*** ***
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 = 240222223528421046.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 240222223528421046.atom to be opened.
Openam> File opened: 240222223528421046.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 = 1496
First residue number = 21
Last residue number = 768
Number of atoms found = 24010
Mean number per residue = 16.0
Pdbmat> Coordinate statistics:
= 50.436000 +/- 16.505408 From: 9.443000 To: 91.429000
= 71.772000 +/- 30.595373 From: 9.844000 To: 133.700000
= 87.930836 +/- 27.623470 From: -27.324000 To: 133.093000
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 3.8201 % Filled.
Pdbmat> 17064680 non-zero elements.
Pdbmat> 1880415 atom-atom interactions.
Pdbmat> Number per atom= 156.64 +/- 43.72
Maximum number = 237
Minimum number = 30
Pdbmat> Matrix trace = 3.760830E+07
Pdbmat> Larger element = 859.536
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
1496 non-zero elements, NRBL set to 8
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 = 240222223528421046.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 8
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 240222223528421046.atom to be opened.
Openam> file on opening on unit 11:
240222223528421046.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 24010 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 8 residue(s) per block.
Blocpdb> 1496 residues.
Blocpdb> 134 atoms in block 1
Block first atom: 1
Blocpdb> 129 atoms in block 2
Block first atom: 135
Blocpdb> 126 atoms in block 3
Block first atom: 264
Blocpdb> 127 atoms in block 4
Block first atom: 390
Blocpdb> 124 atoms in block 5
Block first atom: 517
Blocpdb> 110 atoms in block 6
Block first atom: 641
Blocpdb> 138 atoms in block 7
Block first atom: 751
Blocpdb> 123 atoms in block 8
Block first atom: 889
Blocpdb> 134 atoms in block 9
Block first atom: 1012
Blocpdb> 139 atoms in block 10
Block first atom: 1146
Blocpdb> 112 atoms in block 11
Block first atom: 1285
Blocpdb> 136 atoms in block 12
Block first atom: 1397
Blocpdb> 122 atoms in block 13
Block first atom: 1533
Blocpdb> 124 atoms in block 14
Block first atom: 1655
Blocpdb> 111 atoms in block 15
Block first atom: 1779
Blocpdb> 123 atoms in block 16
Block first atom: 1890
Blocpdb> 119 atoms in block 17
Block first atom: 2013
Blocpdb> 139 atoms in block 18
Block first atom: 2132
Blocpdb> 140 atoms in block 19
Block first atom: 2271
Blocpdb> 143 atoms in block 20
Block first atom: 2411
Blocpdb> 138 atoms in block 21
Block first atom: 2554
Blocpdb> 128 atoms in block 22
Block first atom: 2692
Blocpdb> 136 atoms in block 23
Block first atom: 2820
Blocpdb> 108 atoms in block 24
Block first atom: 2956
Blocpdb> 115 atoms in block 25
Block first atom: 3064
Blocpdb> 130 atoms in block 26
Block first atom: 3179
Blocpdb> 138 atoms in block 27
Block first atom: 3309
Blocpdb> 136 atoms in block 28
Block first atom: 3447
Blocpdb> 137 atoms in block 29
Block first atom: 3583
Blocpdb> 116 atoms in block 30
Block first atom: 3720
Blocpdb> 116 atoms in block 31
Block first atom: 3836
Blocpdb> 142 atoms in block 32
Block first atom: 3952
Blocpdb> 128 atoms in block 33
Block first atom: 4094
Blocpdb> 125 atoms in block 34
Block first atom: 4222
Blocpdb> 114 atoms in block 35
Block first atom: 4347
Blocpdb> 136 atoms in block 36
Block first atom: 4461
Blocpdb> 140 atoms in block 37
Block first atom: 4597
Blocpdb> 112 atoms in block 38
Block first atom: 4737
Blocpdb> 125 atoms in block 39
Block first atom: 4849
Blocpdb> 113 atoms in block 40
Block first atom: 4974
Blocpdb> 114 atoms in block 41
Block first atom: 5087
Blocpdb> 123 atoms in block 42
Block first atom: 5201
Blocpdb> 142 atoms in block 43
Block first atom: 5324
Blocpdb> 118 atoms in block 44
Block first atom: 5466
Blocpdb> 126 atoms in block 45
Block first atom: 5584
Blocpdb> 118 atoms in block 46
Block first atom: 5710
Blocpdb> 127 atoms in block 47
Block first atom: 5828
Blocpdb> 114 atoms in block 48
Block first atom: 5955
Blocpdb> 109 atoms in block 49
Block first atom: 6069
