*** 273 ***
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 = 2607131605591085444.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 2607131605591085444.atom to be opened.
Openam> File opened: 2607131605591085444.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 = 3190
First residue number = 1
Last residue number = 373
Number of atoms found = 24745
Mean number per residue = 7.8
Pdbmat> Coordinate statistics:
= -51.915717 +/- 38.782557 From: -146.095000 To: 22.516000
= -8.956603 +/- 28.230487 From: -92.412000 To: 97.970000
= 30.745700 +/- 25.076975 From: -27.142000 To: 102.634000
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 2.1904 % Filled.
Pdbmat> 13317246 non-zero elements.
Pdbmat> 1463424 atom-atom interactions.
Pdbmat> Number per atom= 118.28 +/- 71.16
Maximum number = 402
Minimum number = 8
Pdbmat> Matrix trace = 2.926848E+07
Pdbmat> Larger element = 1403.13
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3190 non-zero elements, NRBL set to 16
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 = 2607131605591085444.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 16
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 2607131605591085444.atom to be opened.
Openam> file on opening on unit 11:
2607131605591085444.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 24745 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 16 residue(s) per block.
Blocpdb> 3190 residues.
Blocpdb> 116 atoms in block 1
Block first atom: 1
Blocpdb> 128 atoms in block 2
Block first atom: 117
Blocpdb> 130 atoms in block 3
Block first atom: 245
Blocpdb> 129 atoms in block 4
Block first atom: 375
Blocpdb> 144 atoms in block 5
Block first atom: 504
Blocpdb> 125 atoms in block 6
Block first atom: 648
Blocpdb> 122 atoms in block 7
Block first atom: 773
Blocpdb> 120 atoms in block 8
Block first atom: 895
Blocpdb> 121 atoms in block 9
Block first atom: 1015
Blocpdb> 134 atoms in block 10
Block first atom: 1136
Blocpdb> 118 atoms in block 11
Block first atom: 1270
Blocpdb> 146 atoms in block 12
Block first atom: 1388
Blocpdb> 133 atoms in block 13
Block first atom: 1534
Blocpdb> 137 atoms in block 14
Block first atom: 1667
Blocpdb> 110 atoms in block 15
Block first atom: 1804
Blocpdb> 121 atoms in block 16
Block first atom: 1914
Blocpdb> 69 atoms in block 17
Block first atom: 2035
Blocpdb> 116 atoms in block 18
Block first atom: 2104
Blocpdb> 128 atoms in block 19
Block first atom: 2220
Blocpdb> 130 atoms in block 20
Block first atom: 2348
Blocpdb> 129 atoms in block 21
Block first atom: 2478
Blocpdb> 144 atoms in block 22
Block first atom: 2607
Blocpdb> 125 atoms in block 23
Block first atom: 2751
Blocpdb> 122 atoms in block 24
Block first atom: 2876
Blocpdb> 120 atoms in block 25
Block first atom: 2998
Blocpdb> 121 atoms in block 26
Block first atom: 3118
Blocpdb> 134 atoms in block 27
Block first atom: 3239
Blocpdb> 118 atoms in block 28
Block first atom: 3373
Blocpdb> 146 atoms in block 29
Block first atom: 3491
Blocpdb> 133 atoms in block 30
Block first atom: 3637
Blocpdb> 137 atoms in block 31
Block first atom: 3770
Blocpdb> 110 atoms in block 32
Block first atom: 3907
Blocpdb> 121 atoms in block 33
Block first atom: 4017
Blocpdb> 69 atoms in block 34
Block first atom: 4138
