*** nompcdar12 ***
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 = 2607020511031885842.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 2607020511031885842.atom to be opened.
Openam> File opened: 2607020511031885842.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 = 5308
First residue number = 1
Last residue number = 1327
Number of atoms found = 40840
Mean number per residue = 7.7
Pdbmat> Coordinate statistics:
= 242.320703 +/- 29.633453 From: 166.439000 To: 323.318000
= 243.037248 +/- 29.789911 From: 160.172000 To: 325.203000
= 279.313377 +/- 49.297280 From: 154.812000 To: 382.338000
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 1.3808 % Filled.
Pdbmat> 14680576 non-zero elements.
Pdbmat> 1604229 atom-atom interactions.
Pdbmat> Number per atom= 78.56 +/- 24.78
Maximum number = 132
Minimum number = 8
Pdbmat> Matrix trace = 3.208458E+07
Pdbmat> Larger element = 520.047
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 = 2607020511031885842.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 18
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 2607020511031885842.atom to be opened.
Openam> file on opening on unit 11:
2607020511031885842.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 40840 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 18 residue(s) per block.
Blocpdb> 5308 residues.
Blocpdb> 117 atoms in block 1
Block first atom: 1
Blocpdb> 125 atoms in block 2
Block first atom: 118
Blocpdb> 127 atoms in block 3
Block first atom: 243
Blocpdb> 134 atoms in block 4
Block first atom: 370
Blocpdb> 126 atoms in block 5
Block first atom: 504
Blocpdb> 152 atoms in block 6
Block first atom: 630
Blocpdb> 132 atoms in block 7
Block first atom: 782
Blocpdb> 132 atoms in block 8
Block first atom: 914
Blocpdb> 145 atoms in block 9
Block first atom: 1046
Blocpdb> 138 atoms in block 10
Block first atom: 1191
Blocpdb> 144 atoms in block 11
Block first atom: 1329
Blocpdb> 136 atoms in block 12
Block first atom: 1473
Blocpdb> 137 atoms in block 13
Block first atom: 1609
Blocpdb> 143 atoms in block 14
Block first atom: 1746
Blocpdb> 140 atoms in block 15
Block first atom: 1889
Blocpdb> 139 atoms in block 16
Block first atom: 2029
Blocpdb> 138 atoms in block 17
Block first atom: 2168
Blocpdb> 138 atoms in block 18
Block first atom: 2306
Blocpdb> 144 atoms in block 19
Block first atom: 2444
Blocpdb> 146 atoms in block 20
Block first atom: 2588
Blocpdb> 126 atoms in block 21
Block first atom: 2734
Blocpdb> 129 atoms in block 22
Block first atom: 2860
Blocpdb> 149 atoms in block 23
Block first atom: 2989
Blocpdb> 125 atoms in block 24
Block first atom: 3138
Blocpdb> 139 atoms in block 25
Block first atom: 3263
Blocpdb> 129 atoms in block 26
Block first atom: 3402
Blocpdb> 123 atoms in block 27
Block first atom: 3531
Blocpdb> 128 atoms in block 28
Block first atom: 3654
Blocpdb> 142 atoms in block 29
Block first atom: 3782
Blocpdb> 133 atoms in block 30
Block first atom: 3924
Blocpdb> 131 atoms in block 31
Block first atom: 4057
Blocpdb> 132 atoms in block 32
Block first atom: 4188
Blocpdb> 128 atoms in block 33
Block first atom: 4320
Blocpdb> 135 atoms in block 34
Block first atom: 4448
Blocpdb> 128 atoms in block 35
Block first atom: 4583
Blocpdb> 137 atoms in block 36
Block first atom: 4711
Blocpdb> 136 atoms in block 37
Block first atom: 4848
Blocpdb> 133 atoms in block 38
Block first atom: 4984
Blocpdb> 129 atoms in block 39
Block first atom: 5117
Blocpdb> 136 atoms in block 40
Block first atom: 5246
Blocpdb> 156 atoms in block 41
Block first atom: 5382
Blocpdb> 152 atoms in block 42
Block first atom: 5538
Blocpdb> 131 atoms in block 43
