*** ***
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 = 2607190354442417949.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 2607190354442417949.atom to be opened.
Openam> File opened: 2607190354442417949.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 = 6444
First residue number = 1
Last residue number = 21
Number of atoms found = 27648
Mean number per residue = 4.3
Pdbmat> Coordinate statistics:
= 159.541897 +/- 41.104556 From: 68.470000 To: 250.615000
= 159.544801 +/- 41.105632 From: 75.023000 To: 252.274000
= 159.554804 +/- 32.040203 From: 101.148000 To: 217.967000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'G ' is not a well known amino-acid.
%Pdbmat-W> residue:'G ' is not a well known amino-acid.
%Pdbmat-W> residue:'G ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'A ' is not a well known amino-acid.
%Pdbmat-W> residue:'G ' is not a well known amino-acid.
%Pdbmat-W> residue:'G ' is not a well known amino-acid.
%Pdbmat-W> residue:'G ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 300 residue(s) not known.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is -0.6296 % Filled.
Pdbmat> 5383532 non-zero elements.
Pdbmat> 579851 atom-atom interactions.
Pdbmat> Number per atom= 41.95 +/- 10.98
Maximum number = 80
Minimum number = 9
Pdbmat> Matrix trace = 1.159702E+07
Pdbmat> Larger element = 367.090
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
6444 non-zero elements, NRBL set to 33
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 = 2607190354442417949.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 33
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 2607190354442417949.atom to be opened.
Openam> file on opening on unit 11:
2607190354442417949.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 27648 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 33 residue(s) per block.
Blocpdb> 6444 residues.
Blocpdb> 132 atoms in block 1
Block first atom: 1
Blocpdb> 132 atoms in block 2
Block first atom: 133
Blocpdb> 61 atoms in block 3
Block first atom: 265
Blocpdb> 132 atoms in block 4
Block first atom: 326
Blocpdb> 40 atoms in block 5
Block first atom: 458
Blocpdb> 124 atoms in block 6
Block first atom: 498
Blocpdb> 132 atoms in block 7
Block first atom: 622
Blocpdb> 68 atoms in block 8
Block first atom: 754
Blocpdb> 132 atoms in block 9
Block first atom: 822
Blocpdb> 132 atoms in block 10
Block first atom: 954
Blocpdb> 132 atoms in block 11
Block first atom: 1086
Blocpdb> 132 atoms in block 12
Block first atom: 1218
Blocpdb> 132 atoms in block 13
Block first atom: 1350
Blocpdb> 132 atoms in block 14
Block first atom: 1482
Blocpdb> 132 atoms in block 15
Block first atom: 1614
Blocpdb> 132 atoms in block 16
Block first atom: 1746
Blocpdb> 20 atoms in block 17
Block first atom: 1878
Blocpdb> 132 atoms in block 18
Block first atom: 1898
Blocpdb> 132 atoms in block 19
Block first atom: 2030
Blocpdb> 132 atoms in block 20
Block first atom: 2162
Blocpdb> 132 atoms in block 21
Block first atom: 2294
Blocpdb> 132 atoms in block 22
Block first atom: 2426
Blocpdb> 132 atoms in block 23
Block first atom: 2558
Blocpdb> 132 atoms in block 24
Block first atom: 2690
Blocpdb> 132 atoms in block 25
Block first atom: 2822
Blocpdb> 132 atoms in block 26
Block first atom: 2954
Blocpdb> 132 atoms in block 27
Block first atom: 3086
Blocpdb> 132 atoms in block 28
Block first atom: 3218
Blocpdb> 132 atoms in block 29
Block first atom: 3350
Blocpdb> 132 atoms in block 30
Block first atom: 3482
Blocpdb> 132 atoms in block 31
