Project name: FG5 R3W4

Status: done

Started: 2021-10-15 04:56:46
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                                                (00:04:00)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:18:05)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:18:08)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:18:11)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:18:14)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:18:17)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:18:20)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:18:23)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:18:26)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:18:28)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:18:32)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:18:34)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:18:37)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:18:40)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:18:44)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:18:45)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:18:45)
[INFO]       Main:     Simulation completed successfully.                                          (01:18:48)
Show buried residues

Minimal score value
-3.5859
Maximal score value
1.8925
Average score
-0.4064
Total score value
-181.241

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 -1.7975
2 I A -0.7901
3 Q A -1.5046
4 M A 0.0000
5 T A -0.5735
6 Q A 0.0000
7 S A -0.5014
8 P A -0.4632
9 S A -0.5973
10 S A -0.7703
11 L A -0.8190
12 S A -1.1703
13 A A -1.0445
14 S A -0.6374
15 V A 0.7135
16 G A -0.5399
17 D A -1.2306
18 R A -1.9855
19 V A 0.0000
20 T A -0.6040
21 I A 0.0000
22 T A -0.3746
23 C A 0.0000
24 K A -1.1808
25 S A 0.0000
26 S A -0.5379
27 Q A -0.2371
28 S A 0.5647
29 L A 1.8111
30 L A 0.9011
31 N A -0.5882
32 S A -1.6015
33 R A -2.7001
34 D A -2.4133
35 G A -1.8920
36 K A -1.4000
37 N A 0.0000
38 Y A 0.5184
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 -0.4877
46 P A -0.5222
47 G A 0.0000
48 K A -0.4305
49 A A 0.0000
50 P A 0.0000
51 K A 0.0000
52 L A -0.0906
53 L A 0.0000
54 I A 0.0000
55 Y A -0.0029
56 D A -0.2095
57 A A 0.0000
58 S A -0.5355
59 N A -0.5524
60 L A -0.7205
61 E A -1.7480
62 T A -1.1650
63 G A -0.7529
64 V A -1.2569
65 P A -1.7151
66 S A -1.6297
67 R A -2.0861
68 F A 0.0000
69 S A -0.6149
70 G A -0.3852
71 S A -0.4758
72 G A -0.7991
73 S A -0.8202
74 G A -0.9303
75 T A -0.5493
76 D A -0.9442
77 F A 0.0000
78 T A -0.3490
79 F A 0.0000
80 T A -0.6944
81 I A 0.0000
82 S A -0.9409
83 S A -0.8857
84 L A -0.8132
85 Q A 0.0000
86 P A 0.0000
87 E A -1.5965
88 D A 0.0000
89 I A -0.7034
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 1.0842
98 W A 1.8907
99 Y A 1.8925
100 W A 1.2773
101 M A 1.1247
102 Y A 0.0000
103 T A 0.0000
104 F A 0.0333
105 G A 0.0000
106 G A -0.3091
107 G A -0.5042
108 T A 0.0000
109 K A -1.1414
110 V A 0.0000
111 E A -1.6958
112 I A 0.0000
113 K A -2.3151
114 R A -1.3974
115 T A -0.2031
116 V A 1.0534
117 A A 0.2639
118 A A 0.7591
119 P A 0.3297
120 S A -0.0287
121 V A 0.1193
122 F A 0.0000
123 I A 0.0000
124 F A 0.0000
125 P A -0.8066
126 P A 0.0000
127 S A -1.0733
128 D A -1.9650
129 E A -2.4745
130 Q A 0.0000
131 L A -1.1703
132 K A -2.2589
133 S A -1.3841
134 G A -1.0430
135 T A -0.8829
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 -1.2727
148 R A -2.2882
149 E A -2.3990
150 A A -1.8315
151 K A -2.3212
152 V A 0.0000
153 Q A -1.0386
154 W A 0.0000
155 K A -0.9673
156 V A 0.0000
157 D A -2.9993
158 N A -2.1277
159 A A -0.7112
160 L A 0.5271
161 Q A -0.5154
162 S A -0.4508
163 G A -0.7466
164 N A -0.4624
165 S A -0.5390
166 Q A -0.5711
167 E A -0.5944
168 S A -0.0102
169 V A -0.1210
170 T A 0.0000
171 E A -0.7977
172 Q A 0.0000
173 D A 0.0000
174 S A 0.0000
175 K A -2.5886
176 D A -2.7006
177 S A 0.0000
178 T A 0.0000
179 Y A -0.8282
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 0.0000
188 S A -1.3369
189 K A -2.1181
190 A A -1.8393
191 D A -2.8728
192 Y A 0.0000
