*** ***
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 = 22121818020150630.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 22121818020150630.atom to be opened.
Openam> File opened: 22121818020150630.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 = 4084
First residue number = 5
Last residue number = 166
Number of atoms found = 32038
Mean number per residue = 7.8
Pdbmat> Coordinate statistics:
= 146.533569 +/- 16.702193 From: 97.972000 To: 190.265000
= 147.196863 +/- 21.758019 From: 87.639000 To: 203.101000
= 133.554071 +/- 69.653081 From: 3.437000 To: 284.593000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 18 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 3.7716 % Filled.
Pdbmat> 12221268 non-zero elements.
Pdbmat> 1336780 atom-atom interactions.
Pdbmat> Number per atom= 83.45 +/- 20.14
Maximum number = 132
Minimum number = 13
Pdbmat> Matrix trace = 2.673560E+07
Pdbmat> Larger element = 511.071
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
4084 non-zero elements, NRBL set to 21
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 = 22121818020150630.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 21
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 22121818020150630.atom to be opened.
Openam> file on opening on unit 11:
22121818020150630.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 32038 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 21 residue(s) per block.
Blocpdb> 4084 residues.
Blocpdb> 139 atoms in block 1
Block first atom: 1
Blocpdb> 156 atoms in block 2
Block first atom: 140
Blocpdb> 159 atoms in block 3
Block first atom: 296
Blocpdb> 188 atoms in block 4
Block first atom: 455
Blocpdb> 171 atoms in block 5
Block first atom: 643
Blocpdb> 174 atoms in block 6
Block first atom: 814
Blocpdb> 152 atoms in block 7
Block first atom: 988
Blocpdb> 156 atoms in block 8
Block first atom: 1140
Blocpdb> 170 atoms in block 9
Block first atom: 1296
Blocpdb> 175 atoms in block 10
Block first atom: 1466
Blocpdb> 154 atoms in block 11
Block first atom: 1641
Blocpdb> 173 atoms in block 12
Block first atom: 1795
Blocpdb> 159 atoms in block 13
Block first atom: 1968
Blocpdb> 172 atoms in block 14
Block first atom: 2127
Blocpdb> 154 atoms in block 15
Block first atom: 2299
Blocpdb> 170 atoms in block 16
Block first atom: 2453
Blocpdb> 163 atoms in block 17
Block first atom: 2623
Blocpdb> 102 atoms in block 18
Block first atom: 2786
Blocpdb> 28 atoms in block 19
Block first atom: 2888
Blocpdb> 139 atoms in block 20
Block first atom: 2916
Blocpdb> 156 atoms in block 21
Block first atom: 3055
Blocpdb> 159 atoms in block 22
Block first atom: 3211
Blocpdb> 188 atoms in block 23
Block first atom: 3370
Blocpdb> 171 atoms in block 24
Block first atom: 3558
Blocpdb> 174 atoms in block 25
Block first atom: 3729
Blocpdb> 152 atoms in block 26
Block first atom: 3903
Blocpdb> 156 atoms in block 27
Block first atom: 4055
Blocpdb> 170 atoms in block 28
Block first atom: 4211
Blocpdb> 175 atoms in block 29
Block first atom: 4381
Blocpdb> 154 atoms in block 30
Block first atom: 4556
Blocpdb> 173 atoms in block 31
Block first atom: 4710
Blocpdb> 159 atoms in block 32
Block first atom: 4883
Blocpdb> 172 atoms in block 33
Block first atom: 5042
Blocpdb> 154 atoms in block 34
Block first atom: 5214
Blocpdb> 170 atoms in block 35
Block first atom: 5368
Blocpdb> 163 atoms in block 36
