*** 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 = 2607020506411885246.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 2607020506411885246.atom to be opened.
Openam> File opened: 2607020506411885246.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 = 2607020506411885246.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 19
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 2607020506411885246.atom to be opened.
Openam> file on opening on unit 11:
2607020506411885246.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> 19 residue(s) per block.
Blocpdb> 5308 residues.
Blocpdb> 126 atoms in block 1
Block first atom: 1
Blocpdb> 132 atoms in block 2
Block first atom: 127
Blocpdb> 131 atoms in block 3
Block first atom: 259
Blocpdb> 137 atoms in block 4
Block first atom: 390
Blocpdb> 148 atoms in block 5
Block first atom: 527
Blocpdb> 147 atoms in block 6
Block first atom: 675
Blocpdb> 140 atoms in block 7
Block first atom: 822
Blocpdb> 152 atoms in block 8
Block first atom: 962
Blocpdb> 149 atoms in block 9
Block first atom: 1114
Blocpdb> 147 atoms in block 10
Block first atom: 1263
Blocpdb> 146 atoms in block 11
Block first atom: 1410
Blocpdb> 142 atoms in block 12
Block first atom: 1556
Blocpdb> 149 atoms in block 13
Block first atom: 1698
Blocpdb> 147 atoms in block 14
Block first atom: 1847
Blocpdb> 154 atoms in block 15
Block first atom: 1994
Blocpdb> 145 atoms in block 16
Block first atom: 2148
Blocpdb> 146 atoms in block 17
Block first atom: 2293
Blocpdb> 149 atoms in block 18
Block first atom: 2439
Blocpdb> 154 atoms in block 19
Block first atom: 2588
Blocpdb> 131 atoms in block 20
Block first atom: 2742
Blocpdb> 141 atoms in block 21
Block first atom: 2873
Blocpdb> 151 atoms in block 22
Block first atom: 3014
Blocpdb> 131 atoms in block 23
Block first atom: 3165
Blocpdb> 153 atoms in block 24
Block first atom: 3296
Blocpdb> 132 atoms in block 25
Block first atom: 3449
Blocpdb> 131 atoms in block 26
Block first atom: 3581
Blocpdb> 139 atoms in block 27
Block first atom: 3712
Blocpdb> 142 atoms in block 28
Block first atom: 3851
Blocpdb> 146 atoms in block 29
Block first atom: 3993
Blocpdb> 133 atoms in block 30
Block first atom: 4139
Blocpdb> 145 atoms in block 31
Block first atom: 4272
Blocpdb> 135 atoms in block 32
Block first atom: 4417
Blocpdb> 139 atoms in block 33
Block first atom: 4552
Blocpdb> 144 atoms in block 34
Block first atom: 4691
Blocpdb> 141 atoms in block 35
Block first atom: 4835
Blocpdb> 141 atoms in block 36
Block first atom: 4976
Blocpdb> 137 atoms in block 37
Block first atom: 5117
Blocpdb> 147 atoms in block 38
Block first atom: 5254
Blocpdb> 166 atoms in block 39
Block first atom: 5401
Blocpdb> 159 atoms in block 40
Block first atom: 5567
Blocpdb> 138 atoms in block 41
Block first atom: 5726
Blocpdb> 143 atoms in block 42
Block first atom: 5864
Blocpdb> 124 atoms in block 43
Block first atom: 6007
Blocpdb> 156 atoms in block 44
Block first atom: 6131
Blocpdb> 167 atoms in block 45
Block first atom: 6287
Blocpdb> 154 atoms in block 46
Block first atom: 6454
Blocpdb> 155 atoms in block 47
Block first atom: 6608
Blocpdb> 161 atoms in block 48
Block first atom: 6763
Blocpdb> 144 atoms in block 49
Block first atom: 6924
Blocpdb> 166 atoms in block 50
Block first atom: 7068
