Project name: FG5 RFRW4

Status: done

Started: 2021-10-15 04:57:54
Settings
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCKSSQSLLNSRDGKNYLAWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQQYWYWMYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHRFRWWWWPVTKSFNRGECEVQLVESGGGLVQPGGSLRLSCAASGFTFSDFSMSWVRQAPGKGLEWVSYISRTSHTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGWYWMDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
input PDB
Selected Chain(s) A
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 A 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                                                (00:04:07)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:19:51)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:19:53)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:19:56)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:19:59)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:20:02)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:20:05)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:20:08)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:20:11)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:20:14)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:20:17)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:20:20)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:20:23)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:20:25)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:20:29)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:20:30)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:20:30)
[INFO]       Main:     Simulation completed successfully.                                          (01:20:33)
Show buried residues

Minimal score value
-3.7511
Maximal score value
2.6536
Average score
-0.4081
Total score value
-182.0222

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 D A -1.6918
2 I A 0.0000
3 Q A -1.9340
4 M A -1.3549
5 T A -1.0057
6 Q A -0.8934
7 S A -0.5617
8 P A -0.3881
9 S A -0.4541
10 S A -0.5322
11 L A -0.6390
12 S A -1.0759
13 A A 0.0000
14 S A -0.8969
15 V A -0.2825
16 G A -0.7967
17 D A -1.5342
18 R A -2.1083
19 V A 0.0000
20 T A -0.4914
21 I A 0.0000
22 T A -0.9256
23 C A 0.0000
24 K A -2.4805
25 S A 0.0000
26 S A -1.5283
27 Q A -1.5314
28 S A -0.4795
29 L A 0.0000
30 L A 0.8807
31 N A -0.4983
32 S A -1.7714
33 R A -3.0384
34 D A -3.1974
35 G A -2.2112
36 K A -1.7966
37 N A 0.0000
38 Y A 0.6453
39 L A 0.0000
40 A A 0.0000
41 W A 0.0000
42 Y A 0.0000
43 Q A 0.0000
44 Q A 0.0000
45 K A 0.0000
46 P A -0.6413
47 G A -0.5341
48 K A 0.0000
49 A A 0.0000
50 P A 0.0000
51 K A 0.1883
52 L A 0.2632
53 L A 0.0000
54 I A 0.0000
55 Y A -0.0041
56 D A -0.4889
57 A A -0.6206
58 S A -0.5334
59 N A -1.1112
60 L A -0.1597
61 E A -1.4235
62 T A -0.7257
63 G A -0.4417
64 V A 0.1308
65 P A 0.0000
66 S A -0.5299
67 R A 0.0000
68 F A 0.0000
69 S A -0.7248
70 G A -0.6856
71 S A -0.8838
72 G A -1.2716
73 S A -1.1712
74 G A -1.1363
75 T A -1.5614
76 D A -2.5729
77 F A 0.0000
78 T A -0.8777
79 F A 0.0000
80 T A -0.4581
81 I A 0.0000
82 S A -0.8530
