Project name: FG5 RVRW4

Status: done

Started: 2021-10-15 06:18:58
Settings
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCKSSQSLLNSRDGKNYLAWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQQYWYWMYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHRVRWWWWPVTKSFNRGECEVQLVESGGGLVQPGGSLRLSCAASGFTFSDFSMSWVRQAPGKGLEWVSYISRTSHTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGWYWMDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
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                                        (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:21)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:27:30)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:27:33)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:27:35)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:27:38)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:27:41)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:27:43)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:27:46)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:27:49)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:27:51)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:27:54)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:27:57)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:27:59)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:28:02)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:28:06)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:28:06)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:28:06)
[INFO]       Main:     Simulation completed successfully.                                          (01:28:09)
Show buried residues

Minimal score value
-3.0926
Maximal score value
2.059
Average score
-0.4461
Total score value
-198.9645

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 -1.9655
2 I A -1.2787
3 Q A -1.6935
4 M A 0.0000
5 T A -0.8427
6 Q A -0.7825
7 S A -0.5322
8 P A -0.3899
9 S A -0.5222
10 S A -0.4518
11 L A -0.3978
12 S A -1.1071
13 A A 0.0000
14 S A -1.7277
15 V A -1.3796
16 G A -1.7535
17 D A -2.8544
18 R A -2.8015
19 V A 0.0000
20 T A -0.7483
21 I A 0.0000
22 T A -0.7240
23 C A 0.0000
24 K A -1.9839
25 S A 0.0000
26 S A -1.8233
27 Q A -1.8464
28 S A -0.6537
29 L A 0.0000
30 L A 0.7582
31 N A -0.4461
32 S A -1.3690
33 R A -2.8892
34 D A -3.0622
35 G A -2.0446
36 K A -1.6348
37 N A 0.0000
38 Y A 0.5105
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 0.0000
47 G A 0.0000
48 K A -0.6800
49 A A 0.0000
50 P A 0.0000
51 K A -0.2268
52 L A 0.1346
53 L A 0.0000
54 I A 0.0000
55 Y A 0.0050
56 D A 0.0232
57 A A 0.0000
58 S A -0.9884
59 N A -0.9201
60 L A -0.8660
61 E A -1.7528
62 T A -1.3093
63 G A -1.1254
64 V A 0.0000
65 P A -1.1442
66 S A -1.2950
67 R A -1.8068
68 F A 0.0000
69 S A -0.7242
70 G A 0.0000
71 S A -0.7665
72 G A -1.4125
73 S A -1.3523
74 G A -1.2549
75 T A -1.5439
76 D A -2.1490
77 F A 0.0000
78 T A -0.7748
79 F A 0.0000
80 T A -0.7408
81 I A 0.0000
82 S A -1.6325
83 S A -1.4129
84 L A 0.0000
85 Q A -1.2971
86 P A -1.2492
87 E A -1.0962
88 D A -0.8245
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 0.0000
98 W A 2.0285
99 Y A 2.0590
100 W A 1.4209
101 M A 1.2526
102 Y A 0.0000
103 T A 0.0000
104 F A 0.2496
105 G A -0.2431
106 G A -0.2982
107 G A -0.5069
108 T A 0.0000
109 K A -0.9276
110 V A 0.0000
111 E A -1.1567
112 I A 0.0000
113 K A -2.1637
114 R A -2.2893
115 T A -0.9417
116 V A 0.2190
117 A A 0.2112
118 A A 0.0629
119 P A -0.1016
120 S A -0.1926
121 V A -0.0967
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 0.0000
129 E A 0.0000
130 Q A 0.0000
131 L A 0.0000
132 K A -1.5254
133 S A -0.9491
134 G A 0.0000
135 T A 0.0000
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 -0.3334
144 N A -0.3877
145 F A 0.0000
146 Y A -0.6093
147 P A -0.8685
148 R A -1.5202
149 E A -2.4507
150 A A 0.0000
151 K A -2.1361
152 V A -1.2051
153 Q A -1.1412
154 W A 0.0000
155 K A -1.1448
156 V A 0.0000
157 D A -1.4506
158 N A -1.6232
159 A A -0.5199
160 L A 0.3678
161 Q A -0.5965
162 S A -0.6999
163 G A -0.7288
164 N A -0.9532
165 S A -0.8843
166 Q A -0.4243
167 E A -0.5458
168 S A 0.0000
169 V A 0.2067
170 T A 0.0000
171 E A 0.0000
172 Q A -1.1415
