*** ***
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 = 2607310935381766634.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 2607310935381766634.atom to be opened.
Openam> File opened: 2607310935381766634.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 = 3580
First residue number = 40
Last residue number = 1104
Number of atoms found = 28568
Mean number per residue = 8.0
Pdbmat> Coordinate statistics:
= 153.000390 +/- 28.805296 From: 87.481000 To: 218.371000
= 153.003665 +/- 28.822821 From: 86.920000 To: 218.434000
= 164.138554 +/- 31.273370 From: 88.324000 To: 218.932000
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 -1.6271 % Filled.
Pdbmat> 10126093 non-zero elements.
Pdbmat> 1106260 atom-atom interactions.
Pdbmat> Number per atom= 77.45 +/- 19.39
Maximum number = 125
Minimum number = 10
Pdbmat> Matrix trace = 2.212520E+07
Pdbmat> Larger element = 501.597
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3580 non-zero elements, NRBL set to 18
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 = 2607310935381766634.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 18
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 2607310935381766634.atom to be opened.
Openam> file on opening on unit 11:
2607310935381766634.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 28568 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 18 residue(s) per block.
Blocpdb> 3580 residues.
Blocpdb> 160 atoms in block 1
Block first atom: 1
Blocpdb> 136 atoms in block 2
Block first atom: 161
Blocpdb> 130 atoms in block 3
Block first atom: 297
Blocpdb> 143 atoms in block 4
Block first atom: 427
Blocpdb> 153 atoms in block 5
Block first atom: 570
Blocpdb> 152 atoms in block 6
Block first atom: 723
Blocpdb> 160 atoms in block 7
Block first atom: 875
Blocpdb> 152 atoms in block 8
Block first atom: 1035
Blocpdb> 161 atoms in block 9
Block first atom: 1187
Blocpdb> 145 atoms in block 10
Block first atom: 1348
Blocpdb> 125 atoms in block 11
Block first atom: 1493
Blocpdb> 152 atoms in block 12
Block first atom: 1618
Blocpdb> 140 atoms in block 13
Block first atom: 1770
Blocpdb> 146 atoms in block 14
Block first atom: 1910
Blocpdb> 131 atoms in block 15
Block first atom: 2056
Blocpdb> 151 atoms in block 16
Block first atom: 2187
Blocpdb> 146 atoms in block 17
Block first atom: 2338
Blocpdb> 156 atoms in block 18
Block first atom: 2484
Blocpdb> 154 atoms in block 19
Block first atom: 2640
Blocpdb> 145 atoms in block 20
Block first atom: 2794
Blocpdb> 132 atoms in block 21
Block first atom: 2939
Blocpdb> 139 atoms in block 22
Block first atom: 3071
Blocpdb> 154 atoms in block 23
Block first atom: 3210
Blocpdb> 149 atoms in block 24
Block first atom: 3364
Blocpdb> 131 atoms in block 25
Block first atom: 3513
Blocpdb> 142 atoms in block 26
Block first atom: 3644
Blocpdb> 153 atoms in block 27
Block first atom: 3786
Blocpdb> 139 atoms in block 28
Block first atom: 3939
Blocpdb> 144 atoms in block 29
Block first atom: 4078
Blocpdb> 128 atoms in block 30
Block first atom: 4222
Blocpdb> 154 atoms in block 31
Block first atom: 4350
Blocpdb> 23 atoms in block 32
Block first atom: 4504
Blocpdb> 152 atoms in block 33
Block first atom: 4527
Blocpdb> 134 atoms in block 34
Block first atom: 4679
Blocpdb> 141 atoms in block 35
Block first atom: 4813