193 E A -3.2546
194 K A -3.5859
195 H A -3.5511
196 K A -3.1918
197 V A -2.3686
198 Y A 0.0000
199 A A -0.9293
200 C A 0.0000
201 E A -1.3570
202 V A 0.0000
203 T A -1.0149
204 H A -1.5738
205 R A -2.4076
206 R A -2.1506
207 R A -1.7807
208 W A 0.5166
209 W A 1.2762
210 W A 0.9391
211 W A 1.1803
212 P A -0.0615
213 V A 0.0916
214 T A -0.4546
215 K A -0.4675
216 S A -0.9659
217 F A 0.0000
218 N A -1.3657
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 -0.5815
432 G A -0.5289
433 L A 0.0007
434 V A 0.0000
435 Q A -0.4073
436 P A -0.2964
437 G A -0.4444
438 G A -0.8595
439 S A -1.0362
440 L A 0.0000
441 R A -1.4438
442 L A 0.0000
443 S A -0.4226
444 C A 0.0000
445 A A 0.0000
446 A A 0.0000
447 S A 0.0000
448 G A -0.0729
449 F A 0.9503
450 T A -0.2148
451 F A 0.0000
452 S A -0.8940
453 D A -0.6844
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 -0.2280
461 Q A 0.0000
462 A A -0.2687
463 P A -0.5189
464 G A -0.7136
465 K A 0.0000
466 G A -0.2102
467 L A -0.0146
468 E A -0.1684
469 W A 0.0000
470 V A 0.0000
471 S A 0.0000
472 Y A 1.1856
473 I A 0.0000
474 S A -0.4483
475 R A -1.5628
476 T A -1.0438
477 S A -0.7513
478 H A -0.9432
479 T A -0.1239
480 T A 0.6957
481 Y A 1.8677
482 Y A 1.6377
483 A A 0.5617
484 D A 0.1021
485 S A 0.5197
486 V A 1.3008
487 K A 0.0000
488 G A 0.2424
489 R A 0.0000
490 F A 0.6352
491 T A 0.5116
492 I A 0.0000
493 S A -0.5840
494 R A -1.2646
495 D A -1.8228
496 N A -1.8720
497 S A -1.5010
498 K A -1.9710
499 N A 0.0000
500 T A 0.0000
501 L A 0.0000
502 Y A -0.3659
503 L A 0.0000
504 Q A -0.7239
505 M A 0.0000
506 N A -0.7709
507 S A 0.0593
508 L A 0.7976
509 R A 0.0000
510 A A -0.6603
511 E A -1.4206
512 D A 0.0000
513 T A -0.5001
514 A A 0.0000
515 V A 0.1530
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 1.1014
523 Y A 0.7837
524 W A 0.0000
525 M A 0.0000
526 D A 0.3727
527 L A 0.0000
528 W A 0.0000
529 G A 0.0000
530 Q A 0.0000
531 G A -0.3390
532 T A 0.0000
533 L A -0.0731
534 V A 0.0000
535 T A 0.0000
536 V A 0.0000
537 S A -0.3326
538 S A -0.1235
539 A A -0.1391
540 S A -0.4924
541 T A -0.8186
542 K A -1.3553
543 G A -1.0150
544 P A -0.4715
545 S A -0.7504
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 -0.9616
554 K A -0.9938
555 S A 0.0000
556 T A -0.5576
557 S A -0.4475
558 G A -0.7639
559 G A -0.8147
560 T A -0.5939
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 -0.0146
570 Y A 0.0000
571 F A -0.5116
572 P A 0.0000
573 E A -1.6848
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 -0.2237
581 S A 0.0000
582 G A 0.0000
583 A A 0.4970
584 L A 0.2631
585 T A 0.0810
586 S A 0.0609
587 G A -0.3941
588 V A 0.0000
589 H A 0.0000
590 T A 0.0000
591 F A 0.0000
592 P A -0.0248
593 A A 0.1922
594 V A 0.0000
595 L A 1.4953
596 Q A 0.0000
597 S A -0.0737
598 S A -0.2433
599 G A -0.1042
600 L A 0.6925
601 Y A 0.7051
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 -0.3206
609 V A 0.0000
610 P A -0.4721
611 S A -0.6665
612 S A -0.5120
613 S A -0.3151
614 L A -0.0739
615 G A -0.4551
616 T A -0.6057
617 Q A 0.0000
618 T A -0.5410
619 Y A 0.0000
620 I A -0.9076
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 -1.3826
627 P A -1.1826
628 S A -1.3298
629 N A -1.8790
630 T A -1.6467
631 K A -1.8209
632 V A -1.4618
633 D A -2.2601
634 K A 0.0000
635 K A -2.0477
636 V A 0.0000
637 E A 0.0000
638 P A 0.0000
639 K A -2.3540
640 S A -1.3716
641 C A -0.4538
642 D A -1.4240
643 K A -2.3204
644 T A -2.0616
645 H A -1.8194
646 T A -1.6849
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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, -0.4064 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_1 -0.4064 View CSV PDB
model_0 -0.4399 View CSV PDB
model_6 -0.4477 View CSV PDB
model_9 -0.4887 View CSV PDB
model_8 -0.489 View CSV PDB
model_7 -0.5017 View CSV PDB
model_2 -0.5025 View CSV PDB
model_3 -0.5097 View CSV PDB
model_5 -0.516 View CSV PDB
model_10 -0.5363 View CSV PDB
model_11 -0.5467 View CSV PDB
model_4 -0.57 View CSV PDB
input -0.7556 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018