*** ***
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 = 2603240600041303070.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 2603240600041303070.atom to be opened.
Openam> File opened: 2603240600041303070.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 = 2038
First residue number = 2
Last residue number = 1020
Number of atoms found = 31132
Mean number per residue = 15.3
Pdbmat> Coordinate statistics:
= 77.571998 +/- 21.669236 From: 23.316000 To: 131.816000
= 56.740786 +/- 17.876467 From: 17.251000 To: 101.408000
= 76.216409 +/- 24.909080 From: 22.886000 To: 136.435000
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 36.9307 % Filled.
Pdbmat> 24553680 non-zero elements.
Pdbmat> 2707887 atom-atom interactions.
Pdbmat> Number per atom= 173.96 +/- 45.30
Maximum number = 254
Minimum number = 21
Pdbmat> Matrix trace = 5.415774E+07
Pdbmat> Larger element = 904.059
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2038 non-zero elements, NRBL set to 11
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 = 2603240600041303070.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 11
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 2603240600041303070.atom to be opened.
Openam> file on opening on unit 11:
2603240600041303070.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 31132 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 11 residue(s) per block.
Blocpdb> 2038 residues.
Blocpdb> 158 atoms in block 1
Block first atom: 1
Blocpdb> 176 atoms in block 2
Block first atom: 159
Blocpdb> 153 atoms in block 3
Block first atom: 335
Blocpdb> 212 atoms in block 4
Block first atom: 488
Blocpdb> 175 atoms in block 5
Block first atom: 700
Blocpdb> 178 atoms in block 6
Block first atom: 875
Blocpdb> 172 atoms in block 7
Block first atom: 1053
Blocpdb> 156 atoms in block 8
Block first atom: 1225
Blocpdb> 166 atoms in block 9
Block first atom: 1381
Blocpdb> 172 atoms in block 10
Block first atom: 1547
Blocpdb> 168 atoms in block 11
Block first atom: 1719
Blocpdb> 140 atoms in block 12
Block first atom: 1887
Blocpdb> 145 atoms in block 13
Block first atom: 2027
Blocpdb> 150 atoms in block 14
Block first atom: 2172
Blocpdb> 178 atoms in block 15
Block first atom: 2322
Blocpdb> 176 atoms in block 16
Block first atom: 2500
Blocpdb> 160 atoms in block 17
Block first atom: 2676
Blocpdb> 149 atoms in block 18
Block first atom: 2836
Blocpdb> 161 atoms in block 19
Block first atom: 2985
Blocpdb> 185 atoms in block 20
Block first atom: 3146
Blocpdb> 154 atoms in block 21
Block first atom: 3331
Blocpdb> 193 atoms in block 22
Block first atom: 3485
Blocpdb> 183 atoms in block 23
Block first atom: 3678
Blocpdb> 164 atoms in block 24
Block first atom: 3861
Blocpdb> 181 atoms in block 25
Block first atom: 4025
Blocpdb> 162 atoms in block 26
Block first atom: 4206
Blocpdb> 168 atoms in block 27
Block first atom: 4368
Blocpdb> 173 atoms in block 28
Block first atom: 4536
Blocpdb> 156 atoms in block 29
Block first atom: 4709
Blocpdb> 154 atoms in block 30
Block first atom: 4865
Blocpdb> 153 atoms in block 31
Block first atom: 5019
Blocpdb> 155 atoms in block 32
Block first atom: 5172
Blocpdb> 191 atoms in block 33
Block first atom: 5327
Blocpdb> 177 atoms in block 34
Block first atom: 5518
Blocpdb> 177 atoms in block 35
Block first atom: 5695
Blocpdb> 198 atoms in block 36
Block first atom: 5872
Blocpdb> 175 atoms in block 37
Block first atom: 6070
Blocpdb> 180 atoms in block 38
Block first atom: 6245
Blocpdb> 176 atoms in block 39
Block first atom: 6425
Blocpdb> 148 atoms in block 40
Block first atom: 6601
Blocpdb> 171 atoms in block 41
Block first atom: 6749
Blocpdb> 192 atoms in block 42
Block first atom: 6920
Blocpdb> 155 atoms in block 43
Block first atom: 7112
Blocpdb> 154 atoms in block 44
Block first atom: 7267
Blocpdb> 143 atoms in block 45
Block first atom: 7421
Blocpdb> 200 atoms in block 46
Block first atom: 7564
Blocpdb> 153 atoms in block 47
Block first atom: 7764
Blocpdb> 181 atoms in block 48
Block first atom: 7917
