*** control ***
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 = 22042815305356454.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 22042815305356454.atom to be opened.
Openam> File opened: 22042815305356454.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 = 3133
First residue number = 15
Last residue number = 1136
Number of atoms found = 24403
Mean number per residue = 7.8
Pdbmat> Coordinate statistics:
= 115.507204 +/- 24.971298 From: 36.603000 To: 169.251000
= 115.284855 +/- 26.842112 From: 53.428000 To: 192.790000
= 115.587419 +/- 32.409396 From: 44.027000 To: 194.056000
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 1.6557 % Filled.
Pdbmat> 8814078 non-zero elements.
Pdbmat> 963240 atom-atom interactions.
Pdbmat> Number per atom= 78.94 +/- 19.34
Maximum number = 125
Minimum number = 13
Pdbmat> Matrix trace = 1.926480E+07
Pdbmat> Larger element = 479.153
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3133 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 = 22042815305356454.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 22042815305356454.atom to be opened.
Openam> file on opening on unit 11:
22042815305356454.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 24403 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> 3133 residues.
Blocpdb> 29 atoms in block 1
Block first atom: 1
Blocpdb> 128 atoms in block 2
Block first atom: 30
Blocpdb> 132 atoms in block 3
Block first atom: 158
Blocpdb> 105 atoms in block 4
Block first atom: 290
Blocpdb> 137 atoms in block 5
Block first atom: 395
Blocpdb> 121 atoms in block 6
Block first atom: 532
Blocpdb> 119 atoms in block 7
Block first atom: 653
Blocpdb> 132 atoms in block 8
Block first atom: 772
Blocpdb> 19 atoms in block 9
Block first atom: 904
Blocpdb> 135 atoms in block 10
Block first atom: 923
Blocpdb> 6 atoms in block 11
Block first atom: 1058
Blocpdb> 139 atoms in block 12
Block first atom: 1064
Blocpdb> 67 atoms in block 13
Block first atom: 1203
Blocpdb> 120 atoms in block 14
Block first atom: 1270
Blocpdb> 117 atoms in block 15
Block first atom: 1390
Blocpdb> 119 atoms in block 16
Block first atom: 1507
Blocpdb> 132 atoms in block 17
Block first atom: 1626
Blocpdb> 114 atoms in block 18
Block first atom: 1758
Blocpdb> 134 atoms in block 19
Block first atom: 1872
Blocpdb> 128 atoms in block 20
Block first atom: 2006
Blocpdb> 127 atoms in block 21
Block first atom: 2134
Blocpdb> 131 atoms in block 22
Block first atom: 2261
Blocpdb> 124 atoms in block 23
Block first atom: 2392
Blocpdb> 125 atoms in block 24
Block first atom: 2516
Blocpdb> 125 atoms in block 25
Block first atom: 2641
Blocpdb> 128 atoms in block 26
Block first atom: 2766
Blocpdb> 116 atoms in block 27
Block first atom: 2894
Blocpdb> 148 atoms in block 28
Block first atom: 3010
Blocpdb> 127 atoms in block 29
Block first atom: 3158
Blocpdb> 128 atoms in block 30
Block first atom: 3285
Blocpdb> 126 atoms in block 31
Block first atom: 3413
Blocpdb> 115 atoms in block 32
Block first atom: 3539
Blocpdb> 131 atoms in block 33
Block first atom: 3654
Blocpdb> 116 atoms in block 34
Block first atom: 3785
Blocpdb> 126 atoms in block 35
Block first atom: 3901
Blocpdb> 124 atoms in block 36
Block first atom: 4027
Blocpdb> 110 atoms in block 37
Block first atom: 4151
Blocpdb> 84 atoms in block 38