Block first atom: 5690
Blocpdb> 148 atoms in block 44
Block first atom: 5821
Blocpdb> 120 atoms in block 45
Block first atom: 5969
Blocpdb> 131 atoms in block 46
Block first atom: 6089
Blocpdb> 147 atoms in block 47
Block first atom: 6220
Blocpdb> 161 atoms in block 48
Block first atom: 6367
Blocpdb> 140 atoms in block 49
Block first atom: 6528
Blocpdb> 153 atoms in block 50
Block first atom: 6668
Blocpdb> 144 atoms in block 51
Block first atom: 6821
Blocpdb> 157 atoms in block 52
Block first atom: 6965
Blocpdb> 140 atoms in block 53
Block first atom: 7122
Blocpdb> 125 atoms in block 54
Block first atom: 7262
Blocpdb> 144 atoms in block 55
Block first atom: 7387
Blocpdb> 141 atoms in block 56
Block first atom: 7531
Blocpdb> 153 atoms in block 57
Block first atom: 7672
Blocpdb> 137 atoms in block 58
Block first atom: 7825
Blocpdb> 143 atoms in block 59
Block first atom: 7962
Blocpdb> 158 atoms in block 60
Block first atom: 8105
Blocpdb> 153 atoms in block 61
Block first atom: 8263
Blocpdb> 142 atoms in block 62
Block first atom: 8416
Blocpdb> 154 atoms in block 63
Block first atom: 8558
Blocpdb> 139 atoms in block 64
Block first atom: 8712
Blocpdb> 153 atoms in block 65
Block first atom: 8851
Blocpdb> 141 atoms in block 66
Block first atom: 9004
Blocpdb> 157 atoms in block 67
Block first atom: 9145
Blocpdb> 143 atoms in block 68
Block first atom: 9302
Blocpdb> 141 atoms in block 69
Block first atom: 9445
Blocpdb> 130 atoms in block 70
Block first atom: 9586
Blocpdb> 145 atoms in block 71
Block first atom: 9716
Blocpdb> 131 atoms in block 72
Block first atom: 9861
Blocpdb> 118 atoms in block 73
Block first atom: 9992
Blocpdb> 101 atoms in block 74
Block first atom: 10110
Blocpdb> 117 atoms in block 75
Block first atom: 10211
Blocpdb> 125 atoms in block 76
Block first atom: 10328
Blocpdb> 127 atoms in block 77
Block first atom: 10453
Blocpdb> 134 atoms in block 78
Block first atom: 10580
Blocpdb> 126 atoms in block 79
Block first atom: 10714
Blocpdb> 152 atoms in block 80
Block first atom: 10840
Blocpdb> 132 atoms in block 81
Block first atom: 10992
Blocpdb> 132 atoms in block 82
Block first atom: 11124
Blocpdb> 145 atoms in block 83
Block first atom: 11256
Blocpdb> 138 atoms in block 84
Block first atom: 11401
Blocpdb> 144 atoms in block 85
Block first atom: 11539
Blocpdb> 136 atoms in block 86
Block first atom: 11683
Blocpdb> 137 atoms in block 87
Block first atom: 11819
Blocpdb> 143 atoms in block 88
Block first atom: 11956
Blocpdb> 140 atoms in block 89
Block first atom: 12099
Blocpdb> 139 atoms in block 90
Block first atom: 12239
Blocpdb> 138 atoms in block 91
Block first atom: 12378
Blocpdb> 138 atoms in block 92
Block first atom: 12516
Blocpdb> 144 atoms in block 93
Block first atom: 12654
Blocpdb> 146 atoms in block 94
Block first atom: 12798
Blocpdb> 126 atoms in block 95
Block first atom: 12944
Blocpdb> 129 atoms in block 96
Block first atom: 13070
Blocpdb> 149 atoms in block 97
Block first atom: 13199
Blocpdb> 125 atoms in block 98
Block first atom: 13348
Blocpdb> 139 atoms in block 99
Block first atom: 13473
Blocpdb> 129 atoms in block 100
Block first atom: 13612
Blocpdb> 123 atoms in block 101
Block first atom: 13741
Blocpdb> 128 atoms in block 102
Block first atom: 13864
Blocpdb> 142 atoms in block 103
Block first atom: 13992
Blocpdb> 133 atoms in block 104
Block first atom: 14134
Blocpdb> 131 atoms in block 105
Block first atom: 14267
Blocpdb> 132 atoms in block 106
Block first atom: 14398
Blocpdb> 128 atoms in block 107
Block first atom: 14530
Blocpdb> 135 atoms in block 108
Block first atom: 14658
Blocpdb> 128 atoms in block 109
Block first atom: 14793
