Project name: swVacARD1bmut3

Chain sequence(s)	L: TLDLWQSAGLNINAAPEGGKDTVVNINRINTNADGTVRVGGYKASLTTNAAHLHIGKGGINLSNQASGRSLLVENLTGNITVDGPLRVNNQVGGYASAGSNANFEFKAGTDTKNGTATFNNDISLGRNVNLKVDAHTANFKGIDTGNGGNNTLDFSGVTDKVNINKLITASTNVAIKNFNINELLVKTNGVSSGEYTHFSEDIGSQSRINTVRLETGTRSIFSGGVKFKSGEKLVIDEFYYSPWNYFDARNIKNVEITRKFASSTPENPSGTSKLMFNNLTLGQNAVMDYSQFSNLTIQGDFINNQGTINYLVRGGKVATLNVGNAAAMMFNNDIDSATGKLKPLIKINSAQDLIKNTEHVLLKAKSIGYGNVSTGTNGPSNVNLEEQFKESGTAG
Selected Chain(s)	L
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 L 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.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:28)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/9ebd75a3da4682a/tmp/folded.pdb                (00:04:28)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:10)

• Minimal score value: -3.3751
• Maximal score value: 1.251
• Average score: -0.8309
• Total score value: -329.0543

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
2	T	L	-0.7816
3	L	L	-0.9141
4	D	L	-1.8747
5	L	L	0.0000
6	W	L	-0.2559
7	Q	L	-0.9413
8	S	L	-0.3772
9	A	L	-0.2318
10	G	L	-0.5774
11	L	L	-0.3815
12	N	L	-1.3856
13	I	L	-0.7145
14	N	L	-1.5042
15	A	L	-1.1492
16	A	L	-1.4816
17	P	L	-1.7562
18	E	L	-2.6591
19	G	L	-2.2178
20	G	L	-2.5139
21	K	L	-2.9343
22	D	L	-2.5523
23	T	L	-1.1858
24	V	L	0.7543
25	V	L	0.0858
26	N	L	-0.8604
27	I	L	-0.8686
28	N	L	-2.0032
29	R	L	-1.6455
30	I	L	0.0000
31	N	L	-1.3601
32	T	L	0.0000
33	N	L	-1.9694
34	A	L	-1.8227
35	D	L	-2.1247
36	G	L	-1.2757
37	T	L	-0.3078
38	V	L	0.7709
39	R	L	-0.2925
40	V	L	1.1004
41	G	L	-0.0734
42	G	L	-0.6270
43	Y	L	-0.5880
44	K	L	-1.2827
45	A	L	0.0000
46	S	L	-0.5039
47	L	L	0.0000
48	T	L	-0.6832
49	T	L	0.0000
50	N	L	-1.0407
51	A	L	0.0000
52	A	L	-0.8930
53	H	L	-0.6440
54	L	L	0.0000
55	H	L	-0.6920
56	I	L	0.0000
57	G	L	0.0000
58	K	L	-2.2233
59	G	L	-1.5297
60	G	L	0.0000
61	I	L	0.0000
62	N	L	0.0000
63	L	L	0.0000
64	S	L	-1.4566
65	N	L	-1.4268
66	Q	L	-1.2128
67	A	L	-0.5730
68	S	L	-0.3740
69	G	L	-0.6804
70	R	L	0.0000
71	S	L	0.0000
72	L	L	0.0000
73	L	L	-0.5055
74	V	L	0.0000
75	E	L	-0.6464
76	N	L	0.0000
77	L	L	-0.8288
78	T	L	-1.2823
79	G	L	0.0000
80	N	L	-0.9158
81	I	L	0.0000
82	T	L	-0.5747
83	V	L	0.0000
84	D	L	-1.4747
85	G	L	0.0000
86	P	L	-0.8796
87	L	L	0.0000
88	R	L	-0.7627
89	V	L	0.0000
90	N	L	-1.7356
91	N	L	-1.9799
92	Q	L	-1.2166
93	V	L	0.6222
94	G	L	-0.1733
95	G	L	-0.1764
96	Y	L	0.5290
97	A	L	-0.3529
98	S	L	-0.4170
99	A	L	-0.5836
100	G	L	-0.7414
101	S	L	0.0000
