*** 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 = 2607020500381884409.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 2607020500381884409.atom to be opened.
Openam> File opened: 2607020500381884409.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 = 2607020500381884409.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 20
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 2607020500381884409.atom to be opened.
Openam> file on opening on unit 11:
2607020500381884409.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> 20 residue(s) per block.
Blocpdb> 5308 residues.
Blocpdb> 133 atoms in block 1
Block first atom: 1
Blocpdb> 139 atoms in block 2
Block first atom: 134
Blocpdb> 143 atoms in block 3
Block first atom: 273
Blocpdb> 142 atoms in block 4
Block first atom: 416
Blocpdb> 157 atoms in block 5
Block first atom: 558
Blocpdb> 149 atoms in block 6
Block first atom: 715
Blocpdb> 151 atoms in block 7
Block first atom: 864
Blocpdb> 162 atoms in block 8
Block first atom: 1015
Blocpdb> 152 atoms in block 9
Block first atom: 1177
Blocpdb> 163 atoms in block 10
Block first atom: 1329
Blocpdb> 149 atoms in block 11
Block first atom: 1492
Blocpdb> 153 atoms in block 12
Block first atom: 1641
Blocpdb> 156 atoms in block 13
Block first atom: 1794
Blocpdb> 157 atoms in block 14
Block first atom: 1950
Blocpdb> 155 atoms in block 15
Block first atom: 2107
Blocpdb> 155 atoms in block 16
Block first atom: 2262
Blocpdb> 154 atoms in block 17
Block first atom: 2417
Blocpdb> 163 atoms in block 18
Block first atom: 2571
Blocpdb> 139 atoms in block 19
Block first atom: 2734
Blocpdb> 153 atoms in block 20
Block first atom: 2873
Blocpdb> 154 atoms in block 21
Block first atom: 3026
Blocpdb> 142 atoms in block 22
Block first atom: 3180
Blocpdb> 154 atoms in block 23
Block first atom: 3322
Blocpdb> 141 atoms in block 24
Block first atom: 3476
Blocpdb> 139 atoms in block 25
Block first atom: 3617
Blocpdb> 150 atoms in block 26
Block first atom: 3756
Blocpdb> 151 atoms in block 27
Block first atom: 3906
Blocpdb> 146 atoms in block 28
Block first atom: 4057
Blocpdb> 144 atoms in block 29
Block first atom: 4203
Blocpdb> 142 atoms in block 30
Block first atom: 4347
Blocpdb> 150 atoms in block 31
Block first atom: 4489
Blocpdb> 154 atoms in block 32
Block first atom: 4639
Blocpdb> 148 atoms in block 33
Block first atom: 4793
Blocpdb> 148 atoms in block 34
Block first atom: 4941
Blocpdb> 141 atoms in block 35
Block first atom: 5089
Blocpdb> 152 atoms in block 36
Block first atom: 5230
Blocpdb> 178 atoms in block 37
Block first atom: 5382
Blocpdb> 166 atoms in block 38
Block first atom: 5560
Blocpdb> 146 atoms in block 39
Block first atom: 5726
Blocpdb> 149 atoms in block 40
Block first atom: 5872
Blocpdb> 135 atoms in block 41
Block first atom: 6021
Blocpdb> 167 atoms in block 42
Block first atom: 6156
Blocpdb> 166 atoms in block 43
Block first atom: 6323
Blocpdb> 167 atoms in block 44
Block first atom: 6489
Blocpdb> 165 atoms in block 45
Block first atom: 6656
Blocpdb> 158 atoms in block 46
Block first atom: 6821
Blocpdb> 171 atoms in block 47
Block first atom: 6979
Blocpdb> 151 atoms in block 48
