*** PiezoInitial ***
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 = 2403180128323699863.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 2403180128323699863.atom to be opened.
Openam> File opened: 2403180128323699863.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 = 3903
First residue number = 576
Last residue number = 2523
Number of atoms found = 26934
Mean number per residue = 6.9
Pdbmat> Coordinate statistics:
= 184.799787 +/- 41.814568 From: 86.315000 To: 290.596000
= 184.799507 +/- 41.812726 From: 103.424000 To: 292.069000
= 222.008176 +/- 30.477985 From: 146.090000 To: 286.163000
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 -0.8117 % Filled.
Pdbmat> 8364048 non-zero elements.
Pdbmat> 911531 atom-atom interactions.
Pdbmat> Number per atom= 67.69 +/- 19.83
Maximum number = 122
Minimum number = 11
Pdbmat> Matrix trace = 1.823062E+07
Pdbmat> Larger element = 500.677
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3903 non-zero elements, NRBL set to 20
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 = 2403180128323699863.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 20
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 2403180128323699863.atom to be opened.
Openam> file on opening on unit 11:
2403180128323699863.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 26934 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 20 residue(s) per block.
Blocpdb> 3903 residues.
Blocpdb> 98 atoms in block 1
Block first atom: 1
Blocpdb> 99 atoms in block 2
Block first atom: 99
Blocpdb> 100 atoms in block 3
Block first atom: 198
Blocpdb> 75 atoms in block 4
Block first atom: 298
Blocpdb> 99 atoms in block 5
Block first atom: 373
Blocpdb> 75 atoms in block 6
Block first atom: 472
Blocpdb> 100 atoms in block 7
Block first atom: 547
Blocpdb> 100 atoms in block 8
Block first atom: 647
Blocpdb> 129 atoms in block 9
Block first atom: 747
Blocpdb> 120 atoms in block 10
Block first atom: 876
Blocpdb> 55 atoms in block 11
Block first atom: 996
Blocpdb> 97 atoms in block 12
Block first atom: 1051
Blocpdb> 107 atoms in block 13
Block first atom: 1148
Blocpdb> 10 atoms in block 14
Block first atom: 1255
Blocpdb> 128 atoms in block 15
Block first atom: 1265
Blocpdb> 137 atoms in block 16
Block first atom: 1393
Blocpdb> 125 atoms in block 17
Block first atom: 1530
Blocpdb> 151 atoms in block 18
Block first atom: 1655
Blocpdb> 44 atoms in block 19
Block first atom: 1806
Blocpdb> 111 atoms in block 20
Block first atom: 1850
Blocpdb> 36 atoms in block 21
Block first atom: 1961
Blocpdb> 153 atoms in block 22
Block first atom: 1997
Blocpdb> 169 atoms in block 23
Block first atom: 2150
Blocpdb> 156 atoms in block 24
Block first atom: 2319
Blocpdb> 169 atoms in block 25
Block first atom: 2475
Blocpdb> 82 atoms in block 26
Block first atom: 2644
Blocpdb> 168 atoms in block 27
Block first atom: 2726
Blocpdb> 153 atoms in block 28
Block first atom: 2894
Blocpdb> 165 atoms in block 29
Block first atom: 3047
Blocpdb> 171 atoms in block 30
Block first atom: 3212
Blocpdb> 67 atoms in block 31
Block first atom: 3383
Blocpdb> 150 atoms in block 32
Block first atom: 3450
Blocpdb> 167 atoms in block 33
Block first atom: 3600
Blocpdb> 159 atoms in block 34
Block first atom: 3767
Blocpdb> 123 atoms in block 35
Block first atom: 3926
Blocpdb> 161 atoms in block 36
Block first atom: 4049
Blocpdb> 159 atoms in block 37
Block first atom: 4210
Blocpdb> 158 atoms in block 38
