Project name: N_half_og

Chain sequence(s)	A: KKKLVIIYGKKGSGKTKKYEKEKKKAKKTPNAKVVIVSTEEELKKEKEKAKELGIEVK; D: KKKLVIIYGKKGSGKTKKYEKEKKKAKKTPNAKVVIVSTEEELKKEKEKAKELGIEVK; G: KKKLVIIYGKKGSGKTKKYEKEKKKAKKTPNAKVVIVSTEEELKKEKEKAKELGIEVK; J: KKKLVIIYGKKGSGKTKKYEKEKKKAKKTPNAKVVIVSTEEELKKEKEKAKELGIEVK; M: KKKLVIIYGKKGSGKTKKYEKEKKKAKKTPNAKVVIVSTEEELKKEKEKAKELGIEVK; P: KKKLVIIYGKKGSGKTKKYEKEKKKAKKTPNAKVVIVSTEEELKKEKEKAKELGIEVK
Selected Chain(s)	A,D,G,J,M,P
Distance of aggregation	10 Å
FoldX usage	Yes
pH calculations	Yes
alphaCutter usage	Used: no changes made
Dynamic mode	No
Automated mutations	No

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 all chain(s) selected           (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:09)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:09)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:10)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:43:14)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2577bc21df10edf/tmp/folded.pdb                (00:43:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:45:21)

• Minimal score value: -5.3204
• Maximal score value: 0.9993
• Average score: -2.1831
• Total score value: -759.7195

