protein 1BGA -> Q216D
Try to test the Q216D will impede the neighbor same charged residue D289 to rotate its side chain.
Useage:
>> Scwrl4 -i D216_1bga.pdb -o 1bga_D216.pdb
Using parameters from /usr/local/bin/scwrl4/Scwrl4.ini
Using rotamer library: /usr/local/bin/scwrl4/bbDepRotLib.bin
Residue A 448 is being treated as C-terminal
:::::::::::::::::::::::::::::::::::
Initial number of residues - 368
Initial number of rotamers - 4907
1526 redundant edges eliminated
Isolated residues removed - 4
round 1:
199 redundant edges eliminated
Isolated residues removed - 90
Rotamers eliminated - 3118
round 2:
55 redundant edges eliminated
Isolated residues removed - 43
Rotamers eliminated - 489
round 3:
28 redundant edges eliminated
Isolated residues removed - 15
Rotamers eliminated - 148
round 4:
8 redundant edges eliminated
Isolated residues removed - 9
Rotamers eliminated - 36
round 5:
2 redundant edges eliminated
Isolated residues removed - 5
Rotamers eliminated - 17
round 6:
0 redundant edges eliminated
Isolated residues removed - 0
Rotamers eliminated - 0
Energy accumulated during DEE = 305.91
Searching for clusters... 6 clusters found
Processing cluster of 4 vertices
Redundant nodes eliminated : 1
Tree-decomposition has been built. Width+1 = 1
Total combinations to search = 3.6e+1
2 : -> 312 3
1( 2 ) : 312 -> 316
0( 2 ) : 3 -> 1
ArtPts = 0 MaxDegree = 2 MaxBag = 1 AvgBag = 2
===============================
Launching bottom-to-top process
Combinations:
in intersections - 6
in exclusions - 103.2
total to search - 28
Maximal size of a key is 4 elements
Processing nodes ..
Processing cluster of 186 vertices
Redundant nodes eliminated : 36
Tree-decomposition has been built. Width+1 = 8
Total combinations to search = 4.61771e+7
149( 91 ) : 100 26 164 135 136 123 99 -> 117
148( 33 ) : 14 26 143 140 102 -> 150 331
147( 148 ) : 14 26 331 102 140 -> 15
146( 147 ) : 14 15 331 140 102 -> 101
145( 146 ) : 15 331 140 102 101 -> 323
144( 37 ) : 68 81 17 22 85 -> 43 20
143( 145 ) : 140 102 101 323 -> 137 138
142( 149 ) : 100 26 117 164 136 123 99 -> 66
141( 143 ) : 137 138 101 140 323 -> 288 239
140( 32 ) : 81 17 47 50 85 -> 46
139( 140 ) : 81 46 47 50 85 -> 84
138( 141 ) : 239 137 288 101 323 -> 61
137( 113 ) : 135 133 99 123 127 -> 174
136( 100 ) : 100 26 117 110 66 -> 104
135( 137 ) : 135 133 174 99 123 -> 124
134( 62 ) : 164 135 136 203 204 -> 178
133( 68 ) : 195 218 203 199 219 -> 216
132( 144 ) : 68 81 22 43 20 -> 21
131( 142 ) : 100 117 66 99 123 -> 120
130( 141 ) : 239 288 138 140 323 -> 180
129( 100 ) : 100 117 164 110 136 -> 162
128( 28 ) : 143 203 155 219 251 -> 147
127( 99 ) : 68 17 14 26 22 -> 65
126( 51 ) : 82 133 123 99 130 -> 97
125( 139 ) : 46 47 84 50 -> 88
124( 32 ) : 43 47 20 50 -> 51
123( 148 ) : 150 143 331 140 -> 144
122( 28 ) : 195 218 155 251 -> 221
121( 138 ) : 137 288 239 61 -> 287
120( 127 ) : 14 26 22 65 -> 24
119( 120 ) : 14 26 22 24 -> 27
118( 135 ) : 135 133 174 124 -> 177
117( 134 ) : 164 203 178 204 -> 163
116( 118 ) : 133 174 124 177 -> 170
115( 133 ) : 195 216 203 199 -> 198
114( 121 ) : 137 61 287 -> 96
113( 91 ) : 82 135 123 99 85 -> 133 127
112( 114 ) : 61 287 96 -> 285 322
111( 112 ) : 285 61 322 96 -> 132
110( 51 ) : 82 127 130 85 -> 86
109( 117 ) : 164 178 163 204 -> 208
108( 130 ) : 239 288 180 323 -> 241
107( 124 ) : 43 20 51 -> 44
106( 107 ) : 44 43 51 -> 345
105( 106 ) : 44 51 345 -> 45
104( 105 ) : 45 51 345 -> 347
103( 104 ) : 347 45 51 -> 48
102( 103 ) : 48 347 51 -> 52
101( 87 ) : 143 203 199 252 251 -> 195 218
100( 142 ) : 100 26 117 66 164 136 -> 110
99( 98 ) : 14 26 82 85 -> 68 17 22
98( 85 ) : 100 26 143 82 140 85 -> 14
97( 81 ) : 338 -> 289 306 309 305
96( 120 ) : 14 26 65 24 -> 103
95( 97 ) : 289 306 309 338 -> 321
94( 115 ) : 216 203 198 -> 213
93( 94 ) : 198 213 -> 202
92( 93 ) : 202 213 -> 206
91 : -> 100 26 82 164 135 136 123 99 85
