV PDB
model_7 -1.0842 View CSV PDB
model_5 -1.0861 View CSV PDB
model_3 -1.0986 View CSV PDB
model_1 -1.1187 View CSV PDB
model_10 -1.1265 View CSV PDB
model_0 -1.1314 View CSV PDB
model_2 -1.1537 View CSV PDB
model_11 -1.1749 View CSV PDB
input -1.2148 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018