*** ***
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 = 221130214956110655.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 221130214956110655.atom to be opened.
Openam> File opened: 221130214956110655.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 = 1770
First residue number = 1
Last residue number = 1770
Number of atoms found = 26907
Mean number per residue = 15.2
Pdbmat> Coordinate statistics:
= 39.646487 +/- 31.593394 From: -23.894000 To: 109.478000
= 63.510799 +/- 45.521464 From: 0.230000 To: 234.066000
= 195.736028 +/- 44.844620 From: 102.912000 To: 279.047000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 33 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 -1.6929 % Filled.
Pdbmat> 17554727 non-zero elements.
Pdbmat> 1932910 atom-atom interactions.
Pdbmat> Number per atom= 143.67 +/- 43.90
Maximum number = 241
Minimum number = 19
Pdbmat> Matrix trace = 3.865820E+07
Pdbmat> Larger element = 855.235
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
1770 non-zero elements, NRBL set to 9
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 = 221130214956110655.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 9
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 221130214956110655.atom to be opened.
Openam> file on opening on unit 11:
221130214956110655.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 26907 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 9 residue(s) per block.
Blocpdb> 1770 residues.
Blocpdb> 146 atoms in block 1
Block first atom: 1
Blocpdb> 121 atoms in block 2
Block first atom: 147
Blocpdb> 148 atoms in block 3
Block first atom: 268
Blocpdb> 132 atoms in block 4
Block first atom: 416
Blocpdb> 125 atoms in block 5
Block first atom: 548
Blocpdb> 122 atoms in block 6
Block first atom: 673
Blocpdb> 131 atoms in block 7
Block first atom: 795
Blocpdb> 142 atoms in block 8
Block first atom: 926
Blocpdb> 137 atoms in block 9
Block first atom: 1068
Blocpdb> 157 atoms in block 10
Block first atom: 1205
Blocpdb> 114 atoms in block 11
Block first atom: 1362
Blocpdb> 129 atoms in block 12
Block first atom: 1476
Blocpdb> 160 atoms in block 13
Block first atom: 1605
Blocpdb> 141 atoms in block 14
Block first atom: 1765
Blocpdb> 125 atoms in block 15
Block first atom: 1906
Blocpdb> 138 atoms in block 16
Block first atom: 2031
Blocpdb> 138 atoms in block 17
Block first atom: 2169
Blocpdb> 152 atoms in block 18
Block first atom: 2307
Blocpdb> 142 atoms in block 19
Block first atom: 2459
Blocpdb> 117 atoms in block 20
Block first atom: 2601
Blocpdb> 120 atoms in block 21
Block first atom: 2718
Blocpdb> 142 atoms in block 22
Block first atom: 2838
Blocpdb> 134 atoms in block 23
Block first atom: 2980
Blocpdb> 159 atoms in block 24
Block first atom: 3114
Blocpdb> 123 atoms in block 25
Block first atom: 3273
Blocpdb> 135 atoms in block 26
Block first atom: 3396
Blocpdb> 127 atoms in block 27
Block first atom: 3531
Blocpdb> 127 atoms in block 28
Block first atom: 3658
Blocpdb> 133 atoms in block 29
Block first atom: 3785
Blocpdb> 143 atoms in block 30
Block first atom: 3918
Blocpdb> 166 atoms in block 31
Block first atom: 4061
Blocpdb> 141 atoms in block 32
Block first atom: 4227
Blocpdb> 123 atoms in block 33
Block first atom: 4368
Blocpdb> 128 atoms in block 34
Block first atom: 4491
Blocpdb> 138 atoms in block 35
Block first atom: 4619
Blocpdb> 147 atoms in block 36
Block first atom: 4757
Blocpdb> 159 atoms in block 37
Block first atom: 4904
Blocpdb> 122 atoms in block 38
Block first atom: 5063
Blocpdb> 134 atoms in block 39
Block first atom: 5185
Blocpdb> 138 atoms in block 40
Block first atom: 5319
Blocpdb> 129 atoms in block 41
Block first atom: 5457
Blocpdb> 119 atoms in block 42
Block first atom: 5586
Blocpdb> 112 atoms in block 43
Block first atom: 5705
Blocpdb> 142 atoms in block 44
Block first atom: 5817
Blocpdb> 142 atoms in block 45
Block first atom: 5959
Blocpdb> 127 atoms in block 46
Block first atom: 6101
Blocpdb> 129 atoms in block 47
Block first atom: 6228
Blocpdb> 123 atoms in block 48
Block first atom: 6357
Blocpdb> 125 atoms in block 49
Block first atom: 6480
Blocpdb> 138 atoms in block 50
Block first atom: 6605
Blocpdb> 139 atoms in block 51
Block first atom: 6743