Block first atom: 4261
Blocpdb> 132 atoms in block 39
Block first atom: 4345
Blocpdb> 118 atoms in block 40
Block first atom: 4477
Blocpdb> 82 atoms in block 41
Block first atom: 4595
Blocpdb> 115 atoms in block 42
Block first atom: 4677
Blocpdb> 121 atoms in block 43
Block first atom: 4792
Blocpdb> 116 atoms in block 44
Block first atom: 4913
Blocpdb> 117 atoms in block 45
Block first atom: 5029
Blocpdb> 127 atoms in block 46
Block first atom: 5146
Blocpdb> 124 atoms in block 47
Block first atom: 5273
Blocpdb> 130 atoms in block 48
Block first atom: 5397
Blocpdb> 122 atoms in block 49
Block first atom: 5527
Blocpdb> 102 atoms in block 50
Block first atom: 5649
Blocpdb> 91 atoms in block 51
Block first atom: 5751
Blocpdb> 120 atoms in block 52
Block first atom: 5842
Blocpdb> 121 atoms in block 53
Block first atom: 5962
Blocpdb> 108 atoms in block 54
Block first atom: 6083
Blocpdb> 126 atoms in block 55
Block first atom: 6191
Blocpdb> 135 atoms in block 56
Block first atom: 6317
Blocpdb> 87 atoms in block 57
Block first atom: 6452
Blocpdb> 117 atoms in block 58
Block first atom: 6539
Blocpdb> 116 atoms in block 59
Block first atom: 6656
Blocpdb> 126 atoms in block 60
Block first atom: 6772
Blocpdb> 133 atoms in block 61
Block first atom: 6898
Blocpdb> 121 atoms in block 62
Block first atom: 7031
Blocpdb> 117 atoms in block 63
Block first atom: 7152
Blocpdb> 126 atoms in block 64
Block first atom: 7269
Blocpdb> 123 atoms in block 65
Block first atom: 7395
Blocpdb> 118 atoms in block 66
Block first atom: 7518
Blocpdb> 137 atoms in block 67
Block first atom: 7636
Blocpdb> 136 atoms in block 68
Block first atom: 7773
Blocpdb> 114 atoms in block 69
Block first atom: 7909
Blocpdb> 34 atoms in block 70
Block first atom: 8023
Blocpdb> 29 atoms in block 71
Block first atom: 8057
Blocpdb> 131 atoms in block 72
Block first atom: 8086
Blocpdb> 132 atoms in block 73
Block first atom: 8217
Blocpdb> 120 atoms in block 74
Block first atom: 8349
Blocpdb> 131 atoms in block 75
Block first atom: 8469
Blocpdb> 129 atoms in block 76
Block first atom: 8600
Blocpdb> 119 atoms in block 77
Block first atom: 8729
Blocpdb> 128 atoms in block 78
Block first atom: 8848
Blocpdb> 28 atoms in block 79
Block first atom: 8976
Blocpdb> 132 atoms in block 80
Block first atom: 9004
Blocpdb> 27 atoms in block 81
Block first atom: 9136
Blocpdb> 145 atoms in block 82
Block first atom: 9163
Blocpdb> 76 atoms in block 83
Block first atom: 9308
Blocpdb> 124 atoms in block 84
Block first atom: 9384
Blocpdb> 127 atoms in block 85
Block first atom: 9508
Blocpdb> 116 atoms in block 86
Block first atom: 9635
Blocpdb> 133 atoms in block 87
Block first atom: 9751
Blocpdb> 114 atoms in block 88
Block first atom: 9884
Blocpdb> 131 atoms in block 89
Block first atom: 9998
Blocpdb> 131 atoms in block 90
Block first atom: 10129
Blocpdb> 123 atoms in block 91
Block first atom: 10260
Blocpdb> 136 atoms in block 92
Block first atom: 10383
Blocpdb> 125 atoms in block 93
Block first atom: 10519
Blocpdb> 125 atoms in block 94
Block first atom: 10644
Blocpdb> 124 atoms in block 95
Block first atom: 10769
Blocpdb> 131 atoms in block 96
Block first atom: 10893
Blocpdb> 116 atoms in block 97
Block first atom: 11024
Blocpdb> 145 atoms in block 98
Block first atom: 11140
Blocpdb> 127 atoms in block 99
