In [25]:
Image('pr10_1.png', width = 800)
Out[25]:
Начало: установка Modeller в колабе
! cd /tmp/ ; wget https://salilab.org/modeller/10.1/modeller_10.1-1_amd64.deb
! env KEY_MODELLER="MODELIRANJE" dpkg -i /tmp/modeller_10.1-1_amd64.deb
--2023-05-14 00:32:09-- https://salilab.org/modeller/10.1/modeller_10.1-1_amd64.deb Resolving salilab.org (salilab.org)... 169.230.79.19 Connecting to salilab.org (salilab.org)|169.230.79.19|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 14404568 (14M) [application/vnd.debian.binary-package] Saving to: ‘modeller_10.1-1_amd64.deb’ modeller_10.1-1_amd 100%[===================>] 13.74M 43.4MB/s in 0.3s 2023-05-14 00:32:10 (43.4 MB/s) - ‘modeller_10.1-1_amd64.deb’ saved [14404568/14404568] Selecting previously unselected package modeller. (Reading database ... 122519 files and directories currently installed.) Preparing to unpack /tmp/modeller_10.1-1_amd64.deb ... Unpacking modeller (10.1-1) ... Setting up modeller (10.1-1) ...
import os
os.kill(os.getpid(), 9)
! echo -e "install_dir = r'/usr/lib/modeller10.1'\nlicense = 'MODELIRANJE'" > /usr/lib/modeller10.1/modlib/modeller/config.py
! wget https://files.rcsb.org/download/1b8p.pdb
! wget https://files.rcsb.org/download/1bdm.pdb
--2023-05-14 00:32:39-- https://files.rcsb.org/download/1b8p.pdb Resolving files.rcsb.org (files.rcsb.org)... 132.249.210.222 Connecting to files.rcsb.org (files.rcsb.org)|132.249.210.222|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [application/octet-stream] Saving to: ‘1b8p.pdb’ 1b8p.pdb [ <=> ] 239.04K --.-KB/s in 0.1s 2023-05-14 00:32:39 (1.88 MB/s) - ‘1b8p.pdb’ saved [244782] --2023-05-14 00:32:39-- https://files.rcsb.org/download/1bdm.pdb Resolving files.rcsb.org (files.rcsb.org)... 132.249.210.222 Connecting to files.rcsb.org (files.rcsb.org)|132.249.210.222|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [application/octet-stream] Saving to: ‘1bdm.pdb’ 1bdm.pdb [ <=> ] 467.25K 2.95MB/s in 0.2s 2023-05-14 00:32:39 (2.95 MB/s) - ‘1bdm.pdb’ saved [478467]
import sys
sys.path.append('/usr/lib/python3.9/dist-packages')
from modeller import *
from modeller import *
env = Environ()
aln = Alignment(env)
for (pdb, chain) in (('1b8p', 'A'), ('1bdm', 'A') ):
m = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain))
aln.append_model(m, atom_files=pdb, align_codes=pdb+chain)
aln.malign()
aln.malign3d()
aln.compare_structures()
aln.id_table(matrix_file='family.mat')
env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0)
MODELLER 10.1, 2021/03/12, r12156
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2021 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux c33e3efbdda2 5.15.107+ x86_64
Date and time of compilation : 2021/03/12 00:18:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/05/14 00:32:44
Multiple dynamic programming alignment (MALIGN):
Residue-residue metric : $(LIB)/as1.sim.mat
ALIGN_BLOCK : 1
Gap introduction penalty: -900.0000
Gap extension penalty : -50.0000
Length of alignment : 330
fndatmi_285W> Only 317 residues out of 318 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
# Sequence alignment of the structurally conserved regions
# [average distance and standard deviation are with respect
# to the framework (i.e., average structure)]
#
# N av ds st dv 1b8pA 1bdmA
# ===============================
1 0.538 0.000 * K 3 K 1
2 0.103 0.000 T 4 A 2
3 0.127 0.000 * P 5 P 3
4 0.090 0.000 M 6 V 4
5 0.074 0.000 * R 7 R 5
6 0.138 0.000 * V 8 V 6
7 0.134 0.000 * A 9 A 7
8 0.176 0.000 * V 10 V 8
9 0.125 0.000 * T 11 T 9
10 0.320 0.000 * G 12 G 10
11 0.314 0.000 * A 13 A 11
12 0.232 0.000 * A 14 A 12
13 0.184 0.000 * G 15 G 13
14 0.190 0.000 * Q 16 Q 14
15 0.137 0.000 * I 17 I 15
16 0.159 0.000 C 18 G 16
17 0.090 0.000 * Y 19 Y 17
18 0.025 0.000 * S 20 S 18
19 0.081 0.000 * L 21 L 19
20 0.118 0.000 * L 22 L 20
21 0.127 0.000 * F 23 F 21
22 0.160 0.000 * R 24 R 22
23 0.151 0.000 * I 25 I 23
24 0.118 0.000 * A 26 A 24
25 0.210 0.000 N 27 A 25
26 0.201 0.000 * G 28 G 26
27 0.234 0.000 D 29 E 27
28 0.208 0.000 * M 30 M 28
29 0.236 0.000 * L 31 L 29
30 0.217 0.000 * G 32 G 30
31 0.188 0.000 * K 33 K 31
32 0.146 0.000 * D 34 D 32
33 0.158 0.000 * Q 35 Q 33
34 0.114 0.000 * P 36 P 34
35 0.108 0.000 * V 37 V 35
36 0.150 0.000 * I 38 I 36
37 0.159 0.000 * L 39 L 37
38 0.162 0.000 * Q 40 Q 38
39 0.121 0.000 * L 41 L 39
40 0.131 0.000 * L 42 L 40
41 0.125 0.000 * E 43 E 41
42 0.205 0.000 * I 44 I 42
43 0.805 0.000 * P 45 P 43
44 1.024 0.000 N 46 Q 44
# ===============================
45 0.334 0.000 * A 49 A 45
46 0.220 0.000 Q 50 M 46
47 0.215 0.000 * K 51 K 47
48 0.096 0.000 * A 52 A 48
49 0.070 0.000 * L 53 L 49
50 0.100 0.000 Q 54 E 50
51 0.098 0.000 * G 55 G 51
52 0.219 0.000 * V 56 V 52
53 0.206 0.000 M 57 V 53
54 0.143 0.000 * M 58 M 54
55 0.203 0.000 * E 59 E 55
56 0.264 0.000 I 60 L 56
57 0.202 0.000 D 61 E 57
58 0.219 0.000 * D 62 D 58
59 0.241 0.000 * C 63 C 59
60 0.266 0.000 * A 64 A 60
61 0.217 0.000 * F 65 F 61
62 0.173 0.000 * P 66 P 62
63 0.134 0.000 * L 67 L 63
64 0.035 0.000 * L 68 L 64
65 0.087 0.000 * A 69 A 65
66 0.123 0.000 * G 70 G 66
67 0.142 0.000 M 71 L 67
68 0.215 0.000 T 72 E 68
69 0.336 0.000 * A 73 A 69
70 0.339 0.000 H 74 T 70
71 0.319 0.000 A 75 D 71
72 0.468 0.000 * D 76 D 72
73 0.276 0.000 * P 77 P 73
74 0.513 0.000 M 78 D 74
75 0.487 0.000 T 79 V 75
76 0.361 0.000 * A 80 A 76
77 0.215 0.000 * F 81 F 77
78 0.243 0.000 * K 82 K 78
79 0.204 0.000 * D 83 D 79
80 0.161 0.000 * A 84 A 80
81 0.099 0.000 * D 85 D 81
82 0.047 0.000 V 86 Y 82
83 0.022 0.000 * A 87 A 83
84 0.044 0.000 * L 88 L 84
85 0.031 0.000 * L 89 L 85
86 0.075 0.000 * V 90 V 86
87 0.071 0.000 * G 91 G 87
88 0.159 0.000 * A 92 A 88
89 0.413 0.000 R 93 A 89
90 1.137 0.000 * P 94 P 90
91 0.000 0.000 * R 95 R 91
# ===============================
92 0.712 0.000 * L 105 L 101
93 0.728 0.000 E 106 Q 102
94 0.540 0.000 A 107 V 103
95 0.342 0.000 * N 108 N 104
96 0.479 0.000 A 109 G 105
97 0.503 0.000 Q 110 K 106
98 0.276 0.000 * I 111 I 107
99 0.189 0.000 * F 112 F 108
100 0.315 0.000 * T 113 T 109
101 0.286 0.000 V 114 E 110
102 0.109 0.000 * Q 115 Q 111
103 0.124 0.000 * G 116 G 112
104 0.209 0.000 K 117 R 113
105 0.216 0.000 * A 118 A 114
106 0.146 0.000 I 119 L 115
107 0.311 0.000 D 120 A 116
108 0.312 0.000 A 121 E 117
109 0.210 0.000 * V 122 V 118
110 0.135 0.000 * A 123 A 119
111 0.113 0.000 S 124 K 120
112 0.221 0.000 R 125 K 121
113 0.182 0.000 N 126 D 122
114 0.091 0.000 I 127 V 123
115 0.097 0.000 * K 128 K 124
116 0.054 0.000 * V 129 V 125
117 0.079 0.000 * L 130 L 126
118 0.097 0.000 * V 131 V 127
119 0.222 0.000 * V 132 V 128
120 0.215 0.000 * G 133 G 129
121 0.239 0.000 * N 134 N 130
122 0.217 0.000 * P 135 P 131
123 0.280 0.000 * A 136 A 132
124 0.272 0.000 * N 137 N 133
125 0.263 0.000 * T 138 T 134
126 0.254 0.000 * N 139 N 135
127 0.304 0.000 * A 140 A 136
128 0.399 0.000 Y 141 L 137
129 0.319 0.000 * I 142 I 138
130 0.245 0.000 * A 143 A 139
131 0.306 0.000 M 144 Y 140
132 0.226 0.000 * K 145 K 141
133 0.260 0.000 S 146 N 142
134 0.318 0.000 * A 147 A 143
135 0.975 0.000 * P 148 P 144
136 0.114 0.000 S 149 G 145
137 0.186 0.000 * L 150 L 146
138 0.261 0.000 P 151 N 147
139 0.382 0.000 A 152 P 148
140 0.283 0.000 K 153 R 149
141 0.049 0.000 * N 154 N 150
142 0.059 0.000 * F 155 F 151
143 0.098 0.000 * T 156 T 152
144 0.127 0.000 * A 157 A 153
145 0.171 0.000 * M 158 M 154
146 0.275 0.000 L 159 T 155
147 0.139 0.000 * R 160 R 156
148 0.178 0.000 * L 161 L 157
149 0.246 0.000 * D 162 D 158
150 0.103 0.000 * H 163 H 159
151 0.072 0.000 * N 164 N 160
152 0.191 0.000 * R 165 R 161
153 0.175 0.000 * A 166 A 162
154 0.189 0.000 L 167 K 163
155 0.092 0.000 S 168 A 164
156 0.161 0.000 * Q 169 Q 165
157 0.124 0.000 I 170 L 166
158 0.159 0.000 * A 171 A 167
159 0.195 0.000 A 172 K 168
160 0.161 0.000 * K 173 K 169
161 0.134 0.000 * T 174 T 170
162 0.209 0.000 * G 175 G 171
163 0.098 0.000 K 176 T 172
164 0.136 0.000 P 177 G 173
165 0.212 0.000 * V 178 V 174
166 0.285 0.000 S 179 D 175
167 0.248 0.000 S 180 R 176
168 0.312 0.000 * I 181 I 177
169 0.547 0.000 E 182 R 178
170 0.559 0.000 K 183 R 179
171 0.574 0.000 L 184 M 180
172 0.504 0.000 F 185 T 181
173 0.334 0.000 * V 186 V 182
174 0.156 0.000 * W 187 W 183
175 0.137 0.000 * G 188 G 184
176 0.568 0.000 * N 189 N 185
177 0.458 0.000 * H 190 H 186
178 0.390 0.000 * S 191 S 187
179 0.565 0.000 P 192 S 188
180 0.393 0.000 T 193 I 189
181 0.268 0.000 * M 194 M 190
182 0.152 0.000 Y 195 F 191
183 0.150 0.000 A 196 P 192
184 0.079 0.000 * D 197 D 193
185 0.333 0.000 Y 198 L 194
186 0.313 0.000 R 199 F 195
187 0.482 0.000 Y 200 H 196
188 0.442 0.000 * A 201 A 197
189 0.501 0.000 Q 202 E 198
190 1.010 0.000 I 203 V 199
191 1.185 0.000 * D 204 D 200
192 0.793 0.000 * G 205 G 205
193 0.484 0.000 A 206 R 206
194 0.616 0.000 S 207 P 207
195 0.571 0.000 V 208 A 208
196 0.364 0.000 K 209 L 209
197 0.375 0.000 D 210 E 210
198 0.469 0.000 M 211 L 211
199 0.583 0.000 I 212 V 212
# ===============================
200 0.727 0.000 * D 214 D 214
201 0.300 0.000 D 215 M 215
202 0.480 0.000 A 216 E 216
203 0.351 0.000 * W 217 W 217
204 0.325 0.000 N 218 Y 218
205 0.315 0.000 R 219 E 219
206 0.532 0.000 D 220 K 220
207 0.429 0.000 T 221 V 221
208 0.298 0.000 * F 222 F 222
209 0.321 0.000 L 223 I 223
210 0.389 0.000 * P 224 P 224
211 0.411 0.000 * T 225 T 225
212 0.358 0.000 * V 226 V 226
213 0.474 0.000 G 227 A 227
214 0.698 0.000 K 228 Q 228
215 0.396 0.000 * R 229 R 229
216 0.352 0.000 * G 230 G 230
217 0.522 0.000 * A 231 A 231
218 0.569 0.000 * A 232 A 232
219 0.431 0.000 * I 233 I 233
220 0.425 0.000 * I 234 I 234
221 0.503 0.000 D 235 Q 235
222 0.465 0.000 * A 236 A 236
223 0.542 0.000 * R 237 R 237
224 0.562 0.000 * G 238 G 238
225 0.526 0.000 V 239 A 239
226 0.402 0.000 * S 240 S 240
227 0.289 0.000 * S 241 S 241
228 0.194 0.000 * A 242 A 242
229 0.195 0.000 * A 243 A 243
230 0.241 0.000 * S 244 S 244
231 0.218 0.000 * A 245 A 245
232 0.107 0.000 * A 246 A 246
233 0.118 0.000 * N 247 N 247
234 0.100 0.000 * A 248 A 248
235 0.117 0.000 * A 249 A 249
236 0.061 0.000 * I 250 I 250
237 0.120 0.000 D 251 E 251
238 0.076 0.000 * H 252 H 252
239 0.088 0.000 * I 253 I 253
240 0.110 0.000 H 254 R 254
241 0.105 0.000 * D 255 D 255
242 0.079 0.000 * W 256 W 256
243 0.106 0.000 V 257 A 257
244 0.114 0.000 * L 258 L 258
245 0.216 0.000 * G 259 G 259
246 0.363 0.000 * T 260 T 260
247 1.584 0.000 A 261 P 261
248 1.356 0.000 G 262 E 262
# ===============================
249 0.852 0.000 K 263 D 264
250 0.305 0.000 * W 264 W 265
251 0.301 0.000 T 265 V 266
252 0.236 0.000 T 266 S 267
253 0.290 0.000 * M 267 M 268
254 0.262 0.000 G 268 A 269
255 0.211 0.000 I 269 V 270
256 0.226 0.000 * P 270 P 271
257 0.328 0.000 * S 271 S 272
258 0.489 0.000 D 272 Q 273
259 0.203 0.000 * G 273 G 274
260 0.381 0.000 S 274 E 275
261 0.194 0.000 * Y 275 Y 277
262 0.241 0.000 * G 276 G 278
263 0.216 0.000 * I 277 I 279
264 0.443 0.000 * P 278 P 280
265 0.512 0.000 * E 279 E 281
266 0.605 0.000 * G 280 G 282
267 0.490 0.000 V 281 I 283
268 0.257 0.000 I 282 V 284
269 0.263 0.000 F 283 Y 285
270 0.255 0.000 G 284 S 286
271 0.078 0.000 * F 285 F 287
272 0.167 0.000 * P 286 P 288
273 0.344 0.000 * V 287 V 289
274 0.344 0.000 * T 288 T 290
275 0.244 0.000 T 289 A 291
276 0.319 0.000 E 290 K 292
277 0.912 0.000 N 291 D 293
278 0.400 0.000 * G 292 G 294
279 0.217 0.000 E 293 A 295
280 0.195 0.000 * Y 294 Y 296
281 0.406 0.000 K 295 R 297
282 0.353 0.000 I 296 V 298
283 0.361 0.000 * V 297 V 299
284 0.592 0.000 Q 298 E 300
285 0.493 0.000 * G 299 G 301
286 0.434 0.000 * L 300 L 302
287 0.569 0.000 S 301 E 303
288 0.578 0.000 * I 302 I 304
289 0.551 0.000 D 303 N 305
290 0.610 0.000 A 304 E 306
291 0.477 0.000 * F 305 F 307
292 0.367 0.000 S 306 A 308
293 0.477 0.000 Q 307 R 309
294 0.426 0.000 E 308 K 310
295 0.275 0.000 * R 309 R 311
296 0.357 0.000 I 310 M 312
297 0.608 0.000 N 311 E 313
298 0.623 0.000 V 312 I 314
299 0.460 0.000 * T 313 T 315
300 0.496 0.000 L 314 A 316
301 0.752 0.000 N 315 Q 317
302 0.774 0.000 * E 316 E 318
303 0.446 0.000 * L 317 L 319
304 0.728 0.000 * L 318 L 320
305 0.952 0.000 E 319 D 321
306 0.820 0.000 * E 320 E 322
307 0.678 0.000 Q 321 M 323
308 0.905 0.000 N 322 E 324
309 0.991 0.000 G 323 Q 325
310 0.799 0.000 * V 324 V 326
311 0.734 0.000 Q 325 K 327
# ===============================
312 0.874 0.000 H 326 G 330
313 0.909 0.000 * L 327 L 331
314 1.016 0.000 L 328 I 332
# ===============================
# Sequence alignment of the structurally conserved regions
# [average distance and standard deviation are with respect
# to the framework (i.e., average structure)]
#
# N av ds st dv 1b8pA 1bdmA
# ===============================
1 0.567 0.000 * K 3 K 1
2 0.084 0.000 T 4 A 2
3 0.139 0.000 * P 5 P 3