Blocpdb> 129 atoms in block 50
Block first atom: 6178
Blocpdb> 121 atoms in block 51
Block first atom: 6307
Blocpdb> 121 atoms in block 52
Block first atom: 6428
Blocpdb> 140 atoms in block 53
Block first atom: 6549
Blocpdb> 123 atoms in block 54
Block first atom: 6689
Blocpdb> 156 atoms in block 55
Block first atom: 6812
Blocpdb> 140 atoms in block 56
Block first atom: 6968
Blocpdb> 150 atoms in block 57
Block first atom: 7108
Blocpdb> 160 atoms in block 58
Block first atom: 7258
Blocpdb> 114 atoms in block 59
Block first atom: 7418
Blocpdb> 116 atoms in block 60
Block first atom: 7532
Blocpdb> 118 atoms in block 61
Block first atom: 7648
Blocpdb> 149 atoms in block 62
Block first atom: 7766
Blocpdb> 146 atoms in block 63
Block first atom: 7915
Blocpdb> 119 atoms in block 64
Block first atom: 8061
Blocpdb> 121 atoms in block 65
Block first atom: 8180
Blocpdb> 114 atoms in block 66
Block first atom: 8301
Blocpdb> 124 atoms in block 67
Block first atom: 8415
Blocpdb> 134 atoms in block 68
Block first atom: 8539
Blocpdb> 129 atoms in block 69
Block first atom: 8673
Blocpdb> 116 atoms in block 70
Block first atom: 8802
Blocpdb> 147 atoms in block 71
Block first atom: 8918
Blocpdb> 147 atoms in block 72
Block first atom: 9065
Blocpdb> 126 atoms in block 73
Block first atom: 9212
Blocpdb> 117 atoms in block 74
Block first atom: 9338
Blocpdb> 128 atoms in block 75
Block first atom: 9455
Blocpdb> 135 atoms in block 76
Block first atom: 9583
Blocpdb> 125 atoms in block 77
Block first atom: 9718
Blocpdb> 142 atoms in block 78
Block first atom: 9843
Blocpdb> 120 atoms in block 79
Block first atom: 9985
Blocpdb> 151 atoms in block 80
Block first atom: 10105
Blocpdb> 129 atoms in block 81
Block first atom: 10256
Blocpdb> 133 atoms in block 82
Block first atom: 10385
Blocpdb> 142 atoms in block 83
Block first atom: 10518
Blocpdb> 117 atoms in block 84
Block first atom: 10660
Blocpdb> 133 atoms in block 85
Block first atom: 10777
Blocpdb> 142 atoms in block 86
Block first atom: 10910
Blocpdb> 134 atoms in block 87
Block first atom: 11052
Blocpdb> 124 atoms in block 88
Block first atom: 11186
Blocpdb> 116 atoms in block 89
Block first atom: 11310
Blocpdb> 114 atoms in block 90
Block first atom: 11426
Blocpdb> 140 atoms in block 91
Block first atom: 11540
Blocpdb> 114 atoms in block 92
Block first atom: 11680
Blocpdb> 133 atoms in block 93
Block first atom: 11794
Blocpdb> 79 atoms in block 94
Block first atom: 11927
Blocpdb> 134 atoms in block 95
Block first atom: 12006
Blocpdb> 129 atoms in block 96
Block first atom: 12140
Blocpdb> 126 atoms in block 97
Block first atom: 12269
Blocpdb> 127 atoms in block 98
Block first atom: 12395
Blocpdb> 124 atoms in block 99
Block first atom: 12522
Blocpdb> 110 atoms in block 100
Block first atom: 12646
Blocpdb> 138 atoms in block 101
Block first atom: 12756
Blocpdb> 123 atoms in block 102
Block first atom: 12894
Blocpdb> 134 atoms in block 103
Block first atom: 13017
Blocpdb> 139 atoms in block 104
Block first atom: 13151
Blocpdb> 112 atoms in block 105
Block first atom: 13290
Blocpdb> 136 atoms in block 106
Block first atom: 13402
Blocpdb> 122 atoms in block 107
Block first atom: 13538
Blocpdb> 124 atoms in block 108
Block first atom: 13660
Blocpdb> 111 atoms in block 109
Block first atom: 13784
Blocpdb> 123 atoms in block 110
Block first atom: 13895
Blocpdb> 119 atoms in block 111
Block first atom: 14018
Blocpdb> 139 atoms in block 112
Block first atom: 14137
Blocpdb> 140 atoms in block 113
Block first atom: 14276
Blocpdb> 143 atoms in block 114
Block first atom: 14416
Blocpdb> 138 atoms in block 115
Block first atom: 14559
Blocpdb> 128 atoms in block 116
Block first atom: 14697
Blocpdb> 136 atoms in block 117
Block first atom: 14825
Blocpdb> 108 atoms in block 118
Block first atom: 14961
Blocpdb> 115 atoms in block 119
Block first atom: 15069
Blocpdb> 130 atoms in block 120
Block first atom: 15184
Blocpdb> 138 atoms in block 121
Block first atom: 15314
Blocpdb> 136 atoms in block 122
Block first atom: 15452
Blocpdb> 137 atoms in block 123