Block first atom: 7150
Blocpdb> 136 atoms in block 49
Block first atom: 7301
Blocpdb> 179 atoms in block 50
Block first atom: 7437
Blocpdb> 160 atoms in block 51
Block first atom: 7616
Blocpdb> 158 atoms in block 52
Block first atom: 7776
Blocpdb> 158 atoms in block 53
Block first atom: 7934
Blocpdb> 171 atoms in block 54
Block first atom: 8092
Blocpdb> 171 atoms in block 55
Block first atom: 8263
Blocpdb> 150 atoms in block 56
Block first atom: 8434
Blocpdb> 177 atoms in block 57
Block first atom: 8584
Blocpdb> 160 atoms in block 58
Block first atom: 8761
Blocpdb> 170 atoms in block 59
Block first atom: 8921
Blocpdb> 162 atoms in block 60
Block first atom: 9091
Blocpdb> 161 atoms in block 61
Block first atom: 9253
Blocpdb> 159 atoms in block 62
Block first atom: 9414
Blocpdb> 143 atoms in block 63
Block first atom: 9573
Blocpdb> 168 atoms in block 64
Block first atom: 9716
Blocpdb> 133 atoms in block 65
Block first atom: 9884
Blocpdb> 142 atoms in block 66
Block first atom: 10017
Blocpdb> 52 atoms in block 67
Block first atom: 10159
Blocpdb> 133 atoms in block 68
Block first atom: 10211
Blocpdb> 139 atoms in block 69
Block first atom: 10344
Blocpdb> 143 atoms in block 70
Block first atom: 10483
Blocpdb> 142 atoms in block 71
Block first atom: 10626
Blocpdb> 157 atoms in block 72
Block first atom: 10768
Blocpdb> 149 atoms in block 73
Block first atom: 10925
Blocpdb> 151 atoms in block 74
Block first atom: 11074
Blocpdb> 162 atoms in block 75
Block first atom: 11225
Blocpdb> 152 atoms in block 76
Block first atom: 11387
Blocpdb> 163 atoms in block 77
Block first atom: 11539
Blocpdb> 149 atoms in block 78
Block first atom: 11702
Blocpdb> 153 atoms in block 79
Block first atom: 11851
Blocpdb> 156 atoms in block 80
Block first atom: 12004
Blocpdb> 157 atoms in block 81
Block first atom: 12160
Blocpdb> 155 atoms in block 82
Block first atom: 12317
Blocpdb> 155 atoms in block 83
Block first atom: 12472
Blocpdb> 154 atoms in block 84
Block first atom: 12627
Blocpdb> 163 atoms in block 85
Block first atom: 12781
Blocpdb> 139 atoms in block 86
Block first atom: 12944
Blocpdb> 153 atoms in block 87
Block first atom: 13083
Blocpdb> 154 atoms in block 88
Block first atom: 13236
Blocpdb> 142 atoms in block 89
Block first atom: 13390
Blocpdb> 154 atoms in block 90
Block first atom: 13532
Blocpdb> 141 atoms in block 91
Block first atom: 13686
Blocpdb> 139 atoms in block 92
Block first atom: 13827
Blocpdb> 150 atoms in block 93
Block first atom: 13966
Blocpdb> 151 atoms in block 94
Block first atom: 14116
Blocpdb> 146 atoms in block 95
Block first atom: 14267
Blocpdb> 144 atoms in block 96
Block first atom: 14413
Blocpdb> 142 atoms in block 97
Block first atom: 14557
Blocpdb> 150 atoms in block 98
Block first atom: 14699
Blocpdb> 154 atoms in block 99
Block first atom: 14849
Blocpdb> 148 atoms in block 100
Block first atom: 15003
Blocpdb> 148 atoms in block 101
Block first atom: 15151
Blocpdb> 141 atoms in block 102
Block first atom: 15299
Blocpdb> 152 atoms in block 103
Block first atom: 15440
Blocpdb> 178 atoms in block 104
Block first atom: 15592
Blocpdb> 166 atoms in block 105
Block first atom: 15770
