Project name: FG5 R3W4

Status: done

Started: 2021-10-15 04:56:52
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]                                                (00:00:00)
[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                                                (00:04:15)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:20:35)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:20:38)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:20:41)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:20:44)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:20:47)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:20:50)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:20:53)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:20:55)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:20:58)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:21:01)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:21:04)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:21:07)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:21:10)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:21:14)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:21:14)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:21:14)
[INFO]       Main:     Simulation completed successfully.                                          (01:21:17)
Show buried residues

Minimal score value
-2.9426
Maximal score value
1.7866
Average score
-0.4053
Total score value
-180.7783

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 0.1069
2 I A 1.6253
3 Q A 0.3914
4 M A 0.0000
5 T A -0.3696
6 Q A -0.7036
7 S A -0.6305
8 P A -0.4090
9 S A -0.5079
10 S A -0.5704
11 L A -0.3805
12 S A -0.7986
13 A A 0.0000
14 S A -1.7422
15 V A -1.8708
16 G A -1.8269
17 D A -2.9426
18 R A -2.8960
19 V A 0.0000
20 T A -0.7342
21 I A 0.0000
22 T A -0.7878
23 C A 0.0000
24 K A -2.2475
25 S A 0.0000
26 S A -0.8686
27 Q A -0.7243
28 S A -0.5936
29 L A 0.0000
30 L A 0.4627
31 N A -0.5193
32 S A -1.5045
33 R A -2.3688
34 D A -2.1614
35 G A -2.0645
36 K A -2.4062
37 N A -1.2806
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 -0.9944
46 P A -0.4003
47 G A 0.0000
48 K A 0.0000
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 0.0000
56 D A -1.2998
57 A A -0.8071
58 S A -0.6384
59 N A -1.3393
60 L A -0.2957
61 E A 0.0000
62 T A -0.1466
63 G A -0.1674
64 V A 0.0000
65 P A -0.8240
66 S A 0.0000
67 R A -1.9284
68 F A 0.0000
69 S A -0.8729
70 G A -0.8118
71 S A -0.7685
72 G A -1.1828
73 S A -1.3109
74 G A -0.9610
75 T A -1.4746
76 D A -2.5594
77 F A 0.0000
78 T A -0.9340
79 F A 0.0000
80 T A -0.6319
81 I A 0.0000
82 S A -1.4160
83 S A -1.3132
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 -0.0223
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 1.3734
99 Y A 1.7866
100 W A 1.5265
101 M A 1.2109
102 Y A 0.0000
103 T A 0.0000
104 F A 0.5618
105 G A 0.0000
106 G A -0.2736
107 G A -0.8022
108 T A 0.0000
109 K A -1.0362
110 V A 0.0000
111 E A -0.8575
112 I A 0.0000
113 K A -2.4228
114 R A -1.9907
115 T A -1.0726
116 V A -0.5382
117 A A 0.0000
118 A A 0.5295
119 P A 0.1094
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 -2.7956
129 E A -2.3373
130 Q A 0.0000
131 L A -1.9532
132 K A -2.7295
133 S A -1.4707
134 G A -1.0123
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 0.0000
144 N A -0.5365
145 F A 0.0000
146 Y A 0.0000
147 P A -1.6824
148 R A -2.1019
149 E A -1.7651
150 A A -1.8918
151 K A -2.4365
152 V A 0.0000
153 Q A -1.5240
154 W A 0.0000
155 K A -1.1519
156 V A 0.0000
157 D A -1.8154
158 N A -1.6041
159 A A -0.4219
160 L A 0.4325
161 Q A -0.2788
162 S A -0.5928
163 G A -0.5985
164 N A -0.6994
165 S A -0.9500
166 Q A -0.7788
167 E A -1.1270
168 S A 0.0000
169 V A 0.5391
170 T A 0.0000
171 E A 0.0000
172 Q A 0.0000
173 D A 0.0000
174 S A 0.0000
175 K A -1.2200
176 D A -2.0919
177 S A 0.0000
178 T A 0.0000
179 Y A -0.6156
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 -0.3505
188 S A -0.7773
189 K A -1.8685
190 A A -1.9365
191 D A -2.3763
