***  vi  ***
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 = 2402081524491941485.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 2402081524491941485.atom to be opened.
Openam> File opened: 2402081524491941485.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 = 4096
First residue number = 1
Last residue number = 1024
Number of atoms found = 32888
Mean number per residue = 8.0
Pdbmat> Coordinate statistics:
= 122.264218 +/- 38.770090 From: 32.164000 To: 212.341000
= 122.359814 +/- 29.551809 From: 52.547000 To: 192.193000
= 122.294636 +/- 17.886756 From: 78.518000 To: 166.032000
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 2.3812 % Filled.
Pdbmat> 13629544 non-zero elements.
Pdbmat> 1492694 atom-atom interactions.
Pdbmat> Number per atom= 90.77 +/- 21.29
Maximum number = 137
Minimum number = 21
Pdbmat> Matrix trace = 2.985388E+07
Pdbmat> Larger element = 513.638
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
4096 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 = 2402081524491941485.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 2402081524491941485.atom to be opened.
Openam> file on opening on unit 11:
2402081524491941485.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 32888 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> 4096 residues.
Blocpdb> 168 atoms in block 1
Block first atom: 1
Blocpdb> 171 atoms in block 2
Block first atom: 169
Blocpdb> 182 atoms in block 3
Block first atom: 340
Blocpdb> 162 atoms in block 4
Block first atom: 522
Blocpdb> 168 atoms in block 5
Block first atom: 684
Blocpdb> 162 atoms in block 6
Block first atom: 852
Blocpdb> 173 atoms in block 7
Block first atom: 1014
Blocpdb> 174 atoms in block 8
Block first atom: 1187
Blocpdb> 162 atoms in block 9
Block first atom: 1361
Blocpdb> 181 atoms in block 10
Block first atom: 1523
Blocpdb> 170 atoms in block 11
Block first atom: 1704
Blocpdb> 168 atoms in block 12
Block first atom: 1874
Blocpdb> 160 atoms in block 13
Block first atom: 2042
Blocpdb> 164 atoms in block 14
Block first atom: 2202
Blocpdb> 172 atoms in block 15
Block first atom: 2366
Blocpdb> 156 atoms in block 16
Block first atom: 2538
Blocpdb> 165 atoms in block 17
Block first atom: 2694
Blocpdb> 173 atoms in block 18
Block first atom: 2859
Blocpdb> 180 atoms in block 19
Block first atom: 3032
Blocpdb> 170 atoms in block 20
Block first atom: 3212
Blocpdb> 173 atoms in block 21
Block first atom: 3382
Blocpdb> 175 atoms in block 22
Block first atom: 3555
Blocpdb> 167 atoms in block 23
Block first atom: 3730
Blocpdb> 152 atoms in block 24
Block first atom: 3897
Blocpdb> 178 atoms in block 25
Block first atom: 4049
Blocpdb> 156 atoms in block 26
Block first atom: 4227
Blocpdb> 178 atoms in block 27
Block first atom: 4383
Blocpdb> 179 atoms in block 28
Block first atom: 4561
Blocpdb> 164 atoms in block 29
Block first atom: 4740
Blocpdb> 177 atoms in block 30
Block first atom: 4904
Blocpdb> 174 atoms in block 31
Block first atom: 5081
Blocpdb> 158 atoms in block 32
Block first atom: 5255
Blocpdb> 154 atoms in block 33
Block first atom: 5413
Blocpdb> 167 atoms in block 34
Block first atom: 5567
Blocpdb> 165 atoms in block 35
Block first atom: 5734
