Project name: rituximab_HL

Chain sequence(s)	H: QVQLQQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGRGLEWIGAIYPGNGDTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYYCARSTYYGGDWYFNVWGAGTTVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC; L: QIVLSQSPAILSASPGEKVTMTCRASSSVSYIHWFQQKPGSSPKPWIYATSNLASGVPVRFSGSGSGTSYSLTISRVEAEDAATYYCQQWTSNPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
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]                                                (00:00:00)
[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 all 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]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:08)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/baf623c6144fb15/tmp/folded.pdb                (00:04:08)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:44)

• Minimal score value: -3.812
• Maximal score value: 1.7883
• Average score: -0.6959
• Total score value: -304.115

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	Q	H	-1.3624
2	V	H	-0.7599
3	Q	H	-1.8329
4	L	H	0.0000
5	Q	H	-2.1417
6	Q	H	-1.3679
7	P	H	-0.9270
8	G	H	-0.7457
9	A	H	-0.1008
10	E	H	-0.0232
11	L	H	0.9636
12	V	H	0.0000
13	K	H	-1.5297
14	P	H	-1.0467
15	G	H	-1.0888
16	A	H	-0.8999
17	S	H	-1.1949
18	V	H	0.0000
19	K	H	-2.0278
20	M	H	0.0000
21	S	H	-0.9408
22	C	H	0.0000
23	K	H	-2.0992
24	A	H	-1.3968
25	S	H	-1.2286
26	G	H	-0.7896
27	Y	H	-0.2128
28	T	H	-0.0555
29	F	H	0.0000
30	T	H	-0.7065
31	S	H	-0.1250
32	Y	H	0.4584
33	N	H	-0.1980
34	M	H	0.0000
35	H	H	-0.0738
36	W	H	0.0000
37	V	H	0.0000
38	K	H	-0.5687
39	Q	H	-0.8098
40	T	H	0.0000
41	P	H	-1.0284
42	G	H	-1.6124
43	R	H	-2.4388
44	G	H	-1.5491
45	L	H	0.0000
46	E	H	-0.9110
47	W	H	0.0000
48	I	H	0.0000
49	G	H	0.0000
50	A	H	0.0000
51	I	H	0.0000
52	Y	H	-0.6428
52A	P	H	0.0000
53	G	H	-1.3220
54	N	H	-2.1919
55	G	H	-2.1535
56	D	H	-2.3374
57	T	H	-1.1443
58	S	H	-0.8416
59	Y	H	-1.0753
60	N	H	-1.8956
61	Q	H	-2.7834
62	K	H	-2.8611
63	F	H	-2.1927
64	K	H	-2.9501
65	G	H	-2.0829
66	K	H	-1.8039
67	A	H	0.0000
68	T	H	-0.8745
69	L	H	0.0000
70	T	H	-0.6391
71	A	H	-0.9698
72	D	H	-1.6759
73	K	H	-2.4880
74	S	H	-1.3877
75	S	H	-1.2334
76	S	H	-1.2864
77	T	H	0.0000
78	A	H	0.0000
79	Y	H	-0.4862
80	M	H	0.0000
81	Q	H	-1.5448
82	L	H	0.0000
82A	S	H	-1.0432
82B	S	H	-0.6862
82C	L	H	0.0000
83	T	H	-1.1739
84	S	H	-1.1591
85	E	H	-1.9359
86	D	H	0.0000
87	S	H	-0.6063
88	A	H	0.0000
89	V	H	0.2012
90	Y	H	0.0000
91	Y	H	0.0000
92	C	H	0.0000
93	A	H	0.0000
94	R	H	0.0000
95	S	H	0.0000
96	T	H	0.9703
97	Y	H	1.7883
98	Y	H	1.3503
99	G	H	0.0472
100	G	H	-0.0551
100A	D	H	0.4536
100B	W	H	1.1443
100C	Y	H	0.7275
100D	F	H	0.0000
101	N	H	-0.0534