Block first atom: 11285
Blocpdb> 123 atoms in block 100
Block first atom: 11412
Blocpdb> 131 atoms in block 101
Block first atom: 11535
Blocpdb> 115 atoms in block 102
Block first atom: 11666
Blocpdb> 127 atoms in block 103
Block first atom: 11781
Blocpdb> 116 atoms in block 104
Block first atom: 11908
Blocpdb> 132 atoms in block 105
Block first atom: 12024
Blocpdb> 123 atoms in block 106
Block first atom: 12156
Blocpdb> 107 atoms in block 107
Block first atom: 12279
Blocpdb> 93 atoms in block 108
Block first atom: 12386
Blocpdb> 132 atoms in block 109
Block first atom: 12479
Blocpdb> 118 atoms in block 110
Block first atom: 12611
Blocpdb> 89 atoms in block 111
Block first atom: 12729
Blocpdb> 115 atoms in block 112
Block first atom: 12818
Blocpdb> 121 atoms in block 113
Block first atom: 12933
Blocpdb> 116 atoms in block 114
Block first atom: 13054
Blocpdb> 117 atoms in block 115
Block first atom: 13170
Blocpdb> 127 atoms in block 116
Block first atom: 13287
Blocpdb> 124 atoms in block 117
Block first atom: 13414
Blocpdb> 130 atoms in block 118
Block first atom: 13538
Blocpdb> 87 atoms in block 119
Block first atom: 13668
Blocpdb> 134 atoms in block 120
Block first atom: 13755
Blocpdb> 120 atoms in block 121
Block first atom: 13889
Blocpdb> 120 atoms in block 122
Block first atom: 14009
Blocpdb> 121 atoms in block 123
Block first atom: 14129
Blocpdb> 108 atoms in block 124
Block first atom: 14250
Blocpdb> 126 atoms in block 125
Block first atom: 14358
Blocpdb> 135 atoms in block 126
Block first atom: 14484
Blocpdb> 109 atoms in block 127
Block first atom: 14619
Blocpdb> 117 atoms in block 128
Block first atom: 14728
Blocpdb> 116 atoms in block 129
Block first atom: 14845
Blocpdb> 126 atoms in block 130
Block first atom: 14961
Blocpdb> 133 atoms in block 131
Block first atom: 15087
Blocpdb> 121 atoms in block 132
Block first atom: 15220
Blocpdb> 117 atoms in block 133
Block first atom: 15341
Blocpdb> 126 atoms in block 134
Block first atom: 15458
Blocpdb> 123 atoms in block 135
Block first atom: 15584
Blocpdb> 118 atoms in block 136
Block first atom: 15707
Blocpdb> 137 atoms in block 137
Block first atom: 15825
Blocpdb> 136 atoms in block 138
Block first atom: 15962
Blocpdb> 114 atoms in block 139
Block first atom: 16098
Blocpdb> 34 atoms in block 140
Block first atom: 16212
Blocpdb> 29 atoms in block 141
Block first atom: 16246
Blocpdb> 131 atoms in block 142
Block first atom: 16275
Blocpdb> 132 atoms in block 143
Block first atom: 16406
Blocpdb> 120 atoms in block 144
Block first atom: 16538
Blocpdb> 25 atoms in block 145
Block first atom: 16658
Blocpdb> 125 atoms in block 146
Block first atom: 16683
Blocpdb> 127 atoms in block 147
Block first atom: 16808
Blocpdb> 120 atoms in block 148
Block first atom: 16935
Blocpdb> 121 atoms in block 149
Block first atom: 17055
Blocpdb> 135 atoms in block 150
Block first atom: 17176
Blocpdb> 33 atoms in block 151
Block first atom: 17311
Blocpdb> 145 atoms in block 152
Block first atom: 17344
Blocpdb> 76 atoms in block 153
Block first atom: 17489
Blocpdb> 120 atoms in block 154
Block first atom: 17565
Blocpdb> 125 atoms in block 155
Block first atom: 17685
Blocpdb> 116 atoms in block 156
Block first atom: 17810
Blocpdb> 133 atoms in block 157
Block first atom: 17926
Blocpdb> 114 atoms in block 158
