Project name: sFLT01

Status: done

Started: 2020-09-20 05:13:56
Settings
Chain sequence(s) A: RPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTGGGGGGGGGPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
B: RPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTGGGGGGGGGPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
input PDB
Selected Chain(s) A,B
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 all 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                                                (00:07:07)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:52:37)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:52:43)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:52:49)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:52:54)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:52:59)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:53:05)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:53:11)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:53:16)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:53:22)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:53:27)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:53:33)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:53:38)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:53:43)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:53:50)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:53:51)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:53:51)
[INFO]       Main:     Simulation completed successfully.                                          (01:53:57)
Show buried residues

Minimal score value
-4.0416
Maximal score value
2.5295
Average score
-0.6571
Total score value
-438.9371

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
1 R A -1.1249
2 P A 0.0920
3 F A 1.5750
4 V A 0.9928
5 E A -0.0543
6 M A 0.5896
7 Y A 0.7279
8 S A -0.4065
9 E A -1.6522
10 I A -0.4884
11 P A -0.2933
12 E A 0.1992
13 I A 1.7267
14 I A 0.0000
15 H A -1.8309
16 M A 0.0000
17 T A -3.4252
18 E A -3.7755
19 G A -2.5743
20 R A -3.4548
21 E A -2.3739
22 L A 0.0000
23 V A -0.1260
24 I A 0.0000
25 P A -0.7252
26 C A 0.0000
27 R A -0.4948
28 V A 0.7142
29 T A 0.0000
30 S A -0.2534
31 P A -0.7098
32 N A -0.9003
33 I A 1.1620
34 T A 0.7150
35 V A 0.9085
36 T A -0.0712
37 L A 0.0000
38 K A -0.1108
39 K A 0.0000
40 F A 1.3349
41 P A 0.7957
42 L A 0.8741
43 D A 0.3051
44 T A 0.3572
45 L A 0.0000
46 I A 1.6289
47 P A -0.1946
48 D A 0.0000
49 G A -1.7676
50 K A -2.2868
51 R A -1.8542
52 I A 0.7152
53 I A 0.9909
54 W A 0.4438
55 D A -2.2259
56 S A -2.1726
57 R A -3.1887
58 K A -2.8356
59 G A 0.0000
60 F A 0.2438
61 I A 0.0102
62 I A 0.0000
63 S A -1.1403
64 N A -1.7435
65 A A -0.9958
66 T A -0.7587
67 Y A -0.8351
68 K A -1.1175
69 E A 0.0000
70 I A 0.7295
71 G A 0.6572
72 L A 1.2706
73 L A 0.0000
74 T A -0.3516
75 C A 0.0000
76 E A -1.0399
77 A A 0.0000
78 T A 0.0480
79 V A 0.0000
80 N A -1.3455
81 G A -1.0370
82 H A 0.0324
83 L A 0.2586
84 Y A 0.0000
85 K A -1.5599
86 T A 0.0000
87 N A -0.6390
88 Y A 0.0000
89 L A 1.2907
90 T A 0.0368
91 H A -1.4009
92 R A -3.3804
93 Q A -3.4746
94 T A -2.3787
95 G A -1.5551
96 G A -1.1160
