Project name: FG5-R3W4

Status: done

Started: 2021-10-15 01:21:53
Settings
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCKSSQSLLNSRDGKNYLAWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQQYWYWMYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHRRRWWWWPVTKSFNRGECEVQLVESGGGLVQPGGSLRLSCAASGFTFSDFSMSWVRQAPGKGLEWVSYISRTSHTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGWYWMDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
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                                                (00:04:21)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:26:23)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:26:26)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:26:28)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:26:31)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:26:34)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:26:37)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:26:41)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:26:44)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:26:47)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:26:50)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:26:52)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:26:55)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:26:58)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:27:02)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:27:03)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:27:03)
[INFO]       Main:     Simulation completed successfully.                                          (01:27:06)
Show buried residues

Minimal score value
-3.192
Maximal score value
2.1431
Average score
-0.4171
Total score value
-186.0446

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 -2.2534
2 I A 0.0000
3 Q A -2.0751
4 M A 0.0000
5 T A -0.9894
6 Q A -0.7309
7 S A -0.7634
8 P A -0.7282
9 S A -0.7096
10 S A -0.7794
11 L A -0.6889
12 S A -0.9545
13 A A 0.0000
14 S A -0.9168
15 V A -0.2901
16 G A -1.1794
17 D A -2.4715
18 R A -2.3767
19 V A -1.1417
20 T A -0.3207
21 I A 0.0000
22 T A -0.5728
23 C A 0.0000
24 K A -1.8070
25 S A 0.0000
26 S A -1.7389
27 Q A -2.0717
28 S A -0.7530
29 L A 0.3412
30 L A 1.2888
31 N A 0.0000
32 S A -0.8324
33 R A -2.1564
34 D A -1.7073
35 G A -1.2393
36 K A -0.9816
37 N A 0.0000
38 Y A 0.0000
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 -0.6969
47 G A -0.5088
48 K A -0.3655
49 A A 0.0000
50 P A 0.0000
51 K A 0.0000
52 L A 0.0000
53 L A 0.0000
54 I A 0.0000
55 Y A 0.6036
56 D A 0.0000
57 A A 0.0000
58 S A -0.2456
59 N A 0.2314
60 L A 0.7218
61 E A -0.2478
62 T A 0.0000
63 G A -0.7360
64 V A 0.0000
65 P A 0.0000
66 S A -0.9699
67 R A -1.3114
68 F A 0.0000
69 S A -0.2758
70 G A 0.0000
71 S A -0.5422
72 G A -0.8678
73 S A -0.8098
74 G A -0.5260
75 T A -0.8618
76 D A -1.5062
77 F A 0.0000
78 T A -0.6430
79 F A 0.0000
80 T A -0.5394
81 I A 0.0000
82 S A -1.2675
83 S A -0.9599
84 L A 0.0000
85 Q A 0.0000
86 P A 0.0000
87 E A 0.0000
88 D A 0.0000
89 I A -0.6709
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 0.0000
98 W A 1.5153
99 Y A 2.1431
100 W A 2.0329
101 M A 1.2011
102 Y A 0.0000
103 T A 0.0000
104 F A -0.1345
105 G A -0.4673
106 G A -0.6267
107 G A -1.1117
108 T A 0.0000
109 K A -1.4501
110 V A 0.0000
111 E A -1.1687
112 I A 0.0000
113 K A -1.0615
114 R A -1.4177
115 T A -0.5237
116 V A 0.6992
117 A A 0.0000
118 A A 0.4050
119 P A -0.0920
120 S A 0.0000
121 V A 0.0000
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 -1.3986
129 E A -1.1886
130 Q A 0.0000
131 L A -1.0282
132 K A -1.8721
133 S A -1.1216
134 G A -0.7751
135 T A -0.7376
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 -0.6472
145 F A 0.0000
146 Y A -0.9601
147 P A 0.0000
148 R A -2.8794
149 E A -2.2790
150 A A -1.6606
151 K A -2.1931
152 V A -1.1000
153 Q A -1.0025
154 W A 0.0000
155 K A -1.2448
156 V A 0.0000
157 D A -2.3676
158 N A -2.0957
159 A A -0.6953
160 L A -0.0664
161 Q A -0.6706
162 S A -0.7642
163 G A -1.0209
164 N A -1.5278
165 S A -1.1463
166 Q A 0.0000
167 E A -0.4486
168 S A 0.0000
169 V A 0.6103
170 T A 0.0000
171 E A -0.9247
172 Q A 0.0000
173 D A 0.0000
174 S A -0.7844
175 K A -1.3232
176 D A -1.7959