Blocpdb> 167 atoms in block 36
Block first atom: 5899
Blocpdb> 183 atoms in block 37
Block first atom: 6066
Blocpdb> 165 atoms in block 38
Block first atom: 6249
Blocpdb> 173 atoms in block 39
Block first atom: 6414
Blocpdb> 145 atoms in block 40
Block first atom: 6587
Blocpdb> 180 atoms in block 41
Block first atom: 6732
Blocpdb> 151 atoms in block 42
Block first atom: 6912
Blocpdb> 157 atoms in block 43
Block first atom: 7063
Blocpdb> 176 atoms in block 44
Block first atom: 7220
Blocpdb> 170 atoms in block 45
Block first atom: 7396
Blocpdb> 187 atoms in block 46
Block first atom: 7566
Blocpdb> 176 atoms in block 47
Block first atom: 7753
Blocpdb> 154 atoms in block 48
Block first atom: 7929
Blocpdb> 140 atoms in block 49
Block first atom: 8083
Blocpdb> 168 atoms in block 50
Block first atom: 8223
Blocpdb> 171 atoms in block 51
Block first atom: 8391
Blocpdb> 182 atoms in block 52
Block first atom: 8562
Blocpdb> 162 atoms in block 53
Block first atom: 8744
Blocpdb> 168 atoms in block 54
Block first atom: 8906
Blocpdb> 162 atoms in block 55
Block first atom: 9074
Blocpdb> 173 atoms in block 56
Block first atom: 9236
Blocpdb> 174 atoms in block 57
Block first atom: 9409
Blocpdb> 162 atoms in block 58
Block first atom: 9583
Blocpdb> 181 atoms in block 59
Block first atom: 9745
Blocpdb> 170 atoms in block 60
Block first atom: 9926
Blocpdb> 168 atoms in block 61
Block first atom: 10096
Blocpdb> 160 atoms in block 62
Block first atom: 10264
Blocpdb> 164 atoms in block 63
Block first atom: 10424
Blocpdb> 172 atoms in block 64
Block first atom: 10588
Blocpdb> 156 atoms in block 65
Block first atom: 10760
Blocpdb> 165 atoms in block 66
Block first atom: 10916
Blocpdb> 173 atoms in block 67
Block first atom: 11081
Blocpdb> 180 atoms in block 68
Block first atom: 11254
Blocpdb> 170 atoms in block 69
Block first atom: 11434
Blocpdb> 173 atoms in block 70
Block first atom: 11604
Blocpdb> 175 atoms in block 71
Block first atom: 11777
Blocpdb> 167 atoms in block 72
Block first atom: 11952
Blocpdb> 152 atoms in block 73
Block first atom: 12119
Blocpdb> 178 atoms in block 74
Block first atom: 12271
Blocpdb> 156 atoms in block 75
Block first atom: 12449
Blocpdb> 178 atoms in block 76
Block first atom: 12605
Blocpdb> 179 atoms in block 77
Block first atom: 12783
Blocpdb> 164 atoms in block 78
Block first atom: 12962
Blocpdb> 177 atoms in block 79
Block first atom: 13126
Blocpdb> 174 atoms in block 80
Block first atom: 13303
Blocpdb> 158 atoms in block 81
Block first atom: 13477
Blocpdb> 154 atoms in block 82
Block first atom: 13635
Blocpdb> 167 atoms in block 83
Block first atom: 13789
Blocpdb> 165 atoms in block 84
Block first atom: 13956
Blocpdb> 167 atoms in block 85
Block first atom: 14121
Blocpdb> 183 atoms in block 86
Block first atom: 14288
Blocpdb> 165 atoms in block 87
Block first atom: 14471
Blocpdb> 173 atoms in block 88
Block first atom: 14636
Blocpdb> 145 atoms in block 89
Block first atom: 14809
Blocpdb> 180 atoms in block 90
Block first atom: 14954
Blocpdb> 151 atoms in block 91
Block first atom: 15134
Blocpdb> 157 atoms in block 92
Block first atom: 15285
Blocpdb> 176 atoms in block 93
Block first atom: 15442