Blocpdb> 136 atoms in block 51
Block first atom: 7234
Blocpdb> 140 atoms in block 52
Block first atom: 7370
Blocpdb> 156 atoms in block 53
Block first atom: 7510
Blocpdb> 159 atoms in block 54
Block first atom: 7666
Blocpdb> 148 atoms in block 55
Block first atom: 7825
Blocpdb> 149 atoms in block 56
Block first atom: 7973
Blocpdb> 166 atoms in block 57
Block first atom: 8122
Blocpdb> 159 atoms in block 58
Block first atom: 8288
Blocpdb> 146 atoms in block 59
Block first atom: 8447
Blocpdb> 168 atoms in block 60
Block first atom: 8593
Blocpdb> 151 atoms in block 61
Block first atom: 8761
Blocpdb> 158 atoms in block 62
Block first atom: 8912
Blocpdb> 159 atoms in block 63
Block first atom: 9070
Blocpdb> 157 atoms in block 64
Block first atom: 9229
Blocpdb> 144 atoms in block 65
Block first atom: 9386
Blocpdb> 140 atoms in block 66
Block first atom: 9530
Blocpdb> 155 atoms in block 67
Block first atom: 9670
Blocpdb> 140 atoms in block 68
Block first atom: 9825
Blocpdb> 125 atoms in block 69
Block first atom: 9965
Blocpdb> 121 atoms in block 70
Block first atom: 10090
Blocpdb> 126 atoms in block 71
Block first atom: 10211
Blocpdb> 132 atoms in block 72
Block first atom: 10337
Blocpdb> 131 atoms in block 73
Block first atom: 10469
Blocpdb> 137 atoms in block 74
Block first atom: 10600
Blocpdb> 148 atoms in block 75
Block first atom: 10737
Blocpdb> 147 atoms in block 76
Block first atom: 10885
Blocpdb> 140 atoms in block 77
Block first atom: 11032
Blocpdb> 152 atoms in block 78
Block first atom: 11172
Blocpdb> 149 atoms in block 79
Block first atom: 11324
Blocpdb> 147 atoms in block 80
Block first atom: 11473
Blocpdb> 146 atoms in block 81
Block first atom: 11620
Blocpdb> 142 atoms in block 82
Block first atom: 11766
Blocpdb> 149 atoms in block 83
Block first atom: 11908
Blocpdb> 147 atoms in block 84
Block first atom: 12057
Blocpdb> 154 atoms in block 85
Block first atom: 12204
Blocpdb> 145 atoms in block 86
Block first atom: 12358
Blocpdb> 146 atoms in block 87
Block first atom: 12503
Blocpdb> 149 atoms in block 88
Block first atom: 12649
Blocpdb> 154 atoms in block 89
Block first atom: 12798
Blocpdb> 131 atoms in block 90
Block first atom: 12952
Blocpdb> 141 atoms in block 91
Block first atom: 13083
Blocpdb> 151 atoms in block 92
Block first atom: 13224
Blocpdb> 131 atoms in block 93
Block first atom: 13375
Blocpdb> 153 atoms in block 94
Block first atom: 13506
Blocpdb> 132 atoms in block 95
Block first atom: 13659
Blocpdb> 131 atoms in block 96
Block first atom: 13791
Blocpdb> 139 atoms in block 97
Block first atom: 13922
Blocpdb> 142 atoms in block 98
Block first atom: 14061
Blocpdb> 146 atoms in block 99
Block first atom: 14203
Blocpdb> 133 atoms in block 100
Block first atom: 14349
Blocpdb> 145 atoms in block 101
Block first atom: 14482
Blocpdb> 135 atoms in block 102
Block first atom: 14627
Blocpdb> 139 atoms in block 103
Block first atom: 14762
Blocpdb> 144 atoms in block 104
Block first atom: 14901
Blocpdb> 141 atoms in block 105
Block first atom: 15045
Blocpdb> 141 atoms in block 106
Block first atom: 15186
Blocpdb> 137 atoms in block 107
Block first atom: 15327
Blocpdb> 147 atoms in block 108
Block first atom: 15464
Blocpdb> 166 atoms in block 109
Block first atom: 15611
Blocpdb> 159 atoms in block 110
Block first atom: 15777