4 0.094 0.000 M 6 V 4
5 0.050 0.000 * R 7 R 5
6 0.131 0.000 * V 8 V 6
7 0.120 0.000 * A 9 A 7
8 0.166 0.000 * V 10 V 8
9 0.111 0.000 * T 11 T 9
10 0.322 0.000 * G 12 G 10
11 0.314 0.000 * A 13 A 11
12 0.236 0.000 * A 14 A 12
13 0.189 0.000 * G 15 G 13
14 0.195 0.000 * Q 16 Q 14
15 0.129 0.000 * I 17 I 15
16 0.167 0.000 C 18 G 16
17 0.092 0.000 * Y 19 Y 17
18 0.027 0.000 * S 20 S 18
19 0.071 0.000 * L 21 L 19
20 0.107 0.000 * L 22 L 20
21 0.123 0.000 * F 23 F 21
22 0.143 0.000 * R 24 R 22
23 0.132 0.000 * I 25 I 23
24 0.127 0.000 * A 26 A 24
25 0.210 0.000 N 27 A 25
26 0.194 0.000 * G 28 G 26
27 0.218 0.000 D 29 E 27
28 0.187 0.000 * M 30 M 28
29 0.217 0.000 * L 31 L 29
30 0.186 0.000 * G 32 G 30
31 0.183 0.000 * K 33 K 31
32 0.162 0.000 * D 34 D 32
33 0.171 0.000 * Q 35 Q 33
34 0.101 0.000 * P 36 P 34
35 0.112 0.000 * V 37 V 35
36 0.156 0.000 * I 38 I 36
37 0.135 0.000 * L 39 L 37
38 0.151 0.000 * Q 40 Q 38
39 0.132 0.000 * L 41 L 39
40 0.143 0.000 * L 42 L 40
41 0.128 0.000 * E 43 E 41
42 0.203 0.000 * I 44 I 42
43 0.797 0.000 * P 45 P 43
44 1.026 0.000 N 46 Q 44
# ===============================
45 0.348 0.000 * A 49 A 45
46 0.233 0.000 Q 50 M 46
47 0.240 0.000 * K 51 K 47
48 0.105 0.000 * A 52 A 48
49 0.085 0.000 * L 53 L 49
50 0.120 0.000 Q 54 E 50
51 0.108 0.000 * G 55 G 51
52 0.225 0.000 * V 56 V 52
53 0.223 0.000 M 57 V 53
54 0.167 0.000 * M 58 M 54
55 0.222 0.000 * E 59 E 55
56 0.279 0.000 I 60 L 56
57 0.222 0.000 D 61 E 57
58 0.242 0.000 * D 62 D 58
59 0.263 0.000 * C 63 C 59
60 0.288 0.000 * A 64 A 60
61 0.223 0.000 * F 65 F 61
62 0.190 0.000 * P 66 P 62
63 0.145 0.000 * L 67 L 63
64 0.054 0.000 * L 68 L 64
65 0.107 0.000 * A 69 A 65
66 0.148 0.000 * G 70 G 66
67 0.103 0.000 M 71 L 67
68 0.217 0.000 T 72 E 68
69 0.328 0.000 * A 73 A 69
70 0.317 0.000 H 74 T 70
71 0.327 0.000 A 75 D 71
72 0.420 0.000 * D 76 D 72
73 0.231 0.000 * P 77 P 73
74 0.463 0.000 M 78 D 74
75 0.443 0.000 T 79 V 75
76 0.327 0.000 * A 80 A 76
77 0.175 0.000 * F 81 F 77
78 0.213 0.000 * K 82 K 78
79 0.162 0.000 * D 83 D 79
80 0.158 0.000 * A 84 A 80
81 0.112 0.000 * D 85 D 81
82 0.058 0.000 V 86 Y 82
83 0.050 0.000 * A 87 A 83
84 0.051 0.000 * L 88 L 84
85 0.020 0.000 * L 89 L 85
86 0.100 0.000 * V 90 V 86
87 0.100 0.000 * G 91 G 87
88 0.159 0.000 * A 92 A 88
89 0.398 0.000 R 93 A 89
90 1.118 0.000 * P 94 P 90
91 0.000 0.000 * R 95 R 91
# ===============================
92 0.684 0.000 * L 105 L 101
93 0.696 0.000 E 106 Q 102
94 0.503 0.000 A 107 V 103
95 0.318 0.000 * N 108 N 104
96 0.456 0.000 A 109 G 105
97 0.457 0.000 Q 110 K 106
98 0.238 0.000 * I 111 I 107
99 0.169 0.000 * F 112 F 108
100 0.269 0.000 * T 113 T 109
101 0.239 0.000 V 114 E 110
102 0.068 0.000 * Q 115 Q 111
103 0.097 0.000 * G 116 G 112
104 0.155 0.000 K 117 R 113
105 0.164 0.000 * A 118 A 114
106 0.103 0.000 I 119 L 115
107 0.255 0.000 D 120 A 116
108 0.256 0.000 A 121 E 117
109 0.159 0.000 * V 122 V 118
110 0.088 0.000 * A 123 A 119
111 0.138 0.000 S 124 K 120
112 0.260 0.000 R 125 K 121
113 0.170 0.000 N 126 D 122
114 0.080 0.000 I 127 V 123
115 0.094 0.000 * K 128 K 124
116 0.057 0.000 * V 129 V 125
117 0.076 0.000 * L 130 L 126
118 0.110 0.000 * V 131 V 127
119 0.237 0.000 * V 132 V 128
120 0.218 0.000 * G 133 G 129
121 0.233 0.000 * N 134 N 130
122 0.218 0.000 * P 135 P 131
123 0.278 0.000 * A 136 A 132
124 0.277 0.000 * N 137 N 133
125 0.268 0.000 * T 138 T 134
126 0.262 0.000 * N 139 N 135
127 0.314 0.000 * A 140 A 136
128 0.401 0.000 Y 141 L 137
129 0.312 0.000 * I 142 I 138
130 0.246 0.000 * A 143 A 139
131 0.286 0.000 M 144 Y 140
132 0.208 0.000 * K 145 K 141
133 0.261 0.000 S 146 N 142
134 0.310 0.000 * A 147 A 143
135 0.943 0.000 * P 148 P 144
136 0.057 0.000 S 149 G 145
137 0.179 0.000 * L 150 L 146
138 0.264 0.000 P 151 N 147
139 0.381 0.000 A 152 P 148
140 0.302 0.000 K 153 R 149
141 0.043 0.000 * N 154 N 150
142 0.040 0.000 * F 155 F 151
143 0.122 0.000 * T 156 T 152
144 0.138 0.000 * A 157 A 153
145 0.191 0.000 * M 158 M 154
146 0.289 0.000 L 159 T 155
147 0.152 0.000 * R 160 R 156
148 0.188 0.000 * L 161 L 157
149 0.260 0.000 * D 162 D 158
150 0.116 0.000 * H 163 H 159
151 0.080 0.000 * N 164 N 160
152 0.203 0.000 * R 165 R 161
153 0.192 0.000 * A 166 A 162
154 0.197 0.000 L 167 K 163
155 0.098 0.000 S 168 A 164
156 0.180 0.000 * Q 169 Q 165
157 0.136 0.000 I 170 L 166
158 0.162 0.000 * A 171 A 167
159 0.213 0.000 A 172 K 168
160 0.186 0.000 * K 173 K 169
161 0.137 0.000 * T 174 T 170
162 0.212 0.000 * G 175 G 171
163 0.108 0.000 K 176 T 172
164 0.135 0.000 P 177 G 173
165 0.221 0.000 * V 178 V 174
166 0.286 0.000 S 179 D 175
167 0.243 0.000 S 180 R 176
168 0.313 0.000 * I 181 I 177
169 0.546 0.000 E 182 R 178
170 0.555 0.000 K 183 R 179
171 0.568 0.000 L 184 M 180
172 0.509 0.000 F 185 T 181
173 0.342 0.000 * V 186 V 182
174 0.169 0.000 * W 187 W 183
175 0.156 0.000 * G 188 G 184
176 0.558 0.000 * N 189 N 185
177 0.482 0.000 * H 190 H 186
178 0.412 0.000 * S 191 S 187
179 0.575 0.000 P 192 S 188
180 0.425 0.000 T 193 I 189
181 0.286 0.000 * M 194 M 190
182 0.172 0.000 Y 195 F 191
183 0.166 0.000 A 196 P 192
184 0.098 0.000 * D 197 D 193
185 0.342 0.000 Y 198 L 194
186 0.292 0.000 R 199 F 195
187 0.468 0.000 Y 200 H 196
188 0.430 0.000 * A 201 A 197
189 0.494 0.000 Q 202 E 198
190 1.004 0.000 I 203 V 199
191 1.182 0.000 * D 204 D 200
192 0.794 0.000 * G 205 G 205
193 0.473 0.000 A 206 R 206
194 0.597 0.000 S 207 P 207
195 0.550 0.000 V 208 A 208
196 0.370 0.000 K 209 L 209
197 0.398 0.000 D 210 E 210
198 0.468 0.000 M 211 L 211
199 0.556 0.000 I 212 V 212
# ===============================
200 0.726 0.000 * D 214 D 214
201 0.308 0.000 D 215 M 215
202 0.507 0.000 A 216 E 216
203 0.384 0.000 * W 217 W 217
204 0.357 0.000 N 218 Y 218
205 0.346 0.000 R 219 E 219
206 0.565 0.000 D 220 K 220
207 0.460 0.000 T 221 V 221
208 0.327 0.000 * F 222 F 222
209 0.352 0.000 L 223 I 223
210 0.423 0.000 * P 224 P 224
211 0.438 0.000 * T 225 T 225
212 0.381 0.000 * V 226 V 226
213 0.499 0.000 G 227 A 227
214 0.726 0.000 K 228 Q 228
215 0.417 0.000 * R 229 R 229
216 0.371 0.000 * G 230 G 230
217 0.546 0.000 * A 231 A 231
218 0.592 0.000 * A 232 A 232
219 0.447 0.000 * I 233 I 233
220 0.442 0.000 * I 234 I 234
221 0.525 0.000 D 235 Q 235
222 0.485 0.000 * A 236 A 236
223 0.556 0.000 * R 237 R 237
224 0.576 0.000 * G 238 G 238
225 0.534 0.000 V 239 A 239
226 0.413 0.000 * S 240 S 240
227 0.295 0.000 * S 241 S 241
228 0.194 0.000 * A 242 A 242
229 0.191 0.000 * A 243 A 243
230 0.240 0.000 * S 244 S 244
231 0.218 0.000 * A 245 A 245
232 0.098 0.000 * A 246 A 246
233 0.110 0.000 * N 247 N 247
234 0.100 0.000 * A 248 A 248
235 0.124 0.000 * A 249 A 249
236 0.067 0.000 * I 250 I 250
237 0.116 0.000 D 251 E 251
238 0.094 0.000 * H 252 H 252
239 0.111 0.000 * I 253 I 253
240 0.129 0.000 H 254 R 254
241 0.125 0.000 * D 255 D 255
242 0.097 0.000 * W 256 W 256
243 0.115 0.000 V 257 A 257
244 0.138 0.000 * L 258 L 258
245 0.233 0.000 * G 259 G 259
246 0.379 0.000 * T 260 T 260
247 1.583 0.000 A 261 P 261
248 1.345 0.000 G 262 E 262
# ===============================
249 0.864 0.000 K 263 D 264
250 0.298 0.000 * W 264 W 265
251 0.298 0.000 T 265 V 266
252 0.249 0.000 T 266 S 267
253 0.308 0.000 * M 267 M 268
254 0.280 0.000 G 268 A 269
255 0.219 0.000 I 269 V 270
256 0.234 0.000 * P 270 P 271
257 0.333 0.000 * S 271 S 272
258 0.509 0.000 D 272 Q 273
259 0.238 0.000 * G 273 G 274
260 0.372 0.000 S 274 E 275
261 0.162 0.000 * Y 275 Y 277
262 0.225 0.000 * G 276 G 278
263 0.258 0.000 * I 277 I 279
264 0.495 0.000 * P 278 P 280
265 0.561 0.000 * E 279 E 281
266 0.642 0.000 * G 280 G 282
267 0.498 0.000 V 281 I 283
268 0.266 0.000 I 282 V 284
269 0.257 0.000 F 283 Y 285
270 0.238 0.000 G 284 S 286
271 0.092 0.000 * F 285 F 287
272 0.154 0.000 * P 286 P 288
273 0.336 0.000 * V 287 V 289
274 0.341 0.000 * T 288 T 290
275 0.248 0.000 T 289 A 291
276 0.311 0.000 E 290 K 292
277 0.901 0.000 N 291 D 293
278 0.413 0.000 * G 292 G 294
279 0.208 0.000 E 293 A 295
280 0.176 0.000 * Y 294 Y 296
281 0.405 0.000 K 295 R 297
282 0.347 0.000 I 296 V 298
283 0.351 0.000 * V 297 V 299
284 0.585 0.000 Q 298 E 300
285 0.466 0.000 * G 299 G 301
286 0.410 0.000 * L 300 L 302
287 0.557 0.000 S 301 E 303
288 0.568 0.000 * I 302 I 304
289 0.542 0.000 D 303 N 305
290 0.597 0.000 A 304 E 306
291 0.485 0.000 * F 305 F 307
292 0.376 0.000 S 306 A 308
293 0.466 0.000 Q 307 R 309
294 0.399 0.000 E 308 K 310
295 0.239 0.000 * R 309 R 311
296 0.338 0.000 I 310 M 312
297 0.583 0.000 N 311 E 313
298 0.595 0.000 V 312 I 314
299 0.437 0.000 * T 313 T 315
300 0.470 0.000 L 314 A 316
301 0.727 0.000 N 315 Q 317
302 0.758 0.000 * E 316 E 318
303 0.437 0.000 * L 317 L 319
304 0.705 0.000 * L 318 L 320
305 0.929 0.000 E 319 D 321
306 0.808 0.000 * E 320 E 322
307 0.664 0.000 Q 321 M 323
308 0.885 0.000 N 322 E 324
309 0.993 0.000 G 323 Q 325
310 0.812 0.000 * V 324 V 326
311 0.747 0.000 Q 325 K 327
# ===============================
312 0.814 0.000 H 326 G 330
313 0.899 0.000 * L 327 L 331
314 1.027 0.000 L 328 I 332
# ===============================
# Sequence alignment of the structurally conserved regions
# [average distance and standard deviation are with respect
# to the framework (i.e., average structure)]
#
# N av ds st dv 1b8pA 1bdmA
# ===============================
1 0.567 0.000 * K 3 K 1
2 0.084 0.000 T 4 A 2
3 0.139 0.000 * P 5 P 3
4 0.094 0.000 M 6 V 4
5 0.050 0.000 * R 7 R 5
6 0.131 0.000 * V 8 V 6
7 0.120 0.000 * A 9 A 7
8 0.166 0.000 * V 10 V 8
9 0.111 0.000 * T 11 T 9
10 0.322 0.000 * G 12 G 10
11 0.314 0.000 * A 13 A 11
12 0.236 0.000 * A 14 A 12
13 0.189 0.000 * G 15 G 13
14 0.195 0.000 * Q 16 Q 14
15 0.129 0.000 * I 17 I 15
16 0.167 0.000 C 18 G 16
17 0.092 0.000 * Y 19 Y 17
18 0.027 0.000 * S 20 S 18
19 0.071 0.000 * L 21 L 19
20 0.107 0.000 * L 22 L 20
21 0.123 0.000 * F 23 F 21
22 0.143 0.000 * R 24 R 22
23 0.132 0.000 * I 25 I 23
24 0.127 0.000 * A 26 A 24
25 0.210 0.000 N 27 A 25
26 0.194 0.000 * G 28 G 26
27 0.218 0.000 D 29 E 27
28 0.187 0.000 * M 30 M 28
29 0.217 0.000 * L 31 L 29
30 0.186 0.000 * G 32 G 30
31 0.183 0.000 * K 33 K 31
32 0.162 0.000 * D 34 D 32
33 0.171 0.000 * Q 35 Q 33
34 0.101 0.000 * P 36 P 34
35 0.112 0.000 * V 37 V 35
36 0.156 0.000 * I 38 I 36
37 0.135 0.000 * L 39 L 37
38 0.151 0.000 * Q 40 Q 38
39 0.132 0.000 * L 41 L 39
40 0.143 0.000 * L 42 L 40
41 0.128 0.000 * E 43 E 41
42 0.203 0.000 * I 44 I 42
43 0.797 0.000 * P 45 P 43
44 1.026 0.000 N 46 Q 44
# ===============================
45 0.348 0.000 * A 49 A 45
46 0.233 0.000 Q 50 M 46
47 0.240 0.000 * K 51 K 47
48 0.105 0.000 * A 52 A 48
49 0.085 0.000 * L 53 L 49
50 0.120 0.000 Q 54 E 50
51 0.108 0.000 * G 55 G 51
52 0.225 0.000 * V 56 V 52
53 0.223 0.000 M 57 V 53
54 0.167 0.000 * M 58 M 54
55 0.222 0.000 * E 59 E 55
56 0.279 0.000 I 60 L 56
57 0.222 0.000 D 61 E 57
58 0.242 0.000 * D 62 D 58
59 0.263 0.000 * C 63 C 59
60 0.288 0.000 * A 64 A 60
61 0.223 0.000 * F 65 F 61
62 0.190 0.000 * P 66 P 62
63 0.145 0.000 * L 67 L 63
64 0.054 0.000 * L 68 L 64
65 0.107 0.000 * A 69 A 65
66 0.148 0.000 * G 70 G 66
67 0.103 0.000 M 71 L 67
68 0.217 0.000 T 72 E 68
69 0.328 0.000 * A 73 A 69
70 0.317 0.000 H 74 T 70
71 0.327 0.000 A 75 D 71
72 0.420 0.000 * D 76 D 72
73 0.231 0.000 * P 77 P 73
74 0.463 0.000 M 78 D 74
75 0.443 0.000 T 79 V 75
76 0.327 0.000 * A 80 A 76
77 0.175 0.000 * F 81 F 77
78 0.213 0.000 * K 82 K 78
79 0.162 0.000 * D 83 D 79
80 0.158 0.000 * A 84 A 80
81 0.112 0.000 * D 85 D 81
82 0.058 0.000 V 86 Y 82
83 0.050 0.000 * A 87 A 83
84 0.051 0.000 * L 88 L 84
85 0.020 0.000 * L 89 L 85
86 0.100 0.000 * V 90 V 86
87 0.100 0.000 * G 91 G 87
88 0.159 0.000 * A 92 A 88
89 0.398 0.000 R 93 A 89
90 1.118 0.000 * P 94 P 90
91 0.000 0.000 * R 95 R 91
# ===============================
92 0.684 0.000 * L 105 L 101
93 0.696 0.000 E 106 Q 102
94 0.503 0.000 A 107 V 103
95 0.318 0.000 * N 108 N 104
96 0.456 0.000 A 109 G 105
97 0.457 0.000 Q 110 K 106
98 0.238 0.000 * I 111 I 107
99 0.169 0.000 * F 112 F 108
100 0.269 0.000 * T 113 T 109
101 0.239 0.000 V 114 E 110
102 0.068 0.000 * Q 115 Q 111
103 0.097 0.000 * G 116 G 112
104 0.155 0.000 K 117 R 113
105 0.164 0.000 * A 118 A 114
106 0.103 0.000 I 119 L 115
107 0.255 0.000 D 120 A 116
108 0.256 0.000 A 121 E 117
109 0.159 0.000 * V 122 V 118
110 0.088 0.000 * A 123 A 119
111 0.138 0.000 S 124 K 120
112 0.260 0.000 R 125 K 121
113 0.170 0.000 N 126 D 122
114 0.080 0.000 I 127 V 123
115 0.094 0.000 * K 128 K 124
116 0.057 0.000 * V 129 V 125
117 0.076 0.000 * L 130 L 126
118 0.110 0.000 * V 131 V 127
119 0.237 0.000 * V 132 V 128
120 0.218 0.000 * G 133 G 129
121 0.233 0.000 * N 134 N 130
122 0.218 0.000 * P 135 P 131
123 0.278 0.000 * A 136 A 132
124 0.277 0.000 * N 137 N 133
125 0.268 0.000 * T 138 T 134