102	N	L	-1.2307
103	A	L	0.0000
104	N	L	-0.8292
105	F	L	0.0000
106	E	L	-0.9096
107	F	L	0.0000
108	K	L	-1.2372
109	A	L	0.0000
110	G	L	0.0000
111	T	L	-1.8385
112	D	L	-2.4097
113	T	L	-2.0896
114	K	L	-3.0038
115	N	L	-2.5092
116	G	L	0.0000
117	T	L	-1.0578
118	A	L	0.0000
119	T	L	-0.5989
120	F	L	0.0000
121	N	L	-1.5108
122	N	L	-2.0915
123	D	L	-2.7343
124	I	L	0.0000
125	S	L	-0.6565
126	L	L	0.0000
127	G	L	0.0000
128	R	L	-1.4057
129	N	L	0.0000
130	V	L	0.0000
131	N	L	0.0000
132	L	L	0.0000
133	K	L	-1.1016
134	V	L	0.0000
135	D	L	-1.2966
136	A	L	0.0000
137	H	L	-2.0547
138	T	L	-1.5704
139	A	L	0.0000
140	N	L	-0.9308
141	F	L	0.0000
142	K	L	-2.4951
143	G	L	0.0000
144	I	L	0.0000
145	D	L	-1.0539
146	T	L	0.0000
147	G	L	-1.2270
148	N	L	-1.7538
149	G	L	0.0000
150	G	L	0.0000
151	N	L	-2.0596
152	N	L	0.0000
153	T	L	-0.9624
154	L	L	0.0000
155	D	L	-0.8774
156	F	L	0.0000
157	S	L	-1.0154
158	G	L	-1.2311
159	V	L	0.0000
160	T	L	-1.9727
161	D	L	-2.6606
162	K	L	-2.3249
163	V	L	0.0000
164	N	L	-1.3587
165	I	L	0.0000
166	N	L	-2.5183
167	K	L	-2.3123
168	L	L	0.0000
169	I	L	-0.5902
170	T	L	0.0000
171	A	L	0.0000
172	S	L	-1.3579
173	T	L	0.0000
174	N	L	-1.3771
175	V	L	0.0000
176	A	L	-1.4253
177	I	L	0.0000
178	K	L	-2.3232
179	N	L	-2.1495
180	F	L	0.0000
181	N	L	-1.7585
182	I	L	0.0000
183	N	L	-2.3993
184	E	L	-2.6746
185	L	L	0.0000
186	L	L	-0.9212
187	V	L	0.0000
188	K	L	-1.2034
189	T	L	-0.5265
190	N	L	-0.5903
191	G	L	-0.3207
192	V	L	1.1380
193	S	L	0.2848
194	S	L	-0.1998
195	G	L	-0.8814
196	E	L	-1.0948
197	Y	L	-0.6864
198	T	L	0.0000
199	H	L	-1.0657
200	F	L	0.0000
201	S	L	-1.9822
202	E	L	-3.0333
203	D	L	-2.8006
204	I	L	0.0000
205	G	L	-1.8832
206	S	L	-1.7445
207	Q	L	-2.2198
208	S	L	0.0000
209	R	L	-1.5773
210	I	L	0.0000
211	N	L	-1.7744
212	T	L	-1.9551
213	V	L	0.0000
214	R	L	-1.7549
215	L	L	0.0000
216	E	L	-0.8587
217	T	L	-0.7198
218	G	L	-0.2688
219	T	L	-0.3008
220	R	L	-1.3223
221	S	L	-0.3062
222	I	L	0.8710
223	F	L	0.8070
224	S	L	0.0000
225	G	L	0.0000
226	G	L	0.0000
227	V	L	0.0000
228	K	L	-0.9270
229	F	L	0.0000
230	K	L	-2.9408
231	S	L	-2.8209
232	G	L	-2.8583
233	E	L	-3.1483
234	K	L	-2.6473
235	L	L	0.0000
236	V	L	-1.0236
237	I	L	0.0000
238	D	L	-1.6385
239	E	L	-1.7873
240	F	L	0.0000
241	Y	L	0.0000
242	Y	L	0.0000
243	S	L	0.0000
244	P	L	0.0000
245	W	L	0.1161
246	N	L	0.0000
247	Y	L	0.1573
248	F	L	0.0000
249	D	L	-0.8682
250	A	L	0.0000
251	R	L	-2.2481
252	N	L	-3.0595
253	I	L	0.0000
254	K	L	-3.2441
255	N	L	-2.6710
256	V	L	0.0000
257	E	L	-1.3725
258	I	L	0.0000
