Project name: modeller

Status: done

Started: 2020-11-19 09:27:30
Settings
Chain sequence(s) X: LVPRGSASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGNNISFDSTSQGEKPSYVVEFTNSTNIGIKWTMVKKYQLDVPNVSSDMNQVLKNLILEQPLTKYTLNSSLAKEKGKTQREVHLGSGQANQWTSQRNQHDLNNNPSPNASTGFKLTTGNAYRKLSESWPIYEPIDGTKQGKGKDSSGWSSTEENEAKNDAPSVSGGGSSSGTFNKYLNTKQALESIGILFDDQTPRNVITQLYYASTSKLAVTNNHIVVMGNSFLPSMWYWVVERSAQENASNKPTWFANTNLDWGEDKQKQFVENQLGYKETTSTNSHNFHSKSFTQPAYLISGIDSVNDQIIFSGFKAGSVGYDSSSSSSSSSSSSTKDQALAWSTTTSLDSKTGYKDLVTNDTGLNGPINGSFSIQDTFSFVVPYSGNHTNNGTTGPIKTAYPVKKDQKSTVKINSLINATPLNSYGDEGIGVFDALGLNYNFKSNQERLPSRTDQIFVYGIVSPNELRSAKSSADSTGSDTKVNWSNTQSRYLPVPYNYSEGIIDADGFKRPENRGASVTTFSG
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]                                                (00:01:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:01:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with X chain(s) selected             (00:01:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:01:03)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:03)
[INFO]       CABS:     Running CABS flex simulation                                                (00:12:24)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (02:10:48)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (02:10:54)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (02:10:59)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (02:11:04)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (02:11:09)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (02:11:14)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (02:11:20)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (02:11:25)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (02:11:30)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (02:11:35)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (02:11:40)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (02:11:46)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (02:11:51)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (02:11:56)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (02:11:57)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (02:11:57)
[INFO]       Main:     Simulation completed successfully.                                          (02:12:02)
Show buried residues

Minimal score value
-3.8411
Maximal score value
2.4192
Average score
-0.5677
Total score value
-353.1269

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
14 L X 1.7948
15 V X 0.8709
16 P X 0.1880
17 R X -0.9540
18 G X 0.0000
19 S X -0.8622
20 A X 0.0000
21 S X -0.6971
22 M X -0.0353
23 S X -0.7529
24 D X -1.4920
25 S X -1.3867
26 E X -1.8504
27 V X -0.2642
28 N X -1.3022
29 Q X -1.8688
30 E X -1.6381
31 A X -0.7699
32 K X -0.1119
33 P X 0.6623
34 E X 0.7999
35 V X 2.3034
36 K X 0.0000
37 P X 0.5096
38 E X -0.2383
39 V X 0.3098
40 K X -1.1313
41 P X -1.1750
42 E X -1.8630
43 T X -1.8790
44 H X -2.0695
45 I X 0.0000
46 N X -1.5581
47 L X 0.0000
48 K X -0.7994
49 V X 0.0000
50 S X 0.0000
51 D X -1.3807
52 G X -1.3085
53 S X -1.1333
54 S X 0.0000
55 E X -2.3966
56 I X 0.0000
57 F X -0.4808
58 F X -0.8236
59 K X -2.0266
