*** ***
output from eigenvector calculation:
STDOUT:
CUTOFF set to default value (CUTOFF=8)
Build Tirion matrix:
Pdbmat> Computes the Hessian matrix, using an Elastic Network Model.
Pdbmat> Version 3.50, Fevrier 2004.
Pdbmat> Options to be read in pdbmat.dat file.
Pdbmat> Coordinate filename = 241119171016839441.atom
Pdbmat> Distance cutoff = 8.00
Force constant = 10.00
Origin of mass values = CONS
Pdbmat> Levelshift = 1.0E-09
PRINTing level = 2
Pdbmat> Coordinate file 241119171016839441.atom to be opened.
Openam> File opened: 241119171016839441.atom
Pdbmat> Coordinate file in PDB format.
Rdatompdb> Reading pdb file.
Rdatompdb> End of file reached.
Rdatompdb> Number of I/O errors: 0
Rdatompdb> Number of residues found = 12964
First residue number = 12
Last residue number = 4964
Number of atoms found = 99792
Mean number per residue = 7.7
Pdbmat> Coordinate statistics:
= 273.039077 +/- 61.370717 From: 122.799000 To: 423.282000
= 273.042178 +/- 61.370999 From: 122.781000 To: 423.286000
= 267.514320 +/- 35.019774 From: 152.438000 To: 344.147000
Pdbmat> Masses are all set to one.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is -12.9639 % Filled.
Pdbmat> 36819177 non-zero elements.
Pdbmat> 4025190 atom-atom interactions.
Pdbmat> Number per atom= 80.67 +/- 21.81
Maximum number = 134
Minimum number = 10
Pdbmat> Matrix trace = 8.050380E+07
Pdbmat> Larger element = 525.202
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
Diagonalize Tirion matrix using diagrtb
Diagrtb> Diagonalizes a matrix, using the RTB/BNM approximation.
Diagrtb> Version 2.52, November 2004.
Diagrtb> Options to be read in diagrtb.dat file.
Diagrtb> Options taken into account:
MATRix filename = pdbmat.sdijb
COORdinates filename = 241119171016839441.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 100
Origin of MASS values = CONS
MATRix FORMat = BINA
Temporary files cleaning = ALL
Output PRINting level = 2
Diagrtb> Memory allocation for Blocpdb.
Blocpdb> Entering in.
Openam> file on opening on unit 10:
diagrtb_work.xyzm
Blocpdb> Coordinate file 241119171016839441.atom to be opened.
Openam> file on opening on unit 11:
241119171016839441.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 99792 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 100 residue(s) per block.
Blocpdb> 12964 residues.
Blocpdb> 567 atoms in block 1
Block first atom: 1
Blocpdb> 230 atoms in block 2
Block first atom: 568
Blocpdb> 430 atoms in block 3
Block first atom: 798
Blocpdb> 146 atoms in block 4
Block first atom: 1228
Blocpdb> 118 atoms in block 5
Block first atom: 1374
Blocpdb> 73 atoms in block 6
Block first atom: 1492
Blocpdb> 680 atoms in block 7
Block first atom: 1565
Blocpdb> 267 atoms in block 8
Block first atom: 2245
Blocpdb> 455 atoms in block 9
Block first atom: 2512
Blocpdb> 552 atoms in block 10
Block first atom: 2967
Blocpdb> 775 atoms in block 11
Block first atom: 3519
Blocpdb> 356 atoms in block 12
Block first atom: 4294
Blocpdb> 771 atoms in block 13
Block first atom: 4650
Blocpdb> 272 atoms in block 14
Block first atom: 5421
Blocpdb> 389 atoms in block 15
Block first atom: 5693
Blocpdb> 809 atoms in block 16
Block first atom: 6082
Blocpdb> 716 atoms in block 17
Block first atom: 6891
Blocpdb> 205 atoms in block 18
Block first atom: 7607
Blocpdb> 93 atoms in block 19
