Project name: FG5 RMRW4

Status: done

Started: 2021-10-15 06:18:31
Settings
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCKSSQSLLNSRDGKNYLAWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQQYWYWMYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHRMRWWWWPVTKSFNRGECEVQLVESGGGLVQPGGSLRLSCAASGFTFSDFSMSWVRQAPGKGLEWVSYISRTSHTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGWYWMDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
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             (00:00:01)
[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                                                (00:04:02)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:25:19)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:25:22)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:25:25)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:25:28)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:25:31)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:25:33)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:25:36)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:25:39)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:25:42)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:25:44)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:25:47)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:25:50)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:25:53)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:25:57)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:25:57)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:25:57)
[INFO]       Main:     Simulation completed successfully.                                          (01:26:00)
Show buried residues

Minimal score value
-3.2605
Maximal score value
2.0787
Average score
-0.4261
Total score value
-190.0427

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 -1.5167
2 I A -1.0044
3 Q A -1.7046
4 M A 0.0000
5 T A -1.1911
6 Q A -1.1312
7 S A -0.8008
8 P A -0.6658
9 S A -0.7325
10 S A -0.6000
11 L A -0.5471
12 S A -1.2262
13 A A 0.0000
14 S A -0.6390
15 V A 0.6029
16 G A -0.8407
17 D A -1.9195
18 R A -2.0406
19 V A -0.9052
20 T A -0.3539
21 I A 0.0000
22 T A -0.7412
23 C A 0.0000
24 K A -1.6476
25 S A 0.0000
26 S A -1.4763
27 Q A -1.9054
28 S A 0.0000
29 L A 0.3308
30 L A 0.0419
31 N A -1.0938
32 S A -1.8468
33 R A -3.0533
34 D A -3.1478
35 G A -2.1911
36 K A -1.4894
37 N A 0.0000
38 Y A 0.3243
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 -0.4641
46 P A -0.5136
47 G A 0.0000
48 K A -0.3948
49 A A 0.0000
50 P A 0.0000
51 K A 0.2052
52 L A 0.1676
53 L A 0.0000
54 I A 0.0000
55 Y A 0.2480
56 D A -0.3663
57 A A 0.0000
58 S A -0.7359
59 N A -1.1463
60 L A -0.4212
61 E A -1.5404
62 T A -0.5439
63 G A -0.8902
64 V A -0.4807
65 P A -0.9089
66 S A -0.9919
67 R A -1.8365
68 F A 0.0000
69 S A -0.7395
70 G A -0.4764
71 S A -0.6876
72 G A -0.8580
73 S A -0.9194
74 G A -0.7253
75 T A -0.7354
76 D A -1.2059
77 F A 0.0000
78 T A -0.4969
79 F A 0.0000
80 T A -0.6419
81 I A 0.0000
82 S A -1.0443
83 S A 0.0000
84 L A -0.2965
85 Q A -1.0360
86 P A -1.4047
87 E A -0.9627
88 D A 0.0000
89 I A -0.2040
90 A A 0.0000
91 T A -0.5039
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 1.6074
98 W A 2.0787
99 Y A 1.9680
100 W A 1.7748
101 M A 0.8612
102 Y A 0.0000
103 T A 0.0000
104 F A 0.0082
105 G A 0.0000
106 G A -0.5262
107 G A -0.9546
108 T A -0.8599
109 K A -0.8529
110 V A 0.0000
111 E A -1.3352
112 I A -1.3850
113 K A -2.6677
114 R A -2.7137
115 T A -0.8791
116 V A 1.1676
117 A A 0.5884
118 A A 0.3793
119 P A 0.0279
120 S A -0.1966
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 -1.7392
129 E A -1.9467
130 Q A -1.5109
131 L A -1.7257
132 K A -2.3585
133 S A -1.4606
134 G A -0.9712
135 T A -0.7705
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 0.0000
148 R A -2.3219
149 E A -2.0364
150 A A -1.3415
151 K A -1.4995
152 V A 0.0000
153 Q A -1.1500
154 W A 0.0000
155 K A -1.0772
156 V A 0.0000
157 D A -2.1517
158 N A -1.7849
159 A A 0.0000
160 L A -0.0007
161 Q A -0.4441
162 S A -0.6232
163 G A -0.6836
164 N A -0.8202
165 S A -0.7578
166 Q A -0.3938
167 E A -0.4391
168 S A 0.0000
169 V A 0.6446
170 T A 0.0354
171 E A -0.5885
172 Q A -1.1925
