Project name: FG5 RIRW4

Status: done

Started: 2021-10-15 06:17:16
Settings
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCKSSQSLLNSRDGKNYLAWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQQYWYWMYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHRIRWWWWPVTKSFNRGECEVQLVESGGGLVQPGGSLRLSCAASGFTFSDFSMSWVRQAPGKGLEWVSYISRTSHTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGWYWMDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
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                                                (00:04:16)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:23:29)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:23:32)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:23:35)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:23:38)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:23:41)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:23:44)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:23:47)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:23:49)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:23:52)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:23:55)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:23:58)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:24:01)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:24:04)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:24:08)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:24:08)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:24:09)
[INFO]       Main:     Simulation completed successfully.                                          (01:24:12)
Show buried residues

Minimal score value
-3.0895
Maximal score value
2.36
Average score
-0.4709
Total score value
-210.0012

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 -2.3512
2 I A 0.0000
3 Q A -2.1194
4 M A 0.0000
5 T A -1.1122
6 Q A 0.0000
7 S A -0.6696
8 P A -0.4245
9 S A -0.5281
10 S A -0.6381
11 L A -0.6216
12 S A -0.3104
13 A A -0.5791
14 S A -0.2002
15 V A 0.2690
16 G A -0.7040
17 D A -1.5927
18 R A -2.4247
19 V A 0.0000
20 T A -0.5427
21 I A 0.0000
22 T A -0.9036
23 C A 0.0000
24 K A -2.6319
25 S A 0.0000
26 S A -2.0245
27 Q A -2.0610
28 S A -1.1191
29 L A -0.3672
30 L A -0.1017
31 N A -0.8752
32 S A -1.6318
33 R A -2.9663
34 D A -3.0704
35 G A -2.5405
36 K A -2.8865
37 N A -1.6483
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 -0.5147
46 P A -0.5771
47 G A -0.6069
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 0.2381
56 D A -1.1429
57 A A -1.3462
58 S A -0.5174
59 N A -0.5384
60 L A 1.0664
61 E A 0.4460
62 T A 0.4492
63 G A 0.4236
64 V A 0.8599
65 P A -0.1176
66 S A -0.7290
67 R A -1.7963
68 F A -0.4130
69 S A -0.4992
70 G A -0.5726
71 S A -0.7090
72 G A -0.8077
73 S A -1.0261
74 G A -1.0016
75 T A -1.3203
76 D A -2.0952
77 F A 0.0000
78 T A -0.9050
79 F A 0.0000
80 T A -0.6941
81 I A 0.0000
82 S A -1.5072
83 S A -1.2670
84 L A 0.0000
85 Q A -0.7352
86 P A 0.0000
87 E A 0.0000
88 D A 0.0000
89 I A -0.1848
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 1.2755
99 Y A 1.6886
100 W A 2.3600
101 M A 1.2453
102 Y A 0.0000
103 T A 0.0000
104 F A -0.5800
105 G A -1.0819
106 G A -0.9927
107 G A -0.7875
108 T A -0.7184
109 K A -0.9660
110 V A 0.0000
111 E A -0.4504
112 I A -0.5888
113 K A -1.2022
114 R A -1.5167
115 T A -0.5881
116 V A 0.1873
117 A A 0.1693
118 A A 0.3443
119 P A -0.1159
120 S A -0.5262
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 0.0000
129 E A 0.0000
130 Q A 0.0000
131 L A -0.7361
132 K A -1.6252
133 S A -0.9972
134 G A -1.0594
135 T A -0.8650
136 A A 0.0000
137 S A -0.3582
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 -0.8611
145 F A 0.0000
146 Y A 0.0000
147 P A -1.5621
148 R A -2.7498
149 E A -1.8824
150 A A 0.0000
151 K A -1.7966
152 V A -1.1284
153 Q A -0.8941
154 W A -0.6550
155 K A -1.3666
156 V A -1.4569
157 D A -2.4799
158 N A -1.9261
159 A A -0.6111
160 L A 0.2656
161 Q A -0.7017
162 S A -0.6472
163 G A -0.8144
164 N A -1.2580
165 S A -1.1190
166 Q A -1.0746
167 E A -1.5032
168 S A 0.0000
169 V A 0.5818
170 T A 0.0000
171 E A -0.1215
172 Q A 0.0000
173 D A -0.5126
174 S A 0.0000
175 K A -1.2359
176 D A -2.0559
177 S A -1.4193
178 T A 0.0000
179 Y A -0.7313