97 G A -1.1810
98 G A -1.2466
99 G A -1.2730
100 G A -1.1978
101 G A -1.2819
102 G A -1.4476
103 G A -1.6101
104 P A -1.6346
105 K A -2.2057
106 S A -1.4319
107 C A -1.1009
108 D A -2.5531
109 K A -2.4117
110 T A -1.2530
111 H A -0.8679
112 T A -0.6333
113 C A -0.2271
114 P A -0.4427
115 P A -0.3386
116 C A -0.1403
117 P A -0.3981
118 A A -0.2923
119 P A -0.4611
120 E A -0.2620
121 L A 1.3088
122 L A 1.3835
123 G A 0.2862
124 G A 0.0743
125 P A 0.1870
126 S A 0.3796
127 V A 1.1194
128 F A 2.2288
129 L A 0.0000
130 F A 1.7321
131 P A -0.0893
132 P A 0.0000
133 K A -2.1843
134 P A -1.7121
135 K A -1.6766
136 D A -1.3890
137 T A 0.0000
138 L A 0.0000
139 M A -0.0026
140 I A 1.0340
141 S A -0.2562
142 R A -1.5234
143 T A -0.7150
144 P A 0.0000
145 E A -0.7643
146 V A 0.0000
147 T A 0.7808
148 C A 0.0000
149 V A 1.2078
150 V A 0.0000
151 V A 0.0000
152 D A 0.0000
153 V A 0.7164
154 S A -0.3847
155 H A -1.2985
156 E A -2.4963
157 D A 0.0000
158 P A -1.9585
159 E A -2.1304
160 V A -1.0445
161 K A -0.7916
162 F A 0.0000
163 N A 0.0000
164 W A 0.0000
165 Y A -0.3921
166 V A -0.5585
167 D A -2.0520
168 G A -0.4578
169 V A 0.9308
170 E A -0.1752
171 V A 0.0426
172 H A -0.9430
173 N A -1.8125
174 A A -1.6233
175 K A -2.3644
176 T A -1.9739
177 K A -2.7637
178 P A -2.8463
179 R A -4.0416
180 E A -3.6154
181 E A -3.5028
182 Q A -2.4462
183 Y A -0.4698
184 N A -1.1693
185 S A -0.7456
186 T A -1.2129
187 Y A -2.0561
188 R A -2.5305
189 V A 0.0000
190 V A -0.7772
191 S A 0.0000
192 V A -0.4945
193 L A 0.0000
194 T A -0.6096
195 V A 0.0000
196 L A 0.1128
197 H A -0.4933
198 Q A -1.2666
199 D A -1.8040
200 W A 0.0000
201 L A -1.1668
202 N A -2.4366
203 G A -2.1955
204 K A -2.5809
205 E A -2.5112
206 Y A 0.0000
207 K A -1.7694
208 C A 0.0000
209 K A 0.0000
210 V A 0.0000
211 S A 0.0000
212 N A 0.0000
213 K A -1.0465
214 A A -0.5521
215 L A -0.0133
216 P A -0.3633
217 A A 0.0000
218 P A 0.0000
219 I A 0.3323
220 E A -0.2587
221 K A -0.2218
222 T A -0.5077
223 I A 0.0000
224 S A -1.6970
225 K A -2.3925
226 A A -1.8343
227 K A -1.5855
228 G A -1.3892
229 Q A -1.8921
230 P A -1.4713
231 R A -1.7736
232 E A -1.9003
233 P A -0.8764
234 Q A -0.8039
235 V A -0.4419
236 Y A 0.0000
237 T A 0.0000
238 L A 0.0000
239 P A 0.0000
240 P A 0.0000
241 S A 0.0000
242 R A -0.9948
243 D A -1.7171
244 E A 0.0000
245 L A -0.8174
246 T A -1.0185
247 K A -1.6166
248 N A -2.1326
249 Q A -1.6147
250 V A 0.0000
251 S A 0.0000
252 L A 0.0000
253 T A 0.0000
254 C A 0.0000
255 L A 0.0000
256 V A 0.0000
257 K A 0.0000
258 G A 0.0000
259 F A 0.0000
260 Y A -0.6698
261 P A -0.6380
262 S A 0.0000
263 D A -0.9298
264 I A -0.1024
265 A A -0.6580
266 V A 0.0000
267 E A -1.3347
268 W A 0.0000
269 E A -2.8565
270 S A 0.0000
271 N A -2.3611
272 G A -2.2066
273 Q A -2.8694
274 P A -2.5744
275 E A -2.6972
276 N A -2.0597
277 N A -1.0303
278 Y A 0.1799
279 K A 0.2884
280 T A 0.1262
281 T A 0.0000
282 P A -0.2133
283 P A 0.3328
284 V A 0.8700
285 L A 1.1754
286 D A -0.1658
287 S A -0.9329
288 D A -1.8678
289 G A -0.8465
290 S A 0.0000
291 F A 0.1130
292 F A 0.0000
293 L A 0.0000
294 Y A 0.0000
295 S A 0.0000
296 K A 0.0000
297 L A 0.0000
298 T A 0.0000
299 V A 0.0000