Block first atom: 7812
Blocpdb> 172 atoms in block 20
Block first atom: 7905
Blocpdb> 139 atoms in block 21
Block first atom: 8077
Blocpdb> 31 atoms in block 22
Block first atom: 8216
Blocpdb> 77 atoms in block 23
Block first atom: 8247
Blocpdb> 300 atoms in block 24
Block first atom: 8324
Blocpdb> 821 atoms in block 25
Block first atom: 8624
Blocpdb> 585 atoms in block 26
Block first atom: 9445
Blocpdb> 176 atoms in block 27
Block first atom: 10030
Blocpdb> 577 atoms in block 28
Block first atom: 10206
Blocpdb> 427 atoms in block 29
Block first atom: 10783
Blocpdb> 74 atoms in block 30
Block first atom: 11210
Blocpdb> 130 atoms in block 31
Block first atom: 11284
Blocpdb> 594 atoms in block 32
Block first atom: 11414
Blocpdb> 351 atoms in block 33
Block first atom: 12008
Blocpdb> 303 atoms in block 34
Block first atom: 12359
Blocpdb> 271 atoms in block 35
Block first atom: 12662
Blocpdb> 312 atoms in block 36
Block first atom: 12933
Blocpdb> 86 atoms in block 37
Block first atom: 13245
Blocpdb> 139 atoms in block 38
Block first atom: 13331
Blocpdb> 99 atoms in block 39
Block first atom: 13470
Blocpdb> 85 atoms in block 40
Block first atom: 13569
Blocpdb> 141 atoms in block 41
Block first atom: 13654
Blocpdb> 77 atoms in block 42
Block first atom: 13795
Blocpdb> 59 atoms in block 43
Block first atom: 13872
Blocpdb> 144 atoms in block 44
Block first atom: 13931
Blocpdb> 99 atoms in block 45
Block first atom: 14075
Blocpdb> 94 atoms in block 46
Block first atom: 14174
Blocpdb> 100 atoms in block 47
Block first atom: 14268
Blocpdb> 113 atoms in block 48
Block first atom: 14368
Blocpdb> 99 atoms in block 49
Block first atom: 14481
Blocpdb> 109 atoms in block 50
Block first atom: 14580
Blocpdb> 786 atoms in block 51
Block first atom: 14689
Blocpdb> 709 atoms in block 52
Block first atom: 15475
Blocpdb> 118 atoms in block 53
Block first atom: 16184
Blocpdb> 98 atoms in block 54
Block first atom: 16302
Blocpdb> 108 atoms in block 55
Block first atom: 16400
Blocpdb> 109 atoms in block 56
Block first atom: 16508
Blocpdb> 104 atoms in block 57
Block first atom: 16617
Blocpdb> 104 atoms in block 58
Block first atom: 16721
Blocpdb> 88 atoms in block 59
Block first atom: 16825
Blocpdb> 70 atoms in block 60
Block first atom: 16913
Blocpdb> 312 atoms in block 61
Block first atom: 16983
Blocpdb> 325 atoms in block 62
Block first atom: 17295
Blocpdb> 773 atoms in block 63
Block first atom: 17620
Blocpdb> 9 atoms in block 64
Block first atom: 18393
Blocpdb> 818 atoms in block 65
Block first atom: 18402
Blocpdb> 791 atoms in block 66
Block first atom: 19220
Blocpdb> 461 atoms in block 67
Block first atom: 20011
Blocpdb> 820 atoms in block 68
Block first atom: 20472
Blocpdb> 147 atoms in block 69
Block first atom: 21292
Blocpdb> 337 atoms in block 70
Block first atom: 21439
Blocpdb> 840 atoms in block 71
Block first atom: 21776
Blocpdb> 125 atoms in block 72
Block first atom: 22616
Blocpdb> 816 atoms in block 73
Block first atom: 22741
Blocpdb> 791 atoms in block 74
Block first atom: 23557
Blocpdb> 601 atoms in block 75
Block first atom: 24348
Blocpdb> 567 atoms in block 76
Block first atom: 24949
Blocpdb> 230 atoms in block 77
Block first atom: 25516
Blocpdb> 430 atoms in block 78
Block first atom: 25746
Blocpdb> 146 atoms in block 79
Block first atom: 26176
Blocpdb> 118 atoms in block 80