Block first atom: 18059
Blocpdb> 131 atoms in block 159
Block first atom: 18173
Blocpdb> 131 atoms in block 160
Block first atom: 18304
Blocpdb> 123 atoms in block 161
Block first atom: 18435
Blocpdb> 136 atoms in block 162
Block first atom: 18558
Blocpdb> 125 atoms in block 163
Block first atom: 18694
Blocpdb> 125 atoms in block 164
Block first atom: 18819
Blocpdb> 124 atoms in block 165
Block first atom: 18944
Blocpdb> 131 atoms in block 166
Block first atom: 19068
Blocpdb> 116 atoms in block 167
Block first atom: 19199
Blocpdb> 145 atoms in block 168
Block first atom: 19315
Blocpdb> 127 atoms in block 169
Block first atom: 19460
Blocpdb> 123 atoms in block 170
Block first atom: 19587
Blocpdb> 131 atoms in block 171
Block first atom: 19710
Blocpdb> 115 atoms in block 172
Block first atom: 19841
Blocpdb> 127 atoms in block 173
Block first atom: 19956
Blocpdb> 116 atoms in block 174
Block first atom: 20083
Blocpdb> 132 atoms in block 175
Block first atom: 20199
Blocpdb> 123 atoms in block 176
Block first atom: 20331
Blocpdb> 107 atoms in block 177
Block first atom: 20454
Blocpdb> 93 atoms in block 178
Block first atom: 20561
Blocpdb> 132 atoms in block 179
Block first atom: 20654
Blocpdb> 118 atoms in block 180
Block first atom: 20786
Blocpdb> 89 atoms in block 181
Block first atom: 20904
Blocpdb> 115 atoms in block 182
Block first atom: 20993
Blocpdb> 121 atoms in block 183
Block first atom: 21108
Blocpdb> 116 atoms in block 184
Block first atom: 21229
Blocpdb> 117 atoms in block 185
Block first atom: 21345
Blocpdb> 127 atoms in block 186
Block first atom: 21462
Blocpdb> 124 atoms in block 187
Block first atom: 21589
Blocpdb> 130 atoms in block 188
Block first atom: 21713
Blocpdb> 122 atoms in block 189
Block first atom: 21843
Blocpdb> 107 atoms in block 190
Block first atom: 21965
Blocpdb> 114 atoms in block 191
Block first atom: 22072
Blocpdb> 120 atoms in block 192
Block first atom: 22186
Blocpdb> 121 atoms in block 193
Block first atom: 22306
Blocpdb> 108 atoms in block 194
Block first atom: 22427
Blocpdb> 126 atoms in block 195
Block first atom: 22535
Blocpdb> 135 atoms in block 196
Block first atom: 22661
Blocpdb> 90 atoms in block 197
Block first atom: 22796
Blocpdb> 117 atoms in block 198
Block first atom: 22886
Blocpdb> 116 atoms in block 199
Block first atom: 23003
Blocpdb> 126 atoms in block 200
Block first atom: 23119
Blocpdb> 133 atoms in block 201
Block first atom: 23245
Blocpdb> 121 atoms in block 202
Block first atom: 23378
Blocpdb> 117 atoms in block 203
Block first atom: 23499
Blocpdb> 126 atoms in block 204
Block first atom: 23616
Blocpdb> 123 atoms in block 205
Block first atom: 23742
Blocpdb> 118 atoms in block 206
Block first atom: 23865
Blocpdb> 137 atoms in block 207
Block first atom: 23983
Blocpdb> 136 atoms in block 208
Block first atom: 24120
Blocpdb> 114 atoms in block 209
Block first atom: 24256
Blocpdb> 34 atoms in block 210
Block first atom: 24369
Blocpdb> 210 blocks.
Blocpdb> At most, 148 atoms in each of them.
Blocpdb> At least, 6 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: 32701933 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 0m0.094s
user 0m0.092s
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: October 18th, 2018.
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