Project name: jrk_6FRV

Status: done

Started: 2026-02-08 17:33:24
Chain sequence(s) A: ATLDSWLSNEATVARTAILNNIGADGAWVSGADSGIVVASPSTDNPDYFYTWTRDSGLVLKTLVDLFRNGDTSLLSTIENYISAQAIVQGISNPSGDLSSGAGLGEPKFNVDETAYTGSWGRPQRDGPALRATAMIGFGQWLLDNGYTSTATDIVWPLVRNDLSYVAQYWNQTGYDLWEEVNGSSFFTIAVQHRALVEGSAFATAVGSSCSWCDSQAPEILCYLQSFWTGSFILANFDSSRSGKDANTLLGSIHTFDPEAACDDSTFQPCSPRALANHKEVVDSFRSIYTLNDGLSDSEAVAVGRYPEDTYYNGNPWFLCTLAAAEQLYDALYQWDKQGSLEVTDVSLDFFKALYSDAATGTYSSSSSTYSSIVDAVKTFADGFVSIVETHAASNGSMSEQYDKSDGEQLSARDLTWSYAALLTANNRRNSVVPASWGETSASSVPGTCAATSAIGTYSSVTVTSWP
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
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 minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:23)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:50:17)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:50:21)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:50:25)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:50:29)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:50:33)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:50:37)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:50:41)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:50:44)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:50:48)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:50:52)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:50:56)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:51:00)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:51:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:51:15)
[INFO]       Main:     Simulation completed successfully.                                          (01:51:18)
Show buried residues

Minimal score value
-3.4305
Maximal score value
2.5282
Average score
-0.2689
Total score value
-125.5972

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
25 A A 0.0234
26 T A 0.1446
27 L A -0.0190
28 D A -0.5959
29 S A -0.1821
30 W A 0.3877
31 L A 0.0000
32 S A -0.5213
33 N A -0.9064
34 E A 0.0000
35 A A 0.0000
36 T A -0.3428
37 V A -0.2091
38 A A 0.0000
39 R A -0.4246
40 T A -0.1018
41 A A 0.0000
42 I A 0.0000
43 L A 0.5567
44 N A -0.9335
45 N A -0.5617
46 I A 0.0000
47 G A -0.8559
48 A A -0.9467
49 D A -1.9560
50 G A -0.9022
51 A A -0.1007
52 W A 0.0000
53 V A 1.4436
54 S A -0.1229
55 G A -0.1896
56 A A 0.4594
57 D A 0.0000
58 S A 1.0992
59 G A 0.0000
60 I A 0.0000
61 V A 0.0000
62 V A 0.6426
63 A A 0.0000
64 S A 0.0000
65 P A 0.0216
66 S A -0.5676
67 T A -0.2392
68 D A -0.9000
69 N A -0.4625
70 P A -0.0014
71 D A 0.5223
72 Y A 1.9544
73 F A 2.5282
74 Y A 0.0000
75 T A 0.0000
76 W A 0.0000
77 T A 0.0000
78 R A 0.0000
79 D A 0.0000
80 S A 0.0000
81 G A 0.0000
82 L A 0.0000
83 V A 0.0000
84 L A 0.0000
85 K A 0.0000
86 T A 0.0000
87 L A 0.0000
88 V A 0.0000
89 D A 0.0000
90 L A 0.0000
91 F A -1.2583
92 R A -2.5126
93 N A -2.5165
94 G A -1.9281
95 D A -1.5392
96 T A -0.9048
97 S A -0.0873
98 L A 0.0000
99 L A 0.1807
100 S A -0.2607
101 T A -0.4322
102 I A 0.0000
103 E A -0.3373
104 N A -0.9134
105 Y A 0.0000
106 I A 0.0000
107 S A 0.3900
108 A A 0.0000
109 Q A 0.0000
110 A A 0.0000
111 I A 1.3916
112 V A 0.0000
113 Q A 0.3049
114 G A 0.3911
115 I A 0.5638
116 S A -0.0464
117 N A -0.2374
