Project name: FG5 RYRW4

Status: done

Started: 2021-10-15 06:20:10
Settings
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCKSSQSLLNSRDGKNYLAWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQQYWYWMYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHRYRWWWWPVTKSFNRGECEVQLVESGGGLVQPGGSLRLSCAASGFTFSDFSMSWVRQAPGKGLEWVSYISRTSHTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGWYWMDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
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                                                (00:04:32)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:28:05)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:28:08)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:28:11)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:28:13)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:28:16)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:28:19)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:28:22)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:28:25)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:28:28)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:28:30)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:28:33)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:28:36)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:28:39)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:28:43)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:28:43)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:28:43)
[INFO]       Main:     Simulation completed successfully.                                          (01:28:46)
Show buried residues

Minimal score value
-3.0535
Maximal score value
2.5052
Average score
-0.465
Total score value
-207.3919

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 -1.9132
2 I A 0.0000
3 Q A -1.2373
4 M A -0.9878
5 T A -0.9149
6 Q A -0.7025
7 S A -0.5796
8 P A -0.3527
9 S A -0.4583
10 S A -0.4623
11 L A -0.3424
12 S A -0.9918
13 A A 0.0000
14 S A -1.3978
15 V A -1.1700
16 G A -1.3703
17 D A -1.9447
18 R A 0.0000
19 V A -0.2268
20 T A -0.0003
21 I A 0.0000
22 T A -0.6729
23 C A 0.0000
24 K A -1.8451
25 S A -1.5312
26 S A -1.3451
27 Q A -1.6577
28 S A -1.1559
29 L A 0.0000
30 L A 0.2552
31 N A 0.0000
32 S A -0.6231
33 R A -0.7169
34 D A -2.1114
35 G A -1.5980
36 K A 0.0000
37 N A -1.0047
38 Y A -0.5547
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 -0.3404
47 G A 0.0000
48 K A 0.0000
49 A A 0.0000
50 P A 0.0000
51 K A -0.3890
52 L A 0.0000
53 L A 0.0000
54 I A 0.0000
55 Y A 0.0000
56 D A -0.6753
57 A A -0.6845
58 S A -1.0806
59 N A -1.7547
60 L A -1.4435
61 E A -1.6042
62 T A -1.2004
63 G A -0.8985
64 V A -0.9004
65 P A -0.9760
66 S A 0.0000
67 R A -2.0068
68 F A 0.0000
69 S A -0.8777
70 G A -0.6034
71 S A -0.6179
72 G A -1.1391
73 S A -1.0464
74 G A -1.0625
75 T A -1.5743
76 D A -2.1909
77 F A 0.0000
78 T A -0.8172
79 F A 0.0000
80 T A -0.3695
81 I A 0.0000
82 S A -1.0245
83 S A -1.0101
84 L A 0.0000
85 Q A -1.4362
86 P A 0.0000
87 E A -1.0082
88 D A 0.0000
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 0.7236
99 Y A 1.5842
100 W A 1.0531
101 M A 0.0000
102 Y A 0.0000
103 T A -0.7008
104 F A 0.0000
105 G A -0.7745
106 G A -0.6025
107 G A -0.6859
108 T A 0.0000
109 K A -0.6658
110 V A 0.0000
111 E A -1.1357
112 I A 0.0000
113 K A -2.0165
114 R A -1.4684
115 T A 0.1116
116 V A 1.2559
117 A A 0.0000
118 A A 0.9079
119 P A 0.3189
120 S A -0.2271
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 -2.7807
129 E A -2.9867
130 Q A -2.1619
131 L A 0.0000
132 K A -2.9860
133 S A -1.7763
134 G A -1.1837
135 T A -0.8966
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 -0.5766
147 P A 0.0000
148 R A -2.4754
149 E A -2.5720
150 A A -1.6570
151 K A -2.3869
152 V A 0.0000
153 Q A -1.5377
154 W A 0.0000
155 K A -1.4117
156 V A 0.0000
157 D A -2.0737
158 N A -1.6772
159 A A -0.5448
160 L A 0.2680
161 Q A -0.5168
162 S A -0.9598
163 G A -0.7823
164 N A -1.1141
165 S A -1.1799
166 Q A -0.9512
167 E A -1.2836
168 S A 0.0000
169 V A 0.0597
170 T A 0.0000
171 E A -0.4413
172 Q A 0.0000
173 D A 0.0000
174 S A -0.7975
175 K A -1.3551
176 D A -1.9507
177 S A 0.0000
178 T A 0.0000