Block first atom: 4369
Blocpdb> 155 atoms in block 39
Block first atom: 4527
Blocpdb> 165 atoms in block 40
Block first atom: 4682
Blocpdb> 31 atoms in block 41
Block first atom: 4847
Blocpdb> 172 atoms in block 42
Block first atom: 4878
Blocpdb> 43 atoms in block 43
Block first atom: 5050
Blocpdb> 168 atoms in block 44
Block first atom: 5093
Blocpdb> 161 atoms in block 45
Block first atom: 5261
Blocpdb> 14 atoms in block 46
Block first atom: 5422
Blocpdb> 160 atoms in block 47
Block first atom: 5436
Blocpdb> 162 atoms in block 48
Block first atom: 5596
Blocpdb> 120 atoms in block 49
Block first atom: 5758
Blocpdb> 171 atoms in block 50
Block first atom: 5878
Blocpdb> 160 atoms in block 51
Block first atom: 6049
Blocpdb> 178 atoms in block 52
Block first atom: 6209
Blocpdb> 163 atoms in block 53
Block first atom: 6387
Blocpdb> 168 atoms in block 54
Block first atom: 6550
Blocpdb> 168 atoms in block 55
Block first atom: 6718
Blocpdb> 161 atoms in block 56
Block first atom: 6886
Blocpdb> 111 atoms in block 57
Block first atom: 7047
Blocpdb> 98 atoms in block 58
Block first atom: 7158
Blocpdb> 100 atoms in block 59
Block first atom: 7256
Blocpdb> 98 atoms in block 60
Block first atom: 7356
Blocpdb> 99 atoms in block 61
Block first atom: 7454
Blocpdb> 98 atoms in block 62
Block first atom: 7553
Blocpdb> 100 atoms in block 63
Block first atom: 7651
Blocpdb> 99 atoms in block 64
Block first atom: 7751
Blocpdb> 99 atoms in block 65
Block first atom: 7850
Blocpdb> 94 atoms in block 66
Block first atom: 7949
Blocpdb> 99 atoms in block 67
Block first atom: 8043
Blocpdb> 102 atoms in block 68
Block first atom: 8142
Blocpdb> 146 atoms in block 69
Block first atom: 8244
Blocpdb> 166 atoms in block 70
Block first atom: 8390
Blocpdb> 171 atoms in block 71
Block first atom: 8556
Blocpdb> 173 atoms in block 72
Block first atom: 8727
Blocpdb> 79 atoms in block 73
Block first atom: 8900
Blocpdb> 98 atoms in block 74
Block first atom: 8979
Blocpdb> 99 atoms in block 75
Block first atom: 9077
Blocpdb> 100 atoms in block 76
Block first atom: 9176
Blocpdb> 75 atoms in block 77
Block first atom: 9276
Blocpdb> 99 atoms in block 78
Block first atom: 9351
Blocpdb> 75 atoms in block 79
Block first atom: 9450
Blocpdb> 100 atoms in block 80
Block first atom: 9525
Blocpdb> 100 atoms in block 81
Block first atom: 9625
Blocpdb> 129 atoms in block 82
Block first atom: 9725
Blocpdb> 120 atoms in block 83
Block first atom: 9854
Blocpdb> 55 atoms in block 84
Block first atom: 9974
Blocpdb> 97 atoms in block 85
Block first atom: 10029
Blocpdb> 107 atoms in block 86
Block first atom: 10126
Blocpdb> 10 atoms in block 87
Block first atom: 10233
Blocpdb> 128 atoms in block 88
Block first atom: 10243
Blocpdb> 137 atoms in block 89
Block first atom: 10371
Blocpdb> 125 atoms in block 90
Block first atom: 10508
Blocpdb> 151 atoms in block 91
Block first atom: 10633
Blocpdb> 44 atoms in block 92
Block first atom: 10784
Blocpdb> 111 atoms in block 93
Block first atom: 10828
Blocpdb> 36 atoms in block 94
Block first atom: 10939
Blocpdb> 153 atoms in block 95
Block first atom: 10975
Blocpdb> 169 atoms in block 96
Block first atom: 11128
Blocpdb> 156 atoms in block 97
Block first atom: 11297
Blocpdb> 169 atoms in block 98
Block first atom: 11453
Blocpdb> 82 atoms in block 99
Block first atom: 11622
Blocpdb> 168 atoms in block 100
Block first atom: 11704
Blocpdb> 153 atoms in block 101
Block first atom: 11872
Blocpdb> 165 atoms in block 102
