Project name: Bevacizumab

Chain sequence(s)	H: EVQLVESGGGLVQPGGSLRLSCAASGYTFTNYGMNWVRQAPGKGLEWVGWINTYTGEPTYAADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCAKYPHYYGSSHWYFDVWGQGTLVT; L: DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKVLIYFTSSLHSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTKVEIK
Selected Chain(s)	H,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 all 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                                          (00:01:20)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/230f8d0e7f0ca06/tmp/folded.pdb                (00:01:20)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:56)

• Minimal score value: -3.3296
• Maximal score value: 1.4584
• Average score: -0.532
• Total score value: -120.7544

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	E	H	-1.9231
2	V	H	-0.8625
3	Q	H	-0.9343
4	L	H	0.0000
5	V	H	1.1596
6	E	H	0.0000
7	S	H	-0.2005
8	G	H	-0.4954
9	G	H	0.0602
11	G	H	0.6531
12	L	H	1.2474
13	V	H	0.0000
14	Q	H	-1.4424
15	P	H	-1.9787
16	G	H	-1.6877
17	G	H	-1.3993
18	S	H	-1.4788
19	L	H	-0.9498
20	R	H	-1.7121
21	L	H	0.0000
22	S	H	-0.1769
23	C	H	0.0000
24	A	H	0.0953
25	A	H	0.0000
26	S	H	-0.7574
27	G	H	-1.0527
28	Y	H	-0.5540
29	T	H	-0.3872
30	F	H	0.0000
35	T	H	-0.1153
36	N	H	-0.9523
37	Y	H	-0.3205
38	G	H	-0.2413
39	M	H	0.0000
40	N	H	0.0000
41	W	H	0.0000
42	V	H	0.0000
43	R	H	0.0000
44	Q	H	-0.6750
45	A	H	0.0000
46	P	H	-0.8314
47	G	H	-1.4779
48	K	H	-2.3236
49	G	H	-1.5463
50	L	H	0.0000
51	E	H	-1.0203
52	W	H	0.0000
53	V	H	0.0000
54	G	H	0.0000
55	W	H	-0.0897
56	I	H	0.0000
57	N	H	-0.6126
58	T	H	0.0000
59	Y	H	0.6278
62	T	H	-0.1265
63	G	H	-0.7776
64	E	H	-1.7945
65	P	H	-1.0067
66	T	H	-0.4715
67	Y	H	-0.6655
68	A	H	0.0000
69	A	H	-1.6398
70	D	H	-2.6867
71	F	H	0.0000
72	K	H	-3.1410
74	R	H	-3.3296
75	R	H	-2.4598
76	F	H	0.0000
77	T	H	-1.1694
78	F	H	0.0000
79	S	H	-0.3751
80	L	H	-0.2374
81	D	H	-0.8287
82	T	H	-0.6609
83	S	H	-1.1351
84	K	H	-1.9256
85	S	H	-1.0127
86	T	H	0.0000
87	A	H	0.0000
88	Y	H	-0.2858
89	L	H	0.0000
90	Q	H	-1.2987
91	M	H	0.0000
92	N	H	-2.2053
93	S	H	-1.8012
94	L	H	0.0000
95	R	H	-3.0506
96	A	H	-1.9946
97	E	H	-2.4603
98	D	H	0.0000
99	T	H	-0.5308
100	A	H	0.0000
101	V	H	0.5913
102	Y	H	0.0000
103	Y	H	0.0000
104	C	H	0.0000
105	A	H	0.0000
106	K	H	0.0000
107	Y	H	0.0000
108	P	H	0.0000
109	H	H	0.0584
110	Y	H	1.3803
111	Y	H	1.4584
111A	G	H	0.3592
112B	S	H	0.2342
112A	S	H	0.3756
112	H	H	0.5382
113	W	H	0.4887
114	Y	H	0.0000
115	F	H	0.0000
116	D	H	-0.3956
117	V	H	-0.0952
118	W	H	0.0000
119	G	H	0.0000
120	Q	H	-1.2948
121	G	H	-0.3891
122	T	H	0.0000
123	L	H	1.4317
124	V	H	0.0000
125	T	H	0.1429
1	D	L	-2.0166
2	I	L	0.0000
3	Q	L	-1.9684
4	M	L	0.0000
5	T	L	-0.8891
6	Q	L	0.0000
7	S	L	-0.4509
8	P	L	-0.6001
9	S	L	-0.9622
10	S	L	-1.1475
11	L	L	-0.8432
12	S	L	-0.8930
13	A	L	-1.0109
14	S	L	-0.8140
15	V	L	-0.0430
16	G	L	-0.7547
17	D	L	-1.7222
18	R	L	-2.2744
19	V	L	0.0000
20	T	L	-0.6159
21	I	L	0.0000
22	T	L	-0.5860
23	C	L	0.0000
24	S	L	-1.5093
25	A	L	0.0000
26	S	L	-1.9093
27	Q	L	-2.5288
28	D	L	-2.6465
29	I	L	0.0000
36	S	L	-1.0253
37	N	L	-0.4352
38	Y	L	0.5524
39	L	L	0.0000
40	N	L	0.0000
41	W	L	0.0000
42	Y	L	0.0000
43	Q	L	-0.6843
44	Q	L	0.0000
45	K	L	-1.4740
46	P	L	-1.1026
47	G	L	-1.6341
48	K	L	-2.5291
49	A	L	-1.4928
50	P	L	0.0000
51	K	L	-1.0981
52	V	L	0.0000
53	L	L	0.0000
54	I	L	0.0000
55	Y	L	0.7078
56	F	L	0.8636
57	T	L	0.0000
65	S	L	0.0445
66	S	L	0.2685
67	L	L	0.3709
68	H	L	-0.1982
69	S	L	-0.3669
70	G	L	-0.5002
71	V	L	-0.2707
72	P	L	-0.3472
74	S	L	-0.4074
75	R	L	-0.6894
76	F	L	0.0000
77	S	L	-0.3249
78	G	L	0.0000
79	S	L	-0.6900
80	G	L	-1.0706
83	S	L	-1.2209
84	G	L	-1.7530
85	T	L	-2.1108
86	D	L	-2.4804
87	F	L	0.0000
88	T	L	-0.6563
89	L	L	0.0000
90	T	L	-0.5915
91	I	L	0.0000
92	S	L	-1.2420
93	S	L	-1.1128
94	L	L	0.0000
95	Q	L	-0.7883
96	P	L	-0.9082
97	E	L	-1.5866
98	D	L	0.0000
99	F	L	-0.1072
100	A	L	0.0000
101	T	L	-0.9885
102	Y	L	0.0000
103	Y	L	0.0000
104	C	L	0.0000
105	Q	L	0.0000
106	Q	L	0.0000
107	Y	L	0.0000
108	S	L	-0.0473
109	T	L	0.1540
114	V	L	0.6331
115	P	L	0.0851
116	W	L	0.0000
117	T	L	-0.6889
118	F	L	0.0000
119	G	L	0.0000
120	Q	L	-1.6077
121	G	L	0.0000
122	T	L	0.0000
123	K	L	-1.9711
124	V	L	0.0000
125	E	L	-1.2322
126	I	L	-0.6953
127	K	L	-1.5755

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	-0.5317	2.1715
4.5	-0.5709	2.1715
5.0	-0.6154	2.1715
5.5	-0.6572	2.1715
6.0	-0.6877	2.1715
6.5	-0.7009	2.1715
7.0	-0.698	2.1715
7.5	-0.685	2.1715
8.0	-0.6663	2.1715
8.5	-0.6422	2.1715
9.0	-0.6126	2.1715