Blocpdb> 116 atoms in block 35
Block first atom: 4207
Blocpdb> 128 atoms in block 36
Block first atom: 4323
Blocpdb> 130 atoms in block 37
Block first atom: 4451
Blocpdb> 129 atoms in block 38
Block first atom: 4581
Blocpdb> 144 atoms in block 39
Block first atom: 4710
Blocpdb> 125 atoms in block 40
Block first atom: 4854
Blocpdb> 122 atoms in block 41
Block first atom: 4979
Blocpdb> 120 atoms in block 42
Block first atom: 5101
Blocpdb> 121 atoms in block 43
Block first atom: 5221
Blocpdb> 134 atoms in block 44
Block first atom: 5342
Blocpdb> 118 atoms in block 45
Block first atom: 5476
Blocpdb> 146 atoms in block 46
Block first atom: 5594
Blocpdb> 133 atoms in block 47
Block first atom: 5740
Blocpdb> 137 atoms in block 48
Block first atom: 5873
Blocpdb> 110 atoms in block 49
Block first atom: 6010
Blocpdb> 121 atoms in block 50
Block first atom: 6120
Blocpdb> 69 atoms in block 51
Block first atom: 6241
Blocpdb> 116 atoms in block 52
Block first atom: 6310
Blocpdb> 128 atoms in block 53
Block first atom: 6426
Blocpdb> 130 atoms in block 54
Block first atom: 6554
Blocpdb> 129 atoms in block 55
Block first atom: 6684
Blocpdb> 144 atoms in block 56
Block first atom: 6813
Blocpdb> 125 atoms in block 57
Block first atom: 6957
Blocpdb> 122 atoms in block 58
Block first atom: 7082
Blocpdb> 120 atoms in block 59
Block first atom: 7204
Blocpdb> 121 atoms in block 60
Block first atom: 7324
Blocpdb> 134 atoms in block 61
Block first atom: 7445
Blocpdb> 118 atoms in block 62
Block first atom: 7579
Blocpdb> 146 atoms in block 63
Block first atom: 7697
Blocpdb> 133 atoms in block 64
Block first atom: 7843
Blocpdb> 137 atoms in block 65
Block first atom: 7976
Blocpdb> 110 atoms in block 66
Block first atom: 8113
Blocpdb> 121 atoms in block 67
Block first atom: 8223
Blocpdb> 69 atoms in block 68
Block first atom: 8344
Blocpdb> 116 atoms in block 69
Block first atom: 8413
Blocpdb> 128 atoms in block 70
Block first atom: 8529
Blocpdb> 130 atoms in block 71
Block first atom: 8657
Blocpdb> 129 atoms in block 72
Block first atom: 8787
Blocpdb> 144 atoms in block 73
Block first atom: 8916
Blocpdb> 125 atoms in block 74
Block first atom: 9060
Blocpdb> 122 atoms in block 75
Block first atom: 9185
Blocpdb> 120 atoms in block 76
Block first atom: 9307
Blocpdb> 121 atoms in block 77
Block first atom: 9427
Blocpdb> 134 atoms in block 78
Block first atom: 9548
Blocpdb> 118 atoms in block 79
Block first atom: 9682
Blocpdb> 146 atoms in block 80
Block first atom: 9800
Blocpdb> 133 atoms in block 81
Block first atom: 9946
Blocpdb> 137 atoms in block 82
Block first atom: 10079
Blocpdb> 110 atoms in block 83
Block first atom: 10216
Blocpdb> 121 atoms in block 84
Block first atom: 10326
Blocpdb> 69 atoms in block 85
Block first atom: 10447
Blocpdb> 105 atoms in block 86
Block first atom: 10516
Blocpdb> 127 atoms in block 87
Block first atom: 10621
Blocpdb> 116 atoms in block 88
Block first atom: 10748
Blocpdb> 119 atoms in block 89
Block first atom: 10864
Blocpdb> 125 atoms in block 90
Block first atom: 10983
Blocpdb> 118 atoms in block 91
Block first atom: 11108
Blocpdb> 106 atoms in block 92
Block first atom: 11226
Blocpdb> 111 atoms in block 93
Block first atom: 11332
Blocpdb> 122 atoms in block 94
Block first atom: 11443
Blocpdb> 107 atoms in block 95