83 S A -0.5691
84 L A -0.2300
85 Q A 0.0000
86 P A -0.2038
87 E A -0.1810
88 D A 0.0000
89 I A 0.0000
90 A A 0.0000
91 T A 0.0000
92 Y A 0.0000
93 F A 0.0000
94 C A 0.0000
95 Q A 0.0000
96 Q A 0.0000
97 Y A 1.4197
98 W A 2.1818
99 Y A 2.6536
100 W A 1.9896
101 M A 1.2976
102 Y A 0.6362
103 T A -0.2729
104 F A 0.0000
105 G A 0.0000
106 G A -0.7626
107 G A -0.7373
108 T A 0.0000
109 K A -0.9052
110 V A 0.0000
111 E A -1.2076
112 I A 0.0000
113 K A -1.5656
114 R A -1.4191
115 T A -0.7861
116 V A -0.0447
117 A A 0.2666
118 A A 0.3882
119 P A 0.1420
120 S A 0.0000
121 V A 0.1596
122 F A 0.0000
123 I A 0.0000
124 F A 0.0000
125 P A 0.0000
126 P A 0.0000
127 S A 0.0000
128 D A -1.9332
129 E A -1.9461
130 Q A 0.0000
131 L A -1.8924
132 K A -2.4057
133 S A -1.4941
134 G A -1.3859
135 T A -0.9116
136 A A 0.0000
137 S A -0.2093
138 V A 0.0000
139 V A 0.0000
140 C A 0.0000
141 L A 0.0000
142 L A 0.0000
143 N A 0.0000
144 N A 0.0818
145 F A 0.0000
146 Y A -0.3185
147 P A -0.9077
148 R A 0.0000
149 E A -2.2540
150 A A -1.4150
151 K A -2.3420
152 V A 0.0000
153 Q A -0.9034
154 W A 0.0000
155 K A -0.7082
156 V A 0.0000
157 D A -1.9042
158 N A -1.5449
159 A A -0.4862
160 L A 0.5416
161 Q A -0.1542
162 S A -0.6816
163 G A -1.1152
164 N A -1.0496
165 S A -1.0332
166 Q A -0.7736
167 E A -1.0792
168 S A 0.0000
169 V A 1.4216
170 T A 0.3478
171 E A -0.4436
172 Q A 0.0000
173 D A 0.0000
174 S A -0.3298
175 K A 0.0000
176 D A 0.0000
177 S A -0.7458
178 T A 0.0000
179 Y A 0.5824
180 S A 0.0000
181 L A 0.0000
182 S A 0.0000
183 S A 0.0000
184 T A -0.5220
185 L A 0.0000
186 T A -0.6141
187 L A -0.9986
188 S A -1.3423
189 K A -2.8977
190 A A -2.6065
191 D A -3.1918
192 Y A 0.0000
193 E A -3.6460
194 K A -3.7511
195 H A -3.2023
196 K A -3.2873
197 V A -1.4078
198 Y A 0.0000
199 A A -0.7001
200 C A 0.0000
201 E A -0.4182
202 V A 0.0000
203 T A -0.5212
204 H A 0.0000
205 R A -0.9313
206 F A -0.1699
207 R A -1.1481
208 W A 0.9984
209 W A 1.8729
210 W A 1.9123
211 W A 1.6473
212 P A 0.6171
213 V A 0.8537
214 T A 0.0084
215 K A -0.2715
216 S A -0.5472
217 F A 0.0000
218 N A -1.5734
219 R A -1.8047
220 G A 0.0000
221 E A 0.0000
222 C A 0.0000
423 E A 0.0000
424 V A 0.0000
425 Q A 0.0000
426 L A 0.0000
427 V A 0.0000
428 E A 0.0000
429 S A 0.0000
430 G A 0.0000
431 G A 0.0000
432 G A 0.0000
433 L A 0.4509
434 V A 0.0000
435 Q A -1.2613
436 P A -1.1555
437 G A -1.3334
438 G A -1.0662
439 S A -1.0534
440 L A -1.0829
441 R A -1.9395
442 L A 0.0000
443 S A -0.6280
444 C A 0.0000
445 A A 0.0000
446 A A 0.0000
447 S A 0.3873
448 G A 0.6447
449 F A 0.8767
450 T A -0.3130
451 F A -1.1741
452 S A -1.3212
453 D A -1.5581
454 F A 0.0000
455 S A -0.5320
456 M A 0.0000
457 S A 0.0000
458 W A 0.0000
459 V A 0.0000
460 R A 0.0000
461 Q A 0.0000
462 A A -0.9527
463 P A -0.7435
464 G A -0.7754
465 K A -1.3389
466 G A -1.0588
467 L A 0.0000
468 E A -0.7432
469 W A 0.0000
470 V A 0.0000
471 S A 0.0000
472 Y A 0.7568
473 I A 0.0000
474 S A -0.6738
475 R A -2.0849
476 T A -1.1911
477 S A -0.8720
478 H A -1.0077
479 T A -0.2142
480 T A 0.4759
481 Y A 1.7773
482 Y A 1.4806
483 A A 0.8841
