Project name: FG5 RWRW4

Status: done

Started: 2021-10-15 06:19:36
Settings
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCKSSQSLLNSRDGKNYLAWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQQYWYWMYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHRWRWWWWPVTKSFNRGECEVQLVESGGGLVQPGGSLRLSCAASGFTFSDFSMSWVRQAPGKGLEWVSYISRTSHTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGWYWMDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:06)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:23:39)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:23:42)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:23:45)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:23:48)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:23:51)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:23:54)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:23:56)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:23:59)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:24:02)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:24:05)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:24:08)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:24:11)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:24:14)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:24:17)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:24:18)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:24:18)
[INFO]       Main:     Simulation completed successfully.                                          (01:24:21)
Show buried residues

Minimal score value
-3.339
Maximal score value
1.9451
Average score
-0.4883
Total score value
-217.772

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 -1.8481
2 I A -1.1767
3 Q A -1.7992
4 M A 0.0000
5 T A -1.1212
6 Q A -0.8198
7 S A -0.7179
8 P A -0.5304
9 S A -0.7303
10 S A -0.7526
11 L A -0.2215
12 S A -0.3808
13 A A 0.0000
14 S A -0.2757
15 V A 0.5077
16 G A -0.6513
17 D A -2.1511
18 R A -2.1234
19 V A 0.0000
20 T A -0.6752
21 I A 0.0000
22 T A -0.6622
23 C A 0.0000
24 K A -1.9928
25 S A -1.7217
26 S A -1.6210
27 Q A -1.5503
28 S A -0.8740
29 L A -1.0647
30 L A 0.0000
31 N A -2.7936
32 S A -2.6942
33 R A -3.3390
34 D A -3.2647
35 G A -2.6831
36 K A -2.3782
37 N A -1.6771
38 Y A 0.0275
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 -0.6764
47 G A -0.5553
48 K A -0.4032
49 A A 0.0000
50 P A -0.1444
51 K A 0.0000
52 L A 0.0000
53 L A 0.0000
54 I A 0.0000
55 Y A 0.5081
56 D A -0.2359
57 A A 0.0000
58 S A -0.4063
59 N A -0.1791
60 L A 0.4650
61 E A -0.0103
62 T A 0.2913
63 G A 0.2355
64 V A 0.9259
65 P A 0.0000
66 S A -0.2923
67 R A -1.4013
68 F A 0.0000
69 S A -0.5510
70 G A 0.0000
71 S A -0.5606
72 G A -1.1208
73 S A -1.1676
74 G A -1.3980
75 T A -1.2974
76 D A -1.5837
77 F A 0.0000
78 T A -0.5787
79 F A 0.0000
80 T A -0.7712
81 I A 0.0000
82 S A 0.0000
83 S A -0.6764
84 L A 0.6971
85 Q A 0.0000
86 P A 0.0000
87 E A 0.0000
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 0.7206
98 W A 1.5557
99 Y A 1.7211
100 W A 0.0000
101 M A 0.9879
102 Y A -0.1185
103 T A -0.7084
104 F A 0.0000
105 G A -0.7283
106 G A -1.0421
107 G A -1.1427
108 T A 0.0000
109 K A -1.4751
110 V A 0.0000
111 E A -1.0352
112 I A 0.0000
113 K A -1.3506
114 R A -1.2845
115 T A -0.3675
116 V A 0.6633
117 A A 0.2556
118 A A 0.0562
119 P A -0.3411
120 S A 0.0000
121 V A 0.0298
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 -2.5822
129 E A -2.1106
130 Q A 0.0000
131 L A 0.0000
132 K A -2.5600
133 S A -1.6126
134 G A -1.1992
135 T A -0.9034
136 A A 0.0000
137 S A 0.0000
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 0.0000
145 F A 0.0000
146 Y A 0.0000
147 P A -1.2988
148 R A -2.2030
149 E A -1.8811
150 A A -1.5927
151 K A -2.2616
152 V A -1.6104
153 Q A -1.5599
154 W A 0.0000
155 K A -1.4295
156 V A 0.0000
157 D A -2.7417
158 N A -2.0158
159 A A -0.8811
160 L A -0.2318
161 Q A -0.7542
162 S A -0.8433
163 G A -0.9390
164 N A -0.9368
165 S A -1.0952
166 Q A -0.8994
167 E A -1.2253
168 S A 0.0000
169 V A -0.1501
170 T A 0.0000
171 E A -1.2482
172 Q A 0.0000
173 D A 0.0000
174 S A 0.0000
175 K A -1.4869
176 D A -2.1405
177 S A 0.0000
178 T A 0.0000
179 Y A -0.8276
180 S A 0.0000
181 L A 0.0000
182 S A 0.0000
183 S A 0.0000
184 T A 0.0000