118 P A -0.4329
119 S A -0.7087
120 G A -0.0053
121 D A 0.0000
122 L A 1.3488
123 S A 0.4815
124 S A -0.1938
125 G A -0.1404
126 A A 0.0000
127 G A 0.0000
128 L A 0.0275
129 G A 0.0000
130 E A 0.0000
131 P A 0.0000
132 K A 0.0000
133 F A 0.0000
134 N A 0.0000
135 V A 1.6592
136 D A -0.4183
137 E A 0.0000
138 T A 0.0160
139 A A 0.0000
140 Y A 0.0000
141 T A -0.2721
142 G A 0.0594
143 S A 0.3077
144 W A 0.9956
145 G A 0.1964
146 R A -0.0901
147 P A -0.1600
148 Q A 0.0000
149 R A 0.0000
150 D A 0.0000
151 G A 0.0000
152 P A 0.0000
153 A A 0.0000
154 L A 0.0000
155 R A 0.0000
156 A A 0.0000
157 T A 0.0000
158 A A 0.0000
159 M A 0.0000
160 I A 0.0000
161 G A -0.2567
162 F A 0.0000
163 G A 0.0000
164 Q A -0.6662
165 W A -0.6365
166 L A 0.0000
167 L A -0.7514
168 D A -2.0803
169 N A -1.7305
170 G A -0.8952
171 Y A 0.3744
172 T A -0.0441
173 S A 0.0674
174 T A 0.0000
175 A A 0.0000
176 T A 0.2090
177 D A 0.2508
178 I A 0.0000
179 V A 0.0000
180 W A 0.0000
181 P A 0.0000
182 L A 0.0000
183 V A 0.0000
184 R A 0.0000
185 N A -0.4259
186 D A 0.0000
187 L A 0.0000
188 S A -0.3859
189 Y A 0.0000
190 V A 0.0000
191 A A -0.4126
192 Q A -1.2578
193 Y A 0.0000
194 W A -0.2727
195 N A 0.0000
196 Q A -1.2117
197 T A 0.0000
198 G A -0.9553
199 Y A -0.5977
200 D A 0.0000
201 L A 0.0000
202 W A 0.0000
203 E A 0.0000
204 E A -1.0455
205 V A 0.0000
206 N A -1.3608
207 G A 0.0000
208 S A -0.2728
209 S A 0.0000
210 F A 0.0000
211 F A 0.0000
212 T A 0.0000
213 I A 0.0000
214 A A 0.0000
215 V A 0.0000
216 Q A 0.0000
217 H A 0.0000
218 R A 0.0000
219 A A 0.0000
220 L A 0.0000
221 V A 0.0000
222 E A -0.2705
223 G A 0.0000
224 S A 0.0000
225 A A -0.1034
226 F A 0.0000
227 A A 0.0000
228 T A -0.0539
229 A A -0.0486
230 V A 0.2962
231 G A -0.0387
232 S A -0.0610
233 S A -0.0343
234 C A 0.0000
235 S A 0.0000
236 W A 0.8210
237 C A 0.0000
238 D A 0.0000
239 S A 0.2351
240 Q A 0.0000
241 A A 0.0000
242 P A -0.0665
243 E A -0.5456
244 I A 0.0000
245 L A -0.1755
246 C A 0.1747
247 Y A 0.3061
248 L A 0.0000
249 Q A -1.1753
250 S A -0.2065
251 F A 0.0000
252 W A 0.0000
253 T A -0.4023
254 G A -0.0811
255 S A -0.1503
256 F A 0.2790
257 I A 0.0000
258 L A 1.1895
259 A A 0.0000
260 N A 0.4197
261 F A 1.3837
262 D A -0.3956
263 S A -0.5908
264 S A -1.1071
265 R A 0.0000
266 S A 0.0000
267 G A -0.0438
268 K A -0.1807
269 D A 0.0000
270 A A 0.0000
271 N A 0.0000
272 T A 0.0000
273 L A 0.0000
274 L A 0.0000
275 G A 0.0000
276 S A 0.0000
277 I A 0.0000
278 H A 0.0000
279 T A 0.0000
280 F A 0.0000
281 D A 0.0000
282 P A -1.1151
283 E A -2.6085
284 A A -2.0576
285 A A 0.0000
286 C A 0.0000
287 D A -2.8829
288 D A -2.4108
289 S A -1.7726
290 T A 0.0000
291 F A 0.0000
292 Q A 0.0000
293 P A 0.0000
294 C A 0.0000
295 S A 0.0000
296 P A -1.0563
297 R A -1.1566
298 A A 0.0000
299 L A 0.0000
300 A A 0.0000
301 N A 0.0000
302 H A 0.0000
303 K A 0.0000
304 E A -1.2021
305 V A 0.0000
306 V A 0.0000
307 D A -1.7056
308 S A -0.9090
309 F A -0.2264
310 R A -0.2170
311 S A 0.5194
312 I A 0.6597
313 Y A 0.4508
314 T A -0.4987
315 L A 0.0000
316 N A -1.7053
317 D A -2.5603
318 G A -2.0988
319 L A 0.0000
320 S A -1.8658
321 D A -2.4776
322 S A -1.2832
323 E A -1.5487
324 A A 0.0000
325 V A 0.0000