173 D A -1.5492
174 S A -1.0001
175 K A 0.0000
176 D A 0.0000
177 S A -0.8945
178 T A 0.0000
179 Y A -0.2784
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 0.0000
187 L A -0.8145
188 S A -0.9065
189 K A -1.3169
190 A A -1.4199
191 D A -2.1062
192 Y A 0.0000
193 E A -2.8510
194 K A -3.0743
195 H A -2.8800
196 K A -2.7669
197 V A 0.0000
198 Y A -0.8393
199 A A -0.8777
200 C A 0.0000
201 E A -1.6299
202 V A 0.0000
203 T A -0.8861
204 H A 0.0000
205 R A -1.8947
206 V A 0.0000
207 R A -1.3162
208 W A 0.7725
209 W A 1.5998
210 W A 1.7043
211 W A 1.5655
212 P A 0.1343
213 V A -0.0749
214 T A -0.8926
215 K A -1.0325
216 S A -0.9423
217 F A 0.0000
218 N A -1.3126
219 R A -1.6670
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 0.0242
434 V A 0.0000
435 Q A -1.3887
436 P A -1.4288
437 G A -0.9772
438 G A -1.0513
439 S A -1.3212
440 L A 0.0000
441 R A -2.1151
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 1.0598
450 T A -0.0790
451 F A 0.0000
452 S A -1.0459
453 D A -2.3746
454 F A 0.0000
455 S A -0.2513
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 -0.1816
463 P A -0.5310
464 G A -0.8538
465 K A -0.7187
466 G A -0.3174
467 L A -0.1254
468 E A -0.6676
469 W A -0.0735
470 V A 0.0000
471 S A 0.0000
472 Y A 0.9423
473 I A 0.0000
474 S A -0.7869
475 R A -1.6784
476 T A -1.4103
477 S A -1.1133
478 H A -1.4264
479 T A -0.2121
480 T A 0.5604
481 Y A 1.7760
482 Y A 1.7883
483 A A 0.2831
484 D A -0.7015
485 S A -0.8426
486 V A -1.3362
487 K A -2.4717
488 G A -1.2798
489 R A -0.8621
490 F A -0.1282
491 T A -0.1228
492 I A 0.0000
493 S A -0.8304
494 R A -1.5232
495 D A -1.8478
496 N A 0.0000
497 S A -1.3407
498 K A -1.5470
499 N A 0.0000
500 T A 0.0000
501 L A 0.0000
502 Y A -0.6200
503 L A 0.0000
504 Q A -1.4018
505 M A 0.0000
506 N A -1.7342
507 S A -1.4312
508 L A 0.0000
509 R A -2.2176
510 A A -1.8881
511 E A -3.0926
512 D A -3.0183
513 T A 0.0000
514 A A -0.2699
515 V A 0.4873
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 0.4179
522 W A 0.9321
523 Y A 1.6505
524 W A 1.0674
525 M A 0.0000
526 D A 0.4482
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 0.7272
534 V A 0.0000
535 T A 0.0967
536 V A -0.6460
537 S A -0.3198
538 S A -0.2649
539 A A -0.0236
540 S A -0.2971
541 T A -0.4360
542 K A -0.8375
543 G A -0.8167
544 P A 0.0000
545 S A 0.0000
546 V A -0.1443
547 F A -0.1355
548 P A 0.0000
549 L A 0.0000
550 A A 0.0000
551 P A 0.0000
552 S A -0.7722
553 S A -0.4924
554 K A 0.0000
555 S A 0.0000
556 T A -0.5743
557 S A -0.6225
558 G A -0.8162
559 G A -0.7592
560 T A -0.5841
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 0.0000
570 Y A 0.0000
571 F A -0.1140
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 0.2108
581 S A 0.7746
582 G A 0.0000
583 A A 0.1956
584 L A 0.0000
585 T A -0.0747
586 S A -0.1732
587 G A -0.2784
588 V A 0.0000
589 H A -0.2127
590 T A 0.0000
591 F A 0.0000
592 P A 0.0756
593 A A 0.3847
594 V A 0.0000
595 L A 1.0941
596 Q A 0.3022
597 S A -0.1731
598 S A -0.1688
599 G A 0.0000
600 L A 0.4815
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 -0.2380
609 V A 0.0000
610 P A -0.5819
611 S A -0.6473
612 S A -0.4307
613 S A -0.6391
614 L A -0.6436
615 G A -1.0769
616 T A -0.9545
617 Q A -1.3458
618 T A -0.4263
619 Y A 0.1243
620 I A 0.0000
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 -0.9337
628 S A -1.1986
629 N A -1.5805
630 T A 0.0000
631 K A -1.8275
632 V A 0.0000
633 D A -2.0522
634 K A -1.1939
635 K A -1.5227
636 V A 0.0000
637 E A -1.4237
638 P A -1.6566
639 K A -2.3275
640 S A -1.3717
641 C A 0.0000
642 D A 0.0000
643 K A -1.4153
644 T A -1.4923
645 H A -1.8178
646 T A -0.9489
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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, -0.4461 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_6 -0.4461 View CSV PDB
model_7 -0.4637 View CSV PDB
model_2 -0.4736 View CSV PDB
model_10 -0.501 View CSV PDB
model_1 -0.5015 View CSV PDB
model_0 -0.5119 View CSV PDB
model_9 -0.522 View CSV PDB
model_5 -0.5271 View CSV PDB
model_8 -0.5281 View CSV PDB
model_3 -0.5343 View CSV PDB
model_11 -0.5345 View CSV PDB
model_4 -0.537 View CSV PDB
input -0.7614 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018