Blocpdb> 137 atoms in block 110
Block first atom: 14921
Blocpdb> 136 atoms in block 111
Block first atom: 15058
Blocpdb> 133 atoms in block 112
Block first atom: 15194
Blocpdb> 129 atoms in block 113
Block first atom: 15327
Blocpdb> 136 atoms in block 114
Block first atom: 15456
Blocpdb> 156 atoms in block 115
Block first atom: 15592
Blocpdb> 152 atoms in block 116
Block first atom: 15748
Blocpdb> 131 atoms in block 117
Block first atom: 15900
Blocpdb> 148 atoms in block 118
Block first atom: 16031
Blocpdb> 120 atoms in block 119
Block first atom: 16179
Blocpdb> 131 atoms in block 120
Block first atom: 16299
Blocpdb> 147 atoms in block 121
Block first atom: 16430
Blocpdb> 161 atoms in block 122
Block first atom: 16577
Blocpdb> 140 atoms in block 123
Block first atom: 16738
Blocpdb> 153 atoms in block 124
Block first atom: 16878
Blocpdb> 144 atoms in block 125
Block first atom: 17031
Blocpdb> 157 atoms in block 126
Block first atom: 17175
Blocpdb> 140 atoms in block 127
Block first atom: 17332
Blocpdb> 125 atoms in block 128
Block first atom: 17472
Blocpdb> 144 atoms in block 129
Block first atom: 17597
Blocpdb> 141 atoms in block 130
Block first atom: 17741
Blocpdb> 153 atoms in block 131
Block first atom: 17882
Blocpdb> 137 atoms in block 132
Block first atom: 18035
Blocpdb> 143 atoms in block 133
Block first atom: 18172
Blocpdb> 158 atoms in block 134
Block first atom: 18315
Blocpdb> 153 atoms in block 135
Block first atom: 18473
Blocpdb> 142 atoms in block 136
Block first atom: 18626
Blocpdb> 154 atoms in block 137
Block first atom: 18768
Blocpdb> 139 atoms in block 138
Block first atom: 18922
Blocpdb> 153 atoms in block 139
Block first atom: 19061
Blocpdb> 141 atoms in block 140
Block first atom: 19214
Blocpdb> 157 atoms in block 141
Block first atom: 19355
Blocpdb> 143 atoms in block 142
Block first atom: 19512
Blocpdb> 141 atoms in block 143
Block first atom: 19655
Blocpdb> 130 atoms in block 144
Block first atom: 19796
Blocpdb> 145 atoms in block 145
Block first atom: 19926
Blocpdb> 131 atoms in block 146
Block first atom: 20071
Blocpdb> 118 atoms in block 147
Block first atom: 20202
Blocpdb> 101 atoms in block 148
Block first atom: 20320
Blocpdb> 117 atoms in block 149
Block first atom: 20421
Blocpdb> 125 atoms in block 150
Block first atom: 20538
Blocpdb> 127 atoms in block 151
Block first atom: 20663
Blocpdb> 134 atoms in block 152
Block first atom: 20790
Blocpdb> 126 atoms in block 153
Block first atom: 20924
Blocpdb> 152 atoms in block 154
Block first atom: 21050
Blocpdb> 132 atoms in block 155
Block first atom: 21202
Blocpdb> 132 atoms in block 156
Block first atom: 21334
Blocpdb> 145 atoms in block 157
Block first atom: 21466
Blocpdb> 138 atoms in block 158
Block first atom: 21611
Blocpdb> 144 atoms in block 159
Block first atom: 21749
Blocpdb> 136 atoms in block 160
Block first atom: 21893
Blocpdb> 137 atoms in block 161
Block first atom: 22029
Blocpdb> 143 atoms in block 162
Block first atom: 22166
Blocpdb> 140 atoms in block 163
Block first atom: 22309
Blocpdb> 139 atoms in block 164
Block first atom: 22449
Blocpdb> 138 atoms in block 165
Block first atom: 22588
Blocpdb> 138 atoms in block 166
Block first atom: 22726
Blocpdb> 144 atoms in block 167
Block first atom: 22864
Blocpdb> 146 atoms in block 168
Block first atom: 23008
Blocpdb> 126 atoms in block 169
Block first atom: 23154
Blocpdb> 129 atoms in block 170
Block first atom: 23280
Blocpdb> 149 atoms in block 171
Block first atom: 23409
Blocpdb> 125 atoms in block 172
Block first atom: 23558
Blocpdb> 139 atoms in block 173
Block first atom: 23683
Blocpdb> 129 atoms in block 174
Block first atom: 23822