90( 92 ) : 206 202 -> 280 279
89( 133 ) : 195 218 216 -> 215
88( 109 ) : 163 208 -> 231
87( 62 ) : 143 203 140 -> 199 252 251
86( 88 ) : 231 -> 160 227
85( 91 ) : 100 26 82 164 136 135 85 -> 143 140
84( 86 ) : 160 227 -> 225 112
83( 123 ) : 150 331 144 -> 149
82( 106 ) : 44 43 345 -> 41
81( 102 ) : 347 52 -> 339 338
80( 136 ) : 26 110 104 -> 25
79( 80 ) : 110 104 25 -> 108
78( 81 ) : 52 339 338 -> 353
77( 97 ) : 306 305 338 -> 302
76( 77 ) : 302 306 338 -> 352
75( 111 ) : 132 285 96 -> 236
74( 75 ) : 132 285 236 -> 320
73( 74 ) : 285 320 236 -> 283
72( 134 ) : 136 178 204 -> 139
71( 76 ) : 302 352 338 -> 350
70( 71 ) : 302 352 350 -> 299
69( 70 ) : 302 350 299 -> 336
68( 101 ) : 195 143 218 203 199 251 -> 219
67( 69 ) : 336 350 -> 340 327
66( 74 ) : 132 320 236 -> 176
65( 114 ) : 137 61 96 -> 98
64( 137 ) : 174 123 127 -> 125
63( 64 ) : 125 174 -> 173
62( 85 ) : 143 164 135 136 140 -> 203 204
61( 63 ) : 125 173 -> 121 169
60( 64 ) : 125 123 127 -> 126
59( 60 ) : 126 127 123 -> 79
58( 145 ) : 15 331 323 -> 330
57( 59 ) : 126 79 127 -> 83
56( 74 ) : 132 285 320 -> 10
55( 95 ) : 289 309 321 -> 240
54( 95 ) : 306 321 338 -> 356
53( 110 ) : 130 86 -> 95
52( 89 ) : 195 218 -> 253
51( 113 ) : 82 133 123 127 99 85 -> 130
50( 61 ) : 169 -> 172 168
49( 50 ) : 172 168 -> 171
48( 49 ) : 168 171 -> 232
47( 90 ) : 202 279 -> 276
46( 90 ) : 206 280 -> 210
45( 84 ) : 160 227 -> 212
44( 84 ) : 160 112 -> 161
43( 140 ) : 17 46 -> 42
42( 81 ) : 347 339 -> 326
41( 42 ) : 347 326 -> 49
40( 82 ) : 41 345 -> 40
39( 67 ) : 336 340 -> 294
38( 54 ) : 306 -> 355
37( 99 ) : 68 17 22 82 85 -> 81
36( 38 ) : 355 -> 365 367
35( 56 ) : 132 10 -> 94
34( 55 ) : 309 240 -> 243
33( 98 ) : 100 14 143 26 140 -> 102
32( 144 ) : 81 17 43 20 85 -> 47 50
31( 22 ) : 311 -> 313 271
30( 31 ) : 313 271 -> 317
29( 30 ) : 271 317 -> 275
28( 68 ) : 195 143 218 203 219 251 -> 155
27( 29 ) : 275 -> 278 318
26( 58 ) : 331 330 -> 332
25( 26 ) : 332 331 -> 264
24( 25 ) : 332 264 -> 335
23( 24 ) : 332 335 -> 35
22( 34 ) : 243 -> 269 311
21( 22 ) : 269 243 -> 267
20( 23 ) : 35 335 -> 334
19( 20 ) : 35 334 -> 36
18( 21 ) : 269 243 -> 272
17( 130 ) : 180 140 -> 200
16( 96 ) : 14 26 -> 329
15( 18 ) : 243 272 -> 183
14( 57 ) : 83 -> 129
13( 131 ) : 120 -> 70
12( 119 ) : 27 -> 23
11( 79 ) : 25 -> 106
10( 11 ) : 106 -> 28
9( 46 ) : 206 -> 211
8( 107 ) : 20 -> 19
7( 102 ) : 51 -> 55
6( 39 ) : 336 -> 292
5( 6 ) : 292 -> 263
4( 77 ) : 305 -> 262
3( 36 ) : 365 -> 363
2( 22 ) : 311 -> 268
1( 54 ) : 356 -> 359
0( 15 ) : 183 -> 184
ArtPts = 0 MaxDegree = 4 MaxBag = 8 AvgBag = 4.33333
===============================
Launching bottom-to-top process
Combinations:
in intersections - 2.6e+06
in exclusions - 53733.2
total to search - 4.2e+07
Maximal size of a key is 508032 elements
Processing nodes .....................................................................................................................................................
Processing cluster of 4 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 1.2e+1
1 : -> 254 196 245
0( 1 ) : 245 -> 244
ArtPts = 0 MaxDegree = 1 MaxBag = 2 AvgBag = 2.5
===============================
Launching bottom-to-top process
Combinations:
in intersections - 2
in exclusions - 23.2
total to search - 4
Maximal size of a key is 2 elements
Processing nodes .
Processing cluster of 3 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 4.8e+1
0 : -> 255 248 246
ArtPts = 0 MaxDegree = 0 MaxBag = 2 AvgBag = 3
Processing cluster of 3 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 2.4e+1
0 : -> 351 298 297
ArtPts = 0 MaxDegree = 0 MaxBag = 2 AvgBag = 3
Processing cluster of 2 vertices
Redundant nodes eliminated : 1
Tree-decomposition has been built. Width+1 = 1
Total combinations to search = 8
0 : -> 187 192
ArtPts = 0 MaxDegree = 0 MaxBag = 1 AvgBag = 2
Total minimal energy of the graph = 1017.77
真是落落長 ！ 而且差很多 ～
沒有留言:
張貼留言