60 I X -1.7676
61 K X -2.5114
62 K X -1.9115
63 T X 0.0000
64 T X -0.8005
65 P X -0.3633
66 L X 0.0000
67 R X 0.0000
68 R X -0.5531
69 L X 0.0000
70 M X 0.0000
71 E X 0.0000
72 A X 0.0000
73 F X 0.0000
74 A X 0.0000
75 K X 0.0000
76 R X 0.0000
77 Q X 0.0000
78 G X 0.0000
79 K X 0.0000
80 E X 0.0000
81 M X 0.0000
82 D X 0.0000
83 S X 0.0000
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 0.0000
90 G X 0.0000
91 I X 0.0000
92 R X -0.2857
93 I X 0.0000
94 Q X 0.0000
95 A X 0.0000
96 D X 0.0000
97 Q X 0.0000
98 T X -0.4918
99 P X 0.0000
100 E X -1.4870
101 D X -0.8067
102 L X 0.0000
103 D X -0.8078
104 M X 0.0000
105 E X 0.0000
106 D X -1.4590
107 N X -1.2499
108 D X 0.0000
109 I X 0.0000
110 I X 0.0000
111 E X 0.0000
112 A X 0.0000
113 H X -0.9450
114 R X -1.6222
115 E X -1.6412
116 Q X -1.6755
117 I X -0.8052
118 G X -1.0429
119 G X -1.3782
120 N X -1.5177
121 N X -1.2403
122 I X 0.0000
123 S X -0.2162
124 F X 0.2840
125 D X -0.4272
126 S X -0.4894
127 T X -0.6621
128 S X -0.6808
129 Q X -0.9023
130 G X 0.0000
131 E X -0.3915
132 K X 0.0000
133 P X 0.0000
134 S X 0.0000
135 Y X 0.0000
136 V X 0.0000
137 V X -0.6386
138 E X -0.3980
139 F X 0.5487
140 T X -0.2124
141 N X -1.2956
142 S X -0.7156
143 T X -0.5660
144 N X -0.3041
145 I X 1.7817
146 G X 1.0908
147 I X 2.4192
148 K X 0.9007
149 W X 0.6594
150 T X 0.7021
151 M X 1.2024
152 V X 0.1208
153 K X -1.5251
154 K X -1.6768
155 Y X 0.0000
156 Q X 0.0000
157 L X 0.0000
158 D X 0.0000
159 V X 0.0000
160 P X 0.0000
161 N X 0.0000
162 V X 0.0000
163 S X 0.0000
164 S X -1.4154
165 D X -1.9025
166 M X 0.0000
167 N X 0.0000
168 Q X -1.1730
169 V X 0.0000
170 L X 0.0000
171 K X -1.2045
172 N X -0.8074
173 L X 0.0000
174 I X 0.0000
175 L X 0.0000
176 E X 0.0000
177 Q X 0.0000
178 P X 0.0000
179 L X 0.0000
180 T X 0.0000
181 K X -0.9772
182 Y X 0.0000
183 T X 0.0000
184 L X 0.0000
185 N X 0.0000
186 S X -0.0809
187 S X 0.0000
188 L X 0.0000
189 A X 0.0000
190 K X 0.0000
191 E X -0.9760
192 K X -0.8242
193 G X 0.0000
194 K X 0.0000
195 T X 0.0000
196 Q X 0.0000
197 R X -0.6586
198 E X -0.4858
199 V X 0.0000
200 H X 0.0000
201 L X 0.1794
202 G X -0.7162
203 S X -0.9707
204 G X -1.3640
205 Q X -1.6880
206 A X -1.2483
207 N X -1.6690
208 Q X 0.0000
209 W X 0.0000
210 T X -0.9985
211 S X -1.1835
212 Q X -1.8982
213 R X -2.0486
214 N X -2.6882
215 Q X -2.6648
216 H X -2.5716
217 D X -2.9031
218 L X -2.3878
219 N X -2.3562
220 N X -1.6173
221 N X -1.0494
222 P X -0.5742
223 S X -0.3481
224 P X -0.5456
225 N X 0.0000
226 A X 0.0000
227 S X 0.0000
228 T X 0.0000
229 G X 0.0000
230 F X 0.0000
231 K X -1.2819
232 L X 0.0000
233 T X 0.0000
234 T X 0.0000
235 G X 0.0000
236 N X 0.0000
237 A X 0.0000
238 Y X 0.0000
239 R X 0.0000
240 K X -0.9391
241 L X 0.0000
242 S X -1.0689
243 E X -1.2185
244 S X 0.0000
245 W X 0.0000
246 P X 0.0000
247 I X 0.0000
248 Y X 0.0000
249 E X 0.0000
250 P X 0.0000
251 I X 0.0000
252 D X -1.5909
253 G X -1.4124
254 T X -1.2884
255 K X -2.6078
256 Q X -2.5285
257 G X -2.2205
258 K X -2.4640
259 G X -1.4657
260 K X 0.0000
261 D X -1.6351
262 S X -0.8951
263 S X -0.6892
264 G X 0.0000
265 W X 0.0000
266 S X -0.6774
267 S X -0.6272