Blocpdb> 123 atoms in block 175
Block first atom: 23951
Blocpdb> 128 atoms in block 176
Block first atom: 24074
Blocpdb> 142 atoms in block 177
Block first atom: 24202
Blocpdb> 133 atoms in block 178
Block first atom: 24344
Blocpdb> 131 atoms in block 179
Block first atom: 24477
Blocpdb> 132 atoms in block 180
Block first atom: 24608
Blocpdb> 128 atoms in block 181
Block first atom: 24740
Blocpdb> 135 atoms in block 182
Block first atom: 24868
Blocpdb> 128 atoms in block 183
Block first atom: 25003
Blocpdb> 137 atoms in block 184
Block first atom: 25131
Blocpdb> 136 atoms in block 185
Block first atom: 25268
Blocpdb> 133 atoms in block 186
Block first atom: 25404
Blocpdb> 129 atoms in block 187
Block first atom: 25537
Blocpdb> 136 atoms in block 188
Block first atom: 25666
Blocpdb> 156 atoms in block 189
Block first atom: 25802
Blocpdb> 152 atoms in block 190
Block first atom: 25958
Blocpdb> 131 atoms in block 191
Block first atom: 26110
Blocpdb> 148 atoms in block 192
Block first atom: 26241
Blocpdb> 120 atoms in block 193
Block first atom: 26389
Blocpdb> 131 atoms in block 194
Block first atom: 26509
Blocpdb> 147 atoms in block 195
Block first atom: 26640
Blocpdb> 161 atoms in block 196
Block first atom: 26787
Blocpdb> 140 atoms in block 197
Block first atom: 26948
Blocpdb> 153 atoms in block 198
Block first atom: 27088
Blocpdb> 144 atoms in block 199
Block first atom: 27241
Blocpdb> 157 atoms in block 200
Block first atom: 27385
Blocpdb> 140 atoms in block 201
Block first atom: 27542
Blocpdb> 125 atoms in block 202
Block first atom: 27682
Blocpdb> 144 atoms in block 203
Block first atom: 27807
Blocpdb> 141 atoms in block 204
Block first atom: 27951
Blocpdb> 153 atoms in block 205
Block first atom: 28092
Blocpdb> 137 atoms in block 206
Block first atom: 28245
Blocpdb> 143 atoms in block 207
Block first atom: 28382
Blocpdb> 158 atoms in block 208
Block first atom: 28525
Blocpdb> 153 atoms in block 209
Block first atom: 28683
Blocpdb> 142 atoms in block 210
Block first atom: 28836
Blocpdb> 154 atoms in block 211
Block first atom: 28978
Blocpdb> 139 atoms in block 212
Block first atom: 29132
Blocpdb> 153 atoms in block 213
Block first atom: 29271
Blocpdb> 141 atoms in block 214
Block first atom: 29424
Blocpdb> 157 atoms in block 215
Block first atom: 29565
Blocpdb> 143 atoms in block 216
Block first atom: 29722
Blocpdb> 141 atoms in block 217
Block first atom: 29865
Blocpdb> 130 atoms in block 218
Block first atom: 30006
Blocpdb> 145 atoms in block 219
Block first atom: 30136
Blocpdb> 131 atoms in block 220
Block first atom: 30281
Blocpdb> 118 atoms in block 221
Block first atom: 30412
Blocpdb> 101 atoms in block 222
Block first atom: 30530
Blocpdb> 117 atoms in block 223
Block first atom: 30631
Blocpdb> 125 atoms in block 224
Block first atom: 30748
Blocpdb> 127 atoms in block 225
Block first atom: 30873
Blocpdb> 134 atoms in block 226
Block first atom: 31000
Blocpdb> 126 atoms in block 227
Block first atom: 31134
Blocpdb> 152 atoms in block 228
Block first atom: 31260
Blocpdb> 132 atoms in block 229
Block first atom: 31412
Blocpdb> 132 atoms in block 230
Block first atom: 31544
Blocpdb> 145 atoms in block 231
Block first atom: 31676
Blocpdb> 138 atoms in block 232
Block first atom: 31821
Blocpdb> 144 atoms in block 233
Block first atom: 31959
Blocpdb> 136 atoms in block 234
Block first atom: 32103
Blocpdb> 137 atoms in block 235
Block first atom: 32239
Blocpdb> 143 atoms in block 236
Block first atom: 32376
Blocpdb> 140 atoms in block 237
Block first atom: 32519
Blocpdb> 139 atoms in block 238
Block first atom: 32659
Blocpdb> 138 atoms in block 239
Block first atom: 32798
