Project name: VPS9-WT_AF3-00 [mutate: RP99A] [mutate: PR99A] [mutate: RW99A]

Chain sequence(s)	A: KQPDIALLGFLGVQRKFWPATLSILGESKKVLPTTKDACFASAVECLQQISTTFTPSDKLKVIQQTFEEISQSVLASLHEDFLWSMDDLFPVFLYVVLRARIRNLGSEVHLIEDLMDPYLQHGEQGIMFTTLKACYYQIQREKLN
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	RW99A
Energy difference between WT (input) and mutated protein (by FoldX)	0.536691 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)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:03)
[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                                                       (00:02:18)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:50)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/89afb44097108fc/tmp/folded.pdb                (00:02:50)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:55)

• Minimal score value: -2.4565
• Maximal score value: 2.0423
• Average score: -0.3046
• Total score value: -44.1692

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	-1.8963
2	Q	A	-1.4019
3	P	A	-0.3782
4	D	A	0.0000
5	I	A	0.3934
6	A	A	0.1216
7	L	A	0.3786
8	L	A	0.0000
9	G	A	0.0030
10	F	A	1.9351
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	0.1395
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	-0.7359
29	K	A	-1.2725
30	K	A	-1.8369
31	V	A	0.0579
32	L	A	0.7778
33	P	A	-0.1280
34	T	A	-0.1184
35	T	A	-0.2377
36	K	A	-1.4861
37	D	A	-1.8178
38	A	A	-0.2758
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	-0.0690
52	T	A	-0.0832
53	T	A	0.3272
54	F	A	1.9344
55	T	A	0.3180
56	P	A	-0.0820
57	S	A	-0.3279
58	D	A	-0.8097
59	K	A	0.0000
60	L	A	0.0000
61	K	A	-1.7972
62	V	A	0.0000
63	I	A	0.0000
64	Q	A	-0.6677
65	Q	A	-0.9984
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	1.4191
76	A	A	0.2879
77	S	A	-0.0773
78	L	A	0.1438
79	H	A	-1.2779
80	E	A	-2.3134
81	D	A	-2.0180
82	F	A	0.4694
83	L	A	1.6755
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	0.2656
90	F	A	0.6516
91	P	A	0.0787
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	0.2228
99	W	A	0.0000	mutated: RW99A
100	A	A	0.0000
101	R	A	-1.8021
102	I	A	-0.4460
103	R	A	-2.0337
104	N	A	-1.5813
105	L	A	-0.0809
106	G	A	-0.0794
107	S	A	-0.2672
108	E	A	-0.2697
109	V	A	0.0000
110	H	A	-0.9661
111	L	A	0.3290
112	I	A	0.0000
113	E	A	-1.0937
114	D	A	-1.6342
115	L	A	1.2285
116	M	A	0.0000
117	D	A	-1.5599
118	P	A	-0.2879
119	Y	A	1.3318
120	L	A	0.4880
121	Q	A	-0.6457
122	H	A	-1.1038
123	G	A	-0.6116
124	E	A	-1.8896
125	Q	A	-0.5959
126	G	A	0.0000
127	I	A	2.0423
128	M	A	0.4981
129	F	A	0.0000
130	T	A	-0.1018
131	T	A	0.0000
132	L	A	0.0000
133	K	A	-0.3094
134	A	A	-0.0253
135	C	A	0.0000
136	Y	A	0.2490
137	Y	A	0.5529
138	Q	A	-0.3089
139	I	A	0.0797
140	Q	A	-0.7860
141	R	A	-2.2622
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	-0.2388	4.2642
4.5	-0.2705	4.2642
5.0	-0.3096	4.2642
5.5	-0.3488	4.2642
6.0	-0.3803	4.2642
6.5	-0.3985	4.2642
7.0	-0.4037	4.2642
7.5	-0.4008	4.2642
8.0	-0.3938	4.2642
8.5	-0.3835	4.2642
9.0	-0.3689	4.2642