Block first atom: 26322
Blocpdb> 73 atoms in block 81
Block first atom: 26440
Blocpdb> 680 atoms in block 82
Block first atom: 26513
Blocpdb> 267 atoms in block 83
Block first atom: 27193
Blocpdb> 455 atoms in block 84
Block first atom: 27460
Blocpdb> 552 atoms in block 85
Block first atom: 27915
Blocpdb> 775 atoms in block 86
Block first atom: 28467
Blocpdb> 356 atoms in block 87
Block first atom: 29242
Blocpdb> 771 atoms in block 88
Block first atom: 29598
Blocpdb> 272 atoms in block 89
Block first atom: 30369
Blocpdb> 389 atoms in block 90
Block first atom: 30641
Blocpdb> 809 atoms in block 91
Block first atom: 31030
Blocpdb> 716 atoms in block 92
Block first atom: 31839
Blocpdb> 205 atoms in block 93
Block first atom: 32555
Blocpdb> 93 atoms in block 94
Block first atom: 32760
Blocpdb> 172 atoms in block 95
Block first atom: 32853
Blocpdb> 139 atoms in block 96
Block first atom: 33025
Blocpdb> 31 atoms in block 97
Block first atom: 33164
Blocpdb> 77 atoms in block 98
Block first atom: 33195
Blocpdb> 300 atoms in block 99
Block first atom: 33272
Blocpdb> 821 atoms in block 100
Block first atom: 33572
Blocpdb> 585 atoms in block 101
Block first atom: 34393
Blocpdb> 176 atoms in block 102
Block first atom: 34978
Blocpdb> 577 atoms in block 103
Block first atom: 35154
Blocpdb> 427 atoms in block 104
Block first atom: 35731
Blocpdb> 74 atoms in block 105
Block first atom: 36158
Blocpdb> 130 atoms in block 106
Block first atom: 36232
Blocpdb> 594 atoms in block 107
Block first atom: 36362
Blocpdb> 351 atoms in block 108
Block first atom: 36956
Blocpdb> 303 atoms in block 109
Block first atom: 37307
Blocpdb> 271 atoms in block 110
Block first atom: 37610
Blocpdb> 312 atoms in block 111
Block first atom: 37881
Blocpdb> 86 atoms in block 112
Block first atom: 38193
Blocpdb> 139 atoms in block 113
Block first atom: 38279
Blocpdb> 99 atoms in block 114
Block first atom: 38418
Blocpdb> 85 atoms in block 115
Block first atom: 38517
Blocpdb> 141 atoms in block 116
Block first atom: 38602
Blocpdb> 77 atoms in block 117
Block first atom: 38743
Blocpdb> 59 atoms in block 118
Block first atom: 38820
Blocpdb> 144 atoms in block 119
Block first atom: 38879
Blocpdb> 99 atoms in block 120
Block first atom: 39023
Blocpdb> 94 atoms in block 121
Block first atom: 39122
Blocpdb> 100 atoms in block 122
Block first atom: 39216
Blocpdb> 113 atoms in block 123
Block first atom: 39316
Blocpdb> 99 atoms in block 124
Block first atom: 39429
Blocpdb> 109 atoms in block 125
Block first atom: 39528
Blocpdb> 786 atoms in block 126
Block first atom: 39637
Blocpdb> 709 atoms in block 127
Block first atom: 40423
Blocpdb> 118 atoms in block 128
Block first atom: 41132
Blocpdb> 98 atoms in block 129
Block first atom: 41250
Blocpdb> 108 atoms in block 130
Block first atom: 41348
Blocpdb> 109 atoms in block 131
Block first atom: 41456
Blocpdb> 104 atoms in block 132
Block first atom: 41565
Blocpdb> 104 atoms in block 133
Block first atom: 41669
Blocpdb> 88 atoms in block 134
Block first atom: 41773
Blocpdb> 70 atoms in block 135
Block first atom: 41861
Blocpdb> 312 atoms in block 136
Block first atom: 41931
Blocpdb> 325 atoms in block 137
Block first atom: 42243
Blocpdb> 773 atoms in block 138
Block first atom: 42568
Blocpdb> 9 atoms in block 139
Block first atom: 43341