Blocpdb> 138 atoms in block 240
Block first atom: 32936
Blocpdb> 144 atoms in block 241
Block first atom: 33074
Blocpdb> 146 atoms in block 242
Block first atom: 33218
Blocpdb> 126 atoms in block 243
Block first atom: 33364
Blocpdb> 129 atoms in block 244
Block first atom: 33490
Blocpdb> 149 atoms in block 245
Block first atom: 33619
Blocpdb> 125 atoms in block 246
Block first atom: 33768
Blocpdb> 139 atoms in block 247
Block first atom: 33893
Blocpdb> 129 atoms in block 248
Block first atom: 34032
Blocpdb> 123 atoms in block 249
Block first atom: 34161
Blocpdb> 128 atoms in block 250
Block first atom: 34284
Blocpdb> 142 atoms in block 251
Block first atom: 34412
Blocpdb> 133 atoms in block 252
Block first atom: 34554
Blocpdb> 131 atoms in block 253
Block first atom: 34687
Blocpdb> 132 atoms in block 254
Block first atom: 34818
Blocpdb> 128 atoms in block 255
Block first atom: 34950
Blocpdb> 135 atoms in block 256
Block first atom: 35078
Blocpdb> 128 atoms in block 257
Block first atom: 35213
Blocpdb> 137 atoms in block 258
Block first atom: 35341
Blocpdb> 136 atoms in block 259
Block first atom: 35478
Blocpdb> 133 atoms in block 260
Block first atom: 35614
Blocpdb> 129 atoms in block 261
Block first atom: 35747
Blocpdb> 136 atoms in block 262
Block first atom: 35876
Blocpdb> 156 atoms in block 263
Block first atom: 36012
Blocpdb> 152 atoms in block 264
Block first atom: 36168
Blocpdb> 131 atoms in block 265
Block first atom: 36320
Blocpdb> 148 atoms in block 266
Block first atom: 36451
Blocpdb> 120 atoms in block 267
Block first atom: 36599
Blocpdb> 131 atoms in block 268
Block first atom: 36719
Blocpdb> 147 atoms in block 269
Block first atom: 36850
Blocpdb> 161 atoms in block 270
Block first atom: 36997
Blocpdb> 140 atoms in block 271
Block first atom: 37158
Blocpdb> 153 atoms in block 272
Block first atom: 37298
Blocpdb> 144 atoms in block 273
Block first atom: 37451
Blocpdb> 157 atoms in block 274
Block first atom: 37595
Blocpdb> 140 atoms in block 275
Block first atom: 37752
Blocpdb> 125 atoms in block 276
Block first atom: 37892
Blocpdb> 144 atoms in block 277
Block first atom: 38017
Blocpdb> 141 atoms in block 278
Block first atom: 38161
Blocpdb> 153 atoms in block 279
Block first atom: 38302
Blocpdb> 137 atoms in block 280
Block first atom: 38455
Blocpdb> 143 atoms in block 281
Block first atom: 38592
Blocpdb> 158 atoms in block 282
Block first atom: 38735
Blocpdb> 153 atoms in block 283
Block first atom: 38893
Blocpdb> 142 atoms in block 284
Block first atom: 39046
Blocpdb> 154 atoms in block 285
Block first atom: 39188
Blocpdb> 139 atoms in block 286
Block first atom: 39342
Blocpdb> 153 atoms in block 287
Block first atom: 39481
Blocpdb> 141 atoms in block 288
Block first atom: 39634
Blocpdb> 157 atoms in block 289
Block first atom: 39775
Blocpdb> 143 atoms in block 290
Block first atom: 39932
Blocpdb> 141 atoms in block 291
Block first atom: 40075
Blocpdb> 130 atoms in block 292
Block first atom: 40216
Blocpdb> 145 atoms in block 293
Block first atom: 40346
Blocpdb> 131 atoms in block 294
Block first atom: 40491
Blocpdb> 118 atoms in block 295
Block first atom: 40622
Blocpdb> 101 atoms in block 296
Block first atom: 40739
Blocpdb> 296 blocks.
Blocpdb> At most, 161 atoms in each of them.
Blocpdb> At least, 101 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> IRWKMX up to: 59410450 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 0m0.162s
user 0m0.154s
sys 0m0.009s
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).
Between 2015 and 2025, it was hosted by US2B (Nantes).
Last modification: april 24th, 2026.
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