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 -0.6542
187 L A 0.0000
188 S A -0.9865
189 K A -1.7069
190 A A -1.6708
191 D A -2.3084
192 Y A 0.0000
193 E A -2.2573
194 K A -2.8824
195 H A -2.4644
196 K A -2.2643
197 V A -1.1488
198 Y A 0.0000
199 A A -0.9587
200 C A 0.0000
201 E A -0.6989
202 V A 0.0000
203 T A 0.0000
204 H A 0.0000
205 R A -0.0365
206 I A 0.3204
207 R A -0.8988
208 W A 1.3801
209 W A 2.0151
210 W A 2.0020
211 W A 1.8876
212 P A 0.4687
213 V A 0.0000
214 T A -0.1579
215 K A -0.3353
216 S A -0.2911
217 F A -0.3482
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 0.4751
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 0.1369
434 V A -0.4780
435 Q A -1.3994
436 P A -1.4699
437 G A -1.2443
438 G A -1.3217
439 S A -1.5215
440 L A 0.0000
441 R A -2.0684
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 0.8511
449 F A 1.4135
450 T A -0.0471
451 F A 0.0000
452 S A -1.0624
453 D A -1.6621
454 F A -0.3961
455 S A -0.5686
456 M A 0.0000
457 S A 0.0000
458 W A 0.0000
459 V A 0.0000
460 R A -0.5304
461 Q A -0.8931
462 A A -1.2938
463 P A -1.4115
464 G A -1.5490
465 K A -2.1711
466 G A -1.3946
467 L A 0.0000
468 E A -0.9621
469 W A 0.0000
470 V A 0.0000
471 S A 0.0000
472 Y A 0.7855
473 I A 0.0000
474 S A 0.0000
475 R A -2.6960
476 T A -1.7815
477 S A -1.1879
478 H A -2.0651
479 T A -0.7035
480 T A 0.2497
481 Y A 1.7748
482 Y A 1.6772
483 A A 1.0154
484 D A 0.0910
485 S A 0.0000
486 V A 1.2042
487 K A -0.3815
488 G A -0.6509
489 R A -0.1326
490 F A 0.6341
491 T A 0.4928
492 I A 0.7449
493 S A -0.4744
494 R A -2.0053
495 D A -2.5444
496 N A -2.7694
497 S A -1.9720
498 K A -2.5975
499 N A 0.0000
500 T A -1.2148
501 L A 0.0000
502 Y A 0.0690
503 L A 0.0000
504 Q A -1.0001
505 M A 0.0000
506 N A -1.5812
507 S A -1.4183
508 L A -1.5004
509 R A -2.3635
510 A A -2.3705
511 E A -3.0895
512 D A -2.8808
513 T A -1.6711
514 A A -1.1288
515 V A -0.4175
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 0.5706
523 Y A 1.5352
524 W A 0.0000
525 M A 0.0000
526 D A 0.0000
527 L A 0.1037
528 W A 0.0000
529 G A 0.0000
530 Q A -0.2094
531 G A 0.0000
532 T A 0.0000
533 L A -0.2100
534 V A 0.0000
535 T A 0.0000
536 V A 0.0000
537 S A -1.1775
538 S A -0.6345
539 A A 0.0000
540 S A -0.4382
541 T A -0.8636
542 K A -1.7812
543 G A -1.5278
544 P A -0.8111
545 S A -0.5906
546 V A -0.6643
547 F A -0.6350
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 -1.1780
554 K A 0.0000
555 S A -0.6607
556 T A -0.5309
557 S A -0.4848
558 G A -1.0420
559 G A -0.7413
560 T A -0.6461
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 -0.0848
569 D A -0.3622
570 Y A 0.0000
571 F A 0.0939
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 -0.0099
581 S A -0.4035
582 G A 0.0000
583 A A 0.0000
584 L A 0.8337
585 T A 0.4211
586 S A 0.0996
587 G A -0.3834
588 V A -0.0392
589 H A 0.0000
590 T A 0.0000
591 F A 0.0000
592 P A 0.1501
593 A A 0.3485
594 V A 0.7695
595 L A 1.6254
596 Q A 0.3638
597 S A -0.0221
598 S A 0.0905
599 G A 0.0926
600 L A 1.2456
601 Y A 1.1030
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 -0.3635
611 S A -0.3421
612 S A -0.2604
613 S A 0.0213
614 L A 0.3963
615 G A -0.2828
616 T A -0.0117
617 Q A 0.0000
618 T A 0.0000
619 Y A 0.6831
620 I A -0.4326
621 C A 0.0000
622 N A -1.7317
623 V A 0.0000
624 N A -1.7225
625 H A 0.0000
626 K A -1.8103
627 P A -0.9389
628 S A -1.4048
629 N A -2.0825
630 T A -1.9185
631 K A -2.5739
632 V A -1.8660
633 D A -2.7093
634 K A -2.1062
635 K A -2.1586
636 V A 0.0000
637 E A -1.6390
638 P A -1.4630
639 K A -1.4124
640 S A -1.0042
641 C A -0.9474
642 D A -1.3540
643 K A -2.1845
644 T A -1.4327
645 H A -1.4024
646 T A -0.7151
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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, -0.4709 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 -0.4709 View CSV PDB
model_6 -0.4749 View CSV PDB
model_5 -0.4847 View CSV PDB
model_4 -0.485 View CSV PDB
model_9 -0.4887 View CSV PDB
model_0 -0.4927 View CSV PDB
model_8 -0.493 View CSV PDB
model_10 -0.4938 View CSV PDB
model_3 -0.5015 View CSV PDB
model_7 -0.5021 View CSV PDB
model_2 -0.516 View CSV PDB
model_11 -0.5723 View CSV PDB
input -0.7351 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018