*** Test1 ***
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 = 2604222227431516503.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 2604222227431516503.atom to be opened.
Openam> File opened: 2604222227431516503.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 = 4355
First residue number = 1
Last residue number = 339
Number of atoms found = 33623
Mean number per residue = 7.7
Pdbmat> Coordinate statistics:
= 0.714338 +/- 26.336628 From: -58.553000 To: 61.317000
= 0.713629 +/- 25.547517 From: -59.765000 To: 63.345000
= -0.049776 +/- 28.175882 From: -68.061000 To: 65.391000
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 1.7030 % Filled.
Pdbmat> 13493581 non-zero elements.
Pdbmat> 1477102 atom-atom interactions.
Pdbmat> Number per atom= 87.86 +/- 19.19
Maximum number = 133
Minimum number = 12
Pdbmat> Matrix trace = 2.954204E+07
Pdbmat> Larger element = 551.670
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
4355 non-zero elements, NRBL set to 22
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 = 2604222227431516503.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 22
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 2604222227431516503.atom to be opened.
Openam> file on opening on unit 11:
2604222227431516503.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 33623 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 22 residue(s) per block.
Blocpdb> 4355 residues.
Blocpdb> 168 atoms in block 1
Block first atom: 1
Blocpdb> 166 atoms in block 2
Block first atom: 169
Blocpdb> 183 atoms in block 3
Block first atom: 335
Blocpdb> 165 atoms in block 4
Block first atom: 518
Blocpdb> 166 atoms in block 5
Block first atom: 683
Blocpdb> 180 atoms in block 6
Block first atom: 849
Blocpdb> 165 atoms in block 7
Block first atom: 1029
Blocpdb> 180 atoms in block 8
Block first atom: 1194
Blocpdb> 177 atoms in block 9
Block first atom: 1374
Blocpdb> 182 atoms in block 10
Block first atom: 1551
Blocpdb> 173 atoms in block 11
Block first atom: 1733
Blocpdb> 186 atoms in block 12
Block first atom: 1906
Blocpdb> 172 atoms in block 13
Block first atom: 2092
Blocpdb> 165 atoms in block 14
Block first atom: 2264
Blocpdb> 179 atoms in block 15
Block first atom: 2429
Blocpdb> 176 atoms in block 16
Block first atom: 2608
Blocpdb> 167 atoms in block 17
Block first atom: 2784
Blocpdb> 183 atoms in block 18
Block first atom: 2951
Blocpdb> 169 atoms in block 19
Block first atom: 3134
Blocpdb> 166 atoms in block 20
Block first atom: 3303
Blocpdb> 175 atoms in block 21
Block first atom: 3469
Blocpdb> 171 atoms in block 22
Block first atom: 3644
Blocpdb> 189 atoms in block 23
Block first atom: 3815
Blocpdb> 174 atoms in block 24
Block first atom: 4004
Blocpdb> 162 atoms in block 25
Block first atom: 4178
Blocpdb> 169 atoms in block 26
Block first atom: 4340
Blocpdb> 171 atoms in block 27
Block first atom: 4509
Blocpdb> 169 atoms in block 28
Block first atom: 4680
Blocpdb> 168 atoms in block 29
Block first atom: 4849
Blocpdb> 179 atoms in block 30
Block first atom: 5017
Blocpdb> 182 atoms in block 31
Block first atom: 5196
Blocpdb> 172 atoms in block 32
Block first atom: 5378
Blocpdb> 179 atoms in block 33
Block first atom: 5550
Blocpdb> 171 atoms in block 34
Block first atom: 5729