102	V	H	-0.2504
103	W	H	-0.4439
104	G	H	0.0000
105	A	H	-0.5205
106	G	H	-0.3559
107	T	H	0.0000
108	T	H	0.0643
109	V	H	0.0000
110	T	H	-0.0112
111	V	H	-0.4363
112	S	H	-0.3037
113	A	H	-0.4684
114	A	H	-0.4563
115	S	H	-0.5957
116	T	H	-0.6932
117	K	H	-0.9946
118	G	H	-1.3338
119	P	H	-0.5061
120	S	H	-0.3752
121	V	H	0.0000
122	F	H	0.0000
123	P	H	-0.8846
124	L	H	0.0000
125	A	H	0.0000
126	P	H	0.0000
127	S	H	-0.6266
128	S	H	-0.3802
129	K	H	-0.7531
130	S	H	0.0000
131	T	H	-0.5619
132	S	H	-0.6225
133	G	H	-0.8097
134	G	H	-0.8881
135	T	H	-0.6143
136	A	H	0.0000
137	A	H	0.0000
138	L	H	0.0000
139	G	H	0.0000
140	C	H	0.0000
141	L	H	0.0000
142	V	H	0.0000
143	K	H	-0.3768
144	D	H	-0.4220
145	Y	H	0.0000
146	F	H	0.0000
147	P	H	-0.6173
148	E	H	-1.1314
149	P	H	-1.0726
150	V	H	-0.5992
151	T	H	-0.6230
152	V	H	0.0545
153	S	H	-0.4072
154	W	H	0.0000
155	N	H	-0.8848
156	S	H	-0.6911
157	G	H	-0.4954
158	A	H	-0.2437
159	L	H	-0.0430
160	T	H	-0.2285
161	S	H	-0.2738
162	G	H	-0.4073
163	V	H	0.0490
164	H	H	-0.2085
165	T	H	-0.0720
166	F	H	0.0000
167	P	H	-0.3672
168	A	H	0.1070
169	V	H	0.5255
170	L	H	1.3320
171	Q	H	0.3381
172	S	H	-0.0446
173	S	H	-0.1782
174	G	H	0.1366
175	L	H	0.1024
176	Y	H	0.3609
177	S	H	0.0000
178	L	H	0.0000
179	S	H	-0.0642
180	S	H	0.0000
181	V	H	0.0000
182	V	H	0.0000
183	T	H	-0.2443
184	V	H	0.0000
185	P	H	-0.7019
186	S	H	-0.7568
187	S	H	-0.6587
188	S	H	-0.7788
189	L	H	0.0000
190	G	H	-1.3450
191	T	H	-0.9909
192	Q	H	-1.4631
193	T	H	-1.1655
194	Y	H	0.0000
195	I	H	-1.2256
196	C	H	0.0000
197	N	H	-1.5467
198	V	H	0.0000
199	N	H	-1.9614
200	H	H	0.0000
201	K	H	-2.9010
202	P	H	-1.7749
203	S	H	-1.8100
204	N	H	-2.5860
205	T	H	-2.0940
206	K	H	-2.7353
207	V	H	-1.6201
208	D	H	-2.6123
209	K	H	-1.9606
210	K	H	-2.4119
211	V	H	0.0000
212	E	H	-2.1860
213	P	H	-1.4620
214	K	H	-2.0706
215	S	H	-1.3128
216	C	H	-0.6498
1	Q	L	-1.0613
2	I	L	0.2616
3	V	L	1.2176
4	L	L	0.0000
5	S	L	-0.6343
6	Q	L	-0.9235
7	S	L	-0.4339
8	P	L	0.2330
9	A	L	0.4779
10	I	L	1.4432
11	L	L	0.4887
12	S	L	-0.3369
13	A	L	0.0000
14	S	L	-1.9545
15	P	L	-2.2146
16	G	L	-2.6126
17	E	L	-3.6930
18	K	L	-3.3384
19	V	L	0.0000
20	T	L	-0.5082
21	M	L	0.0000
22	T	L	-0.7348
23	C	L	0.0000
24	R	L	-1.9358
25	A	L	-0.7239
26	S	L	-0.3752
28	S	L	-0.4754
29	S	L	-0.6906
30	V	L	0.0000
31	S	L	-0.1830
32	Y	L	0.1680
33	I	L	0.0000
34	H	L	0.0000
35	W	L	0.0000
36	F	L	0.0000
37	Q	L	-1.1598
38	Q	L	-1.8032
39	K	L	-2.4504
40	P	L	-1.5941
41	G	L	-1.1348
42	S	L	-1.2347
43	S	L	-0.9215
44	P	L	0.0000
45	K	L	-2.0486
46	P	L	-0.8583
47	W	L	0.0000
48	I	L	0.0000
49	Y	L	0.0987
50	A	L	0.0000
51	T	L	-0.2427
52	S	L	-0.4823
53	N	L	-0.5778
54	L	L	0.2853
55	A	L	-0.3575
56	S	L	-0.3985
57	G	L	-0.2666
58	V	L	0.0000
59	P	L	0.5614