268 T X -0.5605
269 E X 0.0000
270 E X 0.0000
271 N X -1.5736
272 E X -2.1152
273 A X 0.0000
274 K X -2.1018
275 N X -2.6813
276 D X -2.7294
277 A X -1.4392
278 P X -0.7237
279 S X 0.0104
280 V X 0.9636
281 S X 0.1271
282 G X -0.5961
283 G X -0.8371
284 G X -0.8726
285 S X -0.6521
286 S X -0.7096
287 S X 0.0000
288 G X -0.4296
289 T X -0.0041
290 F X 0.7327
291 N X -1.4161
292 K X -1.8436
293 Y X -0.9753
294 L X 0.0000
295 N X -0.8241
296 T X 0.0000
297 K X -1.0853
298 Q X -1.3940
299 A X -0.9588
300 L X 0.0000
301 E X -1.1201
302 S X -0.9624
303 I X 0.0000
304 G X 0.0000
305 I X 0.0000
306 L X 0.0000
307 F X 0.0000
308 D X -1.9018
309 D X -2.3047
310 Q X -2.1010
311 T X 0.0000
312 P X 0.0000
313 R X 0.0000
314 N X 0.0000
315 V X 0.0000
316 I X 0.0000
317 T X 0.0000
318 Q X 0.0000
319 L X 0.0000
320 Y X 0.0000
321 Y X 0.0000
322 A X 0.0000
323 S X 0.0000
324 T X 0.0000
325 S X 0.0000
326 K X -0.4566
327 L X 0.7654
328 A X 0.0000
329 V X 1.2106
330 T X 0.0000
331 N X -1.6803
332 N X -1.4653
333 H X -1.1288
334 I X 0.0000
335 V X 0.0000
336 V X 0.0000
337 M X 0.0000
338 G X 0.0000
339 N X -0.3553
340 S X -0.3787
341 F X 0.0000
342 L X 0.0000
343 P X 0.0000
344 S X 0.0000
345 M X 0.0000
346 W X 0.0000
347 Y X 0.0000
348 W X 0.0000
349 V X 0.0000
350 V X 0.0000
351 E X -1.6051
352 R X -1.7388
353 S X -1.1403
354 A X -1.0040
355 Q X -2.0103
356 E X -2.8561
357 N X -2.2262
358 A X -1.6080
359 S X -1.2747
360 N X 0.0000
361 K X -1.1970
362 P X 0.0000
363 T X 0.0000
364 W X 0.0000
365 F X 0.0000
366 A X 0.0000
367 N X 0.0000
368 T X 0.0000
369 N X -1.4907
370 L X 0.0000
371 D X -2.4057
372 W X -1.8114
373 G X -2.2574
374 E X -3.2493
375 D X -3.4831
376 K X -2.6556
377 Q X -2.0908
378 K X -2.2786
379 Q X -2.4097
380 F X 0.0000
381 V X 0.0000
382 E X -1.4054
383 N X -1.4697
384 Q X 0.0000
385 L X 0.0000
386 G X 0.0000
387 Y X -0.5844
388 K X -0.6411
389 E X -0.9097
390 T X -0.6780
391 T X -0.6862
392 S X -0.5863
393 T X -0.5438
394 N X -0.9575
395 S X -1.0206
396 H X 0.0000
397 N X 0.0000
398 F X 0.0000
399 H X -1.4677
400 S X -1.2246
401 K X -1.3356
402 S X -0.9652
403 F X 0.0000
404 T X 0.0000
405 Q X 0.0000
406 P X 0.0000
407 A X 0.0000
408 Y X 0.0000
409 L X 0.0763
410 I X 0.0000
411 S X -0.3796
412 G X -0.3334
413 I X 0.0000
414 D X -0.2952
415 S X 0.3216
416 V X 0.6988
417 N X -0.9706
418 D X -1.4379
419 Q X -0.7165
420 I X 0.0000
421 I X 0.7344
422 F X 0.0000
423 S X 0.0874
424 G X 0.0000
425 F X 0.0000
426 K X 0.0000
427 A X 0.0000
428 G X 0.0000
429 S X 0.0000
430 V X 0.0000
431 G X 0.0000
432 Y X 0.0000
433 D X 0.0000
434 S X -0.6352
435 S X -0.4931
436 S X -0.4166
437 S X -0.8291
438 S X 0.0000
439 S X 0.0000
440 S X -0.9180
441 S X -0.9871
442 S X -0.6732
443 S X -0.2671
444 S X -0.2901
445 S X 0.0000
446 T X -1.2647
447 K X -2.2589
448 D X -2.5418
449 Q X 0.0000
450 A X 0.0000
451 L X 0.0000
452 A X 0.0000
453 W X 0.1249
454 S X -0.0178
455 T X 0.0000
456 T X 0.0000
457 T X 0.0000
458 S X 0.0000
459 L X 0.0000
460 D X -1.2177
461 S X 0.0000
462 K X 0.0000
463 T X 0.0000
464 G X -1.2696
465 Y X -1.0735
466 K X -1.8259
467 D X -1.8354
468 L X 0.0000
469 V X -0.5829
470 T X -1.2869