Blocpdb> 167 atoms in block 35
Block first atom: 5900
Blocpdb> 182 atoms in block 36
Block first atom: 6067
Blocpdb> 170 atoms in block 37
Block first atom: 6249
Blocpdb> 185 atoms in block 38
Block first atom: 6419
Blocpdb> 182 atoms in block 39
Block first atom: 6604
Blocpdb> 171 atoms in block 40
Block first atom: 6786
Blocpdb> 165 atoms in block 41
Block first atom: 6957
Blocpdb> 178 atoms in block 42
Block first atom: 7122
Blocpdb> 181 atoms in block 43
Block first atom: 7300
Blocpdb> 169 atoms in block 44
Block first atom: 7481
Blocpdb> 171 atoms in block 45
Block first atom: 7650
Blocpdb> 178 atoms in block 46
Block first atom: 7821
Blocpdb> 165 atoms in block 47
Block first atom: 7999
Blocpdb> 175 atoms in block 48
Block first atom: 8164
Blocpdb> 178 atoms in block 49
Block first atom: 8339
Blocpdb> 178 atoms in block 50
Block first atom: 8517
Blocpdb> 179 atoms in block 51
Block first atom: 8695
Blocpdb> 168 atoms in block 52
Block first atom: 8874
Blocpdb> 171 atoms in block 53
Block first atom: 9042
Blocpdb> 163 atoms in block 54
Block first atom: 9213
Blocpdb> 165 atoms in block 55
Block first atom: 9376
Blocpdb> 169 atoms in block 56
Block first atom: 9541
Blocpdb> 176 atoms in block 57
Block first atom: 9710
Blocpdb> 170 atoms in block 58
Block first atom: 9886
Blocpdb> 180 atoms in block 59
Block first atom: 10056
Blocpdb> 160 atoms in block 60
Block first atom: 10236
Blocpdb> 155 atoms in block 61
Block first atom: 10396
Blocpdb> 159 atoms in block 62
Block first atom: 10551
Blocpdb> 180 atoms in block 63
Block first atom: 10710
Blocpdb> 180 atoms in block 64
Block first atom: 10890
Blocpdb> 156 atoms in block 65
Block first atom: 11070
Blocpdb> 179 atoms in block 66
Block first atom: 11226
Blocpdb> 180 atoms in block 67
Block first atom: 11405
Blocpdb> 178 atoms in block 68
Block first atom: 11585
Blocpdb> 166 atoms in block 69
Block first atom: 11763
Blocpdb> 175 atoms in block 70
Block first atom: 11929
Blocpdb> 168 atoms in block 71
Block first atom: 12104
Blocpdb> 171 atoms in block 72
Block first atom: 12272
Blocpdb> 178 atoms in block 73
Block first atom: 12443
Blocpdb> 171 atoms in block 74
Block first atom: 12621
Blocpdb> 120 atoms in block 75
Block first atom: 12792
Blocpdb> 163 atoms in block 76
Block first atom: 12912
Blocpdb> 170 atoms in block 77
Block first atom: 13075
Blocpdb> 170 atoms in block 78
Block first atom: 13245
Blocpdb> 161 atoms in block 79
Block first atom: 13415
Blocpdb> 179 atoms in block 80
Block first atom: 13576
Blocpdb> 165 atoms in block 81
Block first atom: 13755
Blocpdb> 161 atoms in block 82
Block first atom: 13920
Blocpdb> 172 atoms in block 83
Block first atom: 14081
Blocpdb> 168 atoms in block 84
Block first atom: 14253
Blocpdb> 178 atoms in block 85
Block first atom: 14421
Blocpdb> 169 atoms in block 86
Block first atom: 14599
Blocpdb> 178 atoms in block 87
Block first atom: 14768
Blocpdb> 158 atoms in block 88
Block first atom: 14946
Blocpdb> 167 atoms in block 89
Block first atom: 15104
Blocpdb> 171 atoms in block 90
Block first atom: 15271
Blocpdb> 59 atoms in block 91
Block first atom: 15442
Blocpdb> 163 atoms in block 92
Block first atom: 15501
Blocpdb> 170 atoms in block 93
Block first atom: 15664