60	V	L	1.5035
61	R	L	-0.4346
62	F	L	0.0000
63	S	L	-0.1486
64	G	L	-0.4670
65	S	L	-0.6163
66	G	L	-0.6137
67	S	L	-0.5710
68	G	L	-0.7482
69	T	L	-1.0137
70	S	L	-1.1970
71	Y	L	0.0000
72	S	L	-0.6559
73	L	L	0.0000
74	T	L	-0.8229
75	I	L	0.0000
76	S	L	-2.3518
77	R	L	-3.7381
78	V	L	0.0000
79	E	L	-2.7173
80	A	L	-1.7787
81	E	L	-2.2170
82	D	L	0.0000
83	A	L	-1.4185
84	A	L	0.0000
85	T	L	0.0000
86	Y	L	0.0000
87	Y	L	-0.2256
88	C	L	0.0000
89	Q	L	0.0000
90	Q	L	0.0000
91	W	L	0.0038
92	T	L	-0.3812
93	S	L	-0.9694
94	N	L	-1.6254
95	P	L	-1.2725
96	P	L	0.0000
97	T	L	-0.0320
98	F	L	0.3130
99	G	L	0.0000
100	G	L	-0.7006
101	G	L	-0.4631
102	T	L	0.0000
103	K	L	-1.0462
104	L	L	0.0000
105	E	L	-0.6470
106	I	L	-1.3152
107	K	L	-1.6846
108	R	L	-1.3687
109	T	L	0.0536
110	V	L	0.9312
111	A	L	0.2292
112	A	L	0.0373
113	P	L	0.0000
114	S	L	-0.2847
115	V	L	-0.1062
116	F	L	0.0000
117	I	L	0.0000
118	F	L	0.0000
119	P	L	-0.4700
120	P	L	0.0000
121	S	L	0.0000
122	D	L	-2.3053
123	E	L	-2.6173
124	Q	L	0.0000
125	L	L	-1.7268
126	K	L	-2.6106
127	S	L	-1.7122
128	G	L	-1.3236
129	T	L	-0.8741
130	A	L	0.0000
131	S	L	0.0000
132	V	L	0.0000
133	V	L	0.0000
134	C	L	0.0000
135	L	L	0.0000
136	L	L	0.0000
137	N	L	0.0000
138	N	L	-1.1209
139	F	L	0.0000
140	Y	L	0.0000
141	P	L	-1.6265
142	R	L	-2.9615
143	E	L	-3.2194
144	A	L	-2.3633
145	K	L	-2.5620
146	V	L	-1.3768
147	Q	L	-1.0934
148	W	L	0.0000
149	K	L	-0.7440
150	V	L	0.0000
151	D	L	-1.8586
152	N	L	-1.3442
153	A	L	-0.2723
154	L	L	0.6285
155	Q	L	-0.3680
156	S	L	-0.6916
157	G	L	-1.2503
158	N	L	-1.5202
159	S	L	-1.6906
160	Q	L	-1.8393
161	E	L	-2.1433
162	S	L	-1.1350
163	V	L	-0.8715
164	T	L	-1.0194
165	E	L	-2.2591
166	Q	L	-2.0636
167	D	L	-2.0411
168	S	L	-1.9996
169	K	L	-2.3893
170	D	L	-2.1268
171	S	L	-1.9852
172	T	L	0.0000
173	Y	L	0.0000
174	S	L	0.0000
175	L	L	0.0000
176	S	L	0.0000
177	S	L	0.0000
178	T	L	-0.9855
179	L	L	0.0000
180	T	L	-0.5875
181	L	L	-0.8095
182	S	L	-1.1523
183	K	L	-2.1160
184	A	L	-2.0239
185	D	L	-2.8128
186	Y	L	0.0000
187	E	L	-3.8120
188	K	L	-3.8112
189	H	L	-3.2432
190	K	L	-3.1311
191	V	L	-1.6742
192	Y	L	0.0000
193	A	L	-0.7956
194	C	L	0.0000
195	E	L	-1.1755
196	V	L	0.0000
197	T	L	-1.2769
198	H	L	0.0000
199	Q	L	-1.6702
200	G	L	-0.2966
201	L	L	-0.3057
202	S	L	-0.4189
203	S	L	-0.3923
204	P	L	-0.6039
205	V	L	-0.0425
206	T	L	-0.6407
207	K	L	-0.9725
208	S	L	-0.7964
209	F	L	0.0000
210	N	L	-1.6454
211	R	L	-2.3636
212	G	L	-1.6538
213	E	L	-1.5636
214	C	L	-0.1466

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	-0.7957	2.5846
4.5	-0.8321	2.5691
5.0	-0.8738	2.5521
5.5	-0.91	2.5345
6.0	-0.9286	2.5168
6.5	-0.9196	2.499
7.0	-0.8832	2.4812
7.5	-0.8292	2.4906
8.0	-0.7667	2.647
8.5	-0.699	2.8073
9.0	-0.6275	2.9682