*** 6000DD01A29101E0 ***
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 = 260507230358735715.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 260507230358735715.atom to be opened.
Openam> File opened: 260507230358735715.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 = 3091
First residue number = 1
Last residue number = 183
Number of atoms found = 23670
Mean number per residue = 7.7
Pdbmat> Coordinate statistics:
= -3.019824 +/- 37.998089 From: -100.617000 To: 89.135000
= -0.856493 +/- 59.479178 From: -136.327000 To: 133.727000
= 0.303921 +/- 39.604078 From: -102.957000 To: 97.607000
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 1.9448 % Filled.
Pdbmat> 7269009 non-zero elements.
Pdbmat> 792011 atom-atom interactions.
Pdbmat> Number per atom= 66.92 +/- 24.96
Maximum number = 173
Minimum number = 7
Pdbmat> Matrix trace = 1.584022E+07
Pdbmat> Larger element = 634.191
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3091 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 = 260507230358735715.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 260507230358735715.atom to be opened.
Openam> file on opening on unit 11:
260507230358735715.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 23670 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> 3091 residues.
Blocpdb> 128 atoms in block 1
Block first atom: 1
Blocpdb> 111 atoms in block 2
Block first atom: 129
Blocpdb> 126 atoms in block 3
Block first atom: 240
Blocpdb> 141 atoms in block 4
Block first atom: 366
Blocpdb> 126 atoms in block 5
Block first atom: 507
Blocpdb> 136 atoms in block 6
Block first atom: 633
Blocpdb> 114 atoms in block 7
Block first atom: 769
Blocpdb> 112 atoms in block 8
Block first atom: 883
Blocpdb> 113 atoms in block 9
Block first atom: 995
Blocpdb> 114 atoms in block 10
Block first atom: 1108
Blocpdb> 132 atoms in block 11
Block first atom: 1222
Blocpdb> 140 atoms in block 12
Block first atom: 1354
Blocpdb> 124 atoms in block 13
Block first atom: 1494
Blocpdb> 127 atoms in block 14
Block first atom: 1618
Blocpdb> 127 atoms in block 15
Block first atom: 1745
Blocpdb> 134 atoms in block 16
Block first atom: 1872
Blocpdb> 122 atoms in block 17
Block first atom: 2006
Blocpdb> 127 atoms in block 18
Block first atom: 2128
Blocpdb> 140 atoms in block 19
Block first atom: 2255
Blocpdb> 126 atoms in block 20
Block first atom: 2395
Blocpdb> 119 atoms in block 21
Block first atom: 2521
Blocpdb> 121 atoms in block 22
Block first atom: 2640
Blocpdb> 125 atoms in block 23
Block first atom: 2761
Blocpdb> 130 atoms in block 24
Block first atom: 2886
Blocpdb> 134 atoms in block 25
Block first atom: 3016
Blocpdb> 129 atoms in block 26
Block first atom: 3150
Blocpdb> 134 atoms in block 27
Block first atom: 3279
Blocpdb> 118 atoms in block 28
Block first atom: 3413
Blocpdb> 119 atoms in block 29
Block first atom: 3531
Blocpdb> 120 atoms in block 30
Block first atom: 3650
Blocpdb> 122 atoms in block 31
Block first atom: 3770
Blocpdb> 127 atoms in block 32
Block first atom: 3892
Blocpdb> 126 atoms in block 33
Block first atom: 4019
Blocpdb> 116 atoms in block 34
Block first atom: 4145
Blocpdb> 117 atoms in block 35
Block first atom: 4261
Blocpdb> 109 atoms in block 36
Block first atom: 4378
Blocpdb> 126 atoms in block 37
Block first atom: 4487
Blocpdb> 124 atoms in block 38
Block first atom: 4613
Blocpdb> 107 atoms in block 39
Block first atom: 4737
Blocpdb> 125 atoms in block 40
Block first atom: 4844
Blocpdb> 118 atoms in block 41
Block first atom: 4969
Blocpdb> 121 atoms in block 42
Block first atom: 5087
Blocpdb> 120 atoms in block 43
Block first atom: 5208
Blocpdb> 122 atoms in block 44
Block first atom: 5328
Blocpdb> 130 atoms in block 45
Block first atom: 5450
Blocpdb> 114 atoms in block 46
Block first atom: 5580
Blocpdb> 130 atoms in block 47
Block first atom: 5694
Blocpdb> 113 atoms in block 48
Block first atom: 5824
Blocpdb> 118 atoms in block 49
Block first atom: 5937
Blocpdb> 114 atoms in block 50
Block first atom: 6055
Blocpdb> 119 atoms in block 51
Block first atom: 6169
Blocpdb> 122 atoms in block 52
Block first atom: 6288
Blocpdb> 109 atoms in block 53