Block first atom: 12025
Blocpdb> 171 atoms in block 103
Block first atom: 12190
Blocpdb> 67 atoms in block 104
Block first atom: 12361
Blocpdb> 150 atoms in block 105
Block first atom: 12428
Blocpdb> 167 atoms in block 106
Block first atom: 12578
Blocpdb> 159 atoms in block 107
Block first atom: 12745
Blocpdb> 123 atoms in block 108
Block first atom: 12904
Blocpdb> 161 atoms in block 109
Block first atom: 13027
Blocpdb> 159 atoms in block 110
Block first atom: 13188
Blocpdb> 158 atoms in block 111
Block first atom: 13347
Blocpdb> 155 atoms in block 112
Block first atom: 13505
Blocpdb> 165 atoms in block 113
Block first atom: 13660
Blocpdb> 31 atoms in block 114
Block first atom: 13825
Blocpdb> 172 atoms in block 115
Block first atom: 13856
Blocpdb> 43 atoms in block 116
Block first atom: 14028
Blocpdb> 168 atoms in block 117
Block first atom: 14071
Blocpdb> 161 atoms in block 118
Block first atom: 14239
Blocpdb> 14 atoms in block 119
Block first atom: 14400
Blocpdb> 160 atoms in block 120
Block first atom: 14414
Blocpdb> 162 atoms in block 121
Block first atom: 14574
Blocpdb> 120 atoms in block 122
Block first atom: 14736
Blocpdb> 171 atoms in block 123
Block first atom: 14856
Blocpdb> 160 atoms in block 124
Block first atom: 15027
Blocpdb> 178 atoms in block 125
Block first atom: 15187
Blocpdb> 163 atoms in block 126
Block first atom: 15365
Blocpdb> 168 atoms in block 127
Block first atom: 15528
Blocpdb> 168 atoms in block 128
Block first atom: 15696
Blocpdb> 161 atoms in block 129
Block first atom: 15864
Blocpdb> 111 atoms in block 130
Block first atom: 16025
Blocpdb> 98 atoms in block 131
Block first atom: 16136
Blocpdb> 100 atoms in block 132
Block first atom: 16234
Blocpdb> 98 atoms in block 133
Block first atom: 16334
Blocpdb> 99 atoms in block 134
Block first atom: 16432
Blocpdb> 98 atoms in block 135
Block first atom: 16531
Blocpdb> 100 atoms in block 136
Block first atom: 16629
Blocpdb> 99 atoms in block 137
Block first atom: 16729
Blocpdb> 99 atoms in block 138
Block first atom: 16828
Blocpdb> 94 atoms in block 139
Block first atom: 16927
Blocpdb> 99 atoms in block 140
Block first atom: 17021
Blocpdb> 102 atoms in block 141
Block first atom: 17120
Blocpdb> 146 atoms in block 142
Block first atom: 17222
Blocpdb> 166 atoms in block 143
Block first atom: 17368
Blocpdb> 171 atoms in block 144
Block first atom: 17534
Blocpdb> 173 atoms in block 145
Block first atom: 17705
Blocpdb> 79 atoms in block 146
Block first atom: 17878
Blocpdb> 98 atoms in block 147
Block first atom: 17957
Blocpdb> 99 atoms in block 148
Block first atom: 18055
Blocpdb> 100 atoms in block 149
Block first atom: 18154
Blocpdb> 75 atoms in block 150
Block first atom: 18254
Blocpdb> 99 atoms in block 151
Block first atom: 18329
Blocpdb> 75 atoms in block 152
Block first atom: 18428
Blocpdb> 100 atoms in block 153
Block first atom: 18503
Blocpdb> 100 atoms in block 154
Block first atom: 18603
Blocpdb> 129 atoms in block 155
Block first atom: 18703
Blocpdb> 120 atoms in block 156
Block first atom: 18832
Blocpdb> 55 atoms in block 157
Block first atom: 18952
Blocpdb> 97 atoms in block 158
Block first atom: 19007
Blocpdb> 107 atoms in block 159
Block first atom: 19104
Blocpdb> 10 atoms in block 160
Block first atom: 19211
Blocpdb> 128 atoms in block 161
Block first atom: 19221
Blocpdb> 137 atoms in block 162
Block first atom: 19349
Blocpdb> 125 atoms in block 163
Block first atom: 19486
Blocpdb> 151 atoms in block 164