Blocpdb> 170 atoms in block 94
Block first atom: 15834
Blocpdb> 161 atoms in block 95
Block first atom: 16004
Blocpdb> 179 atoms in block 96
Block first atom: 16165
Blocpdb> 165 atoms in block 97
Block first atom: 16344
Blocpdb> 161 atoms in block 98
Block first atom: 16509
Blocpdb> 172 atoms in block 99
Block first atom: 16670
Blocpdb> 168 atoms in block 100
Block first atom: 16842
Blocpdb> 178 atoms in block 101
Block first atom: 17010
Blocpdb> 169 atoms in block 102
Block first atom: 17188
Blocpdb> 178 atoms in block 103
Block first atom: 17357
Blocpdb> 158 atoms in block 104
Block first atom: 17535
Blocpdb> 167 atoms in block 105
Block first atom: 17693
Blocpdb> 171 atoms in block 106
Block first atom: 17860
Blocpdb> 59 atoms in block 107
Block first atom: 18031
Blocpdb> 163 atoms in block 108
Block first atom: 18090
Blocpdb> 170 atoms in block 109
Block first atom: 18253
Blocpdb> 170 atoms in block 110
Block first atom: 18423
Blocpdb> 161 atoms in block 111
Block first atom: 18593
Blocpdb> 179 atoms in block 112
Block first atom: 18754
Blocpdb> 165 atoms in block 113
Block first atom: 18933
Blocpdb> 161 atoms in block 114
Block first atom: 19098
Blocpdb> 172 atoms in block 115
Block first atom: 19259
Blocpdb> 168 atoms in block 116
Block first atom: 19431
Blocpdb> 178 atoms in block 117
Block first atom: 19599
Blocpdb> 169 atoms in block 118
Block first atom: 19777
Blocpdb> 178 atoms in block 119
Block first atom: 19946
Blocpdb> 158 atoms in block 120
Block first atom: 20124
Blocpdb> 167 atoms in block 121
Block first atom: 20282
Blocpdb> 171 atoms in block 122
Block first atom: 20449
Blocpdb> 59 atoms in block 123
Block first atom: 20620
Blocpdb> 163 atoms in block 124
Block first atom: 20679
Blocpdb> 170 atoms in block 125
Block first atom: 20842
Blocpdb> 170 atoms in block 126
Block first atom: 21012
Blocpdb> 161 atoms in block 127
Block first atom: 21182
Blocpdb> 179 atoms in block 128
Block first atom: 21343
Blocpdb> 165 atoms in block 129
Block first atom: 21522
Blocpdb> 161 atoms in block 130
Block first atom: 21687
Blocpdb> 172 atoms in block 131
Block first atom: 21848
Blocpdb> 168 atoms in block 132
Block first atom: 22020
Blocpdb> 178 atoms in block 133
Block first atom: 22188
Blocpdb> 169 atoms in block 134
Block first atom: 22366
Blocpdb> 178 atoms in block 135
Block first atom: 22535
Blocpdb> 158 atoms in block 136
Block first atom: 22713
Blocpdb> 167 atoms in block 137
Block first atom: 22871
Blocpdb> 171 atoms in block 138
Block first atom: 23038
Blocpdb> 59 atoms in block 139
Block first atom: 23209
Blocpdb> 163 atoms in block 140
Block first atom: 23268
Blocpdb> 170 atoms in block 141
Block first atom: 23431
Blocpdb> 170 atoms in block 142
Block first atom: 23601
Blocpdb> 161 atoms in block 143
Block first atom: 23771
Blocpdb> 179 atoms in block 144
Block first atom: 23932
Blocpdb> 165 atoms in block 145
Block first atom: 24111
Blocpdb> 161 atoms in block 146
Block first atom: 24276
Blocpdb> 172 atoms in block 147
Block first atom: 24437
Blocpdb> 168 atoms in block 148
Block first atom: 24609
Blocpdb> 178 atoms in block 149
Block first atom: 24777
Blocpdb> 169 atoms in block 150
Block first atom: 24955
Blocpdb> 178 atoms in block 151
Block first atom: 25124