Block first atom: 3614
Blocpdb> 132 atoms in block 32
Block first atom: 3746
Blocpdb> 132 atoms in block 33
Block first atom: 3878
Blocpdb> 89 atoms in block 34
Block first atom: 4010
Blocpdb> 300 atoms in block 35
Block first atom: 4099
Blocpdb> 210 atoms in block 36
Block first atom: 4399
Blocpdb> 132 atoms in block 37
Block first atom: 4609
Blocpdb> 132 atoms in block 38
Block first atom: 4741
Blocpdb> 61 atoms in block 39
Block first atom: 4873
Blocpdb> 132 atoms in block 40
Block first atom: 4934
Blocpdb> 40 atoms in block 41
Block first atom: 5066
Blocpdb> 124 atoms in block 42
Block first atom: 5106
Blocpdb> 132 atoms in block 43
Block first atom: 5230
Blocpdb> 68 atoms in block 44
Block first atom: 5362
Blocpdb> 132 atoms in block 45
Block first atom: 5430
Blocpdb> 132 atoms in block 46
Block first atom: 5562
Blocpdb> 132 atoms in block 47
Block first atom: 5694
Blocpdb> 132 atoms in block 48
Block first atom: 5826
Blocpdb> 132 atoms in block 49
Block first atom: 5958
Blocpdb> 132 atoms in block 50
Block first atom: 6090
Blocpdb> 132 atoms in block 51
Block first atom: 6222
Blocpdb> 132 atoms in block 52
Block first atom: 6354
Blocpdb> 20 atoms in block 53
Block first atom: 6486
Blocpdb> 132 atoms in block 54
Block first atom: 6506
Blocpdb> 132 atoms in block 55
Block first atom: 6638
Blocpdb> 132 atoms in block 56
Block first atom: 6770
Blocpdb> 132 atoms in block 57
Block first atom: 6902
Blocpdb> 132 atoms in block 58
Block first atom: 7034
Blocpdb> 132 atoms in block 59
Block first atom: 7166
Blocpdb> 132 atoms in block 60
Block first atom: 7298
Blocpdb> 132 atoms in block 61
Block first atom: 7430
Blocpdb> 132 atoms in block 62
Block first atom: 7562
Blocpdb> 132 atoms in block 63
Block first atom: 7694
Blocpdb> 132 atoms in block 64
Block first atom: 7826
Blocpdb> 132 atoms in block 65
Block first atom: 7958
Blocpdb> 132 atoms in block 66
Block first atom: 8090
Blocpdb> 132 atoms in block 67
Block first atom: 8222
Blocpdb> 132 atoms in block 68
Block first atom: 8354
Blocpdb> 132 atoms in block 69
Block first atom: 8486
Blocpdb> 89 atoms in block 70
Block first atom: 8618
Blocpdb> 300 atoms in block 71
Block first atom: 8707
Blocpdb> 210 atoms in block 72
Block first atom: 9007
Blocpdb> 132 atoms in block 73
Block first atom: 9217
Blocpdb> 132 atoms in block 74
Block first atom: 9349
Blocpdb> 61 atoms in block 75
Block first atom: 9481
Blocpdb> 132 atoms in block 76
Block first atom: 9542
Blocpdb> 40 atoms in block 77
Block first atom: 9674
Blocpdb> 124 atoms in block 78
Block first atom: 9714
Blocpdb> 132 atoms in block 79
Block first atom: 9838
Blocpdb> 68 atoms in block 80
Block first atom: 9970
Blocpdb> 132 atoms in block 81
Block first atom: 10038
Blocpdb> 132 atoms in block 82
Block first atom: 10170
Blocpdb> 132 atoms in block 83
Block first atom: 10302
Blocpdb> 132 atoms in block 84
Block first atom: 10434
Blocpdb> 132 atoms in block 85
Block first atom: 10566
Blocpdb> 132 atoms in block 86
Block first atom: 10698
Blocpdb> 132 atoms in block 87
Block first atom: 10830
Blocpdb> 132 atoms in block 88
Block first atom: 10962
Blocpdb> 20 atoms in block 89
Block first atom: 11094
Blocpdb> 132 atoms in block 90
Block first atom: 11114
Blocpdb> 132 atoms in block 91
Block first atom: 11246
Blocpdb> 132 atoms in block 92
Block first atom: 11378
Blocpdb> 132 atoms in block 93
Block first atom: 11510
Blocpdb> 132 atoms in block 94
Block first atom: 11642
Blocpdb> 132 atoms in block 95
Block first atom: 11774
Blocpdb> 132 atoms in block 96
