Project name: HMGA1

Chain sequence(s)	A: MSESSSKSSQPLASKQEKDGTEKRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ
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 partially or entirely disordered. Average 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                                          (00:02:04)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/9137d995ffefb17/tmp/folded.pdb                (00:02:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:13)

• Minimal score value: -4.9155
• Maximal score value: 2.1469
• Average score: -2.2634
• Total score value: -242.182

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	0.4794
2	S	A	-0.6697
3	E	A	-1.8421
4	S	A	-1.4056
5	S	A	-1.3978
6	S	A	-1.4693
7	K	A	-2.1801
8	S	A	-1.5605
9	S	A	-1.1833
10	Q	A	-1.2118
11	P	A	-0.1893
12	L	A	0.8031
13	A	A	-0.2265
14	S	A	-1.3279
15	K	A	-3.0113
16	Q	A	-3.7907
17	E	A	-4.3977
18	K	A	-4.2679
19	D	A	-3.8206
20	G	A	-3.1173
21	T	A	-3.0901
22	E	A	-3.8608
23	K	A	-4.7900
24	R	A	-4.9155
25	G	A	-3.8161
26	R	A	-3.6031
27	G	A	-3.1283
28	R	A	-4.1916
29	P	A	-3.5019
30	R	A	-4.6139
31	K	A	-3.7851
32	Q	A	-2.5028
33	P	A	-1.2232
34	P	A	-0.1723
35	V	A	1.1598
36	S	A	0.2509
37	P	A	-0.0574
38	G	A	-0.1979
39	T	A	0.3641
40	A	A	0.8381
41	L	A	2.1469
42	V	A	2.0202
43	G	A	0.0652
44	S	A	-0.8536
45	Q	A	-2.5052
46	K	A	-3.4160
47	E	A	-3.4400
48	P	A	-1.9551
49	S	A	-1.6843
50	E	A	-1.4128
51	V	A	0.5908
52	P	A	-0.3143
53	T	A	-0.8836
54	P	A	-1.4788
55	K	A	-3.1675
56	R	A	-3.4652
57	P	A	-2.9120
58	R	A	-3.4841
59	G	A	-2.8930
60	R	A	-3.3093
61	P	A	-2.6505
62	K	A	-2.7957
63	G	A	-2.2952
64	S	A	-2.7674
65	K	A	-3.4560
66	N	A	-3.1149
67	K	A	-2.9873
68	G	A	-2.1156
69	A	A	-1.3489
70	A	A	-1.7109
71	K	A	-2.5847
72	T	A	-2.3063
73	R	A	-3.2325
74	K	A	-2.9748
75	T	A	-1.5945
76	T	A	-1.0206
77	T	A	-1.2829
78	T	A	-1.1197
79	P	A	-1.2653
80	G	A	-1.9282
81	R	A	-3.3131
82	K	A	-3.4231
83	P	A	-2.9705
84	R	A	-3.2914
85	G	A	-2.7352
86	R	A	-3.2785
87	P	A	-2.7925
88	K	A	-2.9117
89	K	A	-2.8743
90	L	A	-1.4822
91	E	A	-3.7164
92	K	A	-4.5538
93	E	A	-4.7916
94	E	A	-4.7524
95	E	A	-4.3606
96	E	A	-3.9363
97	G	A	-2.5865
98	I	A	-0.7455
99	S	A	-1.4004
100	Q	A	-2.4155
101	E	A	-2.7742
102	S	A	-2.0125
103	S	A	-2.6807
104	E	A	-4.0685
105	E	A	-4.2029
106	E	A	-3.8155
107	Q	A	-2.7686

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 partially or entirely disordered. Average score is recommended for pH analysis.

pH	Average A4D Score	Max A4D Score
4.0	-2.3415	2.9755
4.5	-2.4539	2.9755
5.0	-2.5956	2.9755
5.5	-2.7276	2.9755
6.0	-2.8035	2.9755
6.5	-2.791	2.9755
7.0	-2.6928	2.9755
7.5	-2.5385	2.9755
8.0	-2.3574	2.9755
8.5	-2.1662	2.9755
9.0	-1.9725	2.9755