192 Y A 0.0000
193 E A -2.4428
194 K A -2.7428
195 H A -2.2790
196 K A -1.5174
197 V A -0.5392
198 Y A 0.0000
199 A A -0.5801
200 C A 0.0000
201 E A -1.4507
202 V A 0.0000
203 T A -1.1920
204 H A -1.5681
205 R A -1.9141
206 R A -1.2816
207 R A -1.4665
208 W A 0.2931
209 W A 0.0000
210 W A 0.6234
211 W A 0.7015
212 P A -0.0017
213 V A 0.1778
214 T A -0.3776
215 K A -0.6367
216 S A -0.4608
217 F A 0.0900
218 N A 0.0000
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 -0.4690
433 L A 0.2520
434 V A 0.0000
435 Q A -1.1429
436 P A -0.5179
437 G A -0.7273
438 G A -0.8501
439 S A -0.9870
440 L A 0.0000
441 R A -1.9512
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 -0.6095
448 G A 0.0000
449 F A -0.0343
450 T A -0.8637
451 F A 0.0000
452 S A -1.5757
453 D A -1.6204
454 F A -0.5635
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 -0.3539
461 Q A 0.0000
462 A A -0.4395
463 P A -0.6562
464 G A -0.9717
465 K A -0.9880
466 G A 0.0000
467 L A 0.0000
468 E A -0.3768
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 0.0000
475 R A -2.5190
476 T A -1.8484
477 S A -1.6133
478 H A -1.6862
479 T A -0.7045
480 T A 0.1256
481 Y A 1.3329
482 Y A 0.0000
483 A A 0.0490
484 D A -0.8724
485 S A -0.0535
486 V A 1.3637
487 K A 0.2854
488 G A -0.2878
489 R A -0.1348
490 F A 0.3815
491 T A 0.2383
492 I A 0.2330
493 S A -0.6326
494 R A 0.0000
495 D A -2.2047
496 N A -2.1731
497 S A -1.5571
498 K A -2.3172
499 N A -1.4967
500 T A -0.9444
501 L A 0.0000
502 Y A -0.3701
503 L A 0.0000
504 Q A -1.0624
505 M A 0.0000
506 N A -0.8945
507 S A 0.0000
508 L A 0.8775
509 R A 0.0000
510 A A -0.3453
511 E A -0.6735
512 D A 0.0000
513 T A -0.2568
514 A A 0.0000
515 V A 0.1223
516 Y A 0.0000
517 Y A 0.0000
518 C A 0.0000
519 A A 0.0000
520 R A -0.2607
521 G A 0.0000
522 W A 0.0000
523 Y A 0.6458
524 W A 0.4001
525 M A 0.0000
526 D A -0.1840
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 0.3162
534 V A 0.0000
535 T A 0.0000
536 V A 0.0000
537 S A -0.4080
538 S A -0.1308
539 A A 0.2493
540 S A 0.3921
541 T A 0.1767
542 K A 0.0000
543 G A -0.5461
544 P A -0.2070
545 S A -0.5506
546 V A -0.5421
547 F A -0.7706
548 P A 0.0000
549 L A 0.0000
550 A A 0.0000
551 P A -0.8499
552 S A -0.8373
553 S A 0.0000
554 K A -1.7019
555 S A 0.0000
556 T A -0.7186
557 S A -0.5020
558 G A -0.7620
559 G A -0.8623
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 0.0402
570 Y A 0.0000
571 F A 1.2398
572 P A 0.4894
573 E A 0.0000
574 P A 0.2080
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 -0.8883
581 S A -0.1877
582 G A -0.0858
583 A A -0.1712
584 L A 0.0000
585 T A -0.0365
586 S A -0.1927
587 G A 0.0000
588 V A 0.0000
589 H A 0.0000
590 T A 0.0000
591 F A 0.0000
592 P A 0.0868
593 A A 0.7053
594 V A 0.0000
595 L A 1.5624
596 Q A 0.0000
597 S A 0.0429
598 S A 0.0228
599 G A 0.2734
600 L A 1.1404
601 Y A 1.1408
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 -0.2393
611 S A -0.1796
612 S A -0.0890
613 S A 0.2703
614 L A 1.0275
615 G A 0.0409
616 T A -0.2083
617 Q A -0.4802
618 T A -0.9424
619 Y A 0.0000
620 I A -1.2548
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 -0.5321
628 S A -0.7662
629 N A -1.0208
630 T A -1.2735
631 K A -1.8859
632 V A 0.0000
633 D A -2.1613
634 K A 0.0000
635 K A -2.3451
636 V A 0.0000
637 E A -2.0885
638 P A -1.4455
639 K A -1.5879
640 S A 0.0000
641 C A 0.0000
642 D A 0.0000
643 K A -2.6442
644 T A -1.7880
645 H A -1.3628
646 T A -1.0665
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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, -0.4053 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_0 -0.4053 View CSV PDB
model_8 -0.4435 View CSV PDB
model_11 -0.4537 View CSV PDB
model_2 -0.4553 View CSV PDB
model_7 -0.4601 View CSV PDB
model_6 -0.4709 View CSV PDB
model_9 -0.4766 View CSV PDB
model_1 -0.4866 View CSV PDB
model_4 -0.4879 View CSV PDB
model_3 -0.4996 View CSV PDB
model_5 -0.516 View CSV PDB
model_10 -0.573 View CSV PDB
input -0.7556 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018