Project name: example

Chain sequence(s)	A: MAIPANEIDLARYLEHSLLHPAATEAQVKECCEAAVQFDFPAVCLYPTAIKTARDFLHQRPIQICSVVGFPAGAHTTATKLYEAQEAVENGATELDVMLNLAFVKMGESEKLYQEVAQIVELTKVPIKGILETALLTDTEKRLAAEICLDAGVSYLKTSTGWFGGTTVADVKLLYGITKGRIGIKAAGGIKTVDQAIALIQAGATRLGTSRSIKIMQEREQVSDNPTW
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]                                                (00:00:01)
[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)
[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]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:29)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ac4cce3b5a07b00/tmp/folded.pdb                (00:02:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:37)

• Minimal score value: -3.3379
• Maximal score value: 1.4216
• Average score: -0.7811
• Total score value: -178.0978

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	1.1667
2	A	A	0.6813
3	I	A	0.2625
4	P	A	-0.6287
5	A	A	-1.4588
6	N	A	-2.2908
7	E	A	-2.6006
8	I	A	0.0000
9	D	A	-2.4153
10	L	A	0.0000
11	A	A	-1.5405
12	R	A	-2.4528
13	Y	A	-0.9735
14	L	A	0.0000
15	E	A	0.0000
16	H	A	-0.1707
17	S	A	-0.2547
18	L	A	-0.4686
19	L	A	-0.2005
20	H	A	-0.9898
21	P	A	-0.5777
22	A	A	-0.6173
23	A	A	-0.8851
24	T	A	-1.6242
25	E	A	-2.5468
26	A	A	-1.9903
27	Q	A	-2.5633
28	V	A	0.0000
29	K	A	-3.0837
30	E	A	-3.3206
31	C	A	0.0000
32	C	A	0.0000
33	E	A	-3.0185
34	A	A	-1.8841
35	A	A	0.0000
36	V	A	-1.5739
37	Q	A	-1.7381
38	F	A	-1.3292
39	D	A	-2.4874
40	F	A	0.0000
41	P	A	-1.0397
42	A	A	0.0000
43	V	A	0.0000
44	C	A	0.0000
45	L	A	0.0000
46	Y	A	0.1062
47	P	A	-0.4348
48	T	A	-0.6887
49	A	A	-1.1361
50	I	A	0.0000
51	K	A	-2.6966
52	T	A	-2.1604
53	A	A	0.0000
54	R	A	-2.8309
55	D	A	-3.0184
56	F	A	-2.1315
57	L	A	0.0000
58	H	A	-2.5777
59	Q	A	-2.4546
60	R	A	-2.1332
61	P	A	-1.3889
62	I	A	0.0000
63	Q	A	-0.7128
64	I	A	0.0000
65	C	A	0.0000
66	S	A	0.0000
67	V	A	0.0000
68	V	A	0.0000
69	G	A	0.0000
70	F	A	0.2651
71	P	A	0.3612
72	A	A	0.2474
73	G	A	0.0000
74	A	A	-0.2384
75	H	A	-0.7298
76	T	A	-0.3926
77	T	A	-0.3335
78	A	A	0.2164
79	T	A	0.1819
80	K	A	0.0000
81	L	A	0.5732
82	Y	A	0.9532
83	E	A	-0.2470
84	A	A	0.0000
85	Q	A	-0.8868
86	E	A	-1.5003
87	A	A	0.0000
88	V	A	-1.3901
89	E	A	-2.4567
90	N	A	-2.2072
91	G	A	-1.8840
92	A	A	0.0000
93	T	A	-0.5394
94	E	A	0.0000
95	L	A	0.0000
96	D	A	0.0000
97	V	A	0.0000