Block first atom: 19611
Blocpdb> 44 atoms in block 165
Block first atom: 19762
Blocpdb> 111 atoms in block 166
Block first atom: 19806
Blocpdb> 36 atoms in block 167
Block first atom: 19917
Blocpdb> 153 atoms in block 168
Block first atom: 19953
Blocpdb> 169 atoms in block 169
Block first atom: 20106
Blocpdb> 156 atoms in block 170
Block first atom: 20275
Blocpdb> 169 atoms in block 171
Block first atom: 20431
Blocpdb> 82 atoms in block 172
Block first atom: 20600
Blocpdb> 168 atoms in block 173
Block first atom: 20682
Blocpdb> 153 atoms in block 174
Block first atom: 20850
Blocpdb> 165 atoms in block 175
Block first atom: 21003
Blocpdb> 171 atoms in block 176
Block first atom: 21168
Blocpdb> 67 atoms in block 177
Block first atom: 21339
Blocpdb> 150 atoms in block 178
Block first atom: 21406
Blocpdb> 167 atoms in block 179
Block first atom: 21556
Blocpdb> 159 atoms in block 180
Block first atom: 21723
Blocpdb> 123 atoms in block 181
Block first atom: 21882
Blocpdb> 161 atoms in block 182
Block first atom: 22005
Blocpdb> 159 atoms in block 183
Block first atom: 22166
Blocpdb> 158 atoms in block 184
Block first atom: 22325
Blocpdb> 155 atoms in block 185
Block first atom: 22483
Blocpdb> 165 atoms in block 186
Block first atom: 22638
Blocpdb> 31 atoms in block 187
Block first atom: 22803
Blocpdb> 172 atoms in block 188
Block first atom: 22834
Blocpdb> 43 atoms in block 189
Block first atom: 23006
Blocpdb> 168 atoms in block 190
Block first atom: 23049
Blocpdb> 161 atoms in block 191
Block first atom: 23217
Blocpdb> 14 atoms in block 192
Block first atom: 23378
Blocpdb> 160 atoms in block 193
Block first atom: 23392
Blocpdb> 162 atoms in block 194
Block first atom: 23552
Blocpdb> 120 atoms in block 195
Block first atom: 23714
Blocpdb> 171 atoms in block 196
Block first atom: 23834
Blocpdb> 160 atoms in block 197
Block first atom: 24005
Blocpdb> 178 atoms in block 198
Block first atom: 24165
Blocpdb> 163 atoms in block 199
Block first atom: 24343
Blocpdb> 168 atoms in block 200
Block first atom: 24506
Blocpdb> 168 atoms in block 201
Block first atom: 24674
Blocpdb> 161 atoms in block 202
Block first atom: 24842
Blocpdb> 111 atoms in block 203
Block first atom: 25003
Blocpdb> 98 atoms in block 204
Block first atom: 25114
Blocpdb> 100 atoms in block 205
Block first atom: 25212
Blocpdb> 98 atoms in block 206
Block first atom: 25312
Blocpdb> 99 atoms in block 207
Block first atom: 25410
Blocpdb> 98 atoms in block 208
Block first atom: 25509
Blocpdb> 100 atoms in block 209
Block first atom: 25607
Blocpdb> 99 atoms in block 210
Block first atom: 25707
Blocpdb> 99 atoms in block 211
Block first atom: 25806
Blocpdb> 94 atoms in block 212
Block first atom: 25905
Blocpdb> 99 atoms in block 213
Block first atom: 25999
Blocpdb> 102 atoms in block 214
Block first atom: 26098
Blocpdb> 146 atoms in block 215
Block first atom: 26200
Blocpdb> 166 atoms in block 216
Block first atom: 26346
Blocpdb> 171 atoms in block 217
Block first atom: 26512
Blocpdb> 173 atoms in block 218
Block first atom: 26683
Blocpdb> 79 atoms in block 219
Block first atom: 26855
Blocpdb> 219 blocks.
Blocpdb> At most, 178 atoms in each of them.
Blocpdb> At least, 10 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: 43433425 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 0m0.122s
user 0m0.118s
sys 0m0.004s
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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