Block first atom: 6410
Blocpdb> 129 atoms in block 54
Block first atom: 6519
Blocpdb> 132 atoms in block 55
Block first atom: 6648
Blocpdb> 118 atoms in block 56
Block first atom: 6780
Blocpdb> 122 atoms in block 57
Block first atom: 6898
Blocpdb> 112 atoms in block 58
Block first atom: 7020
Blocpdb> 121 atoms in block 59
Block first atom: 7132
Blocpdb> 104 atoms in block 60
Block first atom: 7253
Blocpdb> 125 atoms in block 61
Block first atom: 7357
Blocpdb> 114 atoms in block 62
Block first atom: 7482
Blocpdb> 132 atoms in block 63
Block first atom: 7596
Blocpdb> 115 atoms in block 64
Block first atom: 7728
Blocpdb> 113 atoms in block 65
Block first atom: 7843
Blocpdb> 122 atoms in block 66
Block first atom: 7956
Blocpdb> 134 atoms in block 67
Block first atom: 8078
Blocpdb> 111 atoms in block 68
Block first atom: 8212
Blocpdb> 115 atoms in block 69
Block first atom: 8323
Blocpdb> 108 atoms in block 70
Block first atom: 8438
Blocpdb> 127 atoms in block 71
Block first atom: 8546
Blocpdb> 125 atoms in block 72
Block first atom: 8673
Blocpdb> 133 atoms in block 73
Block first atom: 8798
Blocpdb> 128 atoms in block 74
Block first atom: 8931
Blocpdb> 116 atoms in block 75
Block first atom: 9059
Blocpdb> 138 atoms in block 76
Block first atom: 9175
Blocpdb> 145 atoms in block 77
Block first atom: 9313
Blocpdb> 121 atoms in block 78
Block first atom: 9458
Blocpdb> 112 atoms in block 79
Block first atom: 9579
Blocpdb> 128 atoms in block 80
Block first atom: 9691
Blocpdb> 83 atoms in block 81
Block first atom: 9819
Blocpdb> 129 atoms in block 82
Block first atom: 9902
Blocpdb> 124 atoms in block 83
Block first atom: 10031
Blocpdb> 118 atoms in block 84
Block first atom: 10155
Blocpdb> 118 atoms in block 85
Block first atom: 10273
Blocpdb> 120 atoms in block 86
Block first atom: 10391
Blocpdb> 116 atoms in block 87
Block first atom: 10511
Blocpdb> 117 atoms in block 88
Block first atom: 10627
Blocpdb> 124 atoms in block 89
Block first atom: 10744
Blocpdb> 125 atoms in block 90
Block first atom: 10868
Blocpdb> 128 atoms in block 91
Block first atom: 10993
Blocpdb> 130 atoms in block 92
Block first atom: 11121
Blocpdb> 117 atoms in block 93
Block first atom: 11251
Blocpdb> 119 atoms in block 94
Block first atom: 11368
Blocpdb> 116 atoms in block 95
Block first atom: 11487
Blocpdb> 129 atoms in block 96
Block first atom: 11603
Blocpdb> 115 atoms in block 97
Block first atom: 11732
Blocpdb> 127 atoms in block 98
Block first atom: 11847
Blocpdb> 129 atoms in block 99
Block first atom: 11974
Blocpdb> 122 atoms in block 100
Block first atom: 12103
Blocpdb> 115 atoms in block 101
Block first atom: 12225
Blocpdb> 113 atoms in block 102
Block first atom: 12340
Blocpdb> 123 atoms in block 103
Block first atom: 12453
Blocpdb> 117 atoms in block 104
Block first atom: 12576
Blocpdb> 39 atoms in block 105
Block first atom: 12693
Blocpdb> 112 atoms in block 106
Block first atom: 12732
Blocpdb> 124 atoms in block 107
Block first atom: 12844
Blocpdb> 133 atoms in block 108
Block first atom: 12968
Blocpdb> 116 atoms in block 109
Block first atom: 13101
Blocpdb> 120 atoms in block 110
Block first atom: 13217
Blocpdb> 109 atoms in block 111
Block first atom: 13337
Blocpdb> 123 atoms in block 112
Block first atom: 13446
Blocpdb> 118 atoms in block 113
Block first atom: 13569
Blocpdb> 107 atoms in block 114
Block first atom: 13687
Blocpdb> 118 atoms in block 115
Block first atom: 13794
Blocpdb> 112 atoms in block 116
Block first atom: 13912
Blocpdb> 120 atoms in block 117
Block first atom: 14024
Blocpdb> 126 atoms in block 118
Block first atom: 14144
Blocpdb> 110 atoms in block 119
Block first atom: 14270
Blocpdb> 126 atoms in block 120
Block first atom: 14380
Blocpdb> 112 atoms in block 121
Block first atom: 14506
Blocpdb> 128 atoms in block 122
Block first atom: 14618
Blocpdb> 111 atoms in block 123
Block first atom: 14746
Blocpdb> 118 atoms in block 124
Block first atom: 14857
Blocpdb> 105 atoms in block 125
Block first atom: 14975
Blocpdb> 128 atoms in block 126
Block first atom: 15080
Blocpdb> 127 atoms in block 127
Block first atom: 15208
Blocpdb> 128 atoms in block 128
