Project name: Aggregation prone

Chain sequence(s)	A: MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
Selected Chain(s)	A
Distance of aggregation	10 Å
FoldX usage	Yes
pH calculations	Yes
alphaCutter usage	A: MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERG FFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN ; (Red indicates removed residues)
Dynamic mode	No
Automated mutations	No

Simulation log

[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:12)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:12)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:12)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:12)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:13)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:50)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:50)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:50)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:58)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4d153e67287ba51/tmp/folded.pdb                (00:01:58)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:09)

• Minimal score value: -2.6813
• Maximal score value: 3.6469
• Average score: 1.1618
• Total score value: 54.6048

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	M	A	1.7965
2	A	A	1.6203
3	L	A	2.3538
4	W	A	2.4620
5	M	A	1.8070
6	R	A	0.2861
7	L	A	1.4928
8	L	A	1.9339
9	P	A	1.1811
10	L	A	1.9706
11	L	A	2.5044
12	A	A	2.4503
13	L	A	3.2783
14	L	A	3.4481
15	A	A	2.0797
16	L	A	2.7197
17	W	A	2.4911
18	G	A	1.0897
19	P	A	-0.4719
20	D	A	-1.5157
21	P	A	-0.9929
22	A	A	-0.1391
23	A	A	0.5334
24	A	A	0.9970
25	F	A	2.3515
26	V	A	1.5347
27	N	A	-0.5047
28	Q	A	-1.1482
29	H	A	-0.7249
30	L	A	1.0150
31	C	A	0.9993
32	G	A	0.4288
33	S	A	0.1529
34	H	A	0.1510
35	L	A	2.0285
36	V	A	2.2806
37	E	A	0.7455
38	A	A	2.1219
39	L	A	3.6469
40	Y	A	3.4500
41	L	A	3.1561
42	V	A	2.8670
43	C	A	1.4388
44	G	A	0.0376
45	E	A	-2.3347
46	R	A	-2.6813
47	G	A	-1.7837

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 likely a peptide. Results may be inaccurate. The input structure is partially or entirely disordered. Average score is recommended for pH analysis.

pH	Average A4D Score	Max A4D Score
4.0	2.4612	6.2668
4.5	2.4108	6.2158
5.0	2.3438	6.1517
5.5	2.2753	6.0817
6.0	2.2192	6.0096
6.5	2.1789	5.9369
7.0	2.1482	5.8805
7.5	2.1201	5.8805
8.0	2.0925	5.8805
8.5	2.0664	5.8805
9.0	2.0445	5.8805