Blocpdb> 146 atoms in block 106
Block first atom: 15936
Blocpdb> 149 atoms in block 107
Block first atom: 16082
Blocpdb> 135 atoms in block 108
Block first atom: 16231
Blocpdb> 167 atoms in block 109
Block first atom: 16366
Blocpdb> 166 atoms in block 110
Block first atom: 16533
Blocpdb> 167 atoms in block 111
Block first atom: 16699
Blocpdb> 165 atoms in block 112
Block first atom: 16866
Blocpdb> 158 atoms in block 113
Block first atom: 17031
Blocpdb> 171 atoms in block 114
Block first atom: 17189
Blocpdb> 151 atoms in block 115
Block first atom: 17360
Blocpdb> 136 atoms in block 116
Block first atom: 17511
Blocpdb> 179 atoms in block 117
Block first atom: 17647
Blocpdb> 160 atoms in block 118
Block first atom: 17826
Blocpdb> 158 atoms in block 119
Block first atom: 17986
Blocpdb> 158 atoms in block 120
Block first atom: 18144
Blocpdb> 171 atoms in block 121
Block first atom: 18302
Blocpdb> 171 atoms in block 122
Block first atom: 18473
Blocpdb> 150 atoms in block 123
Block first atom: 18644
Blocpdb> 177 atoms in block 124
Block first atom: 18794
Blocpdb> 160 atoms in block 125
Block first atom: 18971
Blocpdb> 170 atoms in block 126
Block first atom: 19131
Blocpdb> 162 atoms in block 127
Block first atom: 19301
Blocpdb> 161 atoms in block 128
Block first atom: 19463
Blocpdb> 159 atoms in block 129
Block first atom: 19624
Blocpdb> 143 atoms in block 130
Block first atom: 19783
Blocpdb> 168 atoms in block 131
Block first atom: 19926
Blocpdb> 133 atoms in block 132
Block first atom: 20094
Blocpdb> 142 atoms in block 133
Block first atom: 20227
Blocpdb> 52 atoms in block 134
Block first atom: 20369
Blocpdb> 133 atoms in block 135
Block first atom: 20421
Blocpdb> 139 atoms in block 136
Block first atom: 20554
Blocpdb> 143 atoms in block 137
Block first atom: 20693
Blocpdb> 142 atoms in block 138
Block first atom: 20836
Blocpdb> 157 atoms in block 139
Block first atom: 20978
Blocpdb> 149 atoms in block 140
Block first atom: 21135
Blocpdb> 151 atoms in block 141
Block first atom: 21284
Blocpdb> 162 atoms in block 142
Block first atom: 21435
Blocpdb> 152 atoms in block 143
Block first atom: 21597
Blocpdb> 163 atoms in block 144
Block first atom: 21749
Blocpdb> 149 atoms in block 145
Block first atom: 21912
Blocpdb> 153 atoms in block 146
Block first atom: 22061
Blocpdb> 156 atoms in block 147
Block first atom: 22214
Blocpdb> 157 atoms in block 148
Block first atom: 22370
Blocpdb> 155 atoms in block 149
Block first atom: 22527
Blocpdb> 155 atoms in block 150
Block first atom: 22682
Blocpdb> 154 atoms in block 151
Block first atom: 22837
Blocpdb> 163 atoms in block 152
Block first atom: 22991
Blocpdb> 139 atoms in block 153
Block first atom: 23154
Blocpdb> 153 atoms in block 154
Block first atom: 23293
Blocpdb> 154 atoms in block 155
Block first atom: 23446
Blocpdb> 142 atoms in block 156
Block first atom: 23600
Blocpdb> 154 atoms in block 157
Block first atom: 23742
Blocpdb> 141 atoms in block 158
Block first atom: 23896
Blocpdb> 139 atoms in block 159
Block first atom: 24037
Blocpdb> 150 atoms in block 160
Block first atom: 24176
Blocpdb> 151 atoms in block 161
Block first atom: 24326
Blocpdb> 146 atoms in block 162