177 S A 0.0000
178 T A 0.0000
179 Y A -0.5246
180 S A 0.0550
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 -0.5357
187 L A -0.8098
188 S A -0.8935
189 K A -1.5827
190 A A -1.6791
191 D A -2.7030
192 Y A 0.0000
193 E A -2.6424
194 K A -3.1532
195 H A -3.1920
196 K A -3.1524
197 V A -1.8787
198 Y A 0.0000
199 A A 0.0000
200 C A 0.0000
201 E A -1.4056
202 V A 0.0000
203 T A -0.7399
204 H A 0.0000
205 R A -1.2834
206 R A 0.0000
207 R A -1.4484
208 W A 0.8752
209 W A 1.2592
210 W A 1.1539
211 W A 1.0241
212 P A 0.2290
213 V A 0.1580
214 T A -0.4247
215 K A -0.6812
216 S A -1.0515
217 F A 0.0000
218 N A -2.2846
219 R A -2.3952
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 0.0000
434 V A -0.2445
435 Q A -0.9985
436 P A -0.9170
437 G A -0.8629
438 G A -0.9516
439 S A -1.1602
440 L A 0.0000
441 R A -2.2496
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 0.0000
448 G A 0.5430
449 F A 1.2426
450 T A 0.0343
451 F A 0.0000
452 S A -1.1049
453 D A -1.7306
454 F A 0.0000
455 S A -0.6179
456 M A 0.0000
457 S A 0.0000
458 W A 0.0000
459 V A 0.0000
460 R A -0.4331
461 Q A 0.0000
462 A A -0.7630
463 P A -0.9193
464 G A -0.8454
465 K A -1.0212
466 G A -0.7595
467 L A 0.0000
468 E A -0.2871
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 -0.9681
475 R A -2.1924
476 T A -1.5443
477 S A -1.1160
478 H A -1.5631
479 T A -0.7448
480 T A 0.0295
481 Y A 1.3115
482 Y A 1.2334
483 A A 0.6165
484 D A -0.0620
485 S A 0.0000
486 V A 1.2250
487 K A -0.5196
488 G A -0.7333
489 R A -0.6531
490 F A 0.0000
491 T A -0.3183
492 I A 0.0000
493 S A -0.8460
494 R A -1.5644
495 D A -1.8925
496 N A -2.4173
497 S A -1.5511
498 K A -1.6738
499 N A -1.1845
500 T A 0.0000
501 L A 0.0000
502 Y A -0.4845
503 L A 0.0000
504 Q A -1.2031
505 M A 0.0000
506 N A -1.5487
507 S A -1.3039
508 L A -1.4211
509 R A -2.0672
510 A A -1.2273
511 E A -1.4387
512 D A -1.9575
513 T A -0.8566
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 -0.5415
521 G A 0.0235
522 W A 0.0000
523 Y A 1.3602
524 W A 1.0998
525 M A 0.0000
526 D A -0.5242
527 L A 0.0000
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 -0.1820
534 V A 0.0000
535 T A -0.5998
536 V A -0.2721
537 S A -0.1442
538 S A -0.1079
539 A A 0.0511
540 S A -0.1545
541 T A -0.4414
542 K A -0.9349
543 G A -0.9387
544 P A -0.4199
545 S A -0.4752
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 -0.8160
554 K A -1.2991
555 S A 0.0000
556 T A -0.5289
557 S A -0.6580
558 G A -0.8023
559 G A -0.8368
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 0.0000
569 D A -0.1089
570 Y A 0.0000
571 F A 0.1864
572 P A 0.0000
573 E A 0.0000
574 P A 0.0000
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 0.0000
581 S A 0.0000
582 G A 0.0000
583 A A -0.0208
584 L A 0.0000
585 T A -0.4141
586 S A -0.4441
587 G A 0.0000
588 V A 0.0000
589 H A 0.0000
590 T A 0.0000
591 F A 0.2979
592 P A 0.4425
593 A A 0.5750
594 V A 0.0000
595 L A 1.4979
596 Q A 0.3301
597 S A -0.1796
598 S A -0.1262
599 G A 0.3353
600 L A 1.1118
601 Y A 1.0318
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 0.0000
610 P A -0.4554
611 S A -0.4791
612 S A -0.3712
613 S A -0.1091
614 L A -0.2118
615 G A -0.5566
616 T A -0.3918
617 Q A -0.3886
618 T A -0.4761
619 Y A 0.2743
620 I A -0.1104
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 -1.5231
627 P A -1.2723
628 S A -1.2002
629 N A -1.9865
630 T A -1.2824
631 K A -1.4014
632 V A -1.0837
633 D A -1.4118
634 K A 0.0000
635 K A -1.6044
636 V A 0.0000
637 E A -1.0398
638 P A -0.8080
639 K A -1.5942
640 S A -1.2902
641 C A -0.9131
642 D A -1.9392
643 K A -1.5615
644 T A -1.0757
645 H A 0.0000
646 T A 0.0000
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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, -0.4171 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_2 -0.4171 View CSV PDB
model_5 -0.4405 View CSV PDB
model_7 -0.4592 View CSV PDB
model_10 -0.4668 View CSV PDB
model_9 -0.4672 View CSV PDB
model_0 -0.4921 View CSV PDB
model_1 -0.4993 View CSV PDB
model_3 -0.5018 View CSV PDB
model_8 -0.5067 View CSV PDB
model_11 -0.5124 View CSV PDB
model_6 -0.5167 View CSV PDB
model_4 -0.5895 View CSV PDB
input -0.7556 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018