179 Y A -0.5517
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 -0.4429
187 L A 0.0000
188 S A -0.9296
189 K A -1.9605
190 A A -1.6548
191 D A -2.0382
192 Y A 0.0000
193 E A -2.2109
194 K A -2.5816
195 H A -2.2913
196 K A -1.3484
197 V A -0.0492
198 Y A 0.0000
199 A A -0.5511
200 C A 0.0000
201 E A -1.4990
202 V A 0.0000
203 T A -0.6294
204 H A 0.0000
205 R A -0.0146
206 Y A 1.0262
207 R A -0.2567
208 W A 1.4529
209 W A 2.5052
210 W A 2.4077
211 W A 2.1641
212 P A 0.3605
213 V A -0.0063
214 T A -0.4625
215 K A -0.4107
216 S A 0.1759
217 F A 1.0711
218 N A -0.0187
219 R A -0.8782
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 0.1004
434 V A 0.0000
435 Q A -1.6247
436 P A -1.2850
437 G A -1.4892
438 G A -1.4229
439 S A -1.6597
440 L A 0.0000
441 R A -2.1591
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 -0.0808
449 F A 0.6296
450 T A -0.6310
451 F A 0.0000
452 S A -1.4393
453 D A -2.3193
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 0.0000
461 Q A 0.0000
462 A A -0.7302
463 P A -0.5614
464 G A -0.4941
465 K A -0.6967
466 G A -0.5372
467 L A -0.1135
468 E A -0.2064
469 W A 0.0000
470 V A 0.0000
471 S A 0.0000
472 Y A 0.3668
473 I A 0.0000
474 S A -0.8062
475 R A -1.7258
476 T A -1.4801
477 S A -1.1688
478 H A -1.3385
479 T A -0.6339
480 T A -0.1309
481 Y A 0.4418
482 Y A 0.0194
483 A A 0.0000
484 D A -1.7216
485 S A 0.0000
486 V A 0.7558
487 K A 0.0000
488 G A 0.0000
489 R A -2.0363
490 F A 0.0000
491 T A -0.7624
492 I A 0.0000
493 S A -0.9760
494 R A -1.6345
495 D A -2.0800
496 N A -2.2404
497 S A -1.5467
498 K A -1.8185
499 N A -1.3499
500 T A 0.0000
501 L A 0.0000
502 Y A -0.5813
503 L A 0.0000
504 Q A -1.5838
505 M A 0.0000
506 N A -1.9249
507 S A -1.7721
508 L A -1.7572
509 R A -2.1231
510 A A -1.9693
511 E A -3.0535
512 D A -2.5644
513 T A -1.4743
514 A A 0.0000
515 V A -0.2468
516 Y A 0.0000
517 Y A 0.0000
518 C A 0.0000
519 A A 0.0000
520 R A -0.1216
521 G A -0.1171
522 W A 0.0000
523 Y A 1.1681
524 W A 0.5510
525 M A 0.0000
526 D A -0.1515
527 L A 0.0914
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 -0.2037
534 V A 0.0000
535 T A -0.8427
536 V A -1.1628
537 S A -1.0074
538 S A -0.6643
539 A A -0.0006
540 S A -0.0623
541 T A -0.4935
542 K A -1.2543
543 G A -1.1843
544 P A -0.7397
545 S A -0.3219
546 V A 0.0000
547 F A 0.0000
548 P A -1.1514
549 L A 0.0000
550 A A 0.0000
551 P A 0.0000
552 S A -0.6862
553 S A -0.3368
554 K A -0.4678
555 S A 0.0000
556 T A -0.5984
557 S A -0.8064
558 G A -0.9166
559 G A -0.7982
560 T A -0.6654
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 -0.1821
570 Y A 0.0000
571 F A 0.2654
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 0.2357
581 S A 0.0000
582 G A 0.0000
583 A A 0.4680
584 L A 0.9156
585 T A 0.3464
586 S A 0.1783
587 G A -0.0891
588 V A 0.0000
589 H A 0.0000
590 T A 0.0205
591 F A 0.0000
592 P A -0.1604
593 A A 0.2728
594 V A 0.0000
595 L A 1.4432
596 Q A 0.4110
597 S A -0.0054
598 S A 0.1071
599 G A 0.0000
600 L A 1.1206
601 Y A 0.9083
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 -0.3295
611 S A -0.1994
612 S A -0.2877
613 S A 0.1485
614 L A 0.9420
615 G A 0.1024
616 T A -0.2700
617 Q A -0.5020
618 T A -0.9056
619 Y A 0.0000
620 I A -0.7317
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 -1.5171
627 P A -1.1158
628 S A -1.4412
629 N A -1.9045
630 T A -1.3925
631 K A -1.6233
632 V A -1.1035
633 D A -1.4246
634 K A -1.5377
635 K A -2.0868
636 V A 0.0000
637 E A -1.7701
638 P A -1.3970
639 K A -2.1234
640 S A -1.0570
641 C A -0.6879
642 D A 0.0000
643 K A -2.2115
644 T A 0.0000
645 H A -2.1984
646 T A -1.4596
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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, -0.465 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_3 -0.465 View CSV PDB
model_4 -0.5089 View CSV PDB
model_6 -0.5124 View CSV PDB
model_0 -0.5131 View CSV PDB
model_7 -0.5161 View CSV PDB
model_10 -0.5161 View CSV PDB
model_9 -0.5184 View CSV PDB
model_11 -0.5485 View CSV PDB
model_2 -0.5735 View CSV PDB
model_8 -0.5736 View CSV PDB
model_5 -0.5761 View CSV PDB
model_1 -0.5973 View CSV PDB
input -0.7514 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018