326 A A 0.0000
327 V A 0.0000
328 G A 0.0000
329 R A 0.0000
330 Y A 0.2092
331 P A -0.7191
332 E A -2.3553
333 D A -2.4578
334 T A -1.0687
335 Y A -0.1968
336 Y A 0.6519
337 N A -0.0407
338 G A 0.3014
339 N A 0.0000
340 P A 0.0000
341 W A 0.0000
342 F A 0.0000
343 L A 0.0000
344 C A 0.0000
345 T A 0.0000
346 L A 0.0000
347 A A 0.0000
348 A A 0.0000
349 A A 0.0000
350 E A 0.0000
351 Q A 0.0000
352 L A 0.0000
353 Y A -0.1726
354 D A 0.0000
355 A A 0.0000
356 L A -0.8232
357 Y A -0.8309
358 Q A 0.0000
359 W A 0.0000
360 D A -2.7874
361 K A -3.4305
362 Q A -3.0144
363 G A -2.1807
364 S A -1.6228
365 L A 0.0000
366 E A -1.8362
367 V A -1.2218
368 T A -1.3940
369 D A -2.1052
370 V A -0.8027
371 S A -1.1069
372 L A 0.0000
373 D A -1.5424
374 F A 0.0000
375 F A 0.0000
376 K A -1.6416
377 A A -0.5234
378 L A 0.0576
379 Y A 0.3526
380 S A -0.1345
381 D A -0.7867
382 A A 0.0000
383 A A -0.8921
384 T A -0.4555
385 G A -0.9789
386 T A -0.6184
387 Y A -0.7483
388 S A -0.4952
389 S A -0.3362
390 S A -0.4677
391 S A -0.4251
392 S A -0.4980
393 T A -0.5801
394 Y A 0.0000
395 S A -0.8987
396 S A -0.9895
397 I A 0.0000
398 V A -0.9520
399 D A -2.1396
400 A A -1.0517
401 V A 0.0000
402 K A -2.0394
403 T A -1.2395
404 F A -0.9447
405 A A 0.0000
406 D A -0.9154
407 G A -1.3349
408 F A 0.0000
409 V A 0.0000
410 S A -0.6467
411 I A 0.0000
412 V A 0.0000
413 E A -0.2660
414 T A -0.5595
415 H A 0.0000
416 A A -0.4060
417 A A 0.0000
418 S A -0.4673
419 N A -0.7626
420 G A -0.7684
421 S A -0.8011
422 M A 0.0000
423 S A 0.0000
424 E A 0.0000
425 Q A 0.0000
426 Y A -0.9028
427 D A 0.0000
428 K A -2.7030
429 S A -2.2580
430 D A -3.0241
431 G A -2.6758
432 E A -2.4131
433 Q A -1.4234
434 L A -0.7970
435 S A 0.0000
436 A A 0.0000
437 R A -0.8899
438 D A 0.0000
439 L A 0.0000
440 T A 0.0000
441 W A 0.0000
442 S A 0.0000
443 Y A 0.0000
444 A A 0.0000
445 A A 0.0000
446 L A 0.0000
447 L A 0.0000
448 T A 0.0000
449 A A 0.0000
450 N A -0.7457
451 N A -0.8424
452 R A 0.0000
453 R A -1.1332
454 N A -1.3456
455 S A -0.8091
456 V A -0.1105
457 V A 0.0000
458 P A -0.5220
459 A A -0.5123
460 S A -0.5809
461 W A 0.0000
462 G A 0.0000
463 E A 0.0000
464 T A -0.7531
465 S A 0.1629
466 A A 0.0000
467 S A -0.5280
468 S A 0.1302
469 V A 1.4515
470 P A 0.5574
471 G A 0.2269
472 T A 0.5091
473 C A 0.6977
474 A A 0.5239
475 A A 0.3843
476 T A 0.2373
477 S A -0.0580
478 A A 0.1336
479 I A 0.0000
480 G A 0.0546
481 T A 0.3957
482 Y A 1.1959
483 S A 0.5535
484 S A 0.7279
485 V A 1.1857
486 T A 1.0540
487 V A 1.4549
488 T A 0.5132
489 S A 0.1966
490 W A 0.1850
491 P A -0.1447
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D 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 A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.2689 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 A4D Score
model_6 -0.2689 View CSV PDB
model_8 -0.2854 View CSV PDB
model_11 -0.2948 View CSV PDB
model_0 -0.2957 View CSV PDB
model_3 -0.3016 View CSV PDB
model_4 -0.3049 View CSV PDB
model_9 -0.308 View CSV PDB
CABS_average -0.3126 View CSV PDB
model_5 -0.3174 View CSV PDB
model_1 -0.3303 View CSV PDB
model_2 -0.3369 View CSV PDB
model_10 -0.3455 View CSV PDB
model_7 -0.3622 View CSV PDB
input -0.4159 View CSV PDB