Blocpdb> 158 atoms in block 152
Block first atom: 25302
Blocpdb> 167 atoms in block 153
Block first atom: 25460
Blocpdb> 171 atoms in block 154
Block first atom: 25627
Blocpdb> 59 atoms in block 155
Block first atom: 25798
Blocpdb> 163 atoms in block 156
Block first atom: 25857
Blocpdb> 170 atoms in block 157
Block first atom: 26020
Blocpdb> 170 atoms in block 158
Block first atom: 26190
Blocpdb> 161 atoms in block 159
Block first atom: 26360
Blocpdb> 179 atoms in block 160
Block first atom: 26521
Blocpdb> 165 atoms in block 161
Block first atom: 26700
Blocpdb> 161 atoms in block 162
Block first atom: 26865
Blocpdb> 172 atoms in block 163
Block first atom: 27026
Blocpdb> 168 atoms in block 164
Block first atom: 27198
Blocpdb> 178 atoms in block 165
Block first atom: 27366
Blocpdb> 169 atoms in block 166
Block first atom: 27544
Blocpdb> 178 atoms in block 167
Block first atom: 27713
Blocpdb> 158 atoms in block 168
Block first atom: 27891
Blocpdb> 167 atoms in block 169
Block first atom: 28049
Blocpdb> 171 atoms in block 170
Block first atom: 28216
Blocpdb> 59 atoms in block 171
Block first atom: 28387
Blocpdb> 163 atoms in block 172
Block first atom: 28446
Blocpdb> 170 atoms in block 173
Block first atom: 28609
Blocpdb> 170 atoms in block 174
Block first atom: 28779
Blocpdb> 161 atoms in block 175
Block first atom: 28949
Blocpdb> 179 atoms in block 176
Block first atom: 29110
Blocpdb> 165 atoms in block 177
Block first atom: 29289
Blocpdb> 161 atoms in block 178
Block first atom: 29454
Blocpdb> 172 atoms in block 179
Block first atom: 29615
Blocpdb> 168 atoms in block 180
Block first atom: 29787
Blocpdb> 178 atoms in block 181
Block first atom: 29955
Blocpdb> 169 atoms in block 182
Block first atom: 30133
Blocpdb> 178 atoms in block 183
Block first atom: 30302
Blocpdb> 158 atoms in block 184
Block first atom: 30480
Blocpdb> 167 atoms in block 185
Block first atom: 30638
Blocpdb> 171 atoms in block 186
Block first atom: 30805
Blocpdb> 59 atoms in block 187
Block first atom: 30976
Blocpdb> 163 atoms in block 188
Block first atom: 31035
Blocpdb> 170 atoms in block 189
Block first atom: 31198
Blocpdb> 170 atoms in block 190
Block first atom: 31368
Blocpdb> 161 atoms in block 191
Block first atom: 31538
Blocpdb> 179 atoms in block 192
Block first atom: 31699
Blocpdb> 165 atoms in block 193
Block first atom: 31878
Blocpdb> 161 atoms in block 194
Block first atom: 32043
Blocpdb> 172 atoms in block 195
Block first atom: 32204
Blocpdb> 168 atoms in block 196
Block first atom: 32376
Blocpdb> 178 atoms in block 197
Block first atom: 32544
Blocpdb> 169 atoms in block 198
Block first atom: 32722
Blocpdb> 178 atoms in block 199
Block first atom: 32891
Blocpdb> 158 atoms in block 200
Block first atom: 33069
Blocpdb> 167 atoms in block 201
Block first atom: 33227
Blocpdb> 171 atoms in block 202
Block first atom: 33394
Blocpdb> 59 atoms in block 203
Block first atom: 33564
Blocpdb> 203 blocks.
Blocpdb> At most, 189 atoms in each of them.
Blocpdb> At least, 59 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: 57514213 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 0m0.166s
user 0m0.155s
sys 0m0.011s
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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