Blocpdb> 141 atoms in block 52
Block first atom: 6882
Blocpdb> 136 atoms in block 53
Block first atom: 7023
Blocpdb> 136 atoms in block 54
Block first atom: 7159
Blocpdb> 118 atoms in block 55
Block first atom: 7295
Blocpdb> 152 atoms in block 56
Block first atom: 7413
Blocpdb> 147 atoms in block 57
Block first atom: 7565
Blocpdb> 167 atoms in block 58
Block first atom: 7712
Blocpdb> 121 atoms in block 59
Block first atom: 7879
Blocpdb> 133 atoms in block 60
Block first atom: 8000
Blocpdb> 134 atoms in block 61
Block first atom: 8133
Blocpdb> 142 atoms in block 62
Block first atom: 8267
Blocpdb> 156 atoms in block 63
Block first atom: 8409
Blocpdb> 132 atoms in block 64
Block first atom: 8565
Blocpdb> 115 atoms in block 65
Block first atom: 8697
Blocpdb> 134 atoms in block 66
Block first atom: 8812
Blocpdb> 139 atoms in block 67
Block first atom: 8946
Blocpdb> 132 atoms in block 68
Block first atom: 9085
Blocpdb> 119 atoms in block 69
Block first atom: 9217
Blocpdb> 127 atoms in block 70
Block first atom: 9336
Blocpdb> 133 atoms in block 71
Block first atom: 9463
Blocpdb> 115 atoms in block 72
Block first atom: 9596
Blocpdb> 129 atoms in block 73
Block first atom: 9711
Blocpdb> 149 atoms in block 74
Block first atom: 9840
Blocpdb> 144 atoms in block 75
Block first atom: 9989
Blocpdb> 159 atoms in block 76
Block first atom: 10133
Blocpdb> 132 atoms in block 77
Block first atom: 10292
Blocpdb> 140 atoms in block 78
Block first atom: 10424
Blocpdb> 134 atoms in block 79
Block first atom: 10564
Blocpdb> 122 atoms in block 80
Block first atom: 10698
Blocpdb> 154 atoms in block 81
Block first atom: 10820
Blocpdb> 148 atoms in block 82
Block first atom: 10974
Blocpdb> 134 atoms in block 83
Block first atom: 11122
Blocpdb> 140 atoms in block 84
Block first atom: 11256
Blocpdb> 122 atoms in block 85
Block first atom: 11396
Blocpdb> 134 atoms in block 86
Block first atom: 11518
Blocpdb> 140 atoms in block 87
Block first atom: 11652
Blocpdb> 128 atoms in block 88
Block first atom: 11792
Blocpdb> 136 atoms in block 89
Block first atom: 11920
Blocpdb> 127 atoms in block 90
Block first atom: 12056
Blocpdb> 157 atoms in block 91
Block first atom: 12183
Blocpdb> 126 atoms in block 92
Block first atom: 12340
Blocpdb> 146 atoms in block 93
Block first atom: 12466
Blocpdb> 134 atoms in block 94
Block first atom: 12612
Blocpdb> 141 atoms in block 95
Block first atom: 12746
Blocpdb> 173 atoms in block 96
Block first atom: 12887
Blocpdb> 146 atoms in block 97
Block first atom: 13060
Blocpdb> 122 atoms in block 98
Block first atom: 13206
Blocpdb> 121 atoms in block 99
Block first atom: 13328
Blocpdb> 150 atoms in block 100
Block first atom: 13449
Blocpdb> 141 atoms in block 101
Block first atom: 13599
Blocpdb> 163 atoms in block 102
Block first atom: 13740
Blocpdb> 148 atoms in block 103
Block first atom: 13903
Blocpdb> 139 atoms in block 104
Block first atom: 14051
Blocpdb> 138 atoms in block 105
Block first atom: 14190
Blocpdb> 144 atoms in block 106
Block first atom: 14328
Blocpdb> 147 atoms in block 107
Block first atom: 14472
Blocpdb> 158 atoms in block 108
Block first atom: 14619
Blocpdb> 139 atoms in block 109
Block first atom: 14777
Blocpdb> 162 atoms in block 110
Block first atom: 14916
Blocpdb> 159 atoms in block 111
Block first atom: 15078
Blocpdb> 126 atoms in block 112
Block first atom: 15237
Blocpdb> 126 atoms in block 113
Block first atom: 15363
Blocpdb> 123 atoms in block 114
Block first atom: 15489
Blocpdb> 125 atoms in block 115
Block first atom: 15612
Blocpdb> 121 atoms in block 116
Block first atom: 15737
Blocpdb> 155 atoms in block 117
Block first atom: 15858
Blocpdb> 128 atoms in block 118
Block first atom: 16013
Blocpdb> 141 atoms in block 119
Block first atom: 16141
Blocpdb> 148 atoms in block 120
Block first atom: 16282
Blocpdb> 106 atoms in block 121
Block first atom: 16430
Blocpdb> 147 atoms in block 122
Block first atom: 16536
Blocpdb> 152 atoms in block 123
Block first atom: 16683
Blocpdb> 155 atoms in block 124
Block first atom: 16835
Blocpdb> 155 atoms in block 125
Block first atom: 16990
Blocpdb> 142 atoms in block 126
Block first atom: 17145
Blocpdb> 142 atoms in block 127
Block first atom: 17287
Blocpdb> 159 atoms in block 128