Block first atom: 24477
Blocpdb> 144 atoms in block 163
Block first atom: 24623
Blocpdb> 142 atoms in block 164
Block first atom: 24767
Blocpdb> 150 atoms in block 165
Block first atom: 24909
Blocpdb> 154 atoms in block 166
Block first atom: 25059
Blocpdb> 148 atoms in block 167
Block first atom: 25213
Blocpdb> 148 atoms in block 168
Block first atom: 25361
Blocpdb> 141 atoms in block 169
Block first atom: 25509
Blocpdb> 152 atoms in block 170
Block first atom: 25650
Blocpdb> 178 atoms in block 171
Block first atom: 25802
Blocpdb> 166 atoms in block 172
Block first atom: 25980
Blocpdb> 146 atoms in block 173
Block first atom: 26146
Blocpdb> 149 atoms in block 174
Block first atom: 26292
Blocpdb> 135 atoms in block 175
Block first atom: 26441
Blocpdb> 167 atoms in block 176
Block first atom: 26576
Blocpdb> 166 atoms in block 177
Block first atom: 26743
Blocpdb> 167 atoms in block 178
Block first atom: 26909
Blocpdb> 165 atoms in block 179
Block first atom: 27076
Blocpdb> 158 atoms in block 180
Block first atom: 27241
Blocpdb> 171 atoms in block 181
Block first atom: 27399
Blocpdb> 151 atoms in block 182
Block first atom: 27570
Blocpdb> 136 atoms in block 183
Block first atom: 27721
Blocpdb> 179 atoms in block 184
Block first atom: 27857
Blocpdb> 160 atoms in block 185
Block first atom: 28036
Blocpdb> 158 atoms in block 186
Block first atom: 28196
Blocpdb> 158 atoms in block 187
Block first atom: 28354
Blocpdb> 171 atoms in block 188
Block first atom: 28512
Blocpdb> 171 atoms in block 189
Block first atom: 28683
Blocpdb> 150 atoms in block 190
Block first atom: 28854
Blocpdb> 177 atoms in block 191
Block first atom: 29004
Blocpdb> 160 atoms in block 192
Block first atom: 29181
Blocpdb> 170 atoms in block 193
Block first atom: 29341
Blocpdb> 162 atoms in block 194
Block first atom: 29511
Blocpdb> 161 atoms in block 195
Block first atom: 29673
Blocpdb> 159 atoms in block 196
Block first atom: 29834
Blocpdb> 143 atoms in block 197
Block first atom: 29993
Blocpdb> 168 atoms in block 198
Block first atom: 30136
Blocpdb> 133 atoms in block 199
Block first atom: 30304
Blocpdb> 142 atoms in block 200
Block first atom: 30437
Blocpdb> 52 atoms in block 201
Block first atom: 30579
Blocpdb> 133 atoms in block 202
Block first atom: 30631
Blocpdb> 139 atoms in block 203
Block first atom: 30764
Blocpdb> 143 atoms in block 204
Block first atom: 30903
Blocpdb> 142 atoms in block 205
Block first atom: 31046
Blocpdb> 157 atoms in block 206
Block first atom: 31188
Blocpdb> 149 atoms in block 207
Block first atom: 31345
Blocpdb> 151 atoms in block 208
Block first atom: 31494
Blocpdb> 162 atoms in block 209
Block first atom: 31645
Blocpdb> 152 atoms in block 210
Block first atom: 31807
Blocpdb> 163 atoms in block 211
Block first atom: 31959
Blocpdb> 149 atoms in block 212
Block first atom: 32122
Blocpdb> 153 atoms in block 213
Block first atom: 32271
Blocpdb> 156 atoms in block 214
Block first atom: 32424
Blocpdb> 157 atoms in block 215
Block first atom: 32580
Blocpdb> 155 atoms in block 216
Block first atom: 32737
Blocpdb> 155 atoms in block 217
Block first atom: 32892
Blocpdb> 154 atoms in block 218