Block first atom: 15588
Blocpdb> 116 atoms in block 124
Block first atom: 15725
Blocpdb> 116 atoms in block 125
Block first atom: 15841
Blocpdb> 142 atoms in block 126
Block first atom: 15957
Blocpdb> 128 atoms in block 127
Block first atom: 16099
Blocpdb> 125 atoms in block 128
Block first atom: 16227
Blocpdb> 114 atoms in block 129
Block first atom: 16352
Blocpdb> 136 atoms in block 130
Block first atom: 16466
Blocpdb> 140 atoms in block 131
Block first atom: 16602
Blocpdb> 112 atoms in block 132
Block first atom: 16742
Blocpdb> 125 atoms in block 133
Block first atom: 16854
Blocpdb> 113 atoms in block 134
Block first atom: 16979
Blocpdb> 114 atoms in block 135
Block first atom: 17092
Blocpdb> 123 atoms in block 136
Block first atom: 17206
Blocpdb> 142 atoms in block 137
Block first atom: 17329
Blocpdb> 118 atoms in block 138
Block first atom: 17471
Blocpdb> 126 atoms in block 139
Block first atom: 17589
Blocpdb> 118 atoms in block 140
Block first atom: 17715
Blocpdb> 127 atoms in block 141
Block first atom: 17833
Blocpdb> 114 atoms in block 142
Block first atom: 17960
Blocpdb> 109 atoms in block 143
Block first atom: 18074
Blocpdb> 129 atoms in block 144
Block first atom: 18183
Blocpdb> 121 atoms in block 145
Block first atom: 18312
Blocpdb> 121 atoms in block 146
Block first atom: 18433
Blocpdb> 140 atoms in block 147
Block first atom: 18554
Blocpdb> 123 atoms in block 148
Block first atom: 18694
Blocpdb> 156 atoms in block 149
Block first atom: 18817
Blocpdb> 140 atoms in block 150
Block first atom: 18973
Blocpdb> 150 atoms in block 151
Block first atom: 19113
Blocpdb> 160 atoms in block 152
Block first atom: 19263
Blocpdb> 114 atoms in block 153
Block first atom: 19423
Blocpdb> 116 atoms in block 154
Block first atom: 19537
Blocpdb> 118 atoms in block 155
Block first atom: 19653
Blocpdb> 149 atoms in block 156
Block first atom: 19771
Blocpdb> 146 atoms in block 157
Block first atom: 19920
Blocpdb> 119 atoms in block 158
Block first atom: 20066
Blocpdb> 121 atoms in block 159
Block first atom: 20185
Blocpdb> 114 atoms in block 160
Block first atom: 20306
Blocpdb> 124 atoms in block 161
Block first atom: 20420
Blocpdb> 134 atoms in block 162
Block first atom: 20544
Blocpdb> 129 atoms in block 163
Block first atom: 20678
Blocpdb> 116 atoms in block 164
Block first atom: 20807
Blocpdb> 147 atoms in block 165
Block first atom: 20923
Blocpdb> 147 atoms in block 166
Block first atom: 21070
Blocpdb> 126 atoms in block 167
Block first atom: 21217
Blocpdb> 117 atoms in block 168
Block first atom: 21343
Blocpdb> 128 atoms in block 169
Block first atom: 21460
Blocpdb> 135 atoms in block 170
Block first atom: 21588
Blocpdb> 125 atoms in block 171
Block first atom: 21723
Blocpdb> 142 atoms in block 172
Block first atom: 21848
Blocpdb> 120 atoms in block 173
Block first atom: 21990
Blocpdb> 151 atoms in block 174
Block first atom: 22110
Blocpdb> 129 atoms in block 175
Block first atom: 22261
Blocpdb> 133 atoms in block 176
Block first atom: 22390
Blocpdb> 142 atoms in block 177
Block first atom: 22523
Blocpdb> 117 atoms in block 178
Block first atom: 22665
Blocpdb> 133 atoms in block 179
Block first atom: 22782
Blocpdb> 142 atoms in block 180
Block first atom: 22915
Blocpdb> 134 atoms in block 181
Block first atom: 23057
Blocpdb> 124 atoms in block 182
Block first atom: 23191
Blocpdb> 116 atoms in block 183
Block first atom: 23315
Blocpdb> 114 atoms in block 184
Block first atom: 23431
Blocpdb> 140 atoms in block 185
Block first atom: 23545
Blocpdb> 114 atoms in block 186
Block first atom: 23685
Blocpdb> 133 atoms in block 187
Block first atom: 23799
Blocpdb> 79 atoms in block 188
Block first atom: 23931
Blocpdb> 188 blocks.
Blocpdb> At most, 160 atoms in each of them.
Blocpdb> At least, 79 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: 34804801 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 0m0.126s
user 0m0.126s
sys 0m0.000s
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).
Last modification: April 25th, 2023.
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