Blocpdb> 818 atoms in block 140
Block first atom: 43350
Blocpdb> 791 atoms in block 141
Block first atom: 44168
Blocpdb> 461 atoms in block 142
Block first atom: 44959
Blocpdb> 820 atoms in block 143
Block first atom: 45420
Blocpdb> 147 atoms in block 144
Block first atom: 46240
Blocpdb> 337 atoms in block 145
Block first atom: 46387
Blocpdb> 840 atoms in block 146
Block first atom: 46724
Blocpdb> 125 atoms in block 147
Block first atom: 47564
Blocpdb> 816 atoms in block 148
Block first atom: 47689
Blocpdb> 791 atoms in block 149
Block first atom: 48505
Blocpdb> 601 atoms in block 150
Block first atom: 49296
Blocpdb> 567 atoms in block 151
Block first atom: 49897
Blocpdb> 230 atoms in block 152
Block first atom: 50464
Blocpdb> 430 atoms in block 153
Block first atom: 50694
Blocpdb> 146 atoms in block 154
Block first atom: 51124
Blocpdb> 118 atoms in block 155
Block first atom: 51270
Blocpdb> 73 atoms in block 156
Block first atom: 51388
Blocpdb> 680 atoms in block 157
Block first atom: 51461
Blocpdb> 267 atoms in block 158
Block first atom: 52141
Blocpdb> 455 atoms in block 159
Block first atom: 52408
Blocpdb> 552 atoms in block 160
Block first atom: 52863
Blocpdb> 775 atoms in block 161
Block first atom: 53415
Blocpdb> 356 atoms in block 162
Block first atom: 54190
Blocpdb> 771 atoms in block 163
Block first atom: 54546
Blocpdb> 272 atoms in block 164
Block first atom: 55317
Blocpdb> 389 atoms in block 165
Block first atom: 55589
Blocpdb> 809 atoms in block 166
Block first atom: 55978
Blocpdb> 716 atoms in block 167
Block first atom: 56787
Blocpdb> 205 atoms in block 168
Block first atom: 57503
Blocpdb> 93 atoms in block 169
Block first atom: 57708
Blocpdb> 172 atoms in block 170
Block first atom: 57801
Blocpdb> 139 atoms in block 171
Block first atom: 57973
Blocpdb> 31 atoms in block 172
Block first atom: 58112
Blocpdb> 77 atoms in block 173
Block first atom: 58143
Blocpdb> 300 atoms in block 174
Block first atom: 58220
Blocpdb> 821 atoms in block 175
Block first atom: 58520
Blocpdb> 585 atoms in block 176
Block first atom: 59341
Blocpdb> 176 atoms in block 177
Block first atom: 59926
Blocpdb> 577 atoms in block 178
Block first atom: 60102
Blocpdb> 427 atoms in block 179
Block first atom: 60679
Blocpdb> 74 atoms in block 180
Block first atom: 61106
Blocpdb> 130 atoms in block 181
Block first atom: 61180
Blocpdb> 594 atoms in block 182
Block first atom: 61310
Blocpdb> 351 atoms in block 183
Block first atom: 61904
Blocpdb> 303 atoms in block 184
Block first atom: 62255
Blocpdb> 271 atoms in block 185
Block first atom: 62558
Blocpdb> 312 atoms in block 186
Block first atom: 62829
Blocpdb> 86 atoms in block 187
Block first atom: 63141
Blocpdb> 139 atoms in block 188
Block first atom: 63227
Blocpdb> 99 atoms in block 189
Block first atom: 63366
Blocpdb> 85 atoms in block 190
Block first atom: 63465
Blocpdb> 141 atoms in block 191
Block first atom: 63550
Blocpdb> 77 atoms in block 192
Block first atom: 63691
Blocpdb> 59 atoms in block 193
Block first atom: 63768
Blocpdb> 144 atoms in block 194
Block first atom: 63827
Blocpdb> 99 atoms in block 195
Block first atom: 63971
Blocpdb> 94 atoms in block 196
Block first atom: 64070
Blocpdb> 100 atoms in block 197
Block first atom: 64164
Blocpdb> 113 atoms in block 198
Block first atom: 64264
Blocpdb> 99 atoms in block 199
