Project name: SOD1 VUS [mutate: VK6A, CY7A, LV9A, GS13A, PS14A, IF19A, NI20A, KD31A, IF36A, VI48A, EK50A, TI55A, SN60A, PL67A, RG70A, HQ72A, GC73A, GR74A, VD82A, DN84A, DV93A, VA95A, AV96A, DE97A, VL98A, GR109A, DY110A, HY111A, HQ121A, DY126A, GS130A, TI136A, GV139A, AG141A, IS152A, AT153A]

Chain sequence(s)	A: MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Selected Chain(s)	A
Distance of aggregation	10 Å
FoldX usage	Yes
pH calculations	Yes
alphaCutter usage	No
Dynamic mode	No
Automated mutations	No
Mutated residues	HY111A,DY110A,AT153A,GC73A,EK50A,GV139A,TI55A,VL98A,VA95A,DE97A,AV96A,TI136A,DV93A,IS152A,PS14A,KD31A,GS130A,IF36A,GS13A,GR74A,IF19A,HQ72A,RG70A,DY126A,CY7A,VK6A,LV9A,VD82A,DN84A,GR109A,AG141A,HQ121A,VI48A,NI20A,PL67A,SN60A
Energy difference between WT (input) and mutated protein (by FoldX)	81.0178 kcal/mol CAUTION: Your mutation/s can destabilize the protein structure

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)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:00:44)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:18:09)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/bf82caefaf9bc/tmp/folded.pdb                  (00:18:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:45)

• Minimal score value: -3.3118
• Maximal score value: 1.4783
• Average score: -0.7354
• Total score value: -113.2544

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	0.2648
2	A	A	-1.1722
3	T	A	-1.2494
4	K	A	-1.5037
5	A	A	0.0000
6	K	A	-0.5605	mutated: VK6A
7	Y	A	0.0000	mutated: CY7A
8	V	A	0.6429
9	V	A	0.0000	mutated: LV9A
10	K	A	-2.3047
11	G	A	-2.3078
12	D	A	-2.5395
13	S	A	-1.6358	mutated: GS13A
14	S	A	-1.5149	mutated: PS14A
15	V	A	0.0000
16	Q	A	-2.1075
17	G	A	0.0000
18	I	A	0.5909
19	F	A	0.0000	mutated: IF19A
20	I	A	-0.0004	mutated: NI20A
21	F	A	0.0000
22	E	A	-2.1404
23	Q	A	0.0000
24	K	A	-2.9789
25	E	A	-3.0496
26	S	A	-2.2727
27	N	A	-2.4007
28	G	A	-1.9996
29	P	A	-1.7987
30	V	A	0.0000
31	D	A	-2.2026	mutated: KD31A
32	V	A	0.0000
33	W	A	-0.5265
34	G	A	-0.2171
35	S	A	-1.0004
36	F	A	0.0000	mutated: IF36A
37	K	A	-1.7421
38	G	A	-1.0436
39	L	A	0.0000
40	T	A	-1.5957
41	E	A	-2.4484
42	G	A	-1.2873
43	L	A	0.0274
44	H	A	0.0000
45	G	A	0.0000
46	F	A	0.0000
47	H	A	0.0000
48	I	A	0.0000	mutated: VI48A
49	H	A	0.0000
50	K	A	-0.8633	mutated: EK50A
51	F	A	0.0110
52	G	A	-0.0923
53	D	A	-0.2140
54	N	A	0.1282
55	I	A	1.3885	mutated: TI55A
56	A	A	0.4867
57	G	A	-0.6733
58	C	A	-0.6054
59	T	A	-0.2700
60	N	A	-0.2698	mutated: SN60A
61	A	A	0.0000
62	G	A	-0.5300
63	P	A	-0.7595
64	H	A	0.0000
65	F	A	0.0000
66	N	A	-0.0536
67	L	A	1.3264	mutated: PL67A
68	L	A	1.4783
69	S	A	0.1284
70	G	A	-1.0437	mutated: RG70A
71	K	A	-1.9604
72	Q	A	0.0000	mutated: HQ72A
73	C	A	0.0000	mutated: GC73A
74	R	A	-2.2394	mutated: GR74A
75	P	A	-2.0516
76	K	A	-2.7602
77	D	A	-2.8095
78	E	A	-3.3118
79	E	A	-3.0128
80	R	A	0.0000
81	H	A	0.0000
82	D	A	0.0000	mutated: VD82A
83	G	A	0.0000
84	N	A	0.0000	mutated: DN84A
85	L	A	0.0000
86	G	A	0.0000
87	N	A	-0.0368
88	V	A	0.0000
89	T	A	-0.7896
90	A	A	0.0000
91	D	A	-2.5423
92	K	A	-2.1249
93	V	A	-0.0661	mutated: DV93A
94	G	A	0.0000
95	A	A	-1.7100	mutated: VA95A
96	V	A	0.0000	mutated: AV96A
97	E	A	-2.2268	mutated: DE97A
98	L	A	0.0000	mutated: VL98A
99	S	A	-0.9478
100	I	A	-1.1519
101	E	A	-2.2070
102	D	A	0.0000
103	S	A	-0.9254
104	V	A	-0.2609
105	I	A	0.0000
106	S	A	0.0000
107	L	A	0.0000
108	S	A	-0.8977
109	R	A	-1.2817	mutated: GR109A
110	Y	A	0.8114	mutated: DY110A
111	Y	A	0.6989	mutated: HY111A
112	C	A	0.1421
113	I	A	0.0000
114	I	A	-0.0343
115	G	A	-0.1678
116	R	A	-0.2120
117	T	A	0.0000
118	L	A	0.0000
119	V	A	0.0000
120	V	A	0.0000
121	Q	A	0.0000	mutated: HQ121A
122	E	A	-1.8124
123	K	A	-1.4077
124	A	A	-0.1647
125	D	A	0.0000
126	Y	A	0.3438	mutated: DY126A
127	L	A	-0.5853
128	G	A	-1.7946
129	K	A	-1.6562
130	S	A	-1.4014	mutated: GS130A
131	G	A	-1.7732
132	N	A	-2.6549
133	E	A	-3.0732
134	E	A	-2.8387
135	S	A	0.0000
136	I	A	-2.0167	mutated: TI136A
137	K	A	-2.5209
138	T	A	-1.3095
139	V	A	0.0000	mutated: GV139A
140	N	A	-1.3817
141	G	A	0.0000	mutated: AG141A
142	G	A	-1.3615
143	S	A	-1.2387
144	R	A	-1.3152
145	L	A	-1.4824
146	A	A	0.0000
147	C	A	0.0000
148	G	A	0.0000
149	V	A	0.5303
150	I	A	0.0000
151	G	A	-0.2962
152	S	A	-0.7382	mutated: IS152A
153	T	A	-1.2329	mutated: AT153A
154	Q	A	-1.4939

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	-0.6933	2.9707
4.5	-0.7589	2.9362
5.0	-0.8419	2.9005
5.5	-0.9256	2.8645
6.0	-0.9898	2.8283
6.5	-1.0159	2.7924
7.0	-0.9997	2.7571
7.5	-0.9532	2.7238
8.0	-0.8905	2.6953
8.5	-0.8188	2.6758
9.0	-0.7411	2.6658