Blocpdb> 161 atoms in block 49
Block first atom: 8098
Blocpdb> 166 atoms in block 50
Block first atom: 8259
Blocpdb> 172 atoms in block 51
Block first atom: 8425
Blocpdb> 156 atoms in block 52
Block first atom: 8597
Blocpdb> 181 atoms in block 53
Block first atom: 8753
Blocpdb> 176 atoms in block 54
Block first atom: 8934
Blocpdb> 137 atoms in block 55
Block first atom: 9110
Blocpdb> 186 atoms in block 56
Block first atom: 9247
Blocpdb> 168 atoms in block 57
Block first atom: 9433
Blocpdb> 168 atoms in block 58
Block first atom: 9601
Blocpdb> 176 atoms in block 59
Block first atom: 9769
Blocpdb> 158 atoms in block 60
Block first atom: 9945
Blocpdb> 154 atoms in block 61
Block first atom: 10103
Blocpdb> 147 atoms in block 62
Block first atom: 10257
Blocpdb> 168 atoms in block 63
Block first atom: 10404
Blocpdb> 192 atoms in block 64
Block first atom: 10572
Blocpdb> 175 atoms in block 65
Block first atom: 10764
Blocpdb> 163 atoms in block 66
Block first atom: 10939
Blocpdb> 136 atoms in block 67
Block first atom: 11102
Blocpdb> 146 atoms in block 68
Block first atom: 11238
Blocpdb> 174 atoms in block 69
Block first atom: 11384
Blocpdb> 150 atoms in block 70
Block first atom: 11558
Blocpdb> 166 atoms in block 71
Block first atom: 11708
Blocpdb> 170 atoms in block 72
Block first atom: 11874
Blocpdb> 135 atoms in block 73
Block first atom: 12044
Blocpdb> 163 atoms in block 74
Block first atom: 12179
Blocpdb> 161 atoms in block 75
Block first atom: 12342
Blocpdb> 169 atoms in block 76
Block first atom: 12503
Blocpdb> 189 atoms in block 77
Block first atom: 12672
Blocpdb> 153 atoms in block 78
Block first atom: 12861
Blocpdb> 180 atoms in block 79
Block first atom: 13014
Blocpdb> 177 atoms in block 80
Block first atom: 13194
Blocpdb> 203 atoms in block 81
Block first atom: 13371
Blocpdb> 192 atoms in block 82
Block first atom: 13574
Blocpdb> 188 atoms in block 83
Block first atom: 13766
Blocpdb> 195 atoms in block 84
Block first atom: 13954
Blocpdb> 163 atoms in block 85
Block first atom: 14149
Blocpdb> 166 atoms in block 86
Block first atom: 14312
Blocpdb> 160 atoms in block 87
Block first atom: 14478
Blocpdb> 155 atoms in block 88
Block first atom: 14638
Blocpdb> 171 atoms in block 89
Block first atom: 14793
Blocpdb> 149 atoms in block 90
Block first atom: 14964
Blocpdb> 158 atoms in block 91
Block first atom: 15113
Blocpdb> 182 atoms in block 92
Block first atom: 15271
Blocpdb> 114 atoms in block 93
Block first atom: 15453
Blocpdb> 158 atoms in block 94
Block first atom: 15567
Blocpdb> 176 atoms in block 95
Block first atom: 15725
Blocpdb> 153 atoms in block 96
Block first atom: 15901
Blocpdb> 212 atoms in block 97
Block first atom: 16054
Blocpdb> 175 atoms in block 98
Block first atom: 16266
Blocpdb> 178 atoms in block 99
Block first atom: 16441
Blocpdb> 172 atoms in block 100
Block first atom: 16619
Blocpdb> 156 atoms in block 101
Block first atom: 16791
Blocpdb> 166 atoms in block 102
Block first atom: 16947
Blocpdb> 172 atoms in block 103
Block first atom: 17113
Blocpdb> 168 atoms in block 104
Block first atom: 17285
Blocpdb> 140 atoms in block 105
Block first atom: 17453
Blocpdb> 145 atoms in block 106
Block first atom: 17593
Blocpdb> 150 atoms in block 107
Block first atom: 17738
Blocpdb> 178 atoms in block 108
Block first atom: 17888
Blocpdb> 176 atoms in block 109
Block first atom: 18066
Blocpdb> 160 atoms in block 110
Block first atom: 18242
Blocpdb> 149 atoms in block 111
Block first atom: 18402
Blocpdb> 161 atoms in block 112
Block first atom: 18551
Blocpdb> 185 atoms in block 113
Block first atom: 18712
Blocpdb> 154 atoms in block 114
Block first atom: 18897
Blocpdb> 193 atoms in block 115
Block first atom: 19051
Blocpdb> 183 atoms in block 116
Block first atom: 19244
Blocpdb> 164 atoms in block 117
Block first atom: 19427
Blocpdb> 181 atoms in block 118
Block first atom: 19591
Blocpdb> 162 atoms in block 119
Block first atom: 19772
Blocpdb> 168 atoms in block 120
Block first atom: 19934
Blocpdb> 173 atoms in block 121
Block first atom: 20102