126 0.262 0.000 * N 139 N 135
127 0.314 0.000 * A 140 A 136
128 0.401 0.000 Y 141 L 137
129 0.312 0.000 * I 142 I 138
130 0.246 0.000 * A 143 A 139
131 0.286 0.000 M 144 Y 140
132 0.208 0.000 * K 145 K 141
133 0.261 0.000 S 146 N 142
134 0.310 0.000 * A 147 A 143
135 0.943 0.000 * P 148 P 144
136 0.057 0.000 S 149 G 145
137 0.179 0.000 * L 150 L 146
138 0.264 0.000 P 151 N 147
139 0.381 0.000 A 152 P 148
140 0.302 0.000 K 153 R 149
141 0.043 0.000 * N 154 N 150
142 0.040 0.000 * F 155 F 151
143 0.122 0.000 * T 156 T 152
144 0.138 0.000 * A 157 A 153
145 0.191 0.000 * M 158 M 154
146 0.289 0.000 L 159 T 155
147 0.152 0.000 * R 160 R 156
148 0.188 0.000 * L 161 L 157
149 0.260 0.000 * D 162 D 158
150 0.116 0.000 * H 163 H 159
151 0.080 0.000 * N 164 N 160
152 0.203 0.000 * R 165 R 161
153 0.192 0.000 * A 166 A 162
154 0.197 0.000 L 167 K 163
155 0.098 0.000 S 168 A 164
156 0.180 0.000 * Q 169 Q 165
157 0.136 0.000 I 170 L 166
158 0.162 0.000 * A 171 A 167
159 0.213 0.000 A 172 K 168
160 0.186 0.000 * K 173 K 169
161 0.137 0.000 * T 174 T 170
162 0.212 0.000 * G 175 G 171
163 0.108 0.000 K 176 T 172
164 0.135 0.000 P 177 G 173
165 0.221 0.000 * V 178 V 174
166 0.286 0.000 S 179 D 175
167 0.243 0.000 S 180 R 176
168 0.313 0.000 * I 181 I 177
169 0.546 0.000 E 182 R 178
170 0.555 0.000 K 183 R 179
171 0.568 0.000 L 184 M 180
172 0.509 0.000 F 185 T 181
173 0.342 0.000 * V 186 V 182
174 0.169 0.000 * W 187 W 183
175 0.156 0.000 * G 188 G 184
176 0.558 0.000 * N 189 N 185
177 0.482 0.000 * H 190 H 186
178 0.412 0.000 * S 191 S 187
179 0.575 0.000 P 192 S 188
180 0.425 0.000 T 193 I 189
181 0.286 0.000 * M 194 M 190
182 0.172 0.000 Y 195 F 191
183 0.166 0.000 A 196 P 192
184 0.098 0.000 * D 197 D 193
185 0.342 0.000 Y 198 L 194
186 0.292 0.000 R 199 F 195
187 0.468 0.000 Y 200 H 196
188 0.430 0.000 * A 201 A 197
189 0.494 0.000 Q 202 E 198
190 1.004 0.000 I 203 V 199
191 1.182 0.000 * D 204 D 200
192 0.794 0.000 * G 205 G 205
193 0.473 0.000 A 206 R 206
194 0.597 0.000 S 207 P 207
195 0.550 0.000 V 208 A 208
196 0.370 0.000 K 209 L 209
197 0.398 0.000 D 210 E 210
198 0.468 0.000 M 211 L 211
199 0.556 0.000 I 212 V 212
# ===============================
200 0.726 0.000 * D 214 D 214
201 0.308 0.000 D 215 M 215
202 0.507 0.000 A 216 E 216
203 0.384 0.000 * W 217 W 217
204 0.357 0.000 N 218 Y 218
205 0.346 0.000 R 219 E 219
206 0.565 0.000 D 220 K 220
207 0.460 0.000 T 221 V 221
208 0.327 0.000 * F 222 F 222
209 0.352 0.000 L 223 I 223
210 0.423 0.000 * P 224 P 224
211 0.438 0.000 * T 225 T 225
212 0.381 0.000 * V 226 V 226
213 0.499 0.000 G 227 A 227
214 0.726 0.000 K 228 Q 228
215 0.417 0.000 * R 229 R 229
216 0.371 0.000 * G 230 G 230
217 0.546 0.000 * A 231 A 231
218 0.592 0.000 * A 232 A 232
219 0.447 0.000 * I 233 I 233
220 0.442 0.000 * I 234 I 234
221 0.525 0.000 D 235 Q 235
222 0.485 0.000 * A 236 A 236
223 0.556 0.000 * R 237 R 237
224 0.576 0.000 * G 238 G 238
225 0.534 0.000 V 239 A 239
226 0.413 0.000 * S 240 S 240
227 0.295 0.000 * S 241 S 241
228 0.194 0.000 * A 242 A 242
229 0.191 0.000 * A 243 A 243
230 0.240 0.000 * S 244 S 244
231 0.218 0.000 * A 245 A 245
232 0.098 0.000 * A 246 A 246
233 0.110 0.000 * N 247 N 247
234 0.100 0.000 * A 248 A 248
235 0.124 0.000 * A 249 A 249
236 0.067 0.000 * I 250 I 250
237 0.116 0.000 D 251 E 251
238 0.094 0.000 * H 252 H 252
239 0.111 0.000 * I 253 I 253
240 0.129 0.000 H 254 R 254
241 0.125 0.000 * D 255 D 255
242 0.097 0.000 * W 256 W 256
243 0.115 0.000 V 257 A 257
244 0.138 0.000 * L 258 L 258
245 0.233 0.000 * G 259 G 259
246 0.379 0.000 * T 260 T 260
247 1.583 0.000 A 261 P 261
248 1.345 0.000 G 262 E 262
# ===============================
249 0.864 0.000 K 263 D 264
250 0.298 0.000 * W 264 W 265
251 0.298 0.000 T 265 V 266
252 0.249 0.000 T 266 S 267
253 0.308 0.000 * M 267 M 268
254 0.280 0.000 G 268 A 269
255 0.219 0.000 I 269 V 270
256 0.234 0.000 * P 270 P 271
257 0.333 0.000 * S 271 S 272
258 0.509 0.000 D 272 Q 273
259 0.238 0.000 * G 273 G 274
260 0.372 0.000 S 274 E 275
261 0.162 0.000 * Y 275 Y 277
262 0.225 0.000 * G 276 G 278
263 0.258 0.000 * I 277 I 279
264 0.495 0.000 * P 278 P 280
265 0.561 0.000 * E 279 E 281
266 0.642 0.000 * G 280 G 282
267 0.498 0.000 V 281 I 283
268 0.266 0.000 I 282 V 284
269 0.257 0.000 F 283 Y 285
270 0.238 0.000 G 284 S 286
271 0.092 0.000 * F 285 F 287
272 0.154 0.000 * P 286 P 288
273 0.336 0.000 * V 287 V 289
274 0.341 0.000 * T 288 T 290
275 0.248 0.000 T 289 A 291
276 0.311 0.000 E 290 K 292
277 0.901 0.000 N 291 D 293
278 0.413 0.000 * G 292 G 294
279 0.208 0.000 E 293 A 295
280 0.176 0.000 * Y 294 Y 296
281 0.405 0.000 K 295 R 297
282 0.347 0.000 I 296 V 298
283 0.351 0.000 * V 297 V 299
284 0.585 0.000 Q 298 E 300
285 0.466 0.000 * G 299 G 301
286 0.410 0.000 * L 300 L 302
287 0.557 0.000 S 301 E 303
288 0.568 0.000 * I 302 I 304
289 0.542 0.000 D 303 N 305
290 0.597 0.000 A 304 E 306
291 0.485 0.000 * F 305 F 307
292 0.376 0.000 S 306 A 308
293 0.466 0.000 Q 307 R 309
294 0.399 0.000 E 308 K 310
295 0.239 0.000 * R 309 R 311
296 0.338 0.000 I 310 M 312
297 0.583 0.000 N 311 E 313
298 0.595 0.000 V 312 I 314
299 0.437 0.000 * T 313 T 315
300 0.470 0.000 L 314 A 316
301 0.727 0.000 N 315 Q 317
302 0.758 0.000 * E 316 E 318
303 0.437 0.000 * L 317 L 319
304 0.705 0.000 * L 318 L 320
305 0.929 0.000 E 319 D 321
306 0.808 0.000 * E 320 E 322
307 0.664 0.000 Q 321 M 323
308 0.885 0.000 N 322 E 324
309 0.993 0.000 G 323 Q 325
310 0.812 0.000 * V 324 V 326
311 0.747 0.000 Q 325 K 327
# ===============================
312 0.814 0.000 H 326 G 330
313 0.899 0.000 * L 327 L 331
314 1.027 0.000 L 328 I 332
# ===============================
Least-squares dynamic programming alignment:
FIT_ATOMS atoms for alignment : CA
Max dist from frw for equivalence : 3.5000
Gap introduction penalty : 0.0000
Gap extension penalty : 1.7500
Numb of residues in framework : 314
fndatmi_285W> Only 317 residues out of 318 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
COMPARISON OF SEVERAL 3D STRUCTURES:
# ALGNMT CODE ATOM FILE
1 1b8pA
2 1bdmA
Variability at a given position is calculated as:
VAR = 1/Nij * sum_ij (feat_i - feat_j)
sum runs over all pairs of proteins with residues present.
>> Least-squares superposition (FIT) : T
Atom types for superposition/RMS (FIT_ATOMS): CA
Atom type for position average/variability (VARATOM): CA
Position comparison (FIT_ATOMS):
Cutoff for RMS calculation: 3.5000
Upper = RMS, Lower = numb equiv positions
1b8pA 1bdmA
1b8pA 0.000 0.804
1bdmA 313 0.000
Distance comparison (FIT_ATOMS):
Cutoff for rms calculation: 3.5000
Upper = Distance RMS, Lower = numb equiv distances
1b8pA 1bdmA
1b8pA 0.000 0.625
1bdmA 48824 0.000
>> Sequence comparison:
Diag=numb res, Upper=numb equiv res, Lower = % seq ID
1b8pA 1bdmA
1b8pA 327 194
1bdmA 61 318
>> Dihedral angle comparison: Alph
Cutoff for rms comparison: 60.0000
Upper = RMS Alph, Lower = numb of equiv angles
1b8pA 1bdmA
1b8pA 0.000 13.112
1bdmA 303 0.000
>> Dihedral angle comparison: Phi
Cutoff for rms comparison: 60.0000
Upper = RMS Phi , Lower = numb of equiv angles
1b8pA 1bdmA
1b8pA 0.000 11.722
1bdmA 304 0.000
>> Dihedral angle comparison: Psi
Cutoff for rms comparison: 15.0000
Upper = RMS Psi , Lower = numb of equiv angles
1b8pA 1bdmA
1b8pA 0.000 6.797
1bdmA 267 0.000
>> Dihedral angle comparison: Omeg
Cutoff for rms comparison: 60.0000
Upper = RMS Omeg, Lower = numb of equiv angles
1b8pA 1bdmA
1b8pA 0.000 3.968
1bdmA 311 0.000
>> Dihedral angle comparison: chi1
Cutoff for rms comparison: 60.0000
Upper = RMS chi1, Lower = numb of equiv angles
1b8pA 1bdmA
1b8pA 0.000 16.420
1bdmA 177 0.000
>> Dihedral angle comparison: chi2
Cutoff for rms comparison: 60.0000
Upper = RMS chi2, Lower = numb of equiv angles
1b8pA 1bdmA
1b8pA 0.000 18.853
1bdmA 116 0.000
>> Dihedral angle comparison: chi3
Cutoff for rms comparison: 60.0000
Upper = RMS chi3, Lower = numb of equiv angles
1b8pA 1bdmA
1b8pA 0.000 27.273
1bdmA 37 0.000
>> Dihedral angle comparison: chi4
Cutoff for rms comparison: 60.0000
Upper = RMS chi4, Lower = numb of equiv angles
1b8pA 1bdmA
1b8pA 0.000 27.741
1bdmA 10 0.000
>> Dihedral angle comparison: chi5
Cutoff for rms comparison: 60.0000
Upper = RMS chi5, Lower = numb of equiv angles
1b8pA 1bdmA
1b8pA 0.000 0.000
1bdmA 0 0.000
>> Ramachandran mainchain class substitution
prot 1 --> prot 2; class on vert --> class on horiz
A P B L E U
A 172 2 1 2 0 2
P 1 34 7 0 0 0
B 0 6 64 0 0 1
L 0 2 0 16 0 0
E 0 0 1 0 2 0
U 0 1 0 0 0 0
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
A 172 7 179 55.0 2.2 57.2
P 34 8 42 10.9 2.6 13.4
B 64 7 71 20.4 2.2 22.7
L 16 2 18 5.1 0.6 5.8
E 2 1 3 0.6 0.3 1.0
--------------------------------------------
SUMS 288 25 313 92.0 8.0 100.0
--------------------------------------------
U 0 1 1 0.0 0.3 0.3
>> Dihedral class substitution: Alph
prot 1 --> prot 2; class on vert --> class on horiz
1 2 3 4
1 12 1 4 0
2 2 170 1 2
3 6 5 106 3
4 0 0 1 1
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
1 12 5 17 3.8 1.6 5.4
2 170 5 175 54.5 1.6 56.1
3 106 14 120 34.0 4.5 38.5
--------------------------------------------
SUMS 288 24 312 92.3 7.7 100.0
--------------------------------------------
4 1 1 2 0.3 0.3 0.6
>> Dihedral class substitution: Phi
prot 1 --> prot 2; class on vert --> class on horiz
1 2 3 4
1 181 2 14 2
2 2 18 1 0
3 5 0 88 0
4 1 0 0 0
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
1 181 18 199 57.8 5.8 63.6
2 18 3 21 5.8 1.0 6.7
3 88 5 93 28.1 1.6 29.7
--------------------------------------------
SUMS 287 26 313 91.7 8.3 100.0
--------------------------------------------
4 0 1 1 0.0 0.3 0.3
>> Dihedral class substitution: Psi
prot 1 --> prot 2; class on vert --> class on horiz
1 2 3 4
1 152 9 1 0
2 2 39 4 1
3 1 2 102 1
4 0 0 0 0
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
1 152 10 162 48.4 3.2 51.6
2 39 7 46 12.4 2.2 14.6
3 102 4 106 32.5 1.3 33.8
--------------------------------------------
SUMS 293 21 314 93.3 6.7 100.0
--------------------------------------------
4 0 0 0 0.0 0.0 0.0
>> Dihedral class substitution: Omeg
prot 1 --> prot 2; class on vert --> class on horiz
1 2 3 4
1 310 0 0 3
2 0 1 0 0
3 0 0 0 0
4 0 0 0 0
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
1 310 3 313 98.7 1.0 99.7
2 1 0 1 0.3 0.0 0.3
3 0 0 0 0.0 0.0 0.0
--------------------------------------------
SUMS 311 3 314 99.0 1.0 100.0
--------------------------------------------
4 0 0 0 0.0 0.0 0.0
>> Dihedral class substitution: chi1
prot 1 --> prot 2; class on vert --> class on horiz
1 2 3 4
1 109 14 8 6
2 18 57 5 9
3 9 1 8 2
4 2 7 4 55
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
1 109 28 137 44.3 11.4 55.7
2 57 32 89 23.2 13.0 36.2
3 8 12 20 3.3 4.9 8.1
--------------------------------------------
SUMS 174 72 246 70.7 29.3 100.0
--------------------------------------------
4 55 13 68 17.5 4.1 21.7
>> Dihedral class substitution: chi2
prot 1 --> prot 2; class on vert --> class on horiz
1 2 3 4
1 84 14 3 11
2 16 32 6 8
3 6 1 6 2
4 16 7 1 101
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
1 84 28 112 44.4 14.8 59.3
2 32 30 62 16.9 15.9 32.8
3 6 9 15 3.2 4.8 7.9
--------------------------------------------
SUMS 122 67 189 64.6 35.4 100.0
--------------------------------------------
4 101 24 125 32.2 7.6 39.8
>> Dihedral class substitution: chi3
prot 1 --> prot 2; class on vert --> class on horiz
1 2 3 4
1 26 6 6 9
2 6 10 1 7
3 2 1 2 1
4 18 11 4 204
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
1 26 21 47 33.8 27.3 61.0
2 10 14 24 13.0 18.2 31.2
3 2 4 6 2.6 5.2 7.8
--------------------------------------------
SUMS 38 39 77 49.4 50.6 100.0
--------------------------------------------
4 204 33 237 65.0 10.5 75.5
>> Dihedral class substitution: chi4
prot 1 --> prot 2; class on vert --> class on horiz
1 2 3 4
1 7 1 6 2
2 1 1 0 1
3 1 2 0 5
4 9 0 4 274
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
1 7 9 16 25.9 33.3 59.3
2 1 2 3 3.7 7.4 11.1
3 0 8 8 0.0 29.6 29.6
--------------------------------------------
SUMS 8 19 27 29.6 70.4 100.0
--------------------------------------------
4 274 13 287 87.3 4.1 91.4
>> Dihedral class substitution: chi5
prot 1 --> prot 2; class on vert --> class on horiz
1 2 3 4
1 0 0 0 0
2 0 0 0 0
3 0 0 0 0
4 0 0 0 314
Summary (% does not count undefined):
CODE # ID # NID # TOT % ID % NID % TOT
1 0 0 0 0.0 0.0 0.0
2 0 0 0 0.0 0.0 0.0
3 0 0 0 0.0 0.0 0.0
--------------------------------------------
SUMS 0 0 0 0.0 0.0 0.0
--------------------------------------------
4 314 0 314 100.0 0.0 100.0
>> Detailed comparison:
Structure : 1
Structure : 2
ALN ... alignment position
RESID... ... residue numbers 1/2/3
AAA ... amino acid types 1/2/3
MNC ... mainchain classes 1/2/3
ALP... ... dihedral angle classes (alpha,phi,psi,...)