Block first atom: 17429
Blocpdb> 147 atoms in block 129
Block first atom: 17588
Blocpdb> 128 atoms in block 130
Block first atom: 17735
Blocpdb> 146 atoms in block 131
Block first atom: 17863
Blocpdb> 133 atoms in block 132
Block first atom: 18009
Blocpdb> 138 atoms in block 133
Block first atom: 18142
Blocpdb> 154 atoms in block 134
Block first atom: 18280
Blocpdb> 151 atoms in block 135
Block first atom: 18434
Blocpdb> 161 atoms in block 136
Block first atom: 18585
Blocpdb> 107 atoms in block 137
Block first atom: 18746
Blocpdb> 131 atoms in block 138
Block first atom: 18853
Blocpdb> 143 atoms in block 139
Block first atom: 18984
Blocpdb> 141 atoms in block 140
Block first atom: 19127
Blocpdb> 144 atoms in block 141
Block first atom: 19268
Blocpdb> 128 atoms in block 142
Block first atom: 19412
Blocpdb> 112 atoms in block 143
Block first atom: 19540
Blocpdb> 127 atoms in block 144
Block first atom: 19652
Blocpdb> 137 atoms in block 145
Block first atom: 19779
Blocpdb> 157 atoms in block 146
Block first atom: 19916
Blocpdb> 140 atoms in block 147
Block first atom: 20073
Blocpdb> 151 atoms in block 148
Block first atom: 20213
Blocpdb> 126 atoms in block 149
Block first atom: 20364
Blocpdb> 128 atoms in block 150
Block first atom: 20490
Blocpdb> 145 atoms in block 151
Block first atom: 20618
Blocpdb> 162 atoms in block 152
Block first atom: 20763
Blocpdb> 135 atoms in block 153
Block first atom: 20925
Blocpdb> 131 atoms in block 154
Block first atom: 21060
Blocpdb> 136 atoms in block 155
Block first atom: 21191
Blocpdb> 127 atoms in block 156
Block first atom: 21327
Blocpdb> 144 atoms in block 157
Block first atom: 21454
Blocpdb> 147 atoms in block 158
Block first atom: 21598
Blocpdb> 146 atoms in block 159
Block first atom: 21745
Blocpdb> 144 atoms in block 160
Block first atom: 21891
Blocpdb> 109 atoms in block 161
Block first atom: 22035
Blocpdb> 134 atoms in block 162
Block first atom: 22144
Blocpdb> 111 atoms in block 163
Block first atom: 22278
Blocpdb> 124 atoms in block 164
Block first atom: 22389
Blocpdb> 117 atoms in block 165
Block first atom: 22513
Blocpdb> 128 atoms in block 166
Block first atom: 22630
Blocpdb> 129 atoms in block 167
Block first atom: 22758
Blocpdb> 122 atoms in block 168
Block first atom: 22887
Blocpdb> 126 atoms in block 169
Block first atom: 23009
Blocpdb> 138 atoms in block 170
Block first atom: 23135
Blocpdb> 138 atoms in block 171
Block first atom: 23273
Blocpdb> 114 atoms in block 172
Block first atom: 23411
Blocpdb> 110 atoms in block 173
Block first atom: 23525
Blocpdb> 133 atoms in block 174
Block first atom: 23635
Blocpdb> 128 atoms in block 175
Block first atom: 23768
Blocpdb> 120 atoms in block 176
Block first atom: 23896
Blocpdb> 115 atoms in block 177
Block first atom: 24016
Blocpdb> 127 atoms in block 178
Block first atom: 24131
Blocpdb> 120 atoms in block 179
Block first atom: 24258
Blocpdb> 136 atoms in block 180
Block first atom: 24378
Blocpdb> 144 atoms in block 181
Block first atom: 24514
Blocpdb> 132 atoms in block 182
Block first atom: 24658
Blocpdb> 151 atoms in block 183
Block first atom: 24790
Blocpdb> 146 atoms in block 184
Block first atom: 24941
Blocpdb> 127 atoms in block 185
Block first atom: 25087
Blocpdb> 142 atoms in block 186
Block first atom: 25214
Blocpdb> 135 atoms in block 187
Block first atom: 25356
Blocpdb> 154 atoms in block 188
Block first atom: 25491
Blocpdb> 125 atoms in block 189
Block first atom: 25645
Blocpdb> 140 atoms in block 190
Block first atom: 25770
Blocpdb> 132 atoms in block 191
Block first atom: 25910
Blocpdb> 174 atoms in block 192
Block first atom: 26042
Blocpdb> 161 atoms in block 193
Block first atom: 26216
Blocpdb> 155 atoms in block 194
Block first atom: 26377
Blocpdb> 142 atoms in block 195
Block first atom: 26532
Blocpdb> 134 atoms in block 196
Block first atom: 26674
Blocpdb> 100 atoms in block 197
Block first atom: 26807
Blocpdb> 197 blocks.
Blocpdb> At most, 174 atoms in each of them.
Blocpdb> At least, 100 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: 42408847 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 0m0.101s
user 0m0.104s
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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