Blocpdb> 138 atoms in block 111
Block first atom: 15936
Blocpdb> 143 atoms in block 112
Block first atom: 16074
Blocpdb> 124 atoms in block 113
Block first atom: 16217
Blocpdb> 156 atoms in block 114
Block first atom: 16341
Blocpdb> 167 atoms in block 115
Block first atom: 16497
Blocpdb> 154 atoms in block 116
Block first atom: 16664
Blocpdb> 155 atoms in block 117
Block first atom: 16818
Blocpdb> 161 atoms in block 118
Block first atom: 16973
Blocpdb> 144 atoms in block 119
Block first atom: 17134
Blocpdb> 166 atoms in block 120
Block first atom: 17278
Blocpdb> 136 atoms in block 121
Block first atom: 17444
Blocpdb> 140 atoms in block 122
Block first atom: 17580
Blocpdb> 156 atoms in block 123
Block first atom: 17720
Blocpdb> 159 atoms in block 124
Block first atom: 17876
Blocpdb> 148 atoms in block 125
Block first atom: 18035
Blocpdb> 149 atoms in block 126
Block first atom: 18183
Blocpdb> 166 atoms in block 127
Block first atom: 18332
Blocpdb> 159 atoms in block 128
Block first atom: 18498
Blocpdb> 146 atoms in block 129
Block first atom: 18657
Blocpdb> 168 atoms in block 130
Block first atom: 18803
Blocpdb> 151 atoms in block 131
Block first atom: 18971
Blocpdb> 158 atoms in block 132
Block first atom: 19122
Blocpdb> 159 atoms in block 133
Block first atom: 19280
Blocpdb> 157 atoms in block 134
Block first atom: 19439
Blocpdb> 144 atoms in block 135
Block first atom: 19596
Blocpdb> 140 atoms in block 136
Block first atom: 19740
Blocpdb> 155 atoms in block 137
Block first atom: 19880
Blocpdb> 140 atoms in block 138
Block first atom: 20035
Blocpdb> 125 atoms in block 139
Block first atom: 20175
Blocpdb> 121 atoms in block 140
Block first atom: 20300
Blocpdb> 126 atoms in block 141
Block first atom: 20421
Blocpdb> 132 atoms in block 142
Block first atom: 20547
Blocpdb> 131 atoms in block 143
Block first atom: 20679
Blocpdb> 137 atoms in block 144
Block first atom: 20810
Blocpdb> 148 atoms in block 145
Block first atom: 20947
Blocpdb> 147 atoms in block 146
Block first atom: 21095
Blocpdb> 140 atoms in block 147
Block first atom: 21242
Blocpdb> 152 atoms in block 148
Block first atom: 21382
Blocpdb> 149 atoms in block 149
Block first atom: 21534
Blocpdb> 147 atoms in block 150
Block first atom: 21683
Blocpdb> 146 atoms in block 151
Block first atom: 21830
Blocpdb> 142 atoms in block 152
Block first atom: 21976
Blocpdb> 149 atoms in block 153
Block first atom: 22118
Blocpdb> 147 atoms in block 154
Block first atom: 22267
Blocpdb> 154 atoms in block 155
Block first atom: 22414
Blocpdb> 145 atoms in block 156
Block first atom: 22568
Blocpdb> 146 atoms in block 157
Block first atom: 22713
Blocpdb> 149 atoms in block 158
Block first atom: 22859
Blocpdb> 154 atoms in block 159
Block first atom: 23008
Blocpdb> 131 atoms in block 160
Block first atom: 23162
Blocpdb> 141 atoms in block 161
Block first atom: 23293
Blocpdb> 151 atoms in block 162
Block first atom: 23434
Blocpdb> 131 atoms in block 163
Block first atom: 23585
Blocpdb> 153 atoms in block 164
Block first atom: 23716
Blocpdb> 132 atoms in block 165
Block first atom: 23869
Blocpdb> 131 atoms in block 166
Block first atom: 24001
Blocpdb> 139 atoms in block 167
Block first atom: 24132
Blocpdb> 142 atoms in block 168
Block first atom: 24271
Blocpdb> 146 atoms in block 169
Block first atom: 24413