300 D A -2.2398
301 K A 0.0000
302 S A -2.3105
303 R A -3.0513
304 W A 0.0000
305 Q A -2.8019
306 Q A -2.5833
307 G A -2.0887
308 N A -1.8511
309 V A -0.2454
310 F A 0.0000
311 S A -1.0881
312 C A 0.0000
313 S A -1.1237
314 V A 0.0000
315 M A -0.3725
316 H A 0.0000
317 E A 0.0000
318 A A 0.3877
319 L A 1.3852
320 H A 0.0000
321 N A -0.7650
322 H A -1.0195
323 Y A -0.4588
324 T A -0.6241
325 Q A -1.3682
326 K A 0.0000
327 S A -0.4663
328 L A 0.0000
329 S A 0.0000
330 L A 0.0000
331 S A -0.5508
332 P A -0.9415
333 G A -1.1050
334 K A -1.5798
335 R B -1.7186
336 P B 0.0000
337 F B 0.4342
338 V B 0.4027
339 E B 0.4285
340 M B 1.5515
341 Y B 1.4202
342 S B 0.3353
343 E B -0.1301
344 I B 0.5915
345 P B 0.5336
346 E B 0.5692
347 I B 1.7199
348 I B 0.0000
349 H B -0.6796
350 M B -0.7715
351 T B 0.0000
352 E B -2.8862
353 G B -1.5649
354 R B -1.9047
355 E B -2.1028
356 L B 0.0000
357 V B 0.8372
358 I B 0.0000
359 P B -0.2835
360 C B 0.0000
361 R B -1.5655
362 V B -1.0249
363 T B -1.6062
364 S B -0.9534
365 P B -1.1353
366 N B -1.8798
367 I B -1.2113
368 T B -1.1605
369 V B 0.0000
370 T B -0.5004
371 L B 0.0000
372 K B -1.0471
373 K B 0.0000
374 F B 1.6842
375 P B 0.8713
376 L B 0.8161
377 D B -1.0169
378 T B -0.5860
379 L B -0.5403
380 I B 0.0000
381 P B 0.0000
382 D B -2.3358
383 G B -1.7001
384 K B -1.7458
385 R B -1.6242
386 I B 0.6670
387 I B 1.6704
388 W B 0.1980
389 D B -2.4134
390 S B 0.0000
391 R B -3.3537
392 K B -2.8357
393 G B -1.1747
394 F B 0.0000
395 I B 0.9981
396 I B 0.0000
397 S B -0.8600
398 N B 0.0000
399 A B -1.3370
400 T B -0.9725
401 Y B -0.8039
402 K B -2.3155
403 E B 0.0000
404 I B 0.0000
405 G B 0.5198
406 L B 1.3583
407 L B 0.0000
408 T B -0.4890
409 C B 0.0000
410 E B -0.7410
411 A B 0.0000
412 T B -0.2577
413 V B -0.6908
414 N B -1.5920
415 G B -0.9293
416 H B -0.7905
417 L B 0.7351
418 Y B 0.0000
419 K B -0.6343
420 T B 0.0000
421 N B 0.0000
422 Y B 0.0000
423 L B 0.5957
424 T B 0.0000
425 H B -1.4298
426 R B -2.6714
427 Q B -2.4990
428 T B -1.8156
429 G B -1.4756
430 G B -1.1203
431 G B -1.2134
432 G B -1.2088
433 G B -1.2081
434 G B -1.2000
435 G B -1.1546
436 G B -1.3921
437 G B -1.6724
438 P B -1.6032
439 K B -2.4150
440 S B -1.5643
441 C B -1.1332
442 D B -2.3957
443 K B -1.7179
444 T B 0.0000
445 H B 0.0000
446 T B -0.7716
447 C B -0.5109
448 P B -0.4140
449 P B -0.2965
450 C B -0.0858
451 P B -0.7306
452 A B -0.8573
453 P B -0.8462
454 E B -0.5586
455 L B 0.4957
456 L B 0.0360
457 G B -0.5902
458 G B -0.9011
459 P B -0.3557
460 S B 0.2974
461 V B 0.9621
462 F B 2.5295
463 L B 1.9405
464 F B 2.2011
465 P B 0.6707
466 P B -0.4177
467 K B -1.0283
468 P B -1.1222
469 K B -1.7909
470 D B -1.2841
471 T B 0.0000
472 L B 0.0000
473 M B -0.2029
474 I B 0.5658
475 S B -0.5835
476 R B -1.5506
477 T B -0.8430
478 P B 0.0000
479 E B -0.3947
480 V B 0.0000
481 T B 0.9145
482 C B 0.0000
483 V B 1.4617
484 V B 0.0000
485 V B 0.4029
486 D B -0.9091
487 V B 0.0000
488 S B -0.7392
489 H B -0.9617
490 E B -1.2269
491 D B -1.9093
492 P B 0.0000
493 E B -2.5418
494 V B -1.8985
495 K B -1.7746
496 F B 0.0000
497 N B -1.9420
498 W B 0.0000
499 Y B -0.4318
500 V B 0.0000
501 D B -1.4557
502 G B -0.5403