Block first atom: 5538
Blocpdb> 102 atoms in block 37
Block first atom: 5701
Blocpdb> 28 atoms in block 38
Block first atom: 5803
Blocpdb> 139 atoms in block 39
Block first atom: 5831
Blocpdb> 156 atoms in block 40
Block first atom: 5970
Blocpdb> 159 atoms in block 41
Block first atom: 6126
Blocpdb> 188 atoms in block 42
Block first atom: 6285
Blocpdb> 171 atoms in block 43
Block first atom: 6473
Blocpdb> 174 atoms in block 44
Block first atom: 6644
Blocpdb> 152 atoms in block 45
Block first atom: 6818
Blocpdb> 156 atoms in block 46
Block first atom: 6970
Blocpdb> 170 atoms in block 47
Block first atom: 7126
Blocpdb> 175 atoms in block 48
Block first atom: 7296
Blocpdb> 154 atoms in block 49
Block first atom: 7471
Blocpdb> 173 atoms in block 50
Block first atom: 7625
Blocpdb> 159 atoms in block 51
Block first atom: 7798
Blocpdb> 172 atoms in block 52
Block first atom: 7957
Blocpdb> 154 atoms in block 53
Block first atom: 8129
Blocpdb> 170 atoms in block 54
Block first atom: 8283
Blocpdb> 163 atoms in block 55
Block first atom: 8453
Blocpdb> 102 atoms in block 56
Block first atom: 8616
Blocpdb> 28 atoms in block 57
Block first atom: 8718
Blocpdb> 139 atoms in block 58
Block first atom: 8746
Blocpdb> 107 atoms in block 59
Block first atom: 8885
Blocpdb> 75 atoms in block 60
Block first atom: 8992
Blocpdb> 177 atoms in block 61
Block first atom: 9067
Blocpdb> 185 atoms in block 62
Block first atom: 9244
Blocpdb> 169 atoms in block 63
Block first atom: 9429
Blocpdb> 159 atoms in block 64
Block first atom: 9598
Blocpdb> 150 atoms in block 65
Block first atom: 9757
Blocpdb> 169 atoms in block 66
Block first atom: 9907
Blocpdb> 174 atoms in block 67
Block first atom: 10076
Blocpdb> 164 atoms in block 68
Block first atom: 10250
Blocpdb> 155 atoms in block 69
Block first atom: 10414
Blocpdb> 167 atoms in block 70
Block first atom: 10569
Blocpdb> 178 atoms in block 71
Block first atom: 10736
Blocpdb> 153 atoms in block 72
Block first atom: 10914
Blocpdb> 160 atoms in block 73
Block first atom: 11067
Blocpdb> 168 atoms in block 74
Block first atom: 11227
Blocpdb> 136 atoms in block 75
Block first atom: 11395
Blocpdb> 28 atoms in block 76
Block first atom: 11531
Blocpdb> 157 atoms in block 77
Block first atom: 11559
Blocpdb> 165 atoms in block 78
Block first atom: 11716
Blocpdb> 171 atoms in block 79
Block first atom: 11881
Blocpdb> 170 atoms in block 80
Block first atom: 12052
Blocpdb> 152 atoms in block 81
Block first atom: 12222
Blocpdb> 171 atoms in block 82
Block first atom: 12374
Blocpdb> 170 atoms in block 83
Block first atom: 12545
Blocpdb> 156 atoms in block 84
Block first atom: 12715
Blocpdb> 160 atoms in block 85
Block first atom: 12871
Blocpdb> 9 atoms in block 86
Block first atom: 13031
Blocpdb> 28 atoms in block 87
Block first atom: 13040
Blocpdb> 157 atoms in block 88
Block first atom: 13068
Blocpdb> 165 atoms in block 89
Block first atom: 13225
Blocpdb> 171 atoms in block 90
Block first atom: 13390
Blocpdb> 170 atoms in block 91
Block first atom: 13561
Blocpdb> 152 atoms in block 92
Block first atom: 13731
Blocpdb> 171 atoms in block 93
Block first atom: 13883
Blocpdb> 170 atoms in block 94
Block first atom: 14054
Blocpdb> 156 atoms in block 95
Block first atom: 14224
Blocpdb> 160 atoms in block 96
Block first atom: 14380
Blocpdb> 9 atoms in block 97
Block first atom: 14540
Blocpdb> 28 atoms in block 98
Block first atom: 14549