471 N X 0.0000
472 D X 0.0000
473 T X 0.0000
474 G X 0.0000
475 L X -0.0007
476 N X 0.0000
477 G X 0.0000
478 P X -0.3289
479 I X 0.0000
480 N X 0.0000
481 G X 0.0000
482 S X 0.0000
483 F X -0.1748
484 S X -0.3738
485 I X 0.4226
486 Q X -1.6299
487 D X -2.7675
488 T X -1.9784
489 F X 0.0000
490 S X 0.0000
491 F X 0.0000
492 V X 0.0000
493 V X 0.0000
494 P X 0.0000
495 Y X 0.0000
496 S X 0.0000
497 G X -0.9145
498 N X -1.7191
499 H X -1.7665
500 T X -1.5763
501 N X -2.5392
502 N X -2.3273
503 G X -1.3945
504 T X -1.1495
505 T X -0.8274
506 G X 0.0000
507 P X -0.8120
508 I X -1.3271
509 K X -2.1083
510 T X -1.7385
511 A X 0.0000
512 Y X 0.0000
513 P X 0.0000
514 V X 0.0000
515 K X 0.0000
516 K X -2.5727
517 D X -2.9872
518 Q X -2.2140
519 K X -2.3187
520 S X 0.0000
521 T X 0.0000
522 V X 0.0000
523 K X -0.7400
524 I X 0.0000
525 N X 0.0000
526 S X 0.0000
527 L X 0.0000
528 I X 0.0000
529 N X 0.0000
530 A X 0.0000
531 T X 0.0000
532 P X 0.0939
533 L X 0.0000
534 N X 0.0000
535 S X 0.0000
536 Y X 0.0000
537 G X 0.0000
538 D X 0.0000
539 E X 0.0000
540 G X 0.0000
541 I X 0.0000
542 G X 0.0000
543 V X 0.0000
544 F X 0.0000
545 D X 0.0000
546 A X 0.0000
547 L X 0.3182
548 G X 0.0000
549 L X -0.2114
550 N X 0.0000
551 Y X -0.7629
552 N X 0.0000
553 F X -1.1186
554 K X -2.2833
555 S X -1.9083
556 N X -1.6998
557 Q X -1.9177
558 E X 0.0000
559 R X -1.7460
560 L X -0.3667
561 P X 0.0000
562 S X 0.0000
563 R X 0.0000
564 T X 0.0000
565 D X 0.0000
566 Q X 0.0000
567 I X 0.0000
568 F X 0.0000
569 V X 0.0000
570 Y X 0.2702
571 G X 0.0000
572 I X 0.5750
573 V X 0.0000
574 S X -0.9049
575 P X -1.9067
576 N X -2.2321
577 E X 0.0000
578 L X 0.0000
579 R X -2.5375
580 S X -1.9298
581 A X 0.0000
582 K X -1.6642
583 S X -1.5966
584 S X 0.0000
585 A X 0.0000
586 D X -2.0925
587 S X -1.2630
588 T X -0.9966
589 G X -1.0197
590 S X -1.0038
591 D X 0.0000
592 T X -1.2917
593 K X -2.1882
594 V X 0.0000
595 N X -2.2418
596 W X 0.0000
597 S X -1.1551
598 N X -1.0973
599 T X 0.0000
600 Q X -0.9383
601 S X -0.3076
602 R X -0.3117
603 Y X 0.5528
604 L X 1.4744
605 P X 0.8833
606 V X 0.4832
607 P X -0.1524
608 Y X 0.0000
609 N X -1.4374
610 Y X 0.0000
611 S X -1.3774
612 E X -2.4608
613 G X -1.7849
614 I X 0.0000
615 I X 0.0000
616 D X -2.6608
617 A X 0.0000
618 D X -2.7980
619 G X -2.2541
620 F X -1.9089
621 K X -3.7057
622 R X -3.6816
623 P X -2.9594
624 E X -3.8411
625 N X -3.4301
626 R X -3.6587
627 G X 0.0000
628 A X -1.2790
629 S X -0.3088
630 V X 0.4873
631 T X 0.0241
632 T X -0.2614
633 F X -0.4858
634 S X -0.7492
635 G X -0.9304
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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, -0.5677 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_3 -0.5677 View CSV PDB
model_8 -0.5809 View CSV PDB
model_1 -0.5866 View CSV PDB
model_2 -0.5874 View CSV PDB
model_7 -0.6003 View CSV PDB
model_0 -0.6214 View CSV PDB
model_5 -0.6339 View CSV PDB
model_6 -0.643 View CSV PDB
input -0.6631 View CSV PDB
model_9 -0.6761 View CSV PDB
model_10 -0.6961 View CSV PDB
model_4 -0.7017 View CSV PDB
model_11 -0.7056 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018