ALN RESIDUE_NUMBERS AAA MNC ALP PHI PSI OMG CH1 CH2 CH3 CH4 CH5
---------------------------------------------------------------
1 ----0 -M -U -4 -4 -3 -1 -1 -2 -3 -4 -4
2 3 1 KK UP 43 41 33 11 31 11 11 11 44
3 4 2 TA PP 33 11 33 11 34 44 44 44 44
4 5 3 PP PP 33 11 22 11 21 12 21 44 44
5 6 4 MV BB 33 33 33 11 12 14 24 44 44
6 7 5 RR BB 33 33 33 11 11 11 31 32 44
7 8 6 VV BB 33 33 33 11 11 44 44 44 44
8 9 7 AA BB 33 33 33 11 44 44 44 44 44
9 10 8 VV BB 33 33 33 11 11 44 44 44 44
10 11 9 TT PP 22 33 33 11 22 44 44 44 44
11 12 10 GG LL 33 22 22 11 44 44 44 44 44
12 13 11 AA AA 22 11 11 11 44 44 44 44 44
13 14 12 AA AA 22 33 22 11 44 44 44 44 44
14 15 13 GG PP 31 11 33 11 44 44 44 44 44
15 16 14 QQ AA 22 11 11 11 21 31 11 44 44
16 17 15 II AA 22 11 11 11 11 11 44 44 44
17 18 16 CG AA 22 11 11 11 14 44 44 44 44
18 19 17 YY AA 22 11 11 11 22 22 44 44 44
19 20 18 SS AA 22 33 11 11 22 44 44 44 44
20 21 19 LL AA 22 13 11 11 22 22 44 44 44
21 22 20 LL AA 22 11 11 11 11 11 44 44 44
22 23 21 FF AA 22 11 11 11 11 22 44 44 44
23 24 22 RR AA 22 11 11 11 11 11 33 11 44
24 25 23 II AA 22 11 11 11 11 11 44 44 44
25 26 24 AA AA 22 11 11 11 44 44 44 44 44
26 27 25 NA AA 33 11 11 11 24 24 44 44 44
27 28 26 GG LL 33 22 22 11 44 44 44 44 44
28 29 27 DE AA 22 11 11 11 11 11 41 44 44
29 30 28 MM AA 22 13 11 11 22 11 22 44 44
30 31 29 LL AA 11 33 22 11 11 11 44 44 44
31 32 30 GG EE 31 22 33 11 44 44 44 44 44
32 33 31 KK AA 22 11 11 11 11 23 11 11 44
33 34 32 DD AA 22 33 22 11 33 11 44 44 44
34 35 33 QQ BB 33 33 33 11 22 33 11 44 44
35 36 34 PP PP 33 11 22 11 13 22 11 44 44
36 37 35 VV BB 33 33 33 11 22 44 44 44 44
37 38 36 II BB 33 33 33 11 11 11 44 44 44
38 39 37 LL BB 33 33 33 11 11 11 44 44 44
39 40 38 QQ BB 33 33 33 11 11 11 22 44 44
40 41 39 LL BB 33 33 33 11 11 11 44 44 44
41 42 40 LL BB 33 33 33 11 22 22 44 44 44
42 43 41 EE BB 13 33 33 11 11 22 11 44 44
43 44 42 II PP 33 11 33 11 22 11 44 44 44
44 45 43 PP AA 32 11 11 11 21 12 21 44 44
45 46 44 NQ PA 32 11 31 11 11 12 42 44 44
46 47 ---- E- A- 2- 1- 1- 1- 2- 1- 1- 4- 4-
47 48 ---- K- A- 2- 1- 1- 1- 2- 1- 1- 3- 4-
48 49 45 AA AA 22 13 12 11 44 44 44 44 44
49 50 46 QM AA 22 11 11 11 11 22 11 44 44
50 51 47 KK AA 22 11 11 11 22 11 13 13 44
51 52 48 AA AA 22 11 11 11 44 44 44 44 44
52 53 49 LL AA 22 11 11 11 22 22 44 44 44
53 54 50 QE AA 22 11 11 11 21 32 11 44 44
54 55 51 GG AA 22 11 11 11 44 44 44 44 44
55 56 52 VV AA 22 11 11 11 11 44 44 44 44
56 57 53 MV AA 22 11 11 11 11 14 24 44 44
57 58 54 MM AA 22 11 11 11 11 11 11 44 44
58 59 55 EE AA 22 11 11 11 11 11 11 44 44
59 60 56 IL AA 22 11 11 11 11 11 44 44 44
60 61 57 DE AA 22 11 11 11 11 11 41 44 44
61 62 58 DD AA 22 11 22 11 11 11 44 44 44
62 63 59 CC AA 33 33 11 11 11 44 44 44 44
63 64 60 AA LL 33 22 22 11 44 44 44 44 44
64 65 61 FF BB 33 11 33 11 11 11 44 44 44
65 66 62 PP AA 22 11 11 11 23 11 22 44 44
66 67 63 LL AA 22 13 12 11 11 11 44 44 44
67 68 64 LL BB 33 11 33 11 22 22 44 44 44
68 69 65 AA AA 11 11 11 11 44 44 44 44 44
69 70 66 GG BB 33 33 33 11 44 44 44 44 44
70 71 67 ML BB 33 33 33 11 22 11 24 44 44
71 72 68 TE BB 33 33 33 11 22 41 41 44 44
72 73 69 AA BB 33 33 33 11 44 44 44 44 44
73 74 70 HT BB 33 33 33 11 13 24 44 44 44
74 75 71 AD AA 22 33 22 11 43 41 44 44 44
75 76 72 DD BB 33 33 33 11 22 11 44 44 44
76 77 73 PP AA 22 11 11 11 21 12 21 44 44
77 78 74 MD AA 22 11 11 11 21 31 24 44 44
78 79 75 TV AA 22 31 11 11 21 44 44 44 44
79 80 76 AA AA 22 11 11 11 44 44 44 44 44
80 81 77 FF AA 33 13 22 11 11 11 44 44 44
81 82 78 KK PP 11 11 33 11 22 21 11 13 44
82 83 79 DD LL 33 22 22 11 11 11 44 44 44
83 84 80 AA PP 33 11 33 11 44 44 44 44 44
84 85 81 DD AA 22 33 11 11 11 11 44 44 44
85 86 82 VY BB 33 33 33 11 11 42 44 44 44
86 87 83 AA BB 33 33 33 11 44 44 44 44 44
87 88 84 LL BB 33 33 33 11 11 22 44 44 44
88 89 85 LL BB 33 33 33 11 11 21 44 44 44
89 90 86 VV AA 22 33 11 11 11 44 44 44 44
90 91 87 GG PP 33 11 33 11 44 44 44 44 44
91 92 88 AA BB 11 33 33 11 44 44 44 44 44
92 93 89 RA BP 34 31 33 11 24 34 14 34 44
93 94 90 PP PP 34 11 22 14 22 11 21 44 44
94 95 91 RR BU 34 14 34 14 24 14 14 34 44
95 96 ---- G- P- 1- 1- 3- 1- 4- 4- 4- 4- 4-
96 97 ---- P- P- 2- 1- 2- 1- 1- 2- 1- 4- 4-
97 98 ---- G- L- 3- 2- 2- 1- 4- 4- 4- 4- 4-
98 99 ---- M- P- 3- 1- 3- 1- 1- 1- 2- 4- 4-
99 100 ---- E- P- 3- 3- 3- 1- 1- 1- 1- 4- 4-
100 101 ---- R- A- 2- 1- 1- 1- 2- 1- 1- 1- 4-
101 102 ---- K- A- 2- 1- 1- 1- 3- 1- 1- 1- 4-
102 103 ---- D- A- 2- 1- 1- 1- 1- 1- 4- 4- 4-
103 104 ---- L- A- 2- 1- 1- 1- 2- 2- 4- 4- 4-
104 105 101 LL AU 24 14 11 11 11 22 44 44 44
105 106 102 EQ AA 22 11 11 11 11 12 11 44 44
106 107 103 AV AA 22 11 11 11 43 44 44 44 44
107 108 104 NN AA 22 11 11 11 11 22 44 44 44
108 109 105 AG AA 22 11 11 11 44 44 44 44 44
109 110 106 QK AA 22 11 11 11 11 22 22 43 44
110 111 107 II AA 22 11 11 11 11 11 44 44 44
111 112 108 FF AA 22 11 11 11 11 22 44 44 44
112 113 109 TT AA 22 11 11 11 22 44 44 44 44
113 114 110 VE AA 22 11 11 11 12 41 41 44 44
114 115 111 QQ AA 22 11 11 11 11 11 12 44 44
115 116 112 GG AA 22 11 11 11 44 44 44 44 44
116 117 113 KR AA 22 11 11 11 11 11 12 13 44
117 118 114 AA AA 22 11 11 11 44 44 44 44 44
118 119 115 IL AA 22 11 11 11 11 11 44 44 44
119 120 116 DA AA 22 11 11 11 24 14 44 44 44
120 121 117 AE AA 22 11 11 11 42 41 41 44 44
121 122 118 VV AA 22 33 11 11 22 44 44 44 44
122 123 119 AA PP 11 13 33 11 44 44 44 44 44
123 124 120 SK PP 33 11 33 11 31 42 41 43 44
124 125 121 RK AA 22 11 11 11 11 23 32 11 44
125 126 122 ND AA 33 33 22 11 12 11 44 44 44
126 127 123 IV PP 33 11 33 11 33 14 44 44 44
127 128 124 KK BB 33 33 33 11 11 12 11 32 44
128 129 125 VV BB 33 33 33 11 11 44 44 44 44
129 130 126 LL BB 33 33 33 11 22 22 44 44 44
130 131 127 VV BB 33 33 33 11 11 44 44 44 44
131 132 128 VV AA 22 33 11 11 11 44 44 44 44
132 133 129 GG PP 11 11 33 11 44 44 44 44 44
133 134 130 NN PP 22 11 33 22 11 21 44 44 44
134 135 131 PP PP 33 11 22 11 22 11 22 44 44
135 136 132 AA AA 22 11 11 11 44 44 44 44 44
136 137 133 NN AA 22 11 11 11 11 21 44 44 44
137 138 134 TT AA 22 11 11 11 11 44 44 44 44
138 139 135 NN AA 22 11 11 11 11 11 44 44 44
139 140 136 AA AA 22 11 11 11 44 44 44 44 44
140 141 137 YL AA 22 11 11 11 22 22 44 44 44
141 142 138 II AA 22 11 11 11 11 11 44 44 44
142 143 139 AA AA 22 11 11 11 44 44 44 44 44
143 144 140 MY AA 22 11 11 11 23 12 24 44 44
144 145 141 KK AA 22 11 11 11 11 23 11 13 44
145 146 142 SN AA 22 13 22 11 21 41 44 44 44
146 147 143 AA BB 33 33 22 11 44 44 44 44 44
147 148 144 PP AP 22 11 12 11 22 11 22 44 44
148 149 145 SG AL 22 12 12 11 14 44 44 44 44
149 150 146 LL BB 33 33 33 11 11 11 44 44 44
150 151 147 PN PP 33 11 23 11 12 21 14 44 44
151 152 148 AP AA 22 11 11 11 42 41 42 44 44
152 153 149 KR AA 22 11 11 11 31 12 12 11 44
153 154 150 NN AA 22 11 22 11 11 11 44 44 44
154 155 151 FF BB 33 33 33 11 11 22 44 44 44
155 156 152 TT BB 33 33 33 11 22 44 44 44 44
156 157 153 AA BB 33 33 33 11 44 44 44 44 44
157 158 154 MM BB 33 13 33 11 22 11 22 44 44
158 159 155 LT AA 22 33 22 11 12 34 44 44 44
159 160 156 RR AA 22 11 11 11 22 33 11 22 44
160 161 157 LL AA 22 11 11 11 22 22 44 44 44
161 162 158 DD AA 22 11 11 11 11 11 44 44 44
162 163 159 HH AA 22 11 11 11 22 22 44 44 44
163 164 160 NN AA 22 11 11 11 11 11 44 44 44
164 165 161 RR AA 22 11 11 11 11 11 11 11 44
165 166 162 AA AA 22 11 11 11 44 44 44 44 44
166 167 163 LK AA 22 11 11 11 21 21 43 41 44
167 168 164 SA AA 22 11 11 11 14 44 44 44 44
168 169 165 QQ AA 22 11 11 11 11 22 22 44 44
169 170 166 IL AA 22 11 11 11 12 22 44 44 44
170 171 167 AA AA 22 11 11 11 44 44 44 44 44
171 172 168 AK AA 22 11 11 11 42 41 42 41 44
172 173 169 KK AA 22 11 11 11 22 33 11 12 44
173 174 170 TT AA 33 11 12 11 22 44 44 44 44
174 175 171 GG LL 33 22 22 11 44 44 44 44 44
175 176 172 KT BP 13 33 33 11 12 24 14 34 44
176 177 173 PG PP 33 11 23 11 24 14 24 44 44
177 178 174 VV AA 22 11 11 11 33 44 44 44 44
178 179 175 SD AA 22 11 11 11 13 41 44 44 44
179 180 176 SR AA 22 33 12 11 11 42 43 41 44
180 181 177 II PP 33 13 33 11 11 12 44 44 44
181 182 178 ER BB 22 33 33 11 13 11 12 41 44
182 183 179 KR LL 33 22 22 11 11 11 11 31 44
183 184 180 LM BP 33 31 33 11 22 23 42 44 44
184 185 181 FT BB 33 33 33 11 31 24 44 44 44
185 186 182 VV BB 33 33 33 11 11 44 44 44 44
186 187 183 WW BB 12 33 33 11 11 11 44 44 44
187 188 184 GG EE 21 22 33 11 44 44 44 44 44
188 189 185 NN PB 31 13 33 11 23 21 44 44 44
189 190 186 HH BB 22 11 33 11 22 22 44 44 44
190 191 187 SS BB 13 33 33 11 11 44 44 44 44
191 192 188 PS AA 22 11 11 11 21 14 24 44 44
192 193 189 TI AA 33 33 22 11 22 41 44 44 44
193 194 190 MM PP 33 11 33 11 33 33 13 44 44
194 195 191 YF BB 33 33 33 11 22 22 44 44 44
195 196 192 AP PB 33 11 32 11 42 41 42 44 44
196 197 193 DD BB 33 33 33 11 22 11 44 44 44
197 198 194 YL AA 22 33 22 11 31 12 44 44 44
198 199 195 RF AA 22 11 11 11 11 11 34 14 44
199 200 196 YH AA 32 33 12 11 11 21 44 44 44
200 201 197 AA PP 33 11 33 11 44 44 44 44 44
201 202 198 QE BB 33 33 33 11 11 11 21 44 44
202 203 199 IV BB 11 33 33 11 11 14 44 44 44
203 204 200 DD LL 11 22 22 11 12 11 44 44 44
204 205 205 GG LL 22 22 22 11 44 44 44 44 44
205 206 206 AR BP 33 33 33 11 41 42 42 41 44
206 207 207 SP PP 33 11 32 11 31 42 42 44 44
207 208 208 VA AA 22 11 11 11 14 44 44 44 44
208 209 209 KL AA 22 11 12 11 21 12 14 34 44
209 210 210 DE AA 22 11 11 11 11 11 41 44 44
210 211 211 ML AA 22 13 11 11 21 11 14 44 44
211 212 212 IV AB 33 13 13 11 13 14 44 44 44
212 213 ---- N- L- 2- 2- 2- 1- 2- 2- 4- 4- 4-
213 214 214 DD BP 33 33 33 11 23 11 44 44 44
214 215 215 DM AA 22 11 11 11 22 13 43 44 44
215 216 216 AE AA 22 11 11 11 42 41 41 44 44
216 217 217 WW AA 22 11 11 11 22 11 44 44 44
217 218 218 NY AA 22 11 11 11 22 12 44 44 44