Blocpdb> 155 atoms in block 36
Block first atom: 4954
Blocpdb> 157 atoms in block 37
Block first atom: 5109
Blocpdb> 135 atoms in block 38
Block first atom: 5266
Blocpdb> 134 atoms in block 39
Block first atom: 5401
Blocpdb> 133 atoms in block 40
Block first atom: 5535
Blocpdb> 59 atoms in block 41
Block first atom: 5668
Blocpdb> 130 atoms in block 42
Block first atom: 5727
Blocpdb> 151 atoms in block 43
Block first atom: 5857
Blocpdb> 128 atoms in block 44
Block first atom: 6008
Blocpdb> 143 atoms in block 45
Block first atom: 6136
Blocpdb> 121 atoms in block 46
Block first atom: 6279
Blocpdb> 144 atoms in block 47
Block first atom: 6400
Blocpdb> 131 atoms in block 48
Block first atom: 6544
Blocpdb> 141 atoms in block 49
Block first atom: 6675
Blocpdb> 150 atoms in block 50
Block first atom: 6816
Blocpdb> 140 atoms in block 51
Block first atom: 6966
Blocpdb> 37 atoms in block 52
Block first atom: 7106
Blocpdb> 160 atoms in block 53
Block first atom: 7143
Blocpdb> 136 atoms in block 54
Block first atom: 7303
Blocpdb> 130 atoms in block 55
Block first atom: 7439
Blocpdb> 143 atoms in block 56
Block first atom: 7569
Blocpdb> 153 atoms in block 57
Block first atom: 7712
Blocpdb> 152 atoms in block 58
Block first atom: 7865
Blocpdb> 160 atoms in block 59
Block first atom: 8017
Blocpdb> 152 atoms in block 60
Block first atom: 8177
Blocpdb> 161 atoms in block 61
Block first atom: 8329
Blocpdb> 145 atoms in block 62
Block first atom: 8490
Blocpdb> 125 atoms in block 63
Block first atom: 8635
Blocpdb> 152 atoms in block 64
Block first atom: 8760
Blocpdb> 140 atoms in block 65
Block first atom: 8912
Blocpdb> 146 atoms in block 66
Block first atom: 9052
Blocpdb> 131 atoms in block 67
Block first atom: 9198
Blocpdb> 151 atoms in block 68
Block first atom: 9329
Blocpdb> 146 atoms in block 69
Block first atom: 9480
Blocpdb> 156 atoms in block 70
Block first atom: 9626
Blocpdb> 154 atoms in block 71
Block first atom: 9782
Blocpdb> 145 atoms in block 72
Block first atom: 9936
Blocpdb> 132 atoms in block 73
Block first atom: 10081
Blocpdb> 139 atoms in block 74
Block first atom: 10213
Blocpdb> 154 atoms in block 75
Block first atom: 10352
Blocpdb> 149 atoms in block 76
Block first atom: 10506
Blocpdb> 131 atoms in block 77
Block first atom: 10655
Blocpdb> 142 atoms in block 78
Block first atom: 10786
Blocpdb> 153 atoms in block 79
Block first atom: 10928
Blocpdb> 139 atoms in block 80
Block first atom: 11081
Blocpdb> 144 atoms in block 81
Block first atom: 11220
Blocpdb> 128 atoms in block 82
Block first atom: 11364
Blocpdb> 154 atoms in block 83
Block first atom: 11492
Blocpdb> 23 atoms in block 84
Block first atom: 11646
Blocpdb> 152 atoms in block 85
Block first atom: 11669
Blocpdb> 134 atoms in block 86
Block first atom: 11821
Blocpdb> 141 atoms in block 87
Block first atom: 11955
Blocpdb> 155 atoms in block 88
Block first atom: 12096
Blocpdb> 157 atoms in block 89
Block first atom: 12251
Blocpdb> 135 atoms in block 90
Block first atom: 12408
Blocpdb> 134 atoms in block 91
Block first atom: 12543
Blocpdb> 133 atoms in block 92
Block first atom: 12677
Blocpdb> 59 atoms in block 93
Block first atom: 12810
Blocpdb> 130 atoms in block 94
Block first atom: 12869
Blocpdb> 151 atoms in block 95
Block first atom: 12999
Blocpdb> 128 atoms in block 96
Block first atom: 13150