Block first atom: 15335
Blocpdb> 128 atoms in block 129
Block first atom: 15463
Blocpdb> 121 atoms in block 130
Block first atom: 15591
Blocpdb> 124 atoms in block 131
Block first atom: 15712
Blocpdb> 127 atoms in block 132
Block first atom: 15836
Blocpdb> 124 atoms in block 133
Block first atom: 15963
Blocpdb> 121 atoms in block 134
Block first atom: 16087
Blocpdb> 121 atoms in block 135
Block first atom: 16208
Blocpdb> 137 atoms in block 136
Block first atom: 16329
Blocpdb> 121 atoms in block 137
Block first atom: 16466
Blocpdb> 113 atoms in block 138
Block first atom: 16587
Blocpdb> 118 atoms in block 139
Block first atom: 16700
Blocpdb> 115 atoms in block 140
Block first atom: 16818
Blocpdb> 128 atoms in block 141
Block first atom: 16933
Blocpdb> 111 atoms in block 142
Block first atom: 17061
Blocpdb> 112 atoms in block 143
Block first atom: 17172
Blocpdb> 129 atoms in block 144
Block first atom: 17284
Blocpdb> 120 atoms in block 145
Block first atom: 17413
Blocpdb> 117 atoms in block 146
Block first atom: 17533
Blocpdb> 131 atoms in block 147
Block first atom: 17650
Blocpdb> 112 atoms in block 148
Block first atom: 17781
Blocpdb> 131 atoms in block 149
Block first atom: 17893
Blocpdb> 123 atoms in block 150
Block first atom: 18024
Blocpdb> 135 atoms in block 151
Block first atom: 18147
Blocpdb> 125 atoms in block 152
Block first atom: 18282
Blocpdb> 117 atoms in block 153
Block first atom: 18407
Blocpdb> 108 atoms in block 154
Block first atom: 18524
Blocpdb> 109 atoms in block 155
Block first atom: 18632
Blocpdb> 120 atoms in block 156
Block first atom: 18741
Blocpdb> 137 atoms in block 157
Block first atom: 18861
Blocpdb> 121 atoms in block 158
Block first atom: 18998
Blocpdb> 115 atoms in block 159
Block first atom: 19119
Blocpdb> 122 atoms in block 160
Block first atom: 19234
Blocpdb> 129 atoms in block 161
Block first atom: 19356
Blocpdb> 105 atoms in block 162
Block first atom: 19485
Blocpdb> 133 atoms in block 163
Block first atom: 19590
Blocpdb> 129 atoms in block 164
Block first atom: 19723
Blocpdb> 119 atoms in block 165
Block first atom: 19852
Blocpdb> 118 atoms in block 166
Block first atom: 19971
Blocpdb> 126 atoms in block 167
Block first atom: 20089
Blocpdb> 133 atoms in block 168
Block first atom: 20215
Blocpdb> 106 atoms in block 169
Block first atom: 20348
Blocpdb> 121 atoms in block 170
Block first atom: 20454
Blocpdb> 115 atoms in block 171
Block first atom: 20575
Blocpdb> 124 atoms in block 172
Block first atom: 20690
Blocpdb> 120 atoms in block 173
Block first atom: 20814
Blocpdb> 105 atoms in block 174
Block first atom: 20934
Blocpdb> 108 atoms in block 175
Block first atom: 21039
Blocpdb> 118 atoms in block 176
Block first atom: 21147
Blocpdb> 102 atoms in block 177
Block first atom: 21265
Blocpdb> 120 atoms in block 178
Block first atom: 21367
Blocpdb> 117 atoms in block 179
Block first atom: 21487
Blocpdb> 114 atoms in block 180
Block first atom: 21604
Blocpdb> 111 atoms in block 181
Block first atom: 21718
Blocpdb> 108 atoms in block 182
Block first atom: 21829
Blocpdb> 133 atoms in block 183
Block first atom: 21937
Blocpdb> 14 atoms in block 184
Block first atom: 22070
Blocpdb> 156 atoms in block 185
Block first atom: 22084
Blocpdb> 120 atoms in block 186
Block first atom: 22240
Blocpdb> 129 atoms in block 187
Block first atom: 22360
Blocpdb> 149 atoms in block 188
Block first atom: 22489
Blocpdb> 131 atoms in block 189
Block first atom: 22638
Blocpdb> 129 atoms in block 190
Block first atom: 22769
Blocpdb> 142 atoms in block 191
Block first atom: 22898
Blocpdb> 143 atoms in block 192
Block first atom: 23040
Blocpdb> 136 atoms in block 193
Block first atom: 23183
Blocpdb> 138 atoms in block 194
Block first atom: 23319
Blocpdb> 145 atoms in block 195
Block first atom: 23457
Blocpdb> 69 atoms in block 196
Block first atom: 23601
Blocpdb> 196 blocks.
Blocpdb> At most, 156 atoms in each of them.
Blocpdb> At least, 14 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: 33451705 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 0m0.130s
user 0m0.118s
sys 0m0.011s
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.
|