Blocpdb> 139 atoms in block 99
Block first atom: 14577
Blocpdb> 107 atoms in block 100
Block first atom: 14716
Blocpdb> 75 atoms in block 101
Block first atom: 14823
Blocpdb> 177 atoms in block 102
Block first atom: 14898
Blocpdb> 185 atoms in block 103
Block first atom: 15075
Blocpdb> 169 atoms in block 104
Block first atom: 15260
Blocpdb> 148 atoms in block 105
Block first atom: 15429
Blocpdb> 168 atoms in block 106
Block first atom: 15577
Blocpdb> 136 atoms in block 107
Block first atom: 15745
Blocpdb> 139 atoms in block 108
Block first atom: 15881
Blocpdb> 107 atoms in block 109
Block first atom: 16020
Blocpdb> 75 atoms in block 110
Block first atom: 16127
Blocpdb> 177 atoms in block 111
Block first atom: 16202
Blocpdb> 185 atoms in block 112
Block first atom: 16379
Blocpdb> 169 atoms in block 113
Block first atom: 16564
Blocpdb> 148 atoms in block 114
Block first atom: 16733
Blocpdb> 168 atoms in block 115
Block first atom: 16881
Blocpdb> 136 atoms in block 116
Block first atom: 17049
Blocpdb> 155 atoms in block 117
Block first atom: 17185
Blocpdb> 169 atoms in block 118
Block first atom: 17340
Blocpdb> 158 atoms in block 119
Block first atom: 17509
Blocpdb> 176 atoms in block 120
Block first atom: 17667
Blocpdb> 179 atoms in block 121
Block first atom: 17843
Blocpdb> 160 atoms in block 122
Block first atom: 18022
Blocpdb> 169 atoms in block 123
Block first atom: 18182
Blocpdb> 117 atoms in block 124
Block first atom: 18351
Blocpdb> 139 atoms in block 125
Block first atom: 18468
Blocpdb> 107 atoms in block 126
Block first atom: 18607
Blocpdb> 75 atoms in block 127
Block first atom: 18714
Blocpdb> 177 atoms in block 128
Block first atom: 18789
Blocpdb> 185 atoms in block 129
Block first atom: 18966
Blocpdb> 169 atoms in block 130
Block first atom: 19151
Blocpdb> 159 atoms in block 131
Block first atom: 19320
Blocpdb> 150 atoms in block 132
Block first atom: 19479
Blocpdb> 169 atoms in block 133
Block first atom: 19629
Blocpdb> 174 atoms in block 134
Block first atom: 19798
Blocpdb> 164 atoms in block 135
Block first atom: 19972
Blocpdb> 155 atoms in block 136
Block first atom: 20136
Blocpdb> 167 atoms in block 137
Block first atom: 20291
Blocpdb> 178 atoms in block 138
Block first atom: 20458
Blocpdb> 153 atoms in block 139
Block first atom: 20636
Blocpdb> 160 atoms in block 140
Block first atom: 20789
Blocpdb> 168 atoms in block 141
Block first atom: 20949
Blocpdb> 136 atoms in block 142
Block first atom: 21117
Blocpdb> 28 atoms in block 143
Block first atom: 21253
Blocpdb> 139 atoms in block 144
Block first atom: 21281
Blocpdb> 107 atoms in block 145
Block first atom: 21420
Blocpdb> 75 atoms in block 146
Block first atom: 21527
Blocpdb> 177 atoms in block 147
Block first atom: 21602
Blocpdb> 185 atoms in block 148
Block first atom: 21779
Blocpdb> 169 atoms in block 149
Block first atom: 21964
Blocpdb> 159 atoms in block 150
Block first atom: 22133
Blocpdb> 150 atoms in block 151
Block first atom: 22292
Blocpdb> 169 atoms in block 152
Block first atom: 22442
Blocpdb> 174 atoms in block 153
Block first atom: 22611
Blocpdb> 164 atoms in block 154
Block first atom: 22785
Blocpdb> 155 atoms in block 155
Block first atom: 22949
Blocpdb> 167 atoms in block 156
Block first atom: 23104
Blocpdb> 178 atoms in block 157
Block first atom: 23271
Blocpdb> 153 atoms in block 158
Block first atom: 23449
Blocpdb> 160 atoms in block 159