Block first atom: 64377
Blocpdb> 109 atoms in block 200
Block first atom: 64476
Blocpdb> 786 atoms in block 201
Block first atom: 64585
Blocpdb> 709 atoms in block 202
Block first atom: 65371
Blocpdb> 118 atoms in block 203
Block first atom: 66080
Blocpdb> 98 atoms in block 204
Block first atom: 66198
Blocpdb> 108 atoms in block 205
Block first atom: 66296
Blocpdb> 109 atoms in block 206
Block first atom: 66404
Blocpdb> 104 atoms in block 207
Block first atom: 66513
Blocpdb> 104 atoms in block 208
Block first atom: 66617
Blocpdb> 88 atoms in block 209
Block first atom: 66721
Blocpdb> 70 atoms in block 210
Block first atom: 66809
Blocpdb> 312 atoms in block 211
Block first atom: 66879
Blocpdb> 325 atoms in block 212
Block first atom: 67191
Blocpdb> 773 atoms in block 213
Block first atom: 67516
Blocpdb> 9 atoms in block 214
Block first atom: 68289
Blocpdb> 818 atoms in block 215
Block first atom: 68298
Blocpdb> 791 atoms in block 216
Block first atom: 69116
Blocpdb> 461 atoms in block 217
Block first atom: 69907
Blocpdb> 820 atoms in block 218
Block first atom: 70368
Blocpdb> 147 atoms in block 219
Block first atom: 71188
Blocpdb> 337 atoms in block 220
Block first atom: 71335
Blocpdb> 840 atoms in block 221
Block first atom: 71672
Blocpdb> 125 atoms in block 222
Block first atom: 72512
Blocpdb> 816 atoms in block 223
Block first atom: 72637
Blocpdb> 791 atoms in block 224
Block first atom: 73453
Blocpdb> 601 atoms in block 225
Block first atom: 74244
Blocpdb> 567 atoms in block 226
Block first atom: 74845
Blocpdb> 230 atoms in block 227
Block first atom: 75412
Blocpdb> 430 atoms in block 228
Block first atom: 75642
Blocpdb> 146 atoms in block 229
Block first atom: 76072
Blocpdb> 118 atoms in block 230
Block first atom: 76218
Blocpdb> 73 atoms in block 231
Block first atom: 76336
Blocpdb> 680 atoms in block 232
Block first atom: 76409
Blocpdb> 267 atoms in block 233
Block first atom: 77089
Blocpdb> 455 atoms in block 234
Block first atom: 77356
Blocpdb> 552 atoms in block 235
Block first atom: 77811
Blocpdb> 775 atoms in block 236
Block first atom: 78363
Blocpdb> 356 atoms in block 237
Block first atom: 79138
Blocpdb> 771 atoms in block 238
Block first atom: 79494
Blocpdb> 272 atoms in block 239
Block first atom: 80265
Blocpdb> 389 atoms in block 240
Block first atom: 80537
Blocpdb> 809 atoms in block 241
Block first atom: 80926
Blocpdb> 716 atoms in block 242
Block first atom: 81735
Blocpdb> 205 atoms in block 243
Block first atom: 82451
Blocpdb> 93 atoms in block 244
Block first atom: 82656
Blocpdb> 172 atoms in block 245
Block first atom: 82749
Blocpdb> 139 atoms in block 246
Block first atom: 82921
Blocpdb> 31 atoms in block 247
Block first atom: 83060
Blocpdb> 77 atoms in block 248
Block first atom: 83091
Blocpdb> 300 atoms in block 249
Block first atom: 83168
Blocpdb> 821 atoms in block 250
Block first atom: 83468
Blocpdb> 585 atoms in block 251
Block first atom: 84289
Blocpdb> 176 atoms in block 252
Block first atom: 84874
Blocpdb> 577 atoms in block 253
Block first atom: 85050
Blocpdb> 427 atoms in block 254
Block first atom: 85627
Blocpdb> 74 atoms in block 255
Block first atom: 86054
Blocpdb> 130 atoms in block 256
Block first atom: 86128
Blocpdb> 594 atoms in block 257
Block first atom: 86258
Blocpdb> 351 atoms in block 258