218 219 219 RE AA 22 11 11 11 12 11 11 24 44
219 220 220 DK AA 22 33 11 11 31 11 41 41 44
220 221 221 TV AA 22 33 11 11 11 44 44 44 44
221 222 222 FF AA 22 11 11 11 22 22 44 44 44
222 223 223 LI AA 22 11 11 11 11 21 44 44 44
223 224 224 PP AA 22 11 11 11 13 22 11 44 44
224 225 225 TT AA 22 11 11 11 11 44 44 44 44
225 226 226 VV AA 22 11 11 11 11 44 44 44 44
226 227 227 GA AA 22 11 11 11 44 44 44 44 44
227 228 228 KQ AA 22 33 22 11 12 12 31 34 44
228 229 229 RR AA 22 11 11 11 22 33 11 11 44
229 230 230 GG AA 22 11 11 11 44 44 44 44 44
230 231 231 AA AA 22 11 11 11 44 44 44 44 44
231 232 232 AA AA 22 11 11 11 44 44 44 44 44
232 233 233 II AA 22 11 11 11 11 11 44 44 44
233 234 234 II AA 22 11 11 11 11 11 44 44 44
234 235 235 DQ AA 22 11 11 11 21 21 41 44 44
235 236 236 AA AA 22 11 11 11 44 44 44 44 44
236 237 237 RR AA 33 33 11 11 11 11 33 21 44
237 238 238 GG LL 22 22 22 11 44 44 44 44 44
238 239 239 VA BB 13 33 33 11 24 44 44 44 44
239 240 240 SS PP 31 11 33 11 21 44 44 44 44
240 241 241 SS BB 33 11 22 11 11 44 44 44 44
241 242 242 AA AA 22 11 11 11 44 44 44 44 44
242 243 243 AA AA 22 11 11 11 44 44 44 44 44
243 244 244 SS AA 22 11 11 11 11 44 44 44 44
244 245 245 AA AA 22 11 11 11 44 44 44 44 44
245 246 246 AA AA 22 11 11 11 44 44 44 44 44
246 247 247 NN AA 22 11 11 11 22 22 44 44 44
247 248 248 AA AA 22 11 11 11 44 44 44 44 44
248 249 249 AA AA 22 11 11 11 44 44 44 44 44
249 250 250 II AA 22 11 11 11 11 11 44 44 44
250 251 251 DE AA 22 11 11 11 11 11 41 44 44
251 252 252 HH AA 22 11 11 11 22 11 44 44 44
252 253 253 II AA 22 11 11 11 11 22 44 44 44
253 254 254 HR AA 22 11 11 11 22 11 43 41 44
254 255 255 DD AA 22 11 11 11 11 11 44 44 44
255 256 256 WW AA 22 11 11 11 22 33 44 44 44
256 257 257 VA AA 22 11 11 11 14 44 44 44 44
257 258 258 LL AA 33 33 11 11 11 11 44 44 44
258 259 259 GG EB 31 23 33 11 44 44 44 44 44
259 260 260 TT AP 33 31 23 11 22 44 44 44 44
260 261 261 AP LP 11 21 22 11 43 42 41 44 44
261 262 262 GE LP 32 21 23 11 41 42 41 44 44
262 ----263 -G -L -2 -2 -2 -1 -4 -4 -4 -4 -4
263 263 264 KD PB 33 13 33 11 22 21 14 14 44
264 264 265 WW PB 33 33 33 11 13 31 44 44 44
265 265 266 TV BB 33 33 33 11 32 44 44 44 44
266 266 267 TS BB 33 33 33 11 12 44 44 44 44
267 267 268 MM BB 33 33 33 11 11 11 22 44 44
268 268 269 GA BB 33 13 33 11 44 44 44 44 44
269 269 270 IV BB 11 33 33 11 22 14 44 44 44
270 270 271 PP PP 33 11 22 11 11 22 11 44 44
271 271 272 SS PP 33 11 33 11 33 44 44 44 44
272 272 273 DQ AA 31 33 22 11 31 11 42 44 44
273 273 274 GG LL 33 22 22 11 44 44 44 44 44
274 274 275 SE PP 22 11 33 11 21 43 41 44 44
275 275 277 YY LL 11 22 22 11 11 11 44 44 44
276 276 278 GG LL 33 22 22 11 44 44 44 44 44
277 277 279 II PP 33 33 33 11 11 23 44 44 44
278 278 280 PP PP 33 11 22 11 13 21 12 44 44
279 279 281 EE PP 22 11 33 11 11 11 11 44 44
280 280 282 GG LL 32 22 21 11 44 44 44 44 44
281 281 283 VI PP 33 11 33 11 12 41 44 44 44
282 282 284 IV BB 33 11 33 11 11 24 44 44 44
283 283 285 FY BB 33 33 33 11 22 22 44 44 44
284 284 286 GS PB 33 11 33 11 43 44 44 44 44
285 285 287 FF BB 33 33 33 11 11 11 44 44 44
286 286 288 PP PP 33 11 22 11 22 11 22 44 44
287 287 289 VV BB 33 33 33 11 22 44 44 44 44
288 288 290 TT BB 33 33 33 11 22 44 44 44 44
289 289 291 TA BB 33 33 33 11 24 44 44 44 44
290 290 292 EK BB 21 33 33 11 22 11 13 43 44
291 291 293 ND LL 11 22 22 11 11 21 44 44 44
292 292 294 GG LL 22 22 22 11 44 44 44 44 44
293 293 295 EA BB 33 33 33 11 14 24 14 44 44
294 294 296 YY PB 33 33 33 11 33 22 44 44 44
295 295 297 KR BB 33 33 33 11 22 13 13 13 44
296 296 298 IV PP 33 11 33 11 11 14 44 44 44
297 297 299 VV PB 33 11 33 11 11 44 44 44 44
298 298 300 QE BP 22 33 33 11 11 21 21 44 44
299 299 301 GG LL 33 22 22 11 44 44 44 44 44
300 300 302 LL PP 33 11 33 11 11 11 44 44 44
301 301 303 SE BB 33 11 33 11 31 41 41 44 44
302 302 304 II BB 33 33 33 11 11 22 44 44 44
303 303 305 DN PP 33 11 33 11 33 11 44 44 44
304 304 306 AE AA 22 11 11 11 42 41 41 44 44
305 305 307 FF AA 22 11 11 11 22 21 44 44 44
306 306 308 SA AA 22 11 11 11 24 44 44 44 44
307 307 309 QR AA 22 11 11 11 23 31 13 41 44
308 308 310 EK AA 22 11 11 11 12 23 12 43 44
309 309 311 RR AA 22 11 11 11 11 21 23 13 44
310 310 312 IM AA 22 11 11 11 11 11 42 44 44
311 311 313 NE AA 22 11 11 11 11 22 41 44 44
312 312 314 VI AA 22 11 11 11 11 41 44 44 44
313 313 315 TT AA 22 11 11 11 33 44 44 44 44
314 314 316 LA AA 22 11 11 11 24 24 44 44 44
315 315 317 NQ AA 22 11 11 11 21 12 42 44 44
316 316 318 EE AA 22 11 11 11 22 13 11 44 44
317 317 319 LL AA 22 11 11 11 11 11 44 44 44
318 318 320 LL AA 22 11 11 11 11 11 44 44 44
319 319 321 ED AA 22 11 11 11 11 11 14 44 44
320 320 322 EE AA 22 11 11 11 11 11 11 44 44
321 321 323 QM AA 22 11 11 11 22 11 13 44 44
322 322 324 NE AA 22 11 11 11 22 11 41 44 44
323 323 325 GQ AA 22 11 21 11 42 41 42 44 44
324 324 326 VV AA 22 31 11 11 21 44 44 44 44
325 325 327 QK AA 22 11 11 11 21 31 11 41 44
326 ----328 -A -A -2 -1 -1 -1 -4 -4 -4 -4 -4
327 ----329 -L -A -3 -1 -2 -1 -1 -1 -4 -4 -4
328 326 330 HG AL 23 12 12 11 34 24 44 44 44
329 327 331 LL AA 24 33 11 11 11 31 44 44 44
330 328 332 LI AU 44 33 24 14 12 11 44 44 44
331 329 ---- G- U- 4- 1- 4- 4- 4- 4- 4- 4- 4-
Sequence identity comparison (ID_TABLE):
Diagonal ... number of residues;
Upper triangle ... number of identical residues;
Lower triangle ... % sequence identity, id/min(length).
1b8pA @11bdmA @1
1b8pA @1 327 194
1bdmA @1 61 318
Weighted pair-group average clustering based on a distance matrix:
! cat /usr/lib/modeller10.1/modlib/modeller/config.py
install_dir = r'/usr/lib/modeller10.1' license = 'MODELIRANJE'
! find /usr/ -name "modeller*"
/usr/include/modeller /usr/include/modeller/modeller.h /usr/lib/python3.0/dist-packages/modeller /usr/lib/python3.7/dist-packages/modeller /usr/lib/python3.8/dist-packages/modeller /usr/lib/python3.5/dist-packages/modeller /usr/lib/modeller10.1 /usr/lib/modeller10.1/src/swig/modeller.i /usr/lib/modeller10.1/modlib/modeller /usr/lib/python3.2/dist-packages/modeller /usr/lib/python2.7/dist-packages/modeller /usr/lib/python2.5/dist-packages/modeller /usr/lib/python2.6/dist-packages/modeller /usr/lib/python3.4/dist-packages/modeller /usr/lib/python2.4/dist-packages/modeller /usr/lib/python3.1/dist-packages/modeller /usr/lib/python2.3/dist-packages/modeller /usr/lib/python3.3/dist-packages/modeller /usr/lib/python3.9/dist-packages/modeller /usr/lib/python3.6/dist-packages/modeller /usr/lib/pkgconfig/modeller.pc /usr/share/doc/modeller-10.1 /usr/share/doc/modeller
! python --version
Python 3.10.11
В данном практикуме мы попытаемся построить модель комплекса лизоцима (а конкретно, был выбран LYS_MERLU) с лигандом.
import sys
import modeller
import _modeller
import modeller.automodel
from IPython.display import Image
Зададим некоторые параметры
env=modeller.environ()
env.io.hetatm=True
environ____W> The class 'environ' is deprecated; use 'Environ' instead
Скачаем белок-заготовку (известную структуру лизоцима форели - как образец)
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2023-05-14 00:47:45-- http://www.pdb.org/pdb/files/1lmp.pdb Resolving www.pdb.org (www.pdb.org)... 132.249.210.232 Connecting to www.pdb.org (www.pdb.org)|132.249.210.232|:80... ^C
Что-то как-то у него не очень получилось скачать. Ну и ладно, скачаю сама...
И можно еще на него посмотреть
Image('pr10_1.png', width = 800)
! wget http://www.uniprot.org/uniprot/P86383.fasta
--2023-05-14 00:47:35-- http://www.uniprot.org/uniprot/P86383.fasta Resolving www.uniprot.org (www.uniprot.org)... 193.62.193.81 Connecting to www.uniprot.org (www.uniprot.org)|193.62.193.81|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.uniprot.org/uniprot/P86383.fasta [following] --2023-05-14 00:47:35-- https://www.uniprot.org/uniprot/P86383.fasta Connecting to www.uniprot.org (www.uniprot.org)|193.62.193.81|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://rest.uniprot.org/uniprot/P86383.fasta [following] --2023-05-14 00:47:36-- https://rest.uniprot.org/uniprot/P86383.fasta Resolving rest.uniprot.org (rest.uniprot.org)... 193.62.193.81 Connecting to rest.uniprot.org (rest.uniprot.org)|193.62.193.81|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://rest.uniprot.org/uniprotkb/P86383.fasta [following] --2023-05-14 00:47:37-- https://rest.uniprot.org/uniprotkb/P86383.fasta Reusing existing connection to rest.uniprot.org:443. HTTP request sent, awaiting response... 200 OK Length: 194 [text/plain] Saving to: ‘P86383.fasta’ P86383.fasta 100%[===================>] 194 --.-KB/s in 0s 2023-05-14 00:47:38 (28.4 MB/s) - ‘P86383.fasta’ saved [194/194]
А вот последовательность LYS_MERLU (P86383) - лизоцима из японского моллюска Meretrix lusoria - скачалась нормально.
Сделаем выравнивание:
# создадим объект выравнивания
alignm=modeller.alignment(env)
alignment__W> The class 'alignment' is deprecated; use 'Alignment' instead
# загрузим целевой белок
alignm.append(file='P86383.fasta', align_codes='all',alignment_format='FASTA')
# создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
# и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
# поправим идентификаторы
alignm[0].code = 'merlu'
alignm[1].code = '1lmp'
model______W> The class 'model' is deprecated; use 'Model' instead
# делаем выравнивание
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
! cat all_in_one.ali
>P1;merlu sequence::: :: :::-1.00:-1.00 FAGGIVSQRCLSCICKMESGCRNVGCKMDMGSLSCGYFQIKEAYWIDCGRPGSSWKSCAASSYCASLCVQNYMKR YAKWAGCPLRCE-------GFAREHNGGPRGCKKGSTIGYWNRLQKISGCHGVQ* >P1;1lmp structureX:1lmp.pdb:1:A:+129:A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV*
Ну, если так смотреть, то последовательности не кажутся особо-то похожими.
Построим модель.
# Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
# Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )
a.name='mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
merlu 1lmp
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
87 1 87 95 E G 13.907
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 9691 8860
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 122
Number of all, selected real atoms : 926 926
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8860 8860
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1762
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 945.9302
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 947 0 0 0.006 0.006 9.3302 1.000
2 Bond angle potential : 1266 0 3 2.094 2.094 110.01 1.000
3 Stereochemical cosine torsion poten: 589 0 37 51.606 51.606 231.60 1.000
4 Stereochemical improper torsion pot: 381 0 0 1.127 1.127 10.783 1.000
5 Soft-sphere overlap restraints : 1762 0 0 0.003 0.003 1.4776 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2101 0 2 0.481 0.481 106.38 1.000
10 Distance restraints 2 (N-O) : 2294 0 17 0.636 0.636 234.28 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 121 0 1 4.228 4.228 25.511 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 0 81.984 81.984 27.070 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 0 84.344 84.344 23.521 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 79.078 79.078 23.839 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 84.196 84.196 12.974 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 756 0 0 0.443 0.443 12.533 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 120 32 24 38.884 89.746 113.17 1.000
26 Distance restraints 4 (SDCH-SDCH) : 73 0 0 1.218 1.218 3.4555 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: merlu.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15889.6963
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3186 3G 4G C N 19 21 -79.93 -80.20 11.88 0.45 82.20 -136.58 7.20
1 4G 4G N CA 21 22 162.22 174.10 8.50
2 3192 9R 10C C N 64 66 -60.15 -63.00 10.90 1.17 -117.90 176.97 7.66
2 10C 10C N CA 66 67 -51.62 -41.10 141.10
3 3198 15C 16K C N 104 106 57.04 56.60 8.53 0.58 -62.90 139.32 24.32
3 16K 16K N CA 106 107 30.09 38.60 -40.80
4 3201 18E 19S C N 130 132 147.90 56.90 136.55 7.53 -64.10 151.09 20.09
4 19S 19S N CA 132 133 -65.40 36.40 -35.00
5 3202 19S 20G C N 136 138 45.05 78.70 36.81 1.37 -80.20 129.97 9.43
5 20G 20G N CA 138 139 -151.19 -166.10 174.10
6 3213 30M 31G C N 215 217 -63.31 -62.40 2.82 0.39 82.20 152.93 11.58
6 31G 31G N CA 217 218 -38.53 -41.20 8.50
7 3217 34S 35C C N 239 241 -114.78 -117.90 65.62 2.54 -63.00 127.63 13.25
7 35C 35C N CA 241 242 75.56 141.10 -41.10
8 3218 35C 36G C N 245 247 134.30 82.20 60.28 2.58 -62.40 164.44 28.52
8 36G 36G N CA 247 248 -21.82 8.50 -41.20
9 3219 36G 37Y C N 249 251 56.35 55.90 1.95 0.17 -63.50 146.81 27.81
9 37Y 37Y N CA 251 252 41.40 39.50 -43.40
10 3220 37Y 38F C N 261 263 61.68 58.10 4.93 0.35 -63.20 145.06 26.13
10 38F 38F N CA 263 264 29.51 32.90 -44.30
11 3223 40I 41K C N 289 291 -109.60 -118.00 87.19 4.11 -62.90 104.17 11.97
11 41K 41K N CA 291 292 52.32 139.10 -40.80
12 3225 42E 43A C N 307 309 -71.68 -62.50 10.58 2.15 -134.00 178.10 10.96
12 43A 43A N CA 309 310 -46.16 -40.90 147.00
13 3226 43A 44Y C N 312 314 24.06 -98.40 122.82 4.95 -124.30 149.26 10.68
13 44Y 44Y N CA 314 315 118.97 128.40 135.40
14 3236 53S 54S C N 392 394 92.23 -136.60 134.87 4.60 -64.10 -148.52 17.81
14 54S 54S N CA 394 395 -177.43 151.20 -35.00
15 3239 56K 57S C N 421 423 55.74 56.90 19.39 1.14 -64.10 150.33 19.31
15 57S 57S N CA 423 424 55.76 36.40 -35.00
16 3249 66S 67L C N 484 486 82.02 60.20 54.71 1.89 -63.50 146.98 26.19
16 67L 67L N CA 486 487 -20.57 29.60 -41.20
17 3258 75R 76Y C N 562 564 -106.26 -98.40 48.42 5.05 -63.50 131.19 18.85
17 76Y 76Y N CA 564 565 80.62 128.40 -43.40
18 3259 76Y 77A C N 574 576 -42.33 -68.20 41.19 2.59 -62.50 155.46 26.51
18 77A 77A N CA 576 577 113.25 145.30 -40.90
19 3268 85R 86C C N 643 645 -95.81 -117.90 25.21 0.69 -63.00 173.20 19.15
19 86C 86C N CA 645 646 128.97 141.10 -41.10
20 3277 94N 95G C N 716 718 61.45 82.20 48.03 1.40 -62.40 154.89 29.13
20 95G 95G N CA 718 719 51.82 8.50 -41.20
21 3278 95G 96G C N 720 722 69.88 82.20 53.11 1.96 -62.40 166.65 31.32
21 96G 96G N CA 722 723 60.16 8.50 -41.20
22 3279 96G 97P C N 724 726 -41.42 -58.70 41.53 2.43 -64.50 146.37 12.17
22 97P 97P N CA 726 727 -68.27 -30.50 147.20
23 3281 98R 99G C N 742 744 -59.77 -62.40 16.34 2.58 82.20 145.88 10.81
23 99G 99G N CA 744 745 -25.07 -41.20 8.50
24 3283 100C 101K C N 752 754 -62.73 -62.90 5.89 0.77 -118.00 -177.42 7.96
24 101K 101K N CA 754 755 -34.91 -40.80 139.10
25 3284 101K 102K C N 761 763 76.37 -62.90 141.94 21.90 -62.90 141.94 21.90
25 102K 102K N CA 763 764 -68.23 -40.80 -40.80
26 3285 102K 103G C N 770 772 -59.06 -62.40 3.97 0.75 82.20 149.05 11.32
26 103G 103G N CA 772 773 -39.05 -41.20 8.50
27 3288 105T 106I C N 787 789 -106.10 -97.30 29.43 2.90 -63.40 148.97 23.13
27 106I 106I N CA 789 790 99.12 127.20 -43.60
28 3289 106I 107G C N 795 797 132.40 82.20 83.35 2.32 -62.40 166.06 30.29
28 107G 107G N CA 797 798 -58.04 8.50 -41.20
29 3295 112L 113Q C N 852 854 -108.59 -121.10 82.61 3.71 -63.80 108.06 14.04
29 113Q 113Q N CA 854 855 58.04 139.70 -40.30
30 3298 115I 116S C N 878 880 -74.86 -72.40 40.00 2.44 -64.10 147.87 10.12
30 116S 116S N CA 880 881 112.48 152.40 -35.00
31 3301 118C 119H C N 894 896 59.81 56.30 9.14 0.66 -63.20 143.89 24.71
31 119H 119H N CA 896 897 32.36 40.80 -42.30
32 3302 119H 120G C N 904 906 -137.78 -167.20 87.59 2.93 82.20 163.07 12.73
32 120G 120G N CA 906 907 92.09 174.60 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 8 19 45 60 78 94 116 130 125 139
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 122
Number of all, selected real atoms : 926 926
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8860 8860
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1866
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 855.6618
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 947 0 0 0.005 0.005 7.0398 1.000
2 Bond angle potential : 1266 0 6 2.066 2.066 104.94 1.000
3 Stereochemical cosine torsion poten: 589 0 35 51.153 51.153 229.89 1.000
4 Stereochemical improper torsion pot: 381 0 0 0.966 0.966 8.3198 1.000
5 Soft-sphere overlap restraints : 1866 0 0 0.003 0.003 1.4736 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2101 1 5 0.503 0.503 111.94 1.000
10 Distance restraints 2 (N-O) : 2294 0 9 0.567 0.567 166.44 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 121 1 3 5.086 5.086 36.911 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 0 82.363 82.363 32.903 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 0 92.227 92.227 27.612 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 87.526 87.526 23.673 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 94.850 94.850 11.222 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 756 0 0 0.534 0.534 18.744 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 120 29 19 31.043 88.386 68.681 1.000
26 Distance restraints 4 (SDCH-SDCH) : 73 0 0 1.757 1.757 5.8811 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: merlu.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15362.3076
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3399 96G 96G CA C 723 724 -154.43 -180.00 25.57 5.11 -180.00 25.57 5.11
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3186 3G 4G C N 19 21 -80.28 -80.20 13.68 0.54 82.20 -137.56 7.23
1 4G 4G N CA 21 22 160.42 174.10 8.50
2 3192 9R 10C C N 64 66 -59.05 -63.00 7.65 0.80 -117.90 -178.91 7.84
2 10C 10C N CA 66 67 -47.64 -41.10 141.10
3 3195 12S 13C C N 84 86 -61.76 -63.00 2.54 0.26 -117.90 -175.66 7.95
3 13C 13C N CA 86 87 -43.32 -41.10 141.10
4 3196 13C 14I C N 90 92 -93.96 -120.60 71.09 3.13 -63.40 112.24 17.47
4 14I 14I N CA 92 93 64.40 130.30 -43.60
5 3198 15C 16K C N 104 106 61.98 56.60 11.82 0.60 -62.90 142.62 24.91
5 16K 16K N CA 106 107 28.08 38.60 -40.80
6 3201 18E 19S C N 130 132 65.90 56.90 20.22 0.83 -64.10 140.50 18.77
6 19S 19S N CA 132 133 18.29 36.40 -35.00
7 3213 30M 31G C N 215 217 -63.71 -62.40 1.51 0.23 82.20 153.91 11.68
7 31G 31G N CA 217 218 -40.45 -41.20 8.50
8 3219 36G 37Y C N 249 251 65.43 55.90 12.18 0.82 -63.50 149.32 28.20
8 37Y 37Y N CA 251 252 31.91 39.50 -43.40
9 3220 37Y 38F C N 261 263 64.59 58.10 9.17 0.62 -63.20 146.05 26.27
9 38F 38F N CA 263 264 26.42 32.90 -44.30
10 3236 53S 54S C N 392 394 97.02 -136.60 131.82 4.36 -64.10 -148.93 18.33
10 54S 54S N CA 394 395 -171.34 151.20 -35.00
11 3239 56K 57S C N 421 423 56.92 56.90 16.38 1.04 -64.10 149.51 19.30
11 57S 57S N CA 423 424 52.78 36.40 -35.00
12 3248 65A 66S C N 478 480 -114.66 -136.60 34.05 1.92 -64.10 156.17 14.86
12 66S 66S N CA 480 481 177.24 151.20 -35.00
13 3250 67L 68C C N 492 494 -145.49 -117.90 55.10 2.44 -63.00 157.79 16.49
13 68C 68C N CA 494 495 93.41 141.10 -41.10
14 3259 76Y 77A C N 574 576 67.48 55.40 15.21 0.96 -62.50 147.56 30.01
14 77A 77A N CA 576 577 28.96 38.20 -40.90
15 3267 84L 85R C N 632 634 -71.13 -63.00 17.50 2.92 -125.20 171.55 9.21
15 85R 85R N CA 634 635 -56.60 -41.10 140.60
16 3268 85R 86C C N 643 645 -137.45 -117.90 78.77 2.78 -63.00 125.87 20.83
16 86C 86C N CA 645 646 -142.59 141.10 -41.10
17 3270 87E 88G C N 658 660 -129.24 -167.20 92.75 2.94 82.20 169.43 13.20
17 88G 88G N CA 660 661 89.97 174.60 8.50
18 3275 92E 93H C N 698 700 -91.27 -63.20 82.76 8.98 -63.20 82.76 8.98
18 93H 93H N CA 700 701 35.55 -42.30 -42.30
19 3276 93H 94N C N 708 710 -74.43 -63.20 13.20 1.61 -119.90 177.10 6.92
19 94N 94N N CA 710 711 -34.17 -41.10 137.00
20 3277 94N 95G C N 716 718 99.88 82.20 50.57 1.61 -62.40 162.30 29.09
20 95G 95G N CA 718 719 -38.87 8.50 -41.20
21 3279 96G 97P C N 724 726 -35.14 -58.70 42.01 2.54 -64.50 150.41 12.82
21 97P 97P N CA 726 727 -65.28 -30.50 147.20
22 3281 98R 99G C N 742 744 -62.91 -62.40 12.59 1.86 82.20 149.78 11.16
22 99G 99G N CA 744 745 -28.62 -41.20 8.50
23 3284 101K 102K C N 761 763 -72.16 -118.00 51.12 2.35 -62.90 157.76 21.01
23 102K 102K N CA 763 764 161.71 139.10 -40.80
24 3288 105T 106I C N 787 789 -104.76 -97.30 34.65 3.50 -63.40 143.08 22.21
24 106I 106I N CA 789 790 93.37 127.20 -43.60
25 3289 106I 107G C N 795 797 129.03 82.20 74.48 2.12 -62.40 168.77 30.47
25 107G 107G N CA 797 798 -49.41 8.50 -41.20
26 3299 116S 117G C N 884 886 -70.89 -62.40 13.82 1.90 82.20 157.93 11.76
26 117G 117G N CA 886 887 -30.29 -41.20 8.50
27 3301 118C 119H C N 894 896 60.01 56.30 30.59 2.44 -63.20 134.02 22.94
27 119H 119H N CA 896 897 10.44 40.80 -42.30
28 3302 119H 120G C N 904 906 -72.76 -62.40 11.15 1.79 82.20 161.53 12.15
28 120G 120G N CA 906 907 -37.07 -41.20 8.50
29 3303 120G 121V C N 908 910 67.70 55.90 26.01 1.24 -125.40 -150.28 11.58
29 121V 121V N CA 910 911 16.32 39.50 143.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 9 51 67 106 91 116 139 124 145
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
merlu.B99990001.pdb 945.93018
merlu.B99990002.pdb 855.66180
Тут было бы славно посмотреть на результат с помощью nglview, но с ним как обычно проблемы, поэтому посмотрим как умеем.
Image('pr10_2.png', width = 800)
Image('pr10_3.png', width = 800)
Image('pr10_4.png', width = 800)
Видим, что получилось очень даже похоже, только некоторые части элементов вторичной структуры потерялись.
А еще лиганда нет. Будем его добавлять.
# Добавим лиганд вручную в виде трех точек на конце
alignm = modeller.alignment(env)
alignm.append_sequence('FAGGIVSQRCLSCICKMESGCRNVGCKMDMGSLSCGYFQIKEAYWIDCGRPGSSWKSCAASSYCASLCVQNYMKRYAKWAGCPLRCEGFAREHNGGPRGCKKGSTIGYWNRLQKISGCHGVQ/...')
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'B'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm[0].code = 'merlu_lig'
alignm[1].code = '1lmp'
alignment__W> The class 'alignment' is deprecated; use 'Alignment' instead
model______W> The class 'model' is deprecated; use 'Model' instead
read_pd_459W> Residue type NDG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type NAG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
alignm.salign()
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
! cat all_in_one2.ali
>P1;merlu_lig sequence::1:A:+125:B:undefined:undefined:-1.00:-1.00 FAGGIVSQRCLSCICKMESGCRNVGCKMDMGSLSCGYFQIKEAYWIDCGRPGSSWKSCAASSYCASLCVQNYMKR YAKWAGCPLRCE-------GFAREHNGGPRGCKKGSTIGYWNRLQKISGCHGVQ/...* >P1;1lmp structureX:1lmp.pdb:1:A:+132:B:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/...*
# Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
# Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
merlu_lig 1lmp
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
AutoModel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the AutoModel defaults. If this is not what you
want, clear them before creating the AutoModel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
87 1 87 95 E G 13.907
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 11090 10259
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 125
Number of all, selected real atoms : 969 969
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10259 10259
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2026
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 998.9112
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 947 0 0 0.006 0.006 11.423 1.000
2 Bond angle potential : 1266 0 5 2.104 2.104 111.38 1.000
3 Stereochemical cosine torsion poten: 589 0 37 52.452 52.452 238.40 1.000
4 Stereochemical improper torsion pot: 381 0 0 1.157 1.157 11.508 1.000
5 Soft-sphere overlap restraints : 2026 2 2 0.009 0.009 19.536 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2101 1 6 0.481 0.481 103.05 1.000
10 Distance restraints 2 (N-O) : 2294 0 17 0.622 0.622 234.87 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 121 0 2 4.705 4.705 31.593 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 0 81.411 81.411 27.455 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 0 99.554 99.554 30.387 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 74.089 74.089 19.486 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 91.562 91.562 11.807 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 756 0 0 0.511 0.511 18.907 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 120 31 22 33.643 86.890 104.35 1.000
26 Distance restraints 4 (SDCH-SDCH) : 73 0 0 1.256 1.256 6.9892 1.000
27 Distance restraints 5 (X-Y) : 1399 0 0 0.038 0.038 17.773 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: merlu_lig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 16325.3301
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3185 2A 3G C N 15 17 82.00 78.70 11.13 0.45 -80.20 165.04 11.75
1 3G 3G N CA 17 18 -155.47 -166.10 174.10
2 3192 9R 10C C N 64 66 -62.83 -63.00 6.41 0.77 -117.90 -179.98 7.76
2 10C 10C N CA 66 67 -47.51 -41.10 141.10
3 3198 15C 16K C N 104 106 -88.59 -70.20 88.92 6.86 -62.90 97.65 11.54
3 16K 16K N CA 106 107 53.40 140.40 -40.80
4 3201 18E 19S C N 130 132 63.35 56.90 20.45 0.87 -64.10 137.65 18.39
4 19S 19S N CA 132 133 16.99 36.40 -35.00
5 3206 23N 24V C N 165 167 -65.95 -62.40 21.00 2.47 -125.40 175.39 6.99
5 24V 24V N CA 167 168 -21.70 -42.40 143.30
6 3207 24V 25G C N 172 174 106.66 82.20 59.38 1.76 -62.40 169.12 30.03
6 25G 25G N CA 174 175 -45.61 8.50 -41.20
7 3213 30M 31G C N 215 217 -65.49 -62.40 5.77 0.79 82.20 154.35 11.64
7 31G 31G N CA 217 218 -36.33 -41.20 8.50