98	M	A	0.0000
99	L	A	0.0000
100	N	A	-0.4575
101	L	A	-0.0179
102	A	A	-0.1346
103	F	A	-0.6179
104	V	A	0.0000
105	K	A	-0.9268
106	M	A	0.0562
107	G	A	-0.9890
108	E	A	-1.5804
109	S	A	-1.8887
110	E	A	-2.7615
111	K	A	-2.4780
112	L	A	0.0000
113	Y	A	-1.7985
114	Q	A	-1.6629
115	E	A	0.0000
116	V	A	0.0000
117	A	A	-1.2495
118	Q	A	-1.1697
119	I	A	0.0000
120	V	A	-1.2268
121	E	A	-2.1239
122	L	A	-0.6105
123	T	A	0.0000
124	K	A	-1.8733
125	V	A	-0.6543
126	P	A	-0.3368
127	I	A	0.0000
128	K	A	0.0000
129	G	A	0.0000
130	I	A	0.0000
131	L	A	0.0000
132	E	A	0.0000
133	T	A	0.0000
134	A	A	0.3213
135	L	A	0.4827
136	L	A	0.0000
137	T	A	-1.2698
138	D	A	-2.2615
139	T	A	-1.5470
140	E	A	-1.6416
141	K	A	-1.7309
142	R	A	-2.4502
143	L	A	-1.5653
144	A	A	0.0000
145	A	A	0.0000
146	E	A	-2.4809
147	I	A	0.0000
148	C	A	0.0000
149	L	A	-1.6011
150	D	A	-2.2416
151	A	A	0.0000
152	G	A	-1.0906
153	V	A	0.0000
154	S	A	-0.2043
155	Y	A	-0.1224
156	L	A	0.0000
157	K	A	0.0000
158	T	A	0.0000
159	S	A	0.0000
160	T	A	0.0000
161	G	A	0.1605
162	W	A	1.1450
163	F	A	1.4216
164	G	A	0.3726
165	G	A	-0.2113
166	T	A	-0.2569
167	T	A	-0.1501
168	V	A	0.0369
169	A	A	-0.1634
170	D	A	-0.6409
171	V	A	0.0000
172	K	A	-1.5324
173	L	A	-1.1186
174	L	A	0.0000
175	Y	A	-0.8283
176	G	A	-1.1628
177	I	A	-1.3367
178	T	A	0.0000
179	K	A	-2.4409
180	G	A	-1.9657
181	R	A	-2.3284
182	I	A	-0.9985
183	G	A	-0.5353
184	I	A	0.0000
185	K	A	0.0000
186	A	A	0.0000
187	A	A	0.0000
188	G	A	-0.4275
189	G	A	-1.0731
190	I	A	0.0000
191	K	A	-2.1588
192	T	A	-1.8663
193	V	A	0.0000
194	D	A	-2.1637
195	Q	A	-1.4817
196	A	A	0.0000
197	I	A	-0.8926
198	A	A	-0.6081
199	L	A	0.0000
200	I	A	0.0000
201	Q	A	-0.4892
202	A	A	0.0000
203	G	A	-0.6607
204	A	A	0.0000
205	T	A	-0.4357
206	R	A	-0.4527
207	L	A	0.0000
208	G	A	0.0000
209	T	A	0.0000
210	S	A	-1.1334
211	R	A	-1.9151
212	S	A	0.0000
213	I	A	-1.1870
214	K	A	-2.7562
215	I	A	0.0000
216	M	A	-1.8745
217	Q	A	-2.4105
218	E	A	-2.3408
219	R	A	-2.5024
220	E	A	-3.3379
221	Q	A	-2.7781
222	V	A	-0.9283
223	S	A	-2.0272
224	D	A	-2.9436
225	N	A	-2.1533
226	P	A	-0.7719
227	T	A	0.0769
228	W	A	0.9152

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	-0.5056	4.0753
4.5	-0.5723	4.0753
5.0	-0.6572	4.0753
5.5	-0.7439	4.0753
6.0	-0.8154	4.0753
6.5	-0.8615	4.0753
7.0	-0.8821	4.0753
7.5	-0.8833	4.0753
8.0	-0.8728	4.0753
8.5	-0.8541	4.0753
9.0	-0.8272	4.0753