Blocpdb> 143 atoms in block 97
Block first atom: 13278
Blocpdb> 121 atoms in block 98
Block first atom: 13421
Blocpdb> 144 atoms in block 99
Block first atom: 13542
Blocpdb> 131 atoms in block 100
Block first atom: 13686
Blocpdb> 141 atoms in block 101
Block first atom: 13817
Blocpdb> 150 atoms in block 102
Block first atom: 13958
Blocpdb> 140 atoms in block 103
Block first atom: 14108
Blocpdb> 37 atoms in block 104
Block first atom: 14248
Blocpdb> 160 atoms in block 105
Block first atom: 14285
Blocpdb> 136 atoms in block 106
Block first atom: 14445
Blocpdb> 130 atoms in block 107
Block first atom: 14581
Blocpdb> 143 atoms in block 108
Block first atom: 14711
Blocpdb> 153 atoms in block 109
Block first atom: 14854
Blocpdb> 152 atoms in block 110
Block first atom: 15007
Blocpdb> 160 atoms in block 111
Block first atom: 15159
Blocpdb> 152 atoms in block 112
Block first atom: 15319
Blocpdb> 161 atoms in block 113
Block first atom: 15471
Blocpdb> 145 atoms in block 114
Block first atom: 15632
Blocpdb> 125 atoms in block 115
Block first atom: 15777
Blocpdb> 152 atoms in block 116
Block first atom: 15902
Blocpdb> 140 atoms in block 117
Block first atom: 16054
Blocpdb> 146 atoms in block 118
Block first atom: 16194
Blocpdb> 131 atoms in block 119
Block first atom: 16340
Blocpdb> 151 atoms in block 120
Block first atom: 16471
Blocpdb> 146 atoms in block 121
Block first atom: 16622
Blocpdb> 156 atoms in block 122
Block first atom: 16768
Blocpdb> 154 atoms in block 123
Block first atom: 16924
Blocpdb> 145 atoms in block 124
Block first atom: 17078
Blocpdb> 132 atoms in block 125
Block first atom: 17223
Blocpdb> 139 atoms in block 126
Block first atom: 17355
Blocpdb> 154 atoms in block 127
Block first atom: 17494
Blocpdb> 149 atoms in block 128
Block first atom: 17648
Blocpdb> 131 atoms in block 129
Block first atom: 17797
Blocpdb> 142 atoms in block 130
Block first atom: 17928
Blocpdb> 153 atoms in block 131
Block first atom: 18070
Blocpdb> 139 atoms in block 132
Block first atom: 18223
Blocpdb> 144 atoms in block 133
Block first atom: 18362
Blocpdb> 128 atoms in block 134
Block first atom: 18506
Blocpdb> 154 atoms in block 135
Block first atom: 18634
Blocpdb> 23 atoms in block 136
Block first atom: 18788
Blocpdb> 152 atoms in block 137
Block first atom: 18811
Blocpdb> 134 atoms in block 138
Block first atom: 18963
Blocpdb> 141 atoms in block 139
Block first atom: 19097
Blocpdb> 155 atoms in block 140
Block first atom: 19238
Blocpdb> 157 atoms in block 141
Block first atom: 19393
Blocpdb> 135 atoms in block 142
Block first atom: 19550
Blocpdb> 134 atoms in block 143
Block first atom: 19685
Blocpdb> 133 atoms in block 144
Block first atom: 19819
Blocpdb> 59 atoms in block 145
Block first atom: 19952
Blocpdb> 130 atoms in block 146
Block first atom: 20011
Blocpdb> 151 atoms in block 147
Block first atom: 20141
Blocpdb> 128 atoms in block 148
Block first atom: 20292
Blocpdb> 143 atoms in block 149
Block first atom: 20420
Blocpdb> 121 atoms in block 150
Block first atom: 20563
Blocpdb> 144 atoms in block 151
Block first atom: 20684
Blocpdb> 131 atoms in block 152
Block first atom: 20828
Blocpdb> 141 atoms in block 153
Block first atom: 20959
Blocpdb> 150 atoms in block 154
Block first atom: 21100
Blocpdb> 140 atoms in block 155
Block first atom: 21250