503 V B 0.4687
504 E B -1.2599
505 V B -0.8607
506 H B -2.0292
507 N B -2.1997
508 A B -1.8195
509 K B -2.1251
510 T B -1.5745
511 K B -1.7690
512 P B -1.9701
513 R B -2.9555
514 E B -2.5074
515 E B -2.5864
516 Q B -1.7916
517 Y B -0.4128
518 N B -1.1322
519 S B -0.9879
520 T B -0.9870
521 Y B 0.0000
522 R B -1.5340
523 V B 0.0000
524 V B -0.3476
525 S B 0.0000
526 V B 0.0362
527 L B 0.0000
528 T B -0.2982
529 V B 0.0000
530 L B 0.8421
531 H B 0.0000
532 Q B -1.2650
533 D B 0.0000
534 W B 0.0000
535 L B -0.7884
536 N B -1.7084
537 G B -1.7306
538 K B -1.4847
539 E B -1.6352
540 Y B 0.0000
541 K B -1.4421
542 C B 0.0000
543 K B -2.0236
544 V B 0.0000
545 S B -1.6841
546 N B 0.0000
547 K B -2.3879
548 A B -1.3932
549 L B 0.0000
550 P B -0.3751
551 A B 0.0000
552 P B -1.1594
553 I B -1.2579
554 E B -2.3433
555 K B 0.0000
556 T B -0.3845
557 I B -0.0657
558 S B -0.8929
559 K B -1.0022
560 A B -0.8741
561 K B -1.4135
562 G B -1.2524
563 Q B 0.0000
564 P B -1.5580
565 R B -2.8066
566 E B -2.9014
567 P B -1.7148
568 Q B -1.2332
569 V B 0.0000
570 Y B -0.5149
571 T B 0.0000
572 L B 0.0000
573 P B 0.0000
574 P B -0.6008
575 S B -0.7892
576 R B -0.9225
577 D B -1.2988
578 E B 0.0000
579 L B -0.2880
580 T B -0.6889
581 K B -1.4123
582 N B -2.1235
583 Q B -1.6363
584 V B -0.7469
585 S B 0.0000
586 L B 0.0000
587 T B 0.0000
588 C B 0.0000
589 L B 0.0000
590 V B 0.0000
591 K B 0.0000
592 G B 0.0000
593 F B 0.0000
594 Y B 0.0000
595 P B -0.5207
596 S B -0.9143
597 D B -0.8981
598 I B 0.0000
599 A B -0.5250
600 V B 0.0000
601 E B -1.0715
602 W B 0.0000
603 E B -2.6097
604 S B -1.9416
605 N B -1.8540
606 G B -1.8709
607 Q B -2.2417
608 P B -2.2677
609 E B -2.0868
610 N B -1.3196
611 N B -1.0210
612 Y B 0.0247
613 K B 0.0000
614 T B 0.2359
615 T B 0.0000
616 P B 0.0000
617 P B 0.1345
618 V B 0.0000
619 L B 1.5245
620 D B 0.4767
621 S B -0.2687
622 D B -1.0087
623 G B -0.9961
624 S B 0.0874
625 F B 0.4863
626 F B 0.0000
627 L B 0.2965
628 Y B 0.0000
629 S B 0.0000
630 K B 0.0000
631 L B 0.0000
632 T B -0.7953
633 V B -1.1844
634 D B -2.5169
635 K B -2.3257
636 S B -2.0709
637 R B -1.7157
638 W B -1.2713
639 Q B -2.0375
640 Q B -1.9985
641 G B -1.2661
642 N B -0.9091
643 V B 0.5063
644 F B 0.0000
645 S B -0.9205
646 C B 0.0000
647 S B 0.0000
648 V B 0.0000
649 M B -0.4241
650 H B 0.0000
651 E B -0.8701
652 A B -0.9871
653 L B -1.2903
654 H B -1.8642
655 N B -1.7355
656 H B -0.7947
657 Y B -0.4059
658 T B -0.7653
659 Q B -1.3024
660 K B 0.0000
661 S B -0.2776
662 L B 0.4907
663 S B 0.1445
664 L B -0.0370
665 S B 0.0000
666 P B -0.9865
667 G B -1.6382
668 K B -2.2786
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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, -0.6571 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 -0.6571 View CSV PDB
model_1 -0.6964 View CSV PDB
model_8 -0.7042 View CSV PDB
model_2 -0.7106 View CSV PDB
model_4 -0.747 View CSV PDB
model_7 -0.7586 View CSV PDB
model_9 -0.7604 View CSV PDB
model_5 -0.762 View CSV PDB
model_11 -0.784 View CSV PDB
model_0 -0.7863 View CSV PDB
model_6 -0.8034 View CSV PDB
model_10 -0.8078 View CSV PDB
input -0.9041 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018