Blocpdb> 133 atoms in block 170
Block first atom: 24559
Blocpdb> 145 atoms in block 171
Block first atom: 24692
Blocpdb> 135 atoms in block 172
Block first atom: 24837
Blocpdb> 139 atoms in block 173
Block first atom: 24972
Blocpdb> 144 atoms in block 174
Block first atom: 25111
Blocpdb> 141 atoms in block 175
Block first atom: 25255
Blocpdb> 141 atoms in block 176
Block first atom: 25396
Blocpdb> 137 atoms in block 177
Block first atom: 25537
Blocpdb> 147 atoms in block 178
Block first atom: 25674
Blocpdb> 166 atoms in block 179
Block first atom: 25821
Blocpdb> 159 atoms in block 180
Block first atom: 25987
Blocpdb> 138 atoms in block 181
Block first atom: 26146
Blocpdb> 143 atoms in block 182
Block first atom: 26284
Blocpdb> 124 atoms in block 183
Block first atom: 26427
Blocpdb> 156 atoms in block 184
Block first atom: 26551
Blocpdb> 167 atoms in block 185
Block first atom: 26707
Blocpdb> 154 atoms in block 186
Block first atom: 26874
Blocpdb> 155 atoms in block 187
Block first atom: 27028
Blocpdb> 161 atoms in block 188
Block first atom: 27183
Blocpdb> 144 atoms in block 189
Block first atom: 27344
Blocpdb> 166 atoms in block 190
Block first atom: 27488
Blocpdb> 136 atoms in block 191
Block first atom: 27654
Blocpdb> 140 atoms in block 192
Block first atom: 27790
Blocpdb> 156 atoms in block 193
Block first atom: 27930
Blocpdb> 159 atoms in block 194
Block first atom: 28086
Blocpdb> 148 atoms in block 195
Block first atom: 28245
Blocpdb> 149 atoms in block 196
Block first atom: 28393
Blocpdb> 166 atoms in block 197
Block first atom: 28542
Blocpdb> 159 atoms in block 198
Block first atom: 28708
Blocpdb> 146 atoms in block 199
Block first atom: 28867
Blocpdb> 168 atoms in block 200
Block first atom: 29013
Blocpdb> 151 atoms in block 201
Block first atom: 29181
Blocpdb> 158 atoms in block 202
Block first atom: 29332
Blocpdb> 159 atoms in block 203
Block first atom: 29490
Blocpdb> 157 atoms in block 204
Block first atom: 29649
Blocpdb> 144 atoms in block 205
Block first atom: 29806
Blocpdb> 140 atoms in block 206
Block first atom: 29950
Blocpdb> 155 atoms in block 207
Block first atom: 30090
Blocpdb> 140 atoms in block 208
Block first atom: 30245
Blocpdb> 125 atoms in block 209
Block first atom: 30385
Blocpdb> 121 atoms in block 210
Block first atom: 30510
Blocpdb> 126 atoms in block 211
Block first atom: 30631
Blocpdb> 132 atoms in block 212
Block first atom: 30757
Blocpdb> 131 atoms in block 213
Block first atom: 30889
Blocpdb> 137 atoms in block 214
Block first atom: 31020
Blocpdb> 148 atoms in block 215
Block first atom: 31157
Blocpdb> 147 atoms in block 216
Block first atom: 31305
Blocpdb> 140 atoms in block 217
Block first atom: 31452
Blocpdb> 152 atoms in block 218
Block first atom: 31592
Blocpdb> 149 atoms in block 219
Block first atom: 31744
Blocpdb> 147 atoms in block 220
Block first atom: 31893
Blocpdb> 146 atoms in block 221
Block first atom: 32040
Blocpdb> 142 atoms in block 222
Block first atom: 32186
Blocpdb> 149 atoms in block 223
Block first atom: 32328
Blocpdb> 147 atoms in block 224
Block first atom: 32477
Blocpdb> 154 atoms in block 225
Block first atom: 32624
Blocpdb> 145 atoms in block 226
Block first atom: 32778
Blocpdb> 146 atoms in block 227
Block first atom: 32923
Blocpdb> 149 atoms in block 228