Blocpdb> 156 atoms in block 122
Block first atom: 20275
Blocpdb> 154 atoms in block 123
Block first atom: 20431
Blocpdb> 153 atoms in block 124
Block first atom: 20585
Blocpdb> 155 atoms in block 125
Block first atom: 20738
Blocpdb> 191 atoms in block 126
Block first atom: 20893
Blocpdb> 177 atoms in block 127
Block first atom: 21084
Blocpdb> 177 atoms in block 128
Block first atom: 21261
Blocpdb> 198 atoms in block 129
Block first atom: 21438
Blocpdb> 175 atoms in block 130
Block first atom: 21636
Blocpdb> 180 atoms in block 131
Block first atom: 21811
Blocpdb> 176 atoms in block 132
Block first atom: 21991
Blocpdb> 148 atoms in block 133
Block first atom: 22167
Blocpdb> 171 atoms in block 134
Block first atom: 22315
Blocpdb> 192 atoms in block 135
Block first atom: 22486
Blocpdb> 155 atoms in block 136
Block first atom: 22678
Blocpdb> 154 atoms in block 137
Block first atom: 22833
Blocpdb> 143 atoms in block 138
Block first atom: 22987
Blocpdb> 200 atoms in block 139
Block first atom: 23130
Blocpdb> 153 atoms in block 140
Block first atom: 23330
Blocpdb> 181 atoms in block 141
Block first atom: 23483
Blocpdb> 161 atoms in block 142
Block first atom: 23664
Blocpdb> 166 atoms in block 143
Block first atom: 23825
Blocpdb> 172 atoms in block 144
Block first atom: 23991
Blocpdb> 156 atoms in block 145
Block first atom: 24163
Blocpdb> 181 atoms in block 146
Block first atom: 24319
Blocpdb> 176 atoms in block 147
Block first atom: 24500
Blocpdb> 137 atoms in block 148
Block first atom: 24676
Blocpdb> 186 atoms in block 149
Block first atom: 24813
Blocpdb> 168 atoms in block 150
Block first atom: 24999
Blocpdb> 168 atoms in block 151
Block first atom: 25167
Blocpdb> 176 atoms in block 152
Block first atom: 25335
Blocpdb> 158 atoms in block 153
Block first atom: 25511
Blocpdb> 154 atoms in block 154
Block first atom: 25669
Blocpdb> 147 atoms in block 155
Block first atom: 25823
Blocpdb> 168 atoms in block 156
Block first atom: 25970
Blocpdb> 192 atoms in block 157
Block first atom: 26138
Blocpdb> 175 atoms in block 158
Block first atom: 26330
Blocpdb> 163 atoms in block 159
Block first atom: 26505
Blocpdb> 136 atoms in block 160
Block first atom: 26668
Blocpdb> 146 atoms in block 161
Block first atom: 26804
Blocpdb> 174 atoms in block 162
Block first atom: 26950
Blocpdb> 150 atoms in block 163
Block first atom: 27124
Blocpdb> 166 atoms in block 164
Block first atom: 27274
Blocpdb> 170 atoms in block 165
Block first atom: 27440
Blocpdb> 135 atoms in block 166
Block first atom: 27610
Blocpdb> 163 atoms in block 167
Block first atom: 27745
Blocpdb> 161 atoms in block 168
Block first atom: 27908
Blocpdb> 169 atoms in block 169
Block first atom: 28069
Blocpdb> 189 atoms in block 170
Block first atom: 28238
Blocpdb> 153 atoms in block 171
Block first atom: 28427
Blocpdb> 180 atoms in block 172
Block first atom: 28580
Blocpdb> 177 atoms in block 173
Block first atom: 28760
Blocpdb> 203 atoms in block 174
Block first atom: 28937
Blocpdb> 192 atoms in block 175
Block first atom: 29140
Blocpdb> 188 atoms in block 176
Block first atom: 29332
Blocpdb> 195 atoms in block 177
Block first atom: 29520
Blocpdb> 163 atoms in block 178
Block first atom: 29715
Blocpdb> 166 atoms in block 179
Block first atom: 29878
Blocpdb> 160 atoms in block 180
Block first atom: 30044
Blocpdb> 155 atoms in block 181
Block first atom: 30204
Blocpdb> 171 atoms in block 182
Block first atom: 30359
Blocpdb> 149 atoms in block 183
Block first atom: 30530
Blocpdb> 158 atoms in block 184
Block first atom: 30679
Blocpdb> 182 atoms in block 185
Block first atom: 30837
Blocpdb> 114 atoms in block 186
Block first atom: 31018
Blocpdb> 186 blocks.
Blocpdb> At most, 212 atoms in each of them.
Blocpdb> At least, 114 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: 59804353 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 0m0.189s
user 0m0.174s
sys 0m0.014s
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: december 26th, 2025.
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