Block first atom: 11906
Blocpdb> 132 atoms in block 97
Block first atom: 12038
Blocpdb> 132 atoms in block 98
Block first atom: 12170
Blocpdb> 132 atoms in block 99
Block first atom: 12302
Blocpdb> 132 atoms in block 100
Block first atom: 12434
Blocpdb> 132 atoms in block 101
Block first atom: 12566
Blocpdb> 132 atoms in block 102
Block first atom: 12698
Blocpdb> 132 atoms in block 103
Block first atom: 12830
Blocpdb> 132 atoms in block 104
Block first atom: 12962
Blocpdb> 132 atoms in block 105
Block first atom: 13094
Blocpdb> 89 atoms in block 106
Block first atom: 13226
Blocpdb> 300 atoms in block 107
Block first atom: 13315
Blocpdb> 210 atoms in block 108
Block first atom: 13615
Blocpdb> 132 atoms in block 109
Block first atom: 13825
Blocpdb> 132 atoms in block 110
Block first atom: 13957
Blocpdb> 61 atoms in block 111
Block first atom: 14089
Blocpdb> 132 atoms in block 112
Block first atom: 14150
Blocpdb> 40 atoms in block 113
Block first atom: 14282
Blocpdb> 124 atoms in block 114
Block first atom: 14322
Blocpdb> 132 atoms in block 115
Block first atom: 14446
Blocpdb> 68 atoms in block 116
Block first atom: 14578
Blocpdb> 132 atoms in block 117
Block first atom: 14646
Blocpdb> 132 atoms in block 118
Block first atom: 14778
Blocpdb> 132 atoms in block 119
Block first atom: 14910
Blocpdb> 132 atoms in block 120
Block first atom: 15042
Blocpdb> 132 atoms in block 121
Block first atom: 15174
Blocpdb> 132 atoms in block 122
Block first atom: 15306
Blocpdb> 132 atoms in block 123
Block first atom: 15438
Blocpdb> 132 atoms in block 124
Block first atom: 15570
Blocpdb> 20 atoms in block 125
Block first atom: 15702
Blocpdb> 132 atoms in block 126
Block first atom: 15722
Blocpdb> 132 atoms in block 127
Block first atom: 15854
Blocpdb> 132 atoms in block 128
Block first atom: 15986
Blocpdb> 132 atoms in block 129
Block first atom: 16118
Blocpdb> 132 atoms in block 130
Block first atom: 16250
Blocpdb> 132 atoms in block 131
Block first atom: 16382
Blocpdb> 132 atoms in block 132
Block first atom: 16514
Blocpdb> 132 atoms in block 133
Block first atom: 16646
Blocpdb> 132 atoms in block 134
Block first atom: 16778
Blocpdb> 132 atoms in block 135
Block first atom: 16910
Blocpdb> 132 atoms in block 136
Block first atom: 17042
Blocpdb> 132 atoms in block 137
Block first atom: 17174
Blocpdb> 132 atoms in block 138
Block first atom: 17306
Blocpdb> 132 atoms in block 139
Block first atom: 17438
Blocpdb> 132 atoms in block 140
Block first atom: 17570
Blocpdb> 132 atoms in block 141
Block first atom: 17702
Blocpdb> 89 atoms in block 142
Block first atom: 17834
Blocpdb> 300 atoms in block 143
Block first atom: 17923
Blocpdb> 210 atoms in block 144
Block first atom: 18223
Blocpdb> 132 atoms in block 145
Block first atom: 18433
Blocpdb> 132 atoms in block 146
Block first atom: 18565
Blocpdb> 61 atoms in block 147
Block first atom: 18697
Blocpdb> 132 atoms in block 148
Block first atom: 18758
Blocpdb> 40 atoms in block 149
Block first atom: 18890
Blocpdb> 124 atoms in block 150
Block first atom: 18930
Blocpdb> 132 atoms in block 151
Block first atom: 19054
Blocpdb> 68 atoms in block 152
Block first atom: 19186
Blocpdb> 132 atoms in block 153
Block first atom: 19254
Blocpdb> 132 atoms in block 154
Block first atom: 19386
Blocpdb> 132 atoms in block 155
Block first atom: 19518
Blocpdb> 132 atoms in block 156
Block first atom: 19650
Blocpdb> 132 atoms in block 157
Block first atom: 19782
Blocpdb> 132 atoms in block 158
Block first atom: 19914
Blocpdb> 132 atoms in block 159
Block first atom: 20046