Block first atom: 11565
Blocpdb> 136 atoms in block 96
Block first atom: 11672
Blocpdb> 127 atoms in block 97
Block first atom: 11808
Blocpdb> 146 atoms in block 98
Block first atom: 11935
Blocpdb> 124 atoms in block 99
Block first atom: 12081
Blocpdb> 140 atoms in block 100
Block first atom: 12205
Blocpdb> 125 atoms in block 101
Block first atom: 12345
Blocpdb> 112 atoms in block 102
Block first atom: 12470
Blocpdb> 132 atoms in block 103
Block first atom: 12582
Blocpdb> 128 atoms in block 104
Block first atom: 12714
Blocpdb> 118 atoms in block 105
Block first atom: 12842
Blocpdb> 126 atoms in block 106
Block first atom: 12960
Blocpdb> 122 atoms in block 107
Block first atom: 13086
Blocpdb> 126 atoms in block 108
Block first atom: 13208
Blocpdb> 28 atoms in block 109
Block first atom: 13334
Blocpdb> 105 atoms in block 110
Block first atom: 13362
Blocpdb> 127 atoms in block 111
Block first atom: 13467
Blocpdb> 116 atoms in block 112
Block first atom: 13594
Blocpdb> 119 atoms in block 113
Block first atom: 13710
Blocpdb> 125 atoms in block 114
Block first atom: 13829
Blocpdb> 118 atoms in block 115
Block first atom: 13954
Blocpdb> 106 atoms in block 116
Block first atom: 14072
Blocpdb> 111 atoms in block 117
Block first atom: 14178
Blocpdb> 122 atoms in block 118
Block first atom: 14289
Blocpdb> 107 atoms in block 119
Block first atom: 14411
Blocpdb> 136 atoms in block 120
Block first atom: 14518
Blocpdb> 127 atoms in block 121
Block first atom: 14654
Blocpdb> 146 atoms in block 122
Block first atom: 14781
Blocpdb> 124 atoms in block 123
Block first atom: 14927
Blocpdb> 140 atoms in block 124
Block first atom: 15051
Blocpdb> 125 atoms in block 125
Block first atom: 15191
Blocpdb> 112 atoms in block 126
Block first atom: 15316
Blocpdb> 132 atoms in block 127
Block first atom: 15428
Blocpdb> 128 atoms in block 128
Block first atom: 15560
Blocpdb> 118 atoms in block 129
Block first atom: 15688
Blocpdb> 126 atoms in block 130
Block first atom: 15806
Blocpdb> 122 atoms in block 131
Block first atom: 15932
Blocpdb> 126 atoms in block 132
Block first atom: 16054
Blocpdb> 28 atoms in block 133
Block first atom: 16180
Blocpdb> 105 atoms in block 134
Block first atom: 16208
Blocpdb> 127 atoms in block 135
Block first atom: 16313
Blocpdb> 116 atoms in block 136
Block first atom: 16440
Blocpdb> 119 atoms in block 137
Block first atom: 16556
Blocpdb> 125 atoms in block 138
Block first atom: 16675
Blocpdb> 118 atoms in block 139
Block first atom: 16800
Blocpdb> 106 atoms in block 140
Block first atom: 16918
Blocpdb> 111 atoms in block 141
Block first atom: 17024
Blocpdb> 122 atoms in block 142
Block first atom: 17135
Blocpdb> 107 atoms in block 143
Block first atom: 17257
Blocpdb> 136 atoms in block 144
Block first atom: 17364
Blocpdb> 127 atoms in block 145
Block first atom: 17500
Blocpdb> 146 atoms in block 146
Block first atom: 17627
Blocpdb> 124 atoms in block 147
Block first atom: 17773
Blocpdb> 140 atoms in block 148
Block first atom: 17897
Blocpdb> 125 atoms in block 149
Block first atom: 18037
Blocpdb> 112 atoms in block 150
Block first atom: 18162
Blocpdb> 132 atoms in block 151
Block first atom: 18274
Blocpdb> 128 atoms in block 152
Block first atom: 18406
Blocpdb> 118 atoms in block 153
Block first atom: 18534