484 D A 0.3379
485 S A 0.4574
486 V A 1.0426
487 K A -0.5931
488 G A -0.5391
489 R A 0.0000
490 F A 0.0000
491 T A 0.1298
492 I A 0.0000
493 S A -0.4714
494 R A -1.3754
495 D A -1.9034
496 N A -2.6363
497 S A -1.9367
498 K A -2.7185
499 N A -1.7426
500 T A -1.1518
501 L A 0.0000
502 Y A -0.3487
503 L A 0.0000
504 Q A -1.1348
505 M A 0.0000
506 N A -1.2347
507 S A -1.2978
508 L A 0.0000
509 R A -2.1493
510 A A -1.7044
511 E A -2.1171
512 D A -1.9820
513 T A -0.9383
514 A A 0.0000
515 V A 0.0000
516 Y A 0.0000
517 Y A 0.0000
518 C A 0.0000
519 A A 0.0000
520 R A 0.1972
521 G A 0.0000
522 W A 1.0480
523 Y A 1.6595
524 W A 0.0000
525 M A 0.0000
526 D A 0.0000
527 L A 0.4402
528 W A 0.0000
529 G A 0.0000
530 Q A 0.0000
531 G A 0.0000
532 T A 0.0000
533 L A -0.0468
534 V A 0.0000
535 T A -0.0427
536 V A 0.4164
537 S A 0.3195
538 S A -0.0521
539 A A 0.1724
540 S A -0.4739
541 T A -0.9696
542 K A -2.1622
543 G A -1.2730
544 P A -0.8165
545 S A -0.4748
546 V A -0.4572
547 F A 0.0000
548 P A 0.0000
549 L A 0.0000
550 A A 0.0000
551 P A 0.0000
552 S A -0.3617
553 S A -0.4717
554 K A -1.0688
555 S A -0.5966
556 T A -0.4502
557 S A -0.5300
558 G A -0.8121
559 G A -0.8429
560 T A 0.0000
561 A A 0.0000
562 A A 0.0000
563 L A 0.0000
564 G A 0.0000
565 C A 0.0000
566 L A 0.0000
567 V A 0.0000
568 K A -0.2278
569 D A -0.5594
570 Y A 0.0000
571 F A -0.1851
572 P A 0.0000
573 E A 0.0000
574 P A 0.1155
575 V A 0.0000
576 T A 0.0000
577 V A 0.0000
578 S A 0.0000
579 W A 0.0000
580 N A 0.1503
581 S A 0.0000
582 G A 0.0000
583 A A 0.0000
584 L A 0.5678
585 T A 0.0000
586 S A 0.0000
587 G A 0.0000
588 V A 0.0000
589 H A 0.0000
590 T A 0.0000
591 F A 0.0000
592 P A 0.4768
593 A A 0.8514
594 V A 1.1296
595 L A 1.4877
596 Q A 0.2592
597 S A 0.0439
598 S A -0.1137
599 G A 0.0256
600 L A 0.8649
601 Y A 0.0000
602 S A 0.2242
603 L A 0.0000
604 S A 0.0000
605 S A 0.0000
606 V A 0.0000
607 V A 0.0000
608 T A 0.0000
609 V A 0.1291
610 P A -0.2557
611 S A -0.5438
612 S A -0.3598
613 S A -0.2207
614 L A -0.1015
615 G A -0.4181
616 T A -0.5459
617 Q A -0.5375
618 T A -0.4521
619 Y A -0.1523
620 I A -0.5249
621 C A 0.0000
622 N A 0.0000
623 V A 0.0000
624 N A 0.0000
625 H A 0.0000
626 K A 0.0000
627 P A -1.1926
628 S A -1.3303
629 N A -1.9245
630 T A -1.7616
631 K A -1.8150
632 V A -1.3645
633 D A -2.2493
634 K A 0.0000
635 K A -1.9477
636 V A 0.0000
637 E A 0.0000
638 P A 0.0000
639 K A 0.0000
640 S A -0.4229
641 C A -0.3347
642 D A -1.4887
643 K A -2.0712
644 T A -1.7761
645 H A -1.8407
646 T A -1.4446
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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, -0.4081 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 -0.4081 View CSV PDB
model_6 -0.444 View CSV PDB
model_4 -0.4587 View CSV PDB
model_2 -0.4587 View CSV PDB
model_10 -0.4624 View CSV PDB
model_7 -0.4707 View CSV PDB
model_9 -0.4772 View CSV PDB
model_1 -0.494 View CSV PDB
model_0 -0.4968 View CSV PDB
model_5 -0.5123 View CSV PDB
model_3 -0.5567 View CSV PDB
model_11 -0.5808 View CSV PDB
input -0.7326 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018