173 D A -0.9815
174 S A -1.0480
175 K A -1.6672
176 D A -2.1570
177 S A 0.0000
178 T A 0.0000
179 Y A -0.6643
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 -0.4660
187 L A 0.0000
188 S A -0.7968
189 K A -1.7826
190 A A -1.4661
191 D A -2.2738
192 Y A 0.0000
193 E A -3.2605
194 K A -3.0684
195 H A -2.6924
196 K A -2.1129
197 V A -0.0789
198 Y A 0.0000
199 A A 0.0000
200 C A 0.0000
201 E A -1.2071
202 V A 0.0000
203 T A -0.4799
204 H A 0.0000
205 R A -0.3254
206 M A 0.0000
207 R A 0.1400
208 W A 1.4519
209 W A 1.6991
210 W A 1.5565
211 W A 0.7717
212 P A 0.0522
213 V A 0.0917
214 T A -0.5407
215 K A -0.3790
216 S A -0.2925
217 F A 0.0000
218 N A -0.5784
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 0.0000
433 L A 0.4443
434 V A 0.0000
435 Q A -1.0475
436 P A -1.2172
437 G A -1.3951
438 G A -1.1319
439 S A -1.0723
440 L A 0.0000
441 R A -1.3714
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 0.0000
449 F A 0.6850
450 T A -0.7138
451 F A -0.6709
452 S A -0.2521
453 D A -0.8902
454 F A 0.9018
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 0.0000
463 P A -0.8668
464 G A -1.0770
465 K A -1.3009
466 G A -0.8893
467 L A -0.1588
468 E A -0.2854
469 W A 0.0000
470 V A 0.0000
471 S A 0.0000
472 Y A 0.8206
473 I A 0.0000
474 S A -0.6268
475 R A -2.2644
476 T A -1.2089
477 S A -0.9354
478 H A -1.4434
479 T A -0.4997
480 T A 0.3478
481 Y A 1.3970
482 Y A 0.7434
483 A A 0.0000
484 D A 0.3159
485 S A 0.2291
486 V A 1.0272
487 K A -0.7389
488 G A -1.4939
489 R A -2.1002
490 F A 0.0000
491 T A -0.4143
492 I A 0.2273
493 S A -0.4748
494 R A -1.6726
495 D A -2.2030
496 N A -2.6776
497 S A -1.8879
498 K A -2.4202
499 N A -1.4781
500 T A -1.1982
501 L A 0.0000
502 Y A -0.3430
503 L A 0.0000
504 Q A -0.9842
505 M A 0.0000
506 N A -1.9298
507 S A -1.7216
508 L A -1.9711
509 R A -2.5547
510 A A -1.5205
511 E A -2.1363
512 D A -1.9913
513 T A -1.2017
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 1.6082
523 Y A 1.3676
524 W A 0.0000
525 M A 0.0000
526 D A -0.0505
527 L A 0.4610
528 W A 0.0561
529 G A 0.0000
530 Q A 0.0000
531 G A -0.0274
532 T A 0.0000
533 L A 0.0043
534 V A 0.0000
535 T A 0.0184
536 V A 0.6023
537 S A 0.1589
538 S A -0.1532
539 A A 0.0396
540 S A 0.2220
541 T A -0.1245
542 K A -0.6437
543 G A -0.5279
544 P A -0.4075
545 S A 0.0000
546 V A -0.5112
547 F A 0.0000
548 P A -0.8518
549 L A 0.0000
550 A A 0.0000
551 P A 0.0000
552 S A 0.0000
553 S A -0.5454
554 K A -0.7764
555 S A 0.0000
556 T A -0.6321
557 S A -0.6011
558 G A -0.8332
559 G A -0.8076
560 T A -0.5426
561 A A -0.4916
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 -0.1845
570 Y A 0.0000
571 F A 0.7597
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 -0.5379
582 G A -0.0513
583 A A 0.5699
584 L A 1.0955
585 T A 0.3126
586 S A 0.0630
587 G A -0.2416
588 V A 0.0000
589 H A -0.3131
590 T A 0.0000
591 F A 0.0000
592 P A 0.4405
593 A A 0.7277
594 V A 1.1043
595 L A 1.7409
596 Q A 0.6239
597 S A -0.0398
598 S A -0.0218
599 G A 0.2936
600 L A 1.1126
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 -0.2544
609 V A 0.0000
610 P A -0.4914
611 S A -0.5393
612 S A -0.5060
613 S A -0.4949
614 L A -0.4341
615 G A -0.7362
616 T A -0.7059
617 Q A -0.8907
618 T A -0.7843
619 Y A 0.0000
620 I A 0.0000
621 C A 0.0000
622 N A -1.3360
623 V A 0.0000
624 N A 0.0000
625 H A 0.0000
626 K A 0.0000
627 P A -0.8220
628 S A -1.1525
629 N A -1.5231
630 T A -1.3268
631 K A -2.0418
632 V A -1.5873
633 D A -2.3580
634 K A 0.0000
635 K A -2.0091
636 V A 0.0000
637 E A -1.3019
638 P A -0.8899
639 K A -1.1514
640 S A -0.7590
641 C A -0.5933
642 D A 0.0000
643 K A -2.1520
644 T A -1.3444
645 H A -1.0318
646 T A -0.7564
Download PDB file
View in 3Dmol
Play the video

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, -0.4261 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 -0.4261 View CSV PDB
model_10 -0.4497 View CSV PDB
model_4 -0.4547 View CSV PDB
model_11 -0.4691 View CSV PDB
model_5 -0.4715 View CSV PDB
model_0 -0.4812 View CSV PDB
model_1 -0.4871 View CSV PDB
model_3 -0.502 View CSV PDB
model_9 -0.5093 View CSV PDB
model_2 -0.5218 View CSV PDB
model_7 -0.5364 View CSV PDB
model_6 -0.566 View CSV PDB
input -0.7645 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018