Blocpdb> 126 atoms in block 154
Block first atom: 18652
Blocpdb> 122 atoms in block 155
Block first atom: 18778
Blocpdb> 126 atoms in block 156
Block first atom: 18900
Blocpdb> 28 atoms in block 157
Block first atom: 19026
Blocpdb> 105 atoms in block 158
Block first atom: 19054
Blocpdb> 127 atoms in block 159
Block first atom: 19159
Blocpdb> 116 atoms in block 160
Block first atom: 19286
Blocpdb> 119 atoms in block 161
Block first atom: 19402
Blocpdb> 125 atoms in block 162
Block first atom: 19521
Blocpdb> 118 atoms in block 163
Block first atom: 19646
Blocpdb> 106 atoms in block 164
Block first atom: 19764
Blocpdb> 111 atoms in block 165
Block first atom: 19870
Blocpdb> 122 atoms in block 166
Block first atom: 19981
Blocpdb> 107 atoms in block 167
Block first atom: 20103
Blocpdb> 136 atoms in block 168
Block first atom: 20210
Blocpdb> 127 atoms in block 169
Block first atom: 20346
Blocpdb> 146 atoms in block 170
Block first atom: 20473
Blocpdb> 124 atoms in block 171
Block first atom: 20619
Blocpdb> 140 atoms in block 172
Block first atom: 20743
Blocpdb> 125 atoms in block 173
Block first atom: 20883
Blocpdb> 112 atoms in block 174
Block first atom: 21008
Blocpdb> 132 atoms in block 175
Block first atom: 21120
Blocpdb> 128 atoms in block 176
Block first atom: 21252
Blocpdb> 118 atoms in block 177
Block first atom: 21380
Blocpdb> 126 atoms in block 178
Block first atom: 21498
Blocpdb> 122 atoms in block 179
Block first atom: 21624
Blocpdb> 126 atoms in block 180
Block first atom: 21746
Blocpdb> 28 atoms in block 181
Block first atom: 21872
Blocpdb> 105 atoms in block 182
Block first atom: 21900
Blocpdb> 127 atoms in block 183
Block first atom: 22005
Blocpdb> 116 atoms in block 184
Block first atom: 22132
Blocpdb> 119 atoms in block 185
Block first atom: 22248
Blocpdb> 125 atoms in block 186
Block first atom: 22367
Blocpdb> 118 atoms in block 187
Block first atom: 22492
Blocpdb> 106 atoms in block 188
Block first atom: 22610
Blocpdb> 111 atoms in block 189
Block first atom: 22716
Blocpdb> 122 atoms in block 190
Block first atom: 22827
Blocpdb> 107 atoms in block 191
Block first atom: 22949
Blocpdb> 136 atoms in block 192
Block first atom: 23056
Blocpdb> 127 atoms in block 193
Block first atom: 23192
Blocpdb> 146 atoms in block 194
Block first atom: 23319
Blocpdb> 124 atoms in block 195
Block first atom: 23465
Blocpdb> 140 atoms in block 196
Block first atom: 23589
Blocpdb> 125 atoms in block 197
Block first atom: 23729
Blocpdb> 112 atoms in block 198
Block first atom: 23854
Blocpdb> 132 atoms in block 199
Block first atom: 23966
Blocpdb> 128 atoms in block 200
Block first atom: 24098
Blocpdb> 118 atoms in block 201
Block first atom: 24226
Blocpdb> 126 atoms in block 202
Block first atom: 24344
Blocpdb> 122 atoms in block 203
Block first atom: 24470
Blocpdb> 126 atoms in block 204
Block first atom: 24592
Blocpdb> 28 atoms in block 205
Block first atom: 24717
Blocpdb> 205 blocks.
Blocpdb> At most, 146 atoms in each of them.
Blocpdb> At least, 28 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: 32706775 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 0m0.106s
user 0m0.098s
sys 0m0.007s
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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