185 L A 0.0000
186 T A -0.4723
187 L A 0.0000
188 S A -0.9522
189 K A -1.7952
190 A A -1.8015
191 D A -2.1051
192 Y A 0.0000
193 E A -2.2563
194 K A -2.8862
195 H A -2.5903
196 K A -2.3470
197 V A -1.3929
198 Y A 0.0000
199 A A -1.0766
200 C A 0.0000
201 E A -1.4623
202 V A 0.0000
203 T A -0.9133
204 H A -0.2548
205 R A 0.0000
206 W A 0.2507
207 R A -0.6311
208 W A 1.0770
209 W A 1.9451
210 W A 1.7671
211 W A 1.0408
212 P A 0.0585
213 V A 0.1141
214 T A -0.5332
215 K A -0.7772
216 S A -1.0777
217 F A 0.0000
218 N A -1.4757
219 R A 0.0000
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 -0.5831
433 L A 0.0243
434 V A 0.0000
435 Q A -1.3459
436 P A -1.1422
437 G A -1.2458
438 G A 0.0000
439 S A -1.3321
440 L A 0.0000
441 R A -2.0257
442 L A 0.0000
443 S A 0.0000
444 C A 0.0000
445 A A 0.0000
446 A A 0.0000
447 S A -0.2780
448 G A 0.0000
449 F A 0.7056
450 T A -0.0498
451 F A 0.0000
452 S A -0.9258
453 D A -0.6371
454 F A 0.0000
455 S A 0.0000
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 -0.4406
463 P A -0.5297
464 G A -0.9276
465 K A 0.0000
466 G A -0.7710
467 L A -0.5232
468 E A -0.4117
469 W A 0.0000
470 V A 0.0000
471 S A 0.0000
472 Y A 0.0000
473 I A 0.0000
474 S A -0.4651
475 R A -1.4114
476 T A -0.7399
477 S A -0.7966
478 H A -1.0099
479 T A -0.1703
480 T A 0.5589
481 Y A 1.5030
482 Y A 1.2236
483 A A 0.0996
484 D A -1.0623
485 S A -0.2132
486 V A 0.7839
487 K A -0.5485
488 G A -1.1344
489 R A -1.9112
490 F A 0.0000
491 T A -0.6757
492 I A 0.0000
493 S A -0.5612
494 R A -1.3644
495 D A -2.0092
496 N A -2.5143
497 S A -1.9596
498 K A -2.8114
499 N A -2.3040
500 T A 0.0000
501 L A 0.0000
502 Y A -0.3488
503 L A 0.0000
504 Q A -1.8530
505 M A 0.0000
506 N A -1.6424
507 S A -0.9356
508 L A -0.4778
509 R A -0.5716
510 A A -1.0759
511 E A -1.9077
512 D A -2.3575
513 T A -1.2561
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 0.0000
521 G A 0.0000
522 W A 1.1653
523 Y A 1.2383
524 W A 1.3881
525 M A 0.0000
526 D A 0.0000
527 L A 0.0000
528 W A 0.0000
529 G A 0.0000
530 Q A -0.2951
531 G A 0.0000
532 T A 0.0000
533 L A 0.0000
534 V A 0.0000
535 T A 0.0000
536 V A -0.8096
537 S A -0.9861
538 S A -0.7204
539 A A -0.2262
540 S A -0.2030
541 T A -0.7904
542 K A -1.9395
543 G A -1.2245
544 P A -0.9603
545 S A -0.6249
546 V A 0.0000
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 0.0000
553 S A -1.1929
554 K A -1.5130
555 S A 0.0000
556 T A -0.6441
557 S A -0.7762
558 G A -0.8541
559 G A -0.9047
560 T A -0.4457
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 -0.7200
569 D A -1.4586
570 Y A 0.0000
571 F A -0.6915
572 P A 0.0000
573 E A 0.0000
574 P A -0.0178
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 -0.0951
581 S A 0.1839
582 G A 0.0000
583 A A 0.3614
584 L A 0.4699
585 T A 0.2460
586 S A 0.2591
587 G A 0.0717
588 V A 0.0000
589 H A 0.0000
590 T A -0.0823
591 F A 0.0000
592 P A 0.1012
593 A A 0.0786
594 V A 0.1964
595 L A 0.4288
596 Q A -0.7455
597 S A -0.2766
598 S A -0.4980
599 G A -0.4867
600 L A -0.3157
601 Y A 0.0000
602 S A 0.0000
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 0.1233
610 P A -0.3287
611 S A -0.3211
612 S A -0.3356
613 S A 0.0205
614 L A 0.1742
615 G A -0.5620
616 T A -0.8113
617 Q A -1.5940
618 T A -1.1005
619 Y A -0.5299
620 I A -0.9411
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 -1.0656
627 P A -0.9088
628 S A -1.1485
629 N A -1.3364
630 T A -1.3041
631 K A -1.4789
632 V A -1.4779
633 D A -2.2810
634 K A -1.8807
635 K A -2.0374
636 V A 0.0000
637 E A -1.4661
638 P A 0.0000
639 K A -2.0286
640 S A -1.3418
641 C A -1.9460
642 D A -2.6466
643 K A -2.6204
644 T A 0.0000
645 H A -2.2376
646 T A -1.6733
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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, -0.4883 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_4 -0.4883 View CSV PDB
model_3 -0.5062 View CSV PDB
model_11 -0.51 View CSV PDB
model_0 -0.513 View CSV PDB
model_7 -0.5224 View CSV PDB
model_2 -0.5287 View CSV PDB
model_8 -0.5389 View CSV PDB
model_10 -0.5415 View CSV PDB
model_5 -0.5472 View CSV PDB
model_9 -0.5477 View CSV PDB
model_6 -0.5608 View CSV PDB
model_1 -0.6041 View CSV PDB
input -0.7429 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018