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
1	K	A	-2.4180
2	K	A	-2.8428
3	K	A	-2.4671
4	L	A	0.0000
5	V	A	-0.3941
6	I	A	0.2816
7	I	A	0.0000
8	Y	A	-0.0641
9	G	A	-1.3133
10	K	A	-2.8733
11	K	A	-2.8990
12	G	A	-2.0671
13	S	A	-1.9283
14	G	A	-2.1708
15	K	A	-2.2246
16	T	A	-2.1505
17	K	A	-3.5560
18	K	A	-3.2489
19	Y	A	-2.2487
20	E	A	-3.0349
21	K	A	-3.2860
22	E	A	-2.5931
23	K	A	-2.5311
24	K	A	-3.0199
25	K	A	-3.2968
26	A	A	-2.4737
27	K	A	-2.9267
28	K	A	-2.4654
29	T	A	-1.7553
30	P	A	-1.5124
31	N	A	-2.1337
32	A	A	-2.1118
33	K	A	0.0000
34	V	A	0.0000
35	V	A	0.6157
36	I	A	0.4340
37	V	A	0.0000
38	S	A	-1.5553
39	T	A	-2.2622
40	E	A	-3.2599
41	E	A	-3.6226
42	E	A	-2.8534
43	L	A	-2.5742
44	K	A	-4.2753
45	K	A	-4.0377
46	E	A	-3.3319
47	K	A	-3.7280
48	E	A	-4.4757
49	K	A	-3.3656
50	A	A	0.0000
51	K	A	-3.6681
52	E	A	-3.0673
53	L	A	-1.5562
54	G	A	-2.0985
55	I	A	0.0000
56	E	A	-2.8204
57	V	A	-2.0344
58	K	A	-2.1835
1	K	D	-3.7381
2	K	D	-3.4831
3	K	D	-3.0065
4	L	D	0.0000
5	V	D	-0.4588
6	I	D	0.3172
7	I	D	0.0000
8	Y	D	0.0221
9	G	D	-1.1382
10	K	D	-2.5819
11	K	D	-2.7596
12	G	D	-1.9946
13	S	D	-1.7498
14	G	D	-1.8844
15	K	D	-1.7435
16	T	D	-1.8144
17	K	D	-3.0666
18	K	D	-2.8273
19	Y	D	-1.8081
20	E	D	-2.8991
21	K	D	-3.6298
22	E	D	-2.6297
23	K	D	-2.9386
24	K	D	-3.3320
25	K	D	-3.7080
26	A	D	-2.9809
27	K	D	-3.1036
28	K	D	-3.2454
29	T	D	-2.2794
30	P	D	-2.0768
31	N	D	-3.2153
32	A	D	-2.8649
33	K	D	-2.3140
34	V	D	0.0000
35	V	D	0.4136
36	I	D	0.6697
37	V	D	0.0000
38	S	D	-1.5349
39	T	D	-2.4880
40	E	D	-3.7092
41	E	D	-4.1581
42	E	D	-3.6806
43	L	D	-3.1937
44	K	D	-4.9868
45	K	D	-5.1194
46	E	D	-4.3569
47	K	D	-4.4282
48	E	D	-5.3204
49	K	D	-4.6384
50	A	D	0.0000
51	K	D	-4.0907
52	E	D	-3.5001
53	L	D	-2.0830
54	G	D	-2.4031
55	I	D	-2.9080
56	E	D	-3.0099
57	V	D	-1.8477
58	K	D	-1.8119
1	K	G	-2.4411
2	K	G	-2.5617
3	K	G	-1.7082
4	L	G	0.0000
5	V	G	0.4091
6	I	G	0.8378
7	I	G	0.0000
8	Y	G	0.2584
9	G	G	-1.1926
10	K	G	-2.8045
11	K	G	-2.8536
12	G	G	-2.0202
13	S	G	-1.8521
14	G	G	-1.8443
15	K	G	-1.7953
16	T	G	-2.0187
17	K	G	-3.2184
18	K	G	-2.5820
19	Y	G	-2.3142
20	E	G	-3.8553
21	K	G	-3.5663
22	E	G	-2.8542
23	K	G	-3.3459
24	K	G	-3.9828
25	K	G	-3.5497
26	A	G	-2.9537
27	K	G	-3.6888
28	K	G	-3.2807
29	T	G	-2.1674
30	P	G	-1.7077
31	N	G	-2.0595
32	A	G	-1.9749
33	K	G	0.0000
34	V	G	0.0000
35	V	G	0.8466
36	I	G	0.9993
37	V	G	0.0000
38	S	G	-1.4147
39	T	G	-1.9934
40	E	G	-2.8849
41	E	G	-2.9942
42	E	G	-2.1227
43	L	G	-1.5146
44	K	G	-2.7913
45	K	G	-2.8257
46	E	G	-1.8435
47	K	G	-1.5351
48	E	G	-2.4540
49	K	G	-1.7313
50	A	G	0.0000
51	K	G	-1.9802
52	E	G	-1.9756
53	L	G	-0.7805
54	G	G	-1.1539
55	I	G	-1.4972
56	E	G	0.0000
57	V	G	-0.8043
58	K	G	-0.4942
1	K	J	-2.9139
2	K	J	-3.1246
3	K	J	-2.6989
4	L	J	0.0000
5	V	J	-0.3687
6	I	J	0.4321
7	I	J	0.0000
8	Y	J	0.2276
9	G	J	-1.1203
10	K	J	-2.6611
11	K	J	-2.8185
12	G	J	-2.0321