8 3215 32S 33L C N 225 227 -69.38 -70.70 19.61 1.54 -63.50 157.74 22.24
8 33L 33L N CA 227 228 161.17 141.60 -41.20
9 3216 33L 34S C N 233 235 72.51 56.90 66.50 3.07 -64.10 136.78 17.75
9 34S 34S N CA 235 236 -28.24 36.40 -35.00
10 3217 34S 35C C N 239 241 -122.09 -117.90 88.86 3.56 -63.00 110.56 11.59
10 35C 35C N CA 241 242 52.35 141.10 -41.10
11 3218 35C 36G C N 245 247 139.60 82.20 64.39 2.94 -62.40 159.33 27.55
11 36G 36G N CA 247 248 -20.68 8.50 -41.20
12 3219 36G 37Y C N 249 251 54.35 55.90 6.67 0.36 -63.50 147.92 28.02
12 37Y 37Y N CA 251 252 45.98 39.50 -43.40
13 3220 37Y 38F C N 261 263 65.29 58.10 10.59 0.68 -63.20 146.05 26.25
13 38F 38F N CA 263 264 25.13 32.90 -44.30
14 3229 46I 47D C N 346 348 -81.00 -96.50 47.60 2.01 -63.30 110.62 12.68
14 47D 47D N CA 348 349 69.20 114.20 -40.00
15 3230 47D 48C C N 354 356 -161.48 -63.00 101.36 15.44 -63.00 101.36 15.44
15 48C 48C N CA 356 357 -17.11 -41.10 -41.10
16 3236 53S 54S C N 392 394 96.53 -136.60 131.43 4.40 -64.10 -147.25 18.28
16 54S 54S N CA 394 395 -174.50 151.20 -35.00
17 3239 56K 57S C N 421 423 60.36 56.90 17.62 1.42 -64.10 152.83 19.77
17 57S 57S N CA 423 424 53.68 36.40 -35.00
18 3248 65A 66S C N 478 480 -115.06 -136.60 24.78 1.29 -64.10 169.40 15.82
18 66S 66S N CA 480 481 163.45 151.20 -35.00
19 3249 66S 67L C N 484 486 -100.67 -108.50 45.57 2.37 -63.50 134.07 16.88
19 67L 67L N CA 486 487 87.61 132.50 -41.20
20 3250 67L 68C C N 492 494 178.42 -63.00 119.25 19.18 -63.00 119.25 19.18
20 68C 68C N CA 494 495 -28.46 -41.10 -41.10
21 3259 76Y 77A C N 574 576 67.77 55.40 12.73 1.21 -62.50 150.85 30.68
21 77A 77A N CA 576 577 35.18 38.20 -40.90
22 3268 85R 86C C N 643 645 -92.41 -117.90 26.01 0.98 -63.00 175.11 23.50
22 86C 86C N CA 645 646 146.28 141.10 -41.10
23 3277 94N 95G C N 716 718 34.16 78.70 52.18 1.68 -62.40 137.37 19.34
23 95G 95G N CA 718 719 -138.91 -166.10 -41.20
24 3278 95G 96G C N 720 722 10.83 82.20 84.34 3.46 -62.40 119.68 21.70
24 96G 96G N CA 722 723 53.45 8.50 -41.20
25 3279 96G 97P C N 724 726 -46.10 -58.70 61.91 4.18 -64.50 123.07 10.18
25 97P 97P N CA 726 727 -91.12 -30.50 147.20
26 3281 98R 99G C N 742 744 -57.84 -62.40 20.94 3.36 82.20 143.07 10.51
26 99G 99G N CA 744 745 -20.76 -41.20 8.50
27 3285 102K 103G C N 770 772 -62.63 -62.40 2.40 0.35 82.20 152.36 11.55
27 103G 103G N CA 772 773 -38.82 -41.20 8.50
28 3298 115I 116S C N 878 880 -84.25 -72.40 48.65 3.27 -64.10 141.66 9.25
28 116S 116S N CA 880 881 105.22 152.40 -35.00
29 3301 118C 119H C N 894 896 62.81 56.30 20.40 1.47 -63.20 141.22 24.25
29 119H 119H N CA 896 897 21.47 40.80 -42.30
30 3302 119H 120G C N 904 906 -69.41 -62.40 9.53 1.36 82.20 157.66 11.83
30 120G 120G N CA 906 907 -34.74 -41.20 8.50
31 3303 120G 121V C N 908 910 67.95 55.90 16.00 1.03 -125.40 -157.91 11.01
31 121V 121V N CA 910 911 28.98 39.50 143.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 17 12 56 81 112 88 116 152 137 132
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 125
Number of all, selected real atoms : 969 969
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10259 10259
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2014
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1092.1924
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 947 0 0 0.006 0.006 11.029 1.000
2 Bond angle potential : 1266 0 7 2.147 2.147 115.00 1.000
3 Stereochemical cosine torsion poten: 589 0 36 51.366 51.366 235.30 1.000
4 Stereochemical improper torsion pot: 381 0 0 1.183 1.183 12.212 1.000
5 Soft-sphere overlap restraints : 2014 1 2 0.009 0.009 18.943 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2101 0 5 0.484 0.484 114.49 1.000
10 Distance restraints 2 (N-O) : 2294 1 26 0.628 0.628 267.39 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 121 1 2 5.419 5.419 41.907 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 1 91.070 91.070 35.768 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 0 88.337 88.337 21.715 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 70.570 70.570 20.044 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 83.546 83.546 10.771 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 756 0 0 0.567 0.567 26.332 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 120 37 24 35.183 93.698 132.02 1.000
26 Distance restraints 4 (SDCH-SDCH) : 73 0 0 1.431 1.431 8.3244 1.000
27 Distance restraints 5 (X-Y) : 1399 0 0 0.041 0.041 20.952 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: merlu_lig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 16822.6953
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6310 31G 27K N O 217 192 5.42 3.02 2.41 5.32 3.02 2.41 5.32
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3399 96G 96G CA C 723 724 -147.79 -180.00 32.21 6.44 -180.00 32.21 6.44
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3184 1F 2A C N 10 12 -64.60 -62.50 6.54 0.99 -134.00 -168.68 11.79
1 2A 2A N CA 12 13 -34.71 -40.90 147.00
2 3185 2A 3G C N 15 17 72.86 78.70 72.63 2.31 -80.20 161.85 8.74
2 3G 3G N CA 17 18 121.50 -166.10 174.10
3 3186 3G 4G C N 19 21 -84.64 -80.20 17.55 0.91 82.20 -136.57 7.47
3 4G 4G N CA 21 22 157.12 174.10 8.50
4 3192 9R 10C C N 64 66 -62.33 -63.00 8.60 1.00 -117.90 178.12 7.69
4 10C 10C N CA 66 67 -49.67 -41.10 141.10
5 3195 12S 13C C N 84 86 -64.03 -63.00 1.07 0.16 -117.90 -173.96 7.99
5 13C 13C N CA 86 87 -40.82 -41.10 141.10
6 3198 15C 16K C N 104 106 73.75 56.60 18.23 1.77 -62.90 155.03 27.09
6 16K 16K N CA 106 107 32.41 38.60 -40.80
7 3200 17M 18E C N 121 123 -56.48 -63.60 8.94 1.11 -117.80 -172.22 10.21
7 18E 18E N CA 123 124 -45.71 -40.30 136.80
8 3202 19S 20G C N 136 138 51.83 78.70 28.37 1.15 -80.20 135.16 9.69
8 20G 20G N CA 138 139 -156.99 -166.10 174.10
9 3203 20G 21C C N 140 142 -62.04 -63.00 5.11 0.56 -117.90 -178.41 7.83
9 21C 21C N CA 142 143 -46.12 -41.10 141.10
10 3204 21C 22R C N 146 148 -167.88 -63.00 120.62 16.05 57.30 136.23 14.92
10 22R 22R N CA 148 149 18.48 -41.10 38.00
11 3207 24V 25G C N 172 174 22.74 -62.40 90.28 14.65 -62.40 90.28 14.65
11 25G 25G N CA 174 175 -71.23 -41.20 -41.20
12 3208 25G 26C C N 176 178 -57.76 -63.00 8.30 0.90 -117.90 -178.38 7.87
12 26C 26C N CA 178 179 -47.53 -41.10 141.10
13 3209 26C 27K C N 182 184 -69.52 -70.20 30.63 2.23 -62.90 148.33 19.63
13 27K 27K N CA 184 185 171.02 140.40 -40.80
14 3210 27K 28M C N 191 193 72.28 56.30 72.53 2.28 -63.40 135.76 25.43
14 28M 28M N CA 193 194 -35.95 34.80 -40.50
15 3213 30M 31G C N 215 217 -61.16 -62.40 1.74 0.32 82.20 151.34 11.50
15 31G 31G N CA 217 218 -39.98 -41.20 8.50
16 3217 34S 35C C N 239 241 -107.88 -117.90 62.07 2.28 -63.00 129.00 13.51
16 35C 35C N CA 241 242 79.85 141.10 -41.10
17 3218 35C 36G C N 245 247 138.57 82.20 64.85 2.80 -62.40 160.01 27.81
17 36G 36G N CA 247 248 -23.57 8.50 -41.20
18 3219 36G 37Y C N 249 251 56.82 55.90 1.26 0.08 -63.50 145.64 27.58
18 37Y 37Y N CA 251 252 38.65 39.50 -43.40
19 3220 37Y 38F C N 261 263 64.15 58.10 11.19 0.59 -63.20 144.27 25.92
19 38F 38F N CA 263 264 23.49 32.90 -44.30
20 3223 40I 41K C N 289 291 -102.82 -62.90 92.95 10.68 -62.90 92.95 10.68
20 41K 41K N CA 291 292 43.14 -40.80 -40.80
21 3236 53S 54S C N 392 394 100.02 -136.60 128.62 4.26 -64.10 -145.91 18.67
21 54S 54S N CA 394 395 -172.47 151.20 -35.00
22 3239 56K 57S C N 421 423 57.33 56.90 20.36 1.33 -64.10 152.20 19.55
22 57S 57S N CA 423 424 56.76 36.40 -35.00
23 3249 66S 67L C N 484 486 66.95 60.20 10.51 0.48 -63.50 144.75 26.68
23 67L 67L N CA 486 487 21.53 29.60 -41.20
24 3250 67L 68C C N 492 494 -140.31 -63.00 88.00 11.74 -63.00 88.00 11.74
24 68C 68C N CA 494 495 0.95 -41.10 -41.10
25 3259 76Y 77A C N 574 576 68.53 55.40 13.17 1.38 -62.50 152.53 31.01
25 77A 77A N CA 576 577 37.19 38.20 -40.90
26 3268 85R 86C C N 643 645 -99.85 -117.90 19.51 0.79 -63.00 174.34 23.98
26 86C 86C N CA 645 646 148.51 141.10 -41.10
27 3278 95G 96G C N 720 722 -74.52 -62.40 47.88 6.66 -62.40 47.88 6.66
27 96G 96G N CA 722 723 5.12 -41.20 -41.20
28 3279 96G 97P C N 724 726 -15.96 -58.70 72.30 4.47 -64.50 133.14 12.55
28 97P 97P N CA 726 727 -88.82 -30.50 147.20
29 3281 98R 99G C N 742 744 -58.18 -62.40 21.57 3.44 82.20 143.26 10.50
29 99G 99G N CA 744 745 -20.05 -41.20 8.50
30 3285 102K 103G C N 770 772 -63.33 -62.40 3.18 0.44 82.20 152.83 11.57
30 103G 103G N CA 772 773 -38.16 -41.20 8.50
31 3293 110N 111R C N 833 835 -76.69 -63.00 18.26 2.21 -72.10 170.97 13.25
31 111R 111R N CA 835 836 -29.01 -41.10 141.90
32 3294 111R 112L C N 844 846 62.02 -70.70 142.08 11.01 -108.50 175.53 7.94
32 112L 112L N CA 846 847 90.89 141.60 132.50
33 3295 112L 113Q C N 852 854 -105.99 -121.10 73.90 3.24 -63.80 115.63 15.17
33 113Q 113Q N CA 854 855 67.36 139.70 -40.30
34 3299 116S 117G C N 884 886 -67.26 -62.40 7.56 1.38 82.20 159.44 12.19
34 117G 117G N CA 886 887 -46.99 -41.20 8.50
35 3301 118C 119H C N 894 896 57.68 56.30 4.37 0.31 -63.20 144.38 24.76
35 119H 119H N CA 896 897 36.65 40.80 -42.30
36 3302 119H 120G C N 904 906 -66.48 -62.40 12.43 1.71 82.20 153.45 11.43
36 120G 120G N CA 906 907 -29.46 -41.20 8.50
37 3303 120G 121V C N 908 910 60.08 55.90 4.20 0.46 -125.40 -156.79 10.84
37 121V 121V N CA 910 911 39.20 39.50 143.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 11 18 68 78 117 109 117 135 145 151
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
merlu_lig.B99990001.pdb 998.91119
merlu_lig.B99990002.pdb 1092.19238
Image('pr10_5.png', width = 800)
Розовое - исходный белок, зеленое - смоделированный. На мой вгляд, ситуации особо-то не изменилась.
Попробуем переместить лиганд в другое место.
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('NH2:50:A','O4:124:B')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance, feature=modeller.features.distance(at[x],at[y]),mean=3.0, stdev=0.1))
a = mymodel(env, alnfile='all_in_one2.ali', knowns= pdb.code, sequence = s.code)
a.name='mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
AutoModel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the AutoModel defaults. If this is not what you
want, clear them before creating the AutoModel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
87 1 87 95 E G 13.907
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
distance___W> The class 'distance' is deprecated; use 'Distance' instead
gaussian___W> The class 'gaussian' is deprecated; use 'Gaussian' instead
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 11091 10260
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 125
Number of all, selected real atoms : 969 969
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10260 10260
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2103
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1351.1951
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 947 0 0 0.009 0.009 19.056 1.000
2 Bond angle potential : 1266 0 9 2.401 2.401 139.86 1.000
3 Stereochemical cosine torsion poten: 589 0 33 50.797 50.797 231.25 1.000
4 Stereochemical improper torsion pot: 381 0 0 1.175 1.175 12.586 1.000
5 Soft-sphere overlap restraints : 2103 2 2 0.009 0.009 19.470 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2101 0 2 0.475 0.475 112.11 1.000
10 Distance restraints 2 (N-O) : 2294 0 21 0.635 0.635 260.39 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 121 1 3 5.256 5.256 39.420 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 0 84.823 84.823 31.564 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 0 90.870 90.870 25.779 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 67.829 67.829 19.744 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 99.653 99.653 10.321 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 756 0 0 0.474 0.474 15.245 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 120 40 29 38.478 97.306 184.43 1.000
26 Distance restraints 4 (SDCH-SDCH) : 73 0 0 1.103 1.103 4.1935 1.000
27 Distance restraints 5 (X-Y) : 1400 1 1 0.085 0.085 225.78 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: merlu_lig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 17473.4473
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3399 96G 96G CA C 723 724 -151.62 -180.00 28.38 5.67 -180.00 28.38 5.67
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3184 1F 2A C N 10 12 -65.42 -62.50 7.42 1.12 -134.00 -168.38 11.80
1 2A 2A N CA 12 13 -34.07 -40.90 147.00
2 3185 2A 3G C N 15 17 62.87 78.70 76.74 2.83 -80.20 153.38 8.02
2 3G 3G N CA 17 18 118.81 -166.10 174.10
3 3186 3G 4G C N 19 21 -84.39 -80.20 11.75 0.67 82.20 -132.71 7.42
3 4G 4G N CA 21 22 163.12 174.10 8.50
4 3188 5I 6V C N 31 33 -75.54 -73.50 27.12 2.29 -62.40 151.92 20.01
4 6V 6V N CA 33 34 166.25 139.20 -42.40
5 3189 6V 7S C N 38 40 76.12 56.90 75.31 3.39 -64.10 140.23 17.94
5 7S 7S N CA 40 41 -36.42 36.40 -35.00
6 3192 9R 10C C N 64 66 -64.63 -63.00 3.78 0.58 -117.90 -177.65 7.84
6 10C 10C N CA 66 67 -44.50 -41.10 141.10
7 3195 12S 13C C N 84 86 -64.04 -63.00 2.12 0.34 -117.90 -175.99 7.91
7 13C 13C N CA 86 87 -42.94 -41.10 141.10
8 3198 15C 16K C N 104 106 77.24 56.60 22.70 2.06 -62.90 156.63 27.36
8 16K 16K N CA 106 107 29.15 38.60 -40.80
9 3200 17M 18E C N 121 123 -50.87 -63.60 13.76 2.35 -117.80 -175.55 7.74
9 18E 18E N CA 123 124 -35.08 -40.30 136.80
10 3201 18E 19S C N 130 132 -142.48 -136.60 107.37 5.57 -64.10 111.28 8.98
10 19S 19S N CA 132 133 43.99 151.20 -35.00
11 3203 20G 21C C N 140 142 57.56 -69.10 146.32 13.59 -117.90 -169.59 7.73
11 21C 21C N CA 142 143 -144.92 141.80 141.10
12 3204 21C 22R C N 146 148 -77.08 -63.00 20.22 2.38 57.30 149.09 18.55
12 22R 22R N CA 148 149 -26.58 -41.10 38.00
13 3206 23N 24V C N 165 167 -73.89 -62.40 18.85 2.09 -125.40 178.36 7.40
13 24V 24V N CA 167 168 -27.45 -42.40 143.30
14 3207 24V 25G C N 172 174 114.28 82.20 66.15 1.85 -62.40 176.86 31.25
14 25G 25G N CA 174 175 -49.36 8.50 -41.20
15 3213 30M 31G C N 215 217 -64.73 -62.40 2.90 0.43 82.20 154.57 11.71
15 31G 31G N CA 217 218 -39.47 -41.20 8.50
16 3217 34S 35C C N 239 241 -108.64 -117.90 70.30 2.62 -63.00 121.42 12.65
16 35C 35C N CA 241 242 71.41 141.10 -41.10
17 3218 35C 36G C N 245 247 136.84 82.20 61.30 2.80 -62.40 162.24 28.01
17 36G 36G N CA 247 248 -19.29 8.50 -41.20
18 3219 36G 37Y C N 249 251 55.93 55.90 3.41 0.24 -63.50 147.35 27.91
18 37Y 37Y N CA 251 252 42.91 39.50 -43.40
19 3220 37Y 38F C N 261 263 66.01 58.10 14.51 0.77 -63.20 144.65 25.93
19 38F 38F N CA 263 264 20.73 32.90 -44.30
20 3223 40I 41K C N 289 291 -101.07 -118.00 82.71 3.75 -62.90 106.05 12.28
20 41K 41K N CA 291 292 58.14 139.10 -40.80
21 3236 53S 54S C N 392 394 91.38 -136.60 135.54 4.64 -64.10 -148.68 17.72
21 54S 54S N CA 394 395 -178.12 151.20 -35.00
22 3239 56K 57S C N 421 423 55.98 56.90 18.02 1.07 -64.10 149.70 19.27
22 57S 57S N CA 423 424 54.40 36.40 -35.00
23 3249 66S 67L C N 484 486 81.71 60.20 53.52 1.85 -63.50 146.84 26.20
23 67L 67L N CA 486 487 -19.41 29.60 -41.20
24 3252 69V 70Q C N 505 507 -64.05 -63.80 23.32 3.44 -121.10 166.75 8.62
24 70Q 70Q N CA 507 508 -63.62 -40.30 139.70
25 3253 70Q 71N C N 514 516 -101.88 -119.90 51.96 1.91 55.90 165.14 15.69
25 71N 71N N CA 516 517 88.26 137.00 39.50
26 3259 76Y 77A C N 574 576 66.83 55.40 11.43 1.24 -62.50 151.55 30.81
26 77A 77A N CA 576 577 38.12 38.20 -40.90
27 3268 85R 86C C N 643 645 -107.35 -117.90 10.97 0.43 -63.00 -179.67 25.28
27 86C 86C N CA 645 646 144.11 141.10 -41.10
28 3277 94N 95G C N 716 718 21.36 -62.40 87.15 14.41 -62.40 87.15 14.41
28 95G 95G N CA 718 719 -65.26 -41.20 -41.20