Block first atom: 33069
Blocpdb> 154 atoms in block 229
Block first atom: 33218
Blocpdb> 131 atoms in block 230
Block first atom: 33372
Blocpdb> 141 atoms in block 231
Block first atom: 33503
Blocpdb> 151 atoms in block 232
Block first atom: 33644
Blocpdb> 131 atoms in block 233
Block first atom: 33795
Blocpdb> 153 atoms in block 234
Block first atom: 33926
Blocpdb> 132 atoms in block 235
Block first atom: 34079
Blocpdb> 131 atoms in block 236
Block first atom: 34211
Blocpdb> 139 atoms in block 237
Block first atom: 34342
Blocpdb> 142 atoms in block 238
Block first atom: 34481
Blocpdb> 146 atoms in block 239
Block first atom: 34623
Blocpdb> 133 atoms in block 240
Block first atom: 34769
Blocpdb> 145 atoms in block 241
Block first atom: 34902
Blocpdb> 135 atoms in block 242
Block first atom: 35047
Blocpdb> 139 atoms in block 243
Block first atom: 35182
Blocpdb> 144 atoms in block 244
Block first atom: 35321
Blocpdb> 141 atoms in block 245
Block first atom: 35465
Blocpdb> 141 atoms in block 246
Block first atom: 35606
Blocpdb> 137 atoms in block 247
Block first atom: 35747
Blocpdb> 147 atoms in block 248
Block first atom: 35884
Blocpdb> 166 atoms in block 249
Block first atom: 36031
Blocpdb> 159 atoms in block 250
Block first atom: 36197
Blocpdb> 138 atoms in block 251
Block first atom: 36356
Blocpdb> 143 atoms in block 252
Block first atom: 36494
Blocpdb> 124 atoms in block 253
Block first atom: 36637
Blocpdb> 156 atoms in block 254
Block first atom: 36761
Blocpdb> 167 atoms in block 255
Block first atom: 36917
Blocpdb> 154 atoms in block 256
Block first atom: 37084
Blocpdb> 155 atoms in block 257
Block first atom: 37238
Blocpdb> 161 atoms in block 258
Block first atom: 37393
Blocpdb> 144 atoms in block 259
Block first atom: 37554
Blocpdb> 166 atoms in block 260
Block first atom: 37698
Blocpdb> 136 atoms in block 261
Block first atom: 37864
Blocpdb> 140 atoms in block 262
Block first atom: 38000
Blocpdb> 156 atoms in block 263
Block first atom: 38140
Blocpdb> 159 atoms in block 264
Block first atom: 38296
Blocpdb> 148 atoms in block 265
Block first atom: 38455
Blocpdb> 149 atoms in block 266
Block first atom: 38603
Blocpdb> 166 atoms in block 267
Block first atom: 38752
Blocpdb> 159 atoms in block 268
Block first atom: 38918
Blocpdb> 146 atoms in block 269
Block first atom: 39077
Blocpdb> 168 atoms in block 270
Block first atom: 39223
Blocpdb> 151 atoms in block 271
Block first atom: 39391
Blocpdb> 158 atoms in block 272
Block first atom: 39542
Blocpdb> 159 atoms in block 273
Block first atom: 39700
Blocpdb> 157 atoms in block 274
Block first atom: 39859
Blocpdb> 144 atoms in block 275
Block first atom: 40016
Blocpdb> 140 atoms in block 276
Block first atom: 40160
Blocpdb> 155 atoms in block 277
Block first atom: 40300
Blocpdb> 140 atoms in block 278
Block first atom: 40455
Blocpdb> 125 atoms in block 279
Block first atom: 40595
Blocpdb> 121 atoms in block 280
Block first atom: 40719
Blocpdb> 280 blocks.
Blocpdb> At most, 168 atoms in each of them.
Blocpdb> At least, 121 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: 62004097 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 0m0.226s
user 0m0.205s
sys 0m0.020s
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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