Project name: 1VII_ph_test

Chain sequence(s)	A: MLSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLF
Selected Chain(s)	A
Distance of aggregation	10 Å
FoldX usage	No
pH calculations	Yes
alphaCutter usage	No
Dynamic mode	No
Automated mutations	No

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)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:01)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:01)
[INFO]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:01)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/3f7e66e654199e2/tmp/folded.pdb                (00:00:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:47)

• Minimal score value: -4.1398
• Maximal score value: 1.9181
• Average score: -1.0602
• Total score value: -38.169

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
41	M	A	0.9357
42	L	A	-0.5788
43	S	A	-2.2275
44	D	A	-3.6196
45	E	A	-4.1398
46	D	A	-3.3597
47	F	A	0.0000
48	K	A	-3.2768
49	A	A	-1.7990
50	V	A	-1.0723
51	F	A	-0.8158
52	G	A	-0.5921
53	M	A	0.0953
54	T	A	-1.1338
55	R	A	-1.4657
56	S	A	-0.8011
57	A	A	-0.5485
58	F	A	0.0000
59	A	A	-0.6900
60	N	A	-1.0126
61	L	A	0.2367
62	P	A	0.5438
63	L	A	1.4223
64	W	A	1.0547
65	K	A	-0.3159
66	Q	A	-1.0494
67	Q	A	-1.9398
68	N	A	-2.5948
69	L	A	-1.7986
70	K	A	-2.5207
71	K	A	-3.0545
72	E	A	-3.1569
73	K	A	-1.6152
74	G	A	-0.3092
75	L	A	1.1125
76	F	A	1.9181

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	-0.4949	4.1243
4.5	-0.6205	4.059
5.0	-0.7708	3.9791
5.5	-0.9214	3.8994
6.0	-1.039	3.8438
6.5	-1.0947	3.8335
7.0	-1.0847	3.8718
7.5	-1.027	3.9468
8.0	-0.9398	4.0443
8.5	-0.8285	4.1582
9.0	-0.6919	4.2873