Project name: Naba_og

Chain sequence(s)	A: MTRDDAKRVAEEAKRRGVGSGRVIIVIVGPSGAGKTTLLELAKEAKKEVWLE
Selected Chain(s)	A
Distance of aggregation	10 Å
FoldX usage	Yes
pH calculations	Yes
alphaCutter usage	No
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 A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:00)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:00)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:45)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/b35593ad5ac0318/tmp/folded.pdb                (00:01:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:06)

• Minimal score value: -4.4252
• Maximal score value: 3.5308
• Average score: -1.1987
• Total score value: -62.332

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	0.0840
2	T	A	-1.5923
3	R	A	-3.5441
4	D	A	-3.6246
5	D	A	-2.8803
6	A	A	0.0000
7	K	A	-4.4252
8	R	A	-3.7480
9	V	A	-2.2052
10	A	A	0.0000
11	E	A	-3.4991
12	E	A	-3.0791
13	A	A	0.0000
14	K	A	-2.9082
15	R	A	-3.4310
16	R	A	-3.4446
17	G	A	-2.3374
18	V	A	-1.2158
19	G	A	-0.8743
20	S	A	-1.2010
21	G	A	-1.4265
22	R	A	-1.4595
23	V	A	0.6563
24	I	A	2.8125
25	I	A	3.2884
26	V	A	3.5308
27	I	A	2.6000
28	V	A	2.2737
29	G	A	0.5913
30	P	A	-0.2857
31	S	A	-0.4846
32	G	A	-0.7866
33	A	A	-0.2307
34	G	A	-0.2267
35	K	A	0.1059
36	T	A	-0.4332
37	T	A	-0.7224
38	L	A	-0.6862
39	L	A	-0.2522
40	E	A	-2.6126
41	L	A	-2.6091
42	A	A	0.0000
43	K	A	-3.7913
44	E	A	-4.4049
45	A	A	0.0000
46	K	A	-3.8725
47	K	A	-3.6691
48	E	A	-3.5173
49	V	A	0.0000
50	W	A	-0.9230
51	L	A	-0.2372
52	E	A	-1.6334

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	-1.4287	3.8022
4.5	-1.5558	3.8022
5.0	-1.7193	3.8022
5.5	-1.8863	3.8022
6.0	-2.02	3.8022
6.5	-2.0906	3.8022
7.0	-2.0932	3.8022
7.5	-2.0483	3.8022
8.0	-1.9793	3.8022
8.5	-1.8977	3.8022
9.0	-1.8051	3.8049