Block first atom: 86852
Blocpdb> 303 atoms in block 259
Block first atom: 87203
Blocpdb> 271 atoms in block 260
Block first atom: 87506
Blocpdb> 312 atoms in block 261
Block first atom: 87777
Blocpdb> 86 atoms in block 262
Block first atom: 88089
Blocpdb> 139 atoms in block 263
Block first atom: 88175
Blocpdb> 99 atoms in block 264
Block first atom: 88314
Blocpdb> 85 atoms in block 265
Block first atom: 88413
Blocpdb> 141 atoms in block 266
Block first atom: 88498
Blocpdb> 77 atoms in block 267
Block first atom: 88639
Blocpdb> 59 atoms in block 268
Block first atom: 88716
Blocpdb> 144 atoms in block 269
Block first atom: 88775
Blocpdb> 99 atoms in block 270
Block first atom: 88919
Blocpdb> 94 atoms in block 271
Block first atom: 89018
Blocpdb> 100 atoms in block 272
Block first atom: 89112
Blocpdb> 113 atoms in block 273
Block first atom: 89212
Blocpdb> 99 atoms in block 274
Block first atom: 89325
Blocpdb> 109 atoms in block 275
Block first atom: 89424
Blocpdb> 786 atoms in block 276
Block first atom: 89533
Blocpdb> 709 atoms in block 277
Block first atom: 90319
Blocpdb> 118 atoms in block 278
Block first atom: 91028
Blocpdb> 98 atoms in block 279
Block first atom: 91146
Blocpdb> 108 atoms in block 280
Block first atom: 91244
Blocpdb> 109 atoms in block 281
Block first atom: 91352
Blocpdb> 104 atoms in block 282
Block first atom: 91461
Blocpdb> 104 atoms in block 283
Block first atom: 91565
Blocpdb> 88 atoms in block 284
Block first atom: 91669
Blocpdb> 70 atoms in block 285
Block first atom: 91757
Blocpdb> 312 atoms in block 286
Block first atom: 91827
Blocpdb> 325 atoms in block 287
Block first atom: 92139
Blocpdb> 773 atoms in block 288
Block first atom: 92464
Blocpdb> 9 atoms in block 289
Block first atom: 93237
Blocpdb> 818 atoms in block 290
Block first atom: 93246
Blocpdb> 791 atoms in block 291
Block first atom: 94064
Blocpdb> 461 atoms in block 292
Block first atom: 94855
Blocpdb> 820 atoms in block 293
Block first atom: 95316
Blocpdb> 147 atoms in block 294
Block first atom: 96136
Blocpdb> 337 atoms in block 295
Block first atom: 96283
Blocpdb> 840 atoms in block 296
Block first atom: 96620
Blocpdb> 125 atoms in block 297
Block first atom: 97460
Blocpdb> 816 atoms in block 298
Block first atom: 97585
Blocpdb> 791 atoms in block 299
Block first atom: 98401
Blocpdb> 601 atoms in block 300
Block first atom: 99191
Blocpdb> 300 blocks.
Blocpdb> At most, 840 atoms in each of them.
Blocpdb> At least, 9 atoms in each of them.
Blocpdb> Normal end of Blocpdb.
Diagrtb> Memory allocation for Prepmat.
Diagrtb> Memory allocation for RTB.
Diagrtb> Memory allocation for Diagstd.
Diagrtb> Memory allocation for RTB_to_modes.
%Diagrtb-Er> IIWKMX up to: 12800801 Maximum allowed is LIWORK= 5000000
%Diagrtb-Er> IRWKMX up to: 760777921 Maximum allowed is LRWORK= 32000000
%Diagrtb-Er> Not enough memory allowed for working arrays. Sorry.
Lower the number of blocks, the sizes of the largest ones...
Or recompile DIAGRTB with larger WORKing arrays.
STDERR:
STOP *Working arrays allocation error*
real 0m0.442s
user 0m0.426s
sys 0m0.016s
If you find results from this site helpful for your research, please cite one of our papers:
elNémo
is maintained by Yves-Henri Sanejouand.
It was developed
by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: April 25th, 2023.
|