259	T	L	-1.6129
260	R	L	-2.2640
261	K	L	-1.5221
262	F	L	0.0000
263	A	L	0.0000
264	S	L	0.0000
265	S	L	-0.8554
266	T	L	-1.1414
267	P	L	-1.5862
268	E	L	-2.5302
269	N	L	-2.2792
270	P	L	-1.5528
271	S	L	-0.5456
272	G	L	-0.3261
273	T	L	-0.2318
274	S	L	0.0000
275	K	L	-0.7141
276	L	L	0.0000
277	M	L	-0.5544
278	F	L	0.0000
279	N	L	-1.8973
280	N	L	0.0000
281	L	L	0.0000
282	T	L	-0.7400
283	L	L	0.0000
284	G	L	0.0000
285	Q	L	-1.7663
286	N	L	-1.8280
287	A	L	0.0000
288	V	L	-0.5687
289	M	L	0.0000
290	D	L	-0.8179
291	Y	L	0.0000
292	S	L	0.0000
293	Q	L	-1.2760
294	F	L	-0.6391
295	S	L	0.0000
296	N	L	-1.3678
297	L	L	0.0000
298	T	L	-0.9270
299	I	L	0.0000
300	Q	L	-2.2239
301	G	L	0.0000
302	D	L	-2.2920
303	F	L	0.0000
304	I	L	-0.1534
305	N	L	0.0000
306	N	L	-0.5607
307	Q	L	-1.1012
308	G	L	0.0000
309	T	L	-0.6121
310	I	L	0.0000
311	N	L	-0.8005
312	Y	L	0.0000
313	L	L	-1.4415
314	V	L	0.0000
315	R	L	-2.6384
316	G	L	-2.1609
317	G	L	0.0000
318	K	L	-2.2172
319	V	L	-0.6964
320	A	L	0.0000
321	T	L	-0.2749
322	L	L	0.0000
323	N	L	-1.6048
324	V	L	0.0000
325	G	L	-2.3573
326	N	L	-2.6070
327	A	L	-1.7609
328	A	L	0.0000
329	A	L	-0.1033
330	M	L	0.0000
331	M	L	0.6767
332	F	L	0.0000
333	N	L	-0.3384
334	N	L	-0.9197
335	D	L	-0.4281
336	I	L	0.4083
337	D	L	-0.4652
338	S	L	-0.5602
339	A	L	-0.4033
340	T	L	-0.7572
341	G	L	-1.0850
342	K	L	-1.7725
343	L	L	-0.6469
344	K	L	-0.6709
345	P	L	-0.7685
346	L	L	0.0000
347	I	L	0.0000
348	K	L	-1.0287
349	I	L	-0.8497
350	N	L	-1.8335
351	S	L	-1.7751
352	A	L	-1.8543
353	Q	L	-2.0783
354	D	L	-2.6668
355	L	L	-1.3494
356	I	L	-1.2085
357	K	L	-2.2414
358	N	L	-2.2488
359	T	L	-1.8942
360	E	L	-2.2176
361	H	L	-0.9726
362	V	L	0.2512
363	L	L	0.3689
364	L	L	0.1703
365	K	L	-1.0083
366	A	L	-1.3164
367	K	L	-2.2123
368	S	L	-1.0644
369	I	L	0.2783
370	G	L	0.0165
371	Y	L	0.1149
372	G	L	0.2392
373	N	L	0.4798
374	V	L	1.2510
375	S	L	0.1563
376	T	L	-0.3196
377	G	L	0.0000
378	T	L	-0.7871
379	N	L	-1.4864
380	G	L	-1.1929
381	P	L	-0.8385
382	S	L	-1.0343
383	N	L	-1.1647
384	V	L	-0.6667
385	N	L	-1.4132
386	L	L	-1.4088
387	E	L	-2.5193
388	E	L	-3.2921
389	Q	L	-2.5067
390	F	L	-2.2113
391	K	L	-3.3450
392	E	L	-3.3751
393	S	L	0.0000
394	G	L	-1.4497
395	T	L	-1.1894
396	A	L	-0.6086
397	G	L	-1.2405

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	-0.6814	2.5917
4.5	-0.728	2.4762
5.0	-0.7856	2.3409
5.5	-0.8423	2.2043
6.0	-0.8854	2.0763
6.5	-0.9053	1.9565
7.0	-0.9017	1.8413
7.5	-0.8823	1.7292
8.0	-0.8542	1.622
8.5	-0.8202	1.5272
9.0	-0.7794	1.4595