29 3278 95G 96G C N 720 722 -71.71 -62.40 48.71 6.88 -62.40 48.71 6.88
29 96G 96G N CA 722 723 6.61 -41.20 -41.20
30 3279 96G 97P C N 724 726 -16.89 -58.70 72.09 4.41 -64.50 132.43 12.45
30 97P 97P N CA 726 727 -89.22 -30.50 147.20
31 3281 98R 99G C N 742 744 -56.81 -62.40 20.14 3.30 82.20 142.29 10.48
31 99G 99G N CA 744 745 -21.85 -41.20 8.50
32 3285 102K 103G C N 770 772 -61.04 -62.40 4.28 0.71 82.20 150.34 11.37
32 103G 103G N CA 772 773 -37.15 -41.20 8.50
33 3289 106I 107G C N 795 797 -168.00 82.20 118.77 9.14 -62.40 142.04 20.30
33 107G 107G N CA 797 798 53.79 8.50 -41.20
34 3290 107G 108Y C N 799 801 -130.70 -63.50 67.71 11.27 -63.50 67.71 11.27
34 108Y 108Y N CA 801 802 -35.16 -43.40 -43.40
35 3297 114K 115I C N 870 872 -59.87 -97.30 51.02 3.75 -63.40 154.56 25.21
35 115I 115I N CA 872 873 161.88 127.20 -43.60
36 3298 115I 116S C N 878 880 77.75 56.90 45.59 1.89 -64.10 145.17 19.33
36 116S 116S N CA 880 881 -4.14 36.40 -35.00
37 3299 116S 117G C N 884 886 -140.26 -62.40 90.31 13.74 82.20 137.59 9.09
37 117G 117G N CA 886 887 4.55 -41.20 8.50
38 3301 118C 119H C N 894 896 62.85 56.30 26.75 1.97 -63.20 138.41 23.72
38 119H 119H N CA 896 897 14.87 40.80 -42.30
39 3302 119H 120G C N 904 906 -69.27 -62.40 9.18 1.31 82.20 157.62 11.84
39 120G 120G N CA 906 907 -35.10 -41.20 8.50
40 3303 120G 121V C N 908 910 56.48 55.90 6.66 0.42 -125.40 -150.42 11.25
40 121V 121V N CA 910 911 32.86 39.50 143.30
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10260 50R 124. NH2 O4 374 952 5.58 3.00 2.58 25.82 3.00 2.58 25.82
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 12 17 62 86 112 98 138 149 150 156
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 125
Number of all, selected real atoms : 969 969
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10260 10260
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1963
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 984.7444
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 947 0 0 0.007 0.007 14.335 1.000
2 Bond angle potential : 1266 0 5 2.146 2.146 113.90 1.000
3 Stereochemical cosine torsion poten: 589 0 33 50.794 50.794 229.83 1.000
4 Stereochemical improper torsion pot: 381 0 0 1.173 1.173 11.817 1.000
5 Soft-sphere overlap restraints : 1963 2 2 0.009 0.009 18.832 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2101 1 5 0.452 0.452 93.649 1.000
10 Distance restraints 2 (N-O) : 2294 0 10 0.551 0.551 170.90 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 121 0 1 4.763 4.763 32.378 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 2 88.945 88.945 33.592 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 2 87.914 87.914 26.308 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 82.376 82.376 19.165 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 81.321 81.321 9.9395 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 756 0 0 0.466 0.466 14.481 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 120 27 19 36.165 82.600 137.95 1.000
26 Distance restraints 4 (SDCH-SDCH) : 73 0 1 1.404 1.404 8.1263 1.000
27 Distance restraints 5 (X-Y) : 1400 1 1 0.052 0.052 49.546 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: merlu_lig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15879.2480
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3186 3G 4G C N 19 21 -88.41 -80.20 14.30 0.95 82.20 -130.23 7.63
1 4G 4G N CA 21 22 162.39 174.10 8.50
2 3192 9R 10C C N 64 66 -63.38 -63.00 2.94 0.39 -117.90 -176.82 7.89
2 10C 10C N CA 66 67 -44.01 -41.10 141.10
3 3195 12S 13C C N 84 86 -63.11 -63.00 1.00 0.11 -117.90 -173.01 8.04
3 13C 13C N CA 86 87 -40.11 -41.10 141.10
4 3198 15C 16K C N 104 106 75.63 56.60 19.38 2.08 -62.90 157.88 27.58
4 16K 16K N CA 106 107 34.92 38.60 -40.80
5 3201 18E 19S C N 130 132 149.05 56.90 148.43 7.53 -64.10 153.58 20.54
5 19S 19S N CA 132 133 -79.97 36.40 -35.00
6 3202 19S 20G C N 136 138 50.49 78.70 31.87 1.11 -80.20 135.19 9.78
6 20G 20G N CA 138 139 -151.29 -166.10 174.10
7 3207 24V 25G C N 172 174 21.68 -62.40 92.05 14.54 -62.40 92.05 14.54
7 25G 25G N CA 174 175 -78.68 -41.20 -41.20
8 3213 30M 31G C N 215 217 -65.02 -62.40 5.09 0.69 82.20 154.04 11.63
8 31G 31G N CA 217 218 -36.83 -41.20 8.50
9 3215 32S 33L C N 225 227 -68.39 -70.70 17.70 1.43 -63.50 159.72 22.46
9 33L 33L N CA 227 228 159.15 141.60 -41.20
10 3216 33L 34S C N 233 235 77.67 56.90 81.56 3.68 -64.10 141.97 17.94
10 34S 34S N CA 235 236 -42.47 36.40 -35.00
11 3218 35C 36G C N 245 247 -176.98 82.20 100.88 6.64 -62.40 123.59 19.75
11 36G 36G N CA 247 248 5.12 8.50 -41.20
12 3219 36G 37Y C N 249 251 58.75 55.90 4.70 0.53 -63.50 149.84 28.38
12 37Y 37Y N CA 251 252 43.24 39.50 -43.40
13 3220 37Y 38F C N 261 263 60.47 58.10 2.38 0.32 -63.20 145.73 26.27
13 38F 38F N CA 263 264 32.78 32.90 -44.30
14 3236 53S 54S C N 392 394 94.96 -136.60 132.58 4.48 -64.10 -147.48 18.11
14 54S 54S N CA 394 395 -175.95 151.20 -35.00
15 3239 56K 57S C N 421 423 56.57 56.90 18.90 1.18 -64.10 150.72 19.39
15 57S 57S N CA 423 424 55.30 36.40 -35.00
16 3249 66S 67L C N 484 486 74.28 60.20 27.10 1.00 -63.50 145.79 26.69
16 67L 67L N CA 486 487 6.45 29.60 -41.20
17 3250 67L 68C C N 492 494 -130.32 -63.00 87.59 10.46 -63.00 87.59 10.46
17 68C 68C N CA 494 495 14.94 -41.10 -41.10
18 3259 76Y 77A C N 574 576 68.23 55.40 13.42 1.23 -62.50 150.80 30.67
18 77A 77A N CA 576 577 34.27 38.20 -40.90
19 3268 85R 86C C N 643 645 -96.22 -117.90 27.07 1.17 -63.00 164.97 22.56
19 86C 86C N CA 645 646 157.31 141.10 -41.10
20 3277 94N 95G C N 716 718 -49.59 78.70 131.40 7.16 -62.40 153.87 22.38
20 95G 95G N CA 718 719 165.46 -166.10 -41.20
21 3278 95G 96G C N 720 722 70.17 82.20 30.55 0.92 -62.40 153.70 29.06
21 96G 96G N CA 722 723 36.58 8.50 -41.20
22 3279 96G 97P C N 724 726 -40.89 -58.70 63.57 4.02 -64.50 123.56 10.50
22 97P 97P N CA 726 727 -91.52 -30.50 147.20
23 3281 98R 99G C N 742 744 -57.68 -62.40 20.84 3.36 82.20 142.94 10.50
23 99G 99G N CA 744 745 -20.90 -41.20 8.50
24 3285 102K 103G C N 770 772 -62.86 -62.40 2.45 0.35 82.20 152.58 11.56
24 103G 103G N CA 772 773 -38.79 -41.20 8.50
25 3299 116S 117G C N 884 886 -72.84 -62.40 13.56 1.96 82.20 160.38 11.98
25 117G 117G N CA 886 887 -32.55 -41.20 8.50
26 3301 118C 119H C N 894 896 63.01 56.30 13.06 1.00 -63.20 145.25 24.95
26 119H 119H N CA 896 897 29.59 40.80 -42.30
27 3302 119H 120G C N 904 906 -153.91 -167.20 96.78 3.61 82.20 142.41 11.11
27 120G 120G N CA 906 907 78.73 174.60 8.50
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10260 50R 124. NH2 O4 374 952 3.89 3.00 0.89 8.93 3.00 0.89 8.93
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 9 17 62 79 101 98 118 146 139 142
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
merlu_lig.B99990001.pdb 1351.19507
merlu_lig.B99990002.pdb 984.74445
Image('pr10_6.png', width = 800)
Ну, мало что поменялось, на самом деле.
И наконец, попробуем построить лизоцим полностью из аланинов.
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'B'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
lys_ala = 'A' * 129 + '/...'
alignm.append_sequence(lys_ala)
alignm[0].code = 'pdb'
alignm[1].code = 'lys_ala'
alignment__W> The class 'alignment' is deprecated; use 'Alignment' instead model______W> The class 'model' is deprecated; use 'Model' instead
alignm.salign()
alignm.write(file='all_in_one3.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='all_in_one3.ali', knowns=pdb.code, sequence=s.code)
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
lys_ala pdb
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
AutoModel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the AutoModel defaults. If this is not what you
want, clear them before creating the AutoModel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 10115 9477
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 132
Number of all, selected real atoms : 689 689
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9477 9477
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1208
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 524.0288
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 645 0 0 0.006 0.006 6.0777 1.000
2 Bond angle potential : 902 0 4 2.157 2.157 86.102 1.000
3 Stereochemical cosine torsion poten: 262 0 34 77.715 77.715 254.10 1.000
4 Stereochemical improper torsion pot: 258 0 0 0.838 0.838 5.0373 1.000
5 Soft-sphere overlap restraints : 1208 2 2 0.011 0.011 16.389 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2404 0 0 0.187 0.187 42.301 1.000
10 Distance restraints 2 (N-O) : 2562 0 0 0.236 0.236 65.383 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 128 0 3 4.608 4.608 32.050 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 726 0 0 0.217 0.217 4.6757 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 127 17 11 24.845 59.046 -2.4637 1.000
26 Distance restraints 4 (SDCH-SDCH) : 62 0 0 0.398 0.398 1.1299 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.032 0.032 13.248 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: lys_ala.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 10443.2627
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2082 15A 16A C N 74 76 78.20 55.40 26.56 1.93 -62.50 155.19 31.53
1 16A 16A N CA 76 77 24.58 38.20 -40.90
2 2085 18A 19A C N 89 91 65.45 55.40 22.34 0.81 -62.50 140.96 28.64
2 19A 19A N CA 91 92 18.25 38.20 -40.90
3 2087 20A 21A C N 99 101 55.70 55.40 7.88 0.45 -62.50 138.00 28.06
3 21A 21A N CA 101 102 30.32 38.20 -40.90
4 2088 21A 22A C N 104 106 62.93 55.40 11.58 0.54 -62.50 143.78 29.24
4 22A 22A N CA 106 107 29.40 38.20 -40.90
5 2103 36A 37A C N 179 181 66.25 55.40 12.89 0.90 -62.50 147.57 30.01
5 37A 37A N CA 181 182 31.23 38.20 -40.90
6 2104 37A 38A C N 184 186 60.81 55.40 7.92 0.40 -62.50 143.45 29.17
6 38A 38A N CA 186 187 32.42 38.20 -40.90
7 2115 48A 49A C N 239 241 85.74 55.40 41.28 2.31 -62.50 156.79 31.67
7 49A 49A N CA 241 242 10.20 38.20 -40.90
8 2120 53A 54A C N 264 266 91.53 -134.00 139.98 3.40 -62.50 -156.34 32.01
8 54A 54A N CA 266 267 -174.14 147.00 -40.90
9 2123 56A 57A C N 279 281 60.44 55.40 11.43 1.09 -62.50 151.98 30.80
9 57A 57A N CA 281 282 48.46 38.20 -40.90
10 2133 66A 67A C N 329 331 81.68 55.40 57.50 2.09 -62.50 146.87 29.22
10 67A 67A N CA 331 332 -12.94 38.20 -40.90
11 2137 70A 71A C N 349 351 54.01 55.40 11.55 0.59 -62.50 147.57 29.85
11 71A 71A N CA 351 352 49.67 38.20 -40.90
12 2140 73A 74A C N 364 366 53.94 55.40 20.83 1.14 -62.50 153.41 30.90
12 74A 74A N CA 366 367 58.98 38.20 -40.90
13 2143 76A 77A C N 379 381 65.07 55.40 10.27 1.22 -62.50 151.95 30.87
13 77A 77A N CA 381 382 41.67 38.20 -40.90
14 2170 103A 104A C N 514 516 81.78 -134.00 158.95 3.61 -62.50 178.60 28.70
14 104A 104A N CA 516 517 -146.18 147.00 -40.90
15 2183 116A 117A C N 579 581 50.85 55.40 9.93 0.36 -62.50 143.44 29.01
15 117A 117A N CA 581 582 47.02 38.20 -40.90
16 2192 125A 126A C N 624 626 70.55 55.40 33.58 1.22 -62.50 141.82 28.70
16 126A 126A N CA 626 627 8.23 38.20 -40.90
17 2194 127A 128A C N 634 636 61.69 55.40 11.06 0.45 -62.50 142.56 28.99
17 128A 128A N CA 636 637 29.10 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 2 2 29 53 66 57 76 104 96 92
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 132
Number of all, selected real atoms : 689 689
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9477 9477
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1199
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 600.5272
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 645 0 0 0.006 0.006 7.2117 1.000
2 Bond angle potential : 902 0 5 2.280 2.280 96.056 1.000
3 Stereochemical cosine torsion poten: 262 0 31 76.983 76.983 248.96 1.000
4 Stereochemical improper torsion pot: 258 0 0 0.934 0.934 6.1038 1.000
5 Soft-sphere overlap restraints : 1199 1 2 0.011 0.011 16.192 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2404 0 2 0.207 0.207 52.557 1.000
10 Distance restraints 2 (N-O) : 2562 0 6 0.294 0.294 97.235 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 128 0 4 4.803 4.803 34.828 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 726 0 0 0.229 0.229 5.1061 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 127 18 15 28.410 60.665 21.138 1.000
26 Distance restraints 4 (SDCH-SDCH) : 62 0 0 0.379 0.379 1.0471 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.033 0.033 14.097 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: lys_ala.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 10699.7998
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2082 15A 16A C N 74 76 78.07 55.40 25.30 2.00 -62.50 156.09 31.72
1 16A 16A N CA 76 77 26.96 38.20 -40.90
2 2084 17A 18A C N 84 86 -56.83 -62.50 7.62 1.19 -134.00 -176.02 11.35
2 18A 18A N CA 86 87 -45.99 -40.90 147.00
3 2087 20A 21A C N 99 101 52.73 55.40 3.11 0.37 -62.50 138.86 28.19
3 21A 21A N CA 101 102 36.59 38.20 -40.90
4 2088 21A 22A C N 104 106 63.98 55.40 18.55 0.68 -62.50 141.15 28.69
4 22A 22A N CA 106 107 21.75 38.20 -40.90
5 2103 36A 37A C N 179 181 66.29 55.40 13.38 0.88 -62.50 147.22 29.94
5 37A 37A N CA 181 182 30.42 38.20 -40.90
6 2104 37A 38A C N 184 186 63.48 55.40 12.74 0.58 -62.50 143.75 29.24
6 38A 38A N CA 186 187 28.35 38.20 -40.90
7 2115 48A 49A C N 239 241 84.44 55.40 38.39 2.24 -62.50 156.54 31.67
7 49A 49A N CA 241 242 13.09 38.20 -40.90
8 2120 53A 54A C N 264 266 93.97 -134.00 137.45 3.34 -62.50 -154.08 32.41
8 54A 54A N CA 266 267 -174.77 147.00 -40.90
9 2123 56A 57A C N 279 281 58.80 55.40 13.52 1.09 -62.50 152.35 30.84
9 57A 57A N CA 281 282 51.29 38.20 -40.90
10 2133 66A 67A C N 329 331 82.86 55.40 60.29 2.19 -62.50 147.56 29.28
10 67A 67A N CA 331 332 -15.48 38.20 -40.90
11 2137 70A 71A C N 349 351 54.06 55.40 11.51 0.59 -62.50 147.59 29.85
11 71A 71A N CA 351 352 49.63 38.20 -40.90
12 2140 73A 74A C N 364 366 55.78 55.40 21.70 1.34 -62.50 155.40 31.31
12 74A 74A N CA 366 367 59.90 38.20 -40.90
13 2143 76A 77A C N 379 381 67.75 55.40 12.40 1.39 -62.50 152.97 31.10
13 77A 77A N CA 381 382 39.32 38.20 -40.90
14 2170 103A 104A C N 514 516 80.87 -134.00 159.65 3.63 -62.50 178.06 28.58
14 104A 104A N CA 516 517 -146.50 147.00 -40.90
15 2183 116A 117A C N 579 581 46.84 55.40 17.22 0.64 -62.50 144.22 29.05
15 117A 117A N CA 581 582 53.14 38.20 -40.90
16 2191 124A 125A C N 619 621 56.96 -68.20 131.88 12.40 -68.20 131.88 12.40
16 125A 125A N CA 621 622 -173.14 145.30 145.30
17 2192 125A 126A C N 624 626 -82.80 -68.20 75.78 6.61 -62.50 113.67 17.74
17 126A 126A N CA 626 627 70.95 145.30 -40.90
18 2194 127A 128A C N 634 636 61.07 55.40 6.52 0.49 -62.50 145.01 29.48
18 128A 128A N CA 636 637 34.98 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 4 2 29 41 64 61 78 102 102 84
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
lys_ala.B99990001.pdb 524.02881
lys_ala.B99990002.pdb 600.52716
Image('pr10_7.png', width = 800)
Розовый - 1lmp, голубой - лизоцим из аланинов.
структуры удивительным образом опять почти идеально наложились друг на друга. Т.е. полностью аланиновая последовательность вдруг дала нам лизоцим. Все это свидетельствует о том, что modeller`у мало важна последовательность - она все равно подгонит вторичную структуру так, как надо.
Какие у нас получались скоры:
Первая модель (без лиганда): 945.93018
Вторая модель (с лигандом): 998.91119
Третья модель (с чуть передвинутым лигандом): 1351.19507
Четвертая модель (аланиновый лизоцим): 524.02881
Видим, что скор модели лизоцима из аланинов меньше, чем остальных. Спасибо и на этом, наверное.