Block first atom: 23602
Blocpdb> 168 atoms in block 160
Block first atom: 23762
Blocpdb> 136 atoms in block 161
Block first atom: 23930
Blocpdb> 28 atoms in block 162
Block first atom: 24066
Blocpdb> 139 atoms in block 163
Block first atom: 24094
Blocpdb> 107 atoms in block 164
Block first atom: 24233
Blocpdb> 75 atoms in block 165
Block first atom: 24340
Blocpdb> 177 atoms in block 166
Block first atom: 24415
Blocpdb> 185 atoms in block 167
Block first atom: 24592
Blocpdb> 169 atoms in block 168
Block first atom: 24777
Blocpdb> 159 atoms in block 169
Block first atom: 24946
Blocpdb> 150 atoms in block 170
Block first atom: 25105
Blocpdb> 169 atoms in block 171
Block first atom: 25255
Blocpdb> 174 atoms in block 172
Block first atom: 25424
Blocpdb> 164 atoms in block 173
Block first atom: 25598
Blocpdb> 155 atoms in block 174
Block first atom: 25762
Blocpdb> 167 atoms in block 175
Block first atom: 25917
Blocpdb> 178 atoms in block 176
Block first atom: 26084
Blocpdb> 153 atoms in block 177
Block first atom: 26262
Blocpdb> 160 atoms in block 178
Block first atom: 26415
Blocpdb> 168 atoms in block 179
Block first atom: 26575
Blocpdb> 136 atoms in block 180
Block first atom: 26743
Blocpdb> 28 atoms in block 181
Block first atom: 26879
Blocpdb> 155 atoms in block 182
Block first atom: 26907
Blocpdb> 169 atoms in block 183
Block first atom: 27062
Blocpdb> 158 atoms in block 184
Block first atom: 27231
Blocpdb> 176 atoms in block 185
Block first atom: 27389
Blocpdb> 179 atoms in block 186
Block first atom: 27565
Blocpdb> 160 atoms in block 187
Block first atom: 27744
Blocpdb> 169 atoms in block 188
Block first atom: 27904
Blocpdb> 117 atoms in block 189
Block first atom: 28073
Blocpdb> 155 atoms in block 190
Block first atom: 28190
Blocpdb> 169 atoms in block 191
Block first atom: 28345
Blocpdb> 158 atoms in block 192
Block first atom: 28514
Blocpdb> 176 atoms in block 193
Block first atom: 28672
Blocpdb> 179 atoms in block 194
Block first atom: 28848
Blocpdb> 160 atoms in block 195
Block first atom: 29027
Blocpdb> 169 atoms in block 196
Block first atom: 29187
Blocpdb> 117 atoms in block 197
Block first atom: 29356
Blocpdb> 155 atoms in block 198
Block first atom: 29473
Blocpdb> 169 atoms in block 199
Block first atom: 29628
Blocpdb> 158 atoms in block 200
Block first atom: 29797
Blocpdb> 176 atoms in block 201
Block first atom: 29955
Blocpdb> 179 atoms in block 202
Block first atom: 30131
Blocpdb> 160 atoms in block 203
Block first atom: 30310
Blocpdb> 169 atoms in block 204
Block first atom: 30470
Blocpdb> 117 atoms in block 205
Block first atom: 30639
Blocpdb> 155 atoms in block 206
Block first atom: 30756
Blocpdb> 169 atoms in block 207
Block first atom: 30911
Blocpdb> 158 atoms in block 208
Block first atom: 31080
Blocpdb> 176 atoms in block 209
Block first atom: 31238
Blocpdb> 179 atoms in block 210
Block first atom: 31414
Blocpdb> 160 atoms in block 211
Block first atom: 31593
Blocpdb> 169 atoms in block 212
Block first atom: 31753
Blocpdb> 117 atoms in block 213
Block first atom: 31921
Blocpdb> 213 blocks.
Blocpdb> At most, 188 atoms in each of them.
Blocpdb> At least, 9 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: 54526393 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 0m0.187s
user 0m0.184s
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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