13	S	J	-1.8702
14	G	J	-1.9984
15	K	J	-2.0461
16	T	J	-2.2684
17	K	J	-3.5396
18	K	J	-3.1159
19	Y	J	-2.7444
20	E	J	-4.2957
21	K	J	-4.4331
22	E	J	-3.5071
23	K	J	-3.8932
24	K	J	-4.6551
25	K	J	-4.3888
26	A	J	0.0000
27	K	J	-3.9747
28	K	J	-3.5536
29	T	J	-2.3578
30	P	J	-1.7142
31	N	J	-2.1475
32	A	J	-2.4181
33	K	J	-1.6018
34	V	J	0.0000
35	V	J	0.7144
36	I	J	0.8248
37	V	J	0.0000
38	S	J	-1.3711
39	T	J	-1.7645
40	E	J	-2.5423
41	E	J	-2.8325
42	E	J	-1.8471
43	L	J	-1.1993
44	K	J	0.0000
45	K	J	-2.5614
46	E	J	-1.7200
47	K	J	-1.9710
48	E	J	0.0000
49	K	J	-2.2395
50	A	J	0.0000
51	K	J	-2.9032
52	E	J	-2.2125
53	L	J	-0.8826
54	G	J	-1.6887
55	I	J	-2.2654
56	E	J	-2.9138
57	V	J	-1.7711
58	K	J	-1.8220
1	K	M	-3.3283
2	K	M	-3.0452
3	K	M	-2.6527
4	L	M	0.0000
5	V	M	-0.2255
6	I	M	0.4021
7	I	M	0.0000
8	Y	M	0.0762
9	G	M	-1.2720
10	K	M	-2.8057
11	K	M	-2.8969
12	G	M	-2.0563
13	S	M	-1.9292
14	G	M	-1.9016
15	K	M	-1.9197
16	T	M	-2.0938
17	K	M	-3.2576
18	K	M	-2.5519
19	Y	M	-2.3695
20	E	M	-3.9740
21	K	M	-3.7925
22	E	M	0.0000
23	K	M	-3.9865
24	K	M	-3.8755
25	K	M	-3.9130
26	A	M	-3.6952
27	K	M	-3.9522
28	K	M	-3.4323
29	T	M	-2.5870
30	P	M	-2.3789
31	N	M	-3.3910
32	A	M	-3.3417
33	K	M	-3.1476
34	V	M	0.0000
35	V	M	0.2701
36	I	M	0.6576
37	V	M	0.0000
38	S	M	0.0000
39	T	M	-2.0861
40	E	M	-2.8633
41	E	M	-3.2592
42	E	M	-3.0277
43	L	M	-2.4889
44	K	M	-4.1067
45	K	M	-4.4968
46	E	M	-3.4414
47	K	M	-3.2078
48	E	M	-4.3820
49	K	M	-3.5564
50	A	M	0.0000
51	K	M	-2.9106
52	E	M	-3.3097
53	L	M	-1.2444
54	G	M	-1.6205
55	I	M	-2.0363
56	E	M	-1.7705
57	V	M	-1.1205
58	K	M	-0.9235
1	K	P	-3.3805
2	K	P	-3.1997
3	K	P	-2.5320
4	L	P	0.0000
5	V	P	-0.1503
6	I	P	0.3451
7	I	P	0.0000
8	Y	P	-0.3719
9	G	P	-1.4807
10	K	P	-2.8902
11	K	P	-2.9188
12	G	P	-2.0536
13	S	P	-1.9681
14	G	P	-1.9551
15	K	P	-2.0078
16	T	P	-2.1541
17	K	P	-3.3197
18	K	P	-2.7154
19	Y	P	-2.5934
20	E	P	-4.0805
21	K	P	-4.5880
22	E	P	-3.5172
23	K	P	-4.2917
24	K	P	-4.8080
25	K	P	-4.6926
26	A	P	-3.9404
27	K	P	-4.2688
28	K	P	-3.8178
29	T	P	-2.6609
30	P	P	-2.3775
31	N	P	-3.3946
32	A	P	-3.3544
33	K	P	-3.1228
34	V	P	0.0000
35	V	P	0.1649
36	I	P	0.4444
37	V	P	0.0000
38	S	P	-1.7418
39	T	P	-2.5386
40	E	P	-3.5567
41	E	P	-4.0318
42	E	P	-3.5948
43	L	P	-3.0513
44	K	P	-4.6835
45	K	P	-4.8319
46	E	P	-3.9594
47	K	P	-3.6501
48	E	P	-4.9750
49	K	P	-4.3651
50	A	P	0.0000
51	K	P	-3.6931
52	E	P	-3.4319
53	L	P	-1.9012
54	G	P	-2.0670
55	I	P	-2.0661
56	E	P	-1.4343
57	V	P	-0.8696
58	K	P	-0.6347

Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is partially or entirely disordered. Average score is recommended for pH analysis.

pH	Average A4D Score	Max A4D Score
4.0	-3.3058	1.1066
4.5	-3.3891	1.093
5.0	-3.4845	1.0783
5.5	-3.5378	1.0727
6.0	-3.4795	1.089
6.5	-3.2677	1.1334
7.0	-2.9232	1.2004
7.5	-2.5012	1.2799
8.0	-2.0459	1.3644
8.5	-1.5803	1.4503
9.0	-1.1165	1.5354