Project name: VPS9-WT_AF3-00 [mutate: RP99A] [mutate: PR99A]

Chain sequence(s)	A: KQPDIALLGFLGVQRKFWPATLSILGESKKVLPTTKDACFASAVECLQQISTTFTPSDKLKVIQQTFEEISQSVLASLHEDFLWSMDDLFPVFLYVVLPARIRNLGSEVHLIEDLMDPYLQHGEQGIMFTTLKACYYQIQREKLN
Selected Chain(s)	A
Distance of aggregation	5 Å
FoldX usage	Yes
pH calculations	Yes
alphaCutter usage	No
Dynamic mode	No
Automated mutations	No
Mutated residues	PR99A
Energy difference between WT (input) and mutated protein (by FoldX)	-4.87622 kcal/mol

Simulation log

[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       FoldX:    Building mutant model                                                       (00:02:40)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:03)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4a6959489d13e54/tmp/folded.pdb                (00:03:03)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:19)

• Minimal score value: -2.4565
• Maximal score value: 2.0423
• Average score: -0.3032
• Total score value: -43.9679

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	-1.8363
2	Q	A	-1.0734
3	P	A	-0.3410
4	D	A	0.0000
5	I	A	0.4012
6	A	A	0.1110
7	L	A	0.0000
8	L	A	0.0000
9	G	A	0.0030
10	F	A	1.9170
11	L	A	0.4786
12	G	A	-0.4280
13	V	A	0.0000
14	Q	A	-1.5282
15	R	A	-2.2913
16	K	A	-1.6278
17	F	A	0.0000
18	W	A	0.1402
19	P	A	0.0000
20	A	A	0.0456
21	T	A	-0.2657
22	L	A	0.1353
23	S	A	-0.0443
24	I	A	1.1144
25	L	A	1.6215
26	G	A	-0.5169
27	E	A	-1.9428
28	S	A	-0.7367
29	K	A	-1.2773
30	K	A	-1.8380
31	V	A	0.0495
32	L	A	0.7379
33	P	A	-0.1351
34	T	A	-0.1184
35	T	A	-0.2434
36	K	A	-1.4683
37	D	A	-1.5422
38	A	A	-0.2254
39	C	A	0.0000
40	F	A	0.0000
41	A	A	-0.0096
42	S	A	-0.1556
43	A	A	0.0000
44	V	A	0.0000
45	E	A	-1.8040
46	C	A	-0.2416
47	L	A	0.0000
48	Q	A	-0.7839
49	Q	A	-0.8931
50	I	A	0.0000
51	S	A	-0.0645
52	T	A	-0.0824
53	T	A	0.3272
54	F	A	1.9343
55	T	A	0.3178
56	P	A	-0.0820
57	S	A	-0.3257
58	D	A	-0.7973
59	K	A	0.0000
60	L	A	0.0000
61	K	A	-1.7957
62	V	A	0.0000
63	I	A	0.0000
64	Q	A	-0.6658
65	Q	A	-0.9981
66	T	A	0.0000
67	F	A	0.0000
68	E	A	-1.9852
69	E	A	-0.8158
70	I	A	0.0000
71	S	A	-0.2779
72	Q	A	-1.2189
73	S	A	-0.2689
74	V	A	0.0000
75	L	A	1.4193
76	A	A	0.2879
77	S	A	-0.0769
78	L	A	0.1460
79	H	A	-1.2775
80	E	A	-2.3134
81	D	A	-2.0185
82	F	A	0.4668
83	L	A	1.6750
84	W	A	0.4616
85	S	A	0.0629
86	M	A	0.1939
87	D	A	-1.7840
88	D	A	-0.7654
89	L	A	0.2650
90	F	A	0.6483
91	P	A	0.0781
92	V	A	0.0000
93	F	A	0.0000
94	L	A	0.0000
95	Y	A	0.0000
96	V	A	0.0000
97	V	A	0.0000
98	L	A	0.2275
99	R	A	0.0000	mutated: PR99A
100	A	A	0.0000
101	R	A	-1.8024
102	I	A	-0.4471
103	R	A	-2.0339
104	N	A	-1.5813
105	L	A	-0.0809
106	G	A	-0.0794
107	S	A	-0.2638
108	E	A	-0.2512
109	V	A	0.0000
110	H	A	-0.9659
111	L	A	0.3343
112	I	A	0.0000
113	E	A	-1.1008
114	D	A	-1.6355
115	L	A	1.2285
116	M	A	0.0000
117	D	A	-1.6661
118	P	A	-0.3068
119	Y	A	1.3321
120	L	A	0.4903
121	Q	A	-0.6426
122	H	A	-1.1032
123	G	A	-0.6110
124	E	A	-1.8893
125	Q	A	-0.5944
126	G	A	0.0000
127	I	A	2.0423
128	M	A	0.4983
129	F	A	0.0000
130	T	A	-0.1019
131	T	A	0.0000
132	L	A	0.0000
133	K	A	-0.3111
134	A	A	-0.0256
135	C	A	0.0000
136	Y	A	0.2477
137	Y	A	0.5479
138	Q	A	-0.3195
139	I	A	0.0762
140	Q	A	-0.7889
141	R	A	-2.2627
142	E	A	-2.4565
143	K	A	-1.7460
144	L	A	1.0111
145	N	A	-0.9934

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 globular. Max score is recommended for pH analysis.

pH	Average A4D Score	Max A4D Score
4.0	-0.2428	4.2425
4.5	-0.275	4.2425
5.0	-0.3142	4.2425
5.5	-0.353	4.2425
6.0	-0.3835	4.2425
6.5	-0.4005	4.2425
7.0	-0.4046	4.2425
7.5	-0.4008	4.2425
8.0	-0.3929	4.2425
8.5	-0.3814	4.2425
9.0	-0.3651	4.2425