Block first atom: 33047
Blocpdb> 163 atoms in block 219
Block first atom: 33201
Blocpdb> 139 atoms in block 220
Block first atom: 33364
Blocpdb> 153 atoms in block 221
Block first atom: 33503
Blocpdb> 154 atoms in block 222
Block first atom: 33656
Blocpdb> 142 atoms in block 223
Block first atom: 33810
Blocpdb> 154 atoms in block 224
Block first atom: 33952
Blocpdb> 141 atoms in block 225
Block first atom: 34106
Blocpdb> 139 atoms in block 226
Block first atom: 34247
Blocpdb> 150 atoms in block 227
Block first atom: 34386
Blocpdb> 151 atoms in block 228
Block first atom: 34536
Blocpdb> 146 atoms in block 229
Block first atom: 34687
Blocpdb> 144 atoms in block 230
Block first atom: 34833
Blocpdb> 142 atoms in block 231
Block first atom: 34977
Blocpdb> 150 atoms in block 232
Block first atom: 35119
Blocpdb> 154 atoms in block 233
Block first atom: 35269
Blocpdb> 148 atoms in block 234
Block first atom: 35423
Blocpdb> 148 atoms in block 235
Block first atom: 35571
Blocpdb> 141 atoms in block 236
Block first atom: 35719
Blocpdb> 152 atoms in block 237
Block first atom: 35860
Blocpdb> 178 atoms in block 238
Block first atom: 36012
Blocpdb> 166 atoms in block 239
Block first atom: 36190
Blocpdb> 146 atoms in block 240
Block first atom: 36356
Blocpdb> 149 atoms in block 241
Block first atom: 36502
Blocpdb> 135 atoms in block 242
Block first atom: 36651
Blocpdb> 167 atoms in block 243
Block first atom: 36786
Blocpdb> 166 atoms in block 244
Block first atom: 36953
Blocpdb> 167 atoms in block 245
Block first atom: 37119
Blocpdb> 165 atoms in block 246
Block first atom: 37286
Blocpdb> 158 atoms in block 247
Block first atom: 37451
Blocpdb> 171 atoms in block 248
Block first atom: 37609
Blocpdb> 151 atoms in block 249
Block first atom: 37780
Blocpdb> 136 atoms in block 250
Block first atom: 37931
Blocpdb> 179 atoms in block 251
Block first atom: 38067
Blocpdb> 160 atoms in block 252
Block first atom: 38246
Blocpdb> 158 atoms in block 253
Block first atom: 38406
Blocpdb> 158 atoms in block 254
Block first atom: 38564
Blocpdb> 171 atoms in block 255
Block first atom: 38722
Blocpdb> 171 atoms in block 256
Block first atom: 38893
Blocpdb> 150 atoms in block 257
Block first atom: 39064
Blocpdb> 177 atoms in block 258
Block first atom: 39214
Blocpdb> 160 atoms in block 259
Block first atom: 39391
Blocpdb> 170 atoms in block 260
Block first atom: 39551
Blocpdb> 162 atoms in block 261
Block first atom: 39721
Blocpdb> 161 atoms in block 262
Block first atom: 39883
Blocpdb> 159 atoms in block 263
Block first atom: 40044
Blocpdb> 143 atoms in block 264
Block first atom: 40203
Blocpdb> 168 atoms in block 265
Block first atom: 40346
Blocpdb> 133 atoms in block 266
Block first atom: 40514
Blocpdb> 142 atoms in block 267
Block first atom: 40647
Blocpdb> 52 atoms in block 268
Block first atom: 40788
Blocpdb> 268 blocks.
Blocpdb> At most, 179 atoms in each of them.
Blocpdb> At least, 52 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: 66081610 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 0m0.168s
user 0m0.160s
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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