Blocpdb> 132 atoms in block 160
Block first atom: 20178
Blocpdb> 20 atoms in block 161
Block first atom: 20310
Blocpdb> 132 atoms in block 162
Block first atom: 20330
Blocpdb> 132 atoms in block 163
Block first atom: 20462
Blocpdb> 132 atoms in block 164
Block first atom: 20594
Blocpdb> 132 atoms in block 165
Block first atom: 20726
Blocpdb> 132 atoms in block 166
Block first atom: 20858
Blocpdb> 132 atoms in block 167
Block first atom: 20990
Blocpdb> 132 atoms in block 168
Block first atom: 21122
Blocpdb> 132 atoms in block 169
Block first atom: 21254
Blocpdb> 132 atoms in block 170
Block first atom: 21386
Blocpdb> 132 atoms in block 171
Block first atom: 21518
Blocpdb> 132 atoms in block 172
Block first atom: 21650
Blocpdb> 132 atoms in block 173
Block first atom: 21782
Blocpdb> 132 atoms in block 174
Block first atom: 21914
Blocpdb> 132 atoms in block 175
Block first atom: 22046
Blocpdb> 132 atoms in block 176
Block first atom: 22178
Blocpdb> 132 atoms in block 177
Block first atom: 22310
Blocpdb> 89 atoms in block 178
Block first atom: 22442
Blocpdb> 300 atoms in block 179
Block first atom: 22531
Blocpdb> 210 atoms in block 180
Block first atom: 22831
Blocpdb> 132 atoms in block 181
Block first atom: 23041
Blocpdb> 132 atoms in block 182
Block first atom: 23173
Blocpdb> 61 atoms in block 183
Block first atom: 23305
Blocpdb> 132 atoms in block 184
Block first atom: 23366
Blocpdb> 40 atoms in block 185
Block first atom: 23498
Blocpdb> 124 atoms in block 186
Block first atom: 23538
Blocpdb> 132 atoms in block 187
Block first atom: 23662
Blocpdb> 68 atoms in block 188
Block first atom: 23794
Blocpdb> 132 atoms in block 189
Block first atom: 23862
Blocpdb> 132 atoms in block 190
Block first atom: 23994
Blocpdb> 132 atoms in block 191
Block first atom: 24126
Blocpdb> 132 atoms in block 192
Block first atom: 24258
Blocpdb> 132 atoms in block 193
Block first atom: 24390
Blocpdb> 132 atoms in block 194
Block first atom: 24522
Blocpdb> 132 atoms in block 195
Block first atom: 24654
Blocpdb> 132 atoms in block 196
Block first atom: 24786
Blocpdb> 20 atoms in block 197
Block first atom: 24918
Blocpdb> 132 atoms in block 198
Block first atom: 24938
Blocpdb> 132 atoms in block 199
Block first atom: 25070
Blocpdb> 132 atoms in block 200
Block first atom: 25202
Blocpdb> 132 atoms in block 201
Block first atom: 25334
Blocpdb> 132 atoms in block 202
Block first atom: 25466
Blocpdb> 132 atoms in block 203
Block first atom: 25598
Blocpdb> 132 atoms in block 204
Block first atom: 25730
Blocpdb> 132 atoms in block 205
Block first atom: 25862
Blocpdb> 132 atoms in block 206
Block first atom: 25994
Blocpdb> 132 atoms in block 207
Block first atom: 26126
Blocpdb> 132 atoms in block 208
Block first atom: 26258
Blocpdb> 132 atoms in block 209
Block first atom: 26390
Blocpdb> 132 atoms in block 210
Block first atom: 26522
Blocpdb> 132 atoms in block 211
Block first atom: 26654
Blocpdb> 132 atoms in block 212
Block first atom: 26786
Blocpdb> 132 atoms in block 213
Block first atom: 26918
Blocpdb> 89 atoms in block 214
Block first atom: 27050
Blocpdb> 300 atoms in block 215
Block first atom: 27139
Blocpdb> 210 atoms in block 216
Block first atom: 27438
Blocpdb> 216 blocks.
Blocpdb> At most, 300 atoms in each of them.
Blocpdb> At least, 20 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: 75459601 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 0m0.127s
user 0m0.119s
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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