Blocpdb> 37 atoms in block 156
Block first atom: 21390
Blocpdb> 160 atoms in block 157
Block first atom: 21427
Blocpdb> 136 atoms in block 158
Block first atom: 21587
Blocpdb> 130 atoms in block 159
Block first atom: 21723
Blocpdb> 143 atoms in block 160
Block first atom: 21853
Blocpdb> 153 atoms in block 161
Block first atom: 21996
Blocpdb> 152 atoms in block 162
Block first atom: 22149
Blocpdb> 160 atoms in block 163
Block first atom: 22301
Blocpdb> 152 atoms in block 164
Block first atom: 22461
Blocpdb> 161 atoms in block 165
Block first atom: 22613
Blocpdb> 145 atoms in block 166
Block first atom: 22774
Blocpdb> 125 atoms in block 167
Block first atom: 22919
Blocpdb> 152 atoms in block 168
Block first atom: 23044
Blocpdb> 140 atoms in block 169
Block first atom: 23196
Blocpdb> 146 atoms in block 170
Block first atom: 23336
Blocpdb> 131 atoms in block 171
Block first atom: 23482
Blocpdb> 151 atoms in block 172
Block first atom: 23613
Blocpdb> 146 atoms in block 173
Block first atom: 23764
Blocpdb> 156 atoms in block 174
Block first atom: 23910
Blocpdb> 154 atoms in block 175
Block first atom: 24066
Blocpdb> 145 atoms in block 176
Block first atom: 24220
Blocpdb> 132 atoms in block 177
Block first atom: 24365
Blocpdb> 139 atoms in block 178
Block first atom: 24497
Blocpdb> 154 atoms in block 179
Block first atom: 24636
Blocpdb> 149 atoms in block 180
Block first atom: 24790
Blocpdb> 131 atoms in block 181
Block first atom: 24939
Blocpdb> 142 atoms in block 182
Block first atom: 25070
Blocpdb> 153 atoms in block 183
Block first atom: 25212
Blocpdb> 139 atoms in block 184
Block first atom: 25365
Blocpdb> 144 atoms in block 185
Block first atom: 25504
Blocpdb> 128 atoms in block 186
Block first atom: 25648
Blocpdb> 154 atoms in block 187
Block first atom: 25776
Blocpdb> 23 atoms in block 188
Block first atom: 25930
Blocpdb> 152 atoms in block 189
Block first atom: 25953
Blocpdb> 134 atoms in block 190
Block first atom: 26105
Blocpdb> 141 atoms in block 191
Block first atom: 26239
Blocpdb> 155 atoms in block 192
Block first atom: 26380
Blocpdb> 157 atoms in block 193
Block first atom: 26535
Blocpdb> 135 atoms in block 194
Block first atom: 26692
Blocpdb> 134 atoms in block 195
Block first atom: 26827
Blocpdb> 133 atoms in block 196
Block first atom: 26961
Blocpdb> 59 atoms in block 197
Block first atom: 27094
Blocpdb> 130 atoms in block 198
Block first atom: 27153
Blocpdb> 151 atoms in block 199
Block first atom: 27283
Blocpdb> 128 atoms in block 200
Block first atom: 27434
Blocpdb> 143 atoms in block 201
Block first atom: 27562
Blocpdb> 121 atoms in block 202
Block first atom: 27705
Blocpdb> 144 atoms in block 203
Block first atom: 27826
Blocpdb> 131 atoms in block 204
Block first atom: 27970
Blocpdb> 141 atoms in block 205
Block first atom: 28101
Blocpdb> 150 atoms in block 206
Block first atom: 28242
Blocpdb> 140 atoms in block 207
Block first atom: 28392
Blocpdb> 37 atoms in block 208
Block first atom: 28531
Blocpdb> 208 blocks.
Blocpdb> At most, 161 atoms in each of them.
Blocpdb> At least, 23 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: 41628322 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 0m0.163s
user 0m0.152s
sys 0m0.010s
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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