Blocpdb> 170 atoms in block 94
Block first atom: 15618
Blocpdb> 187 atoms in block 95
Block first atom: 15788
Blocpdb> 176 atoms in block 96
Block first atom: 15975
Blocpdb> 154 atoms in block 97
Block first atom: 16151
Blocpdb> 140 atoms in block 98
Block first atom: 16305
Blocpdb> 168 atoms in block 99
Block first atom: 16445
Blocpdb> 171 atoms in block 100
Block first atom: 16613
Blocpdb> 182 atoms in block 101
Block first atom: 16784
Blocpdb> 162 atoms in block 102
Block first atom: 16966
Blocpdb> 168 atoms in block 103
Block first atom: 17128
Blocpdb> 162 atoms in block 104
Block first atom: 17296
Blocpdb> 173 atoms in block 105
Block first atom: 17458
Blocpdb> 174 atoms in block 106
Block first atom: 17631
Blocpdb> 162 atoms in block 107
Block first atom: 17805
Blocpdb> 181 atoms in block 108
Block first atom: 17967
Blocpdb> 170 atoms in block 109
Block first atom: 18148
Blocpdb> 168 atoms in block 110
Block first atom: 18318
Blocpdb> 160 atoms in block 111
Block first atom: 18486
Blocpdb> 164 atoms in block 112
Block first atom: 18646
Blocpdb> 172 atoms in block 113
Block first atom: 18810
Blocpdb> 156 atoms in block 114
Block first atom: 18982
Blocpdb> 165 atoms in block 115
Block first atom: 19138
Blocpdb> 173 atoms in block 116
Block first atom: 19303
Blocpdb> 180 atoms in block 117
Block first atom: 19476
Blocpdb> 170 atoms in block 118
Block first atom: 19656
Blocpdb> 173 atoms in block 119
Block first atom: 19826
Blocpdb> 175 atoms in block 120
Block first atom: 19999
Blocpdb> 167 atoms in block 121
Block first atom: 20174
Blocpdb> 152 atoms in block 122
Block first atom: 20341
Blocpdb> 178 atoms in block 123
Block first atom: 20493
Blocpdb> 156 atoms in block 124
Block first atom: 20671
Blocpdb> 178 atoms in block 125
Block first atom: 20827
Blocpdb> 179 atoms in block 126
Block first atom: 21005
Blocpdb> 164 atoms in block 127
Block first atom: 21184
Blocpdb> 177 atoms in block 128
Block first atom: 21348
Blocpdb> 174 atoms in block 129
Block first atom: 21525
Blocpdb> 158 atoms in block 130
Block first atom: 21699
Blocpdb> 154 atoms in block 131
Block first atom: 21857
Blocpdb> 167 atoms in block 132
Block first atom: 22011
Blocpdb> 165 atoms in block 133
Block first atom: 22178
Blocpdb> 167 atoms in block 134
Block first atom: 22343
Blocpdb> 183 atoms in block 135
Block first atom: 22510
Blocpdb> 165 atoms in block 136
Block first atom: 22693
Blocpdb> 173 atoms in block 137
Block first atom: 22858
Blocpdb> 145 atoms in block 138
Block first atom: 23031
Blocpdb> 180 atoms in block 139
Block first atom: 23176
Blocpdb> 151 atoms in block 140
Block first atom: 23356
Blocpdb> 157 atoms in block 141
Block first atom: 23507
Blocpdb> 176 atoms in block 142
Block first atom: 23664
Blocpdb> 170 atoms in block 143
Block first atom: 23840
Blocpdb> 187 atoms in block 144
Block first atom: 24010
Blocpdb> 176 atoms in block 145
Block first atom: 24197
Blocpdb> 154 atoms in block 146
Block first atom: 24373
Blocpdb> 140 atoms in block 147
Block first atom: 24527
Blocpdb> 168 atoms in block 148
Block first atom: 24667
Blocpdb> 171 atoms in block 149
Block first atom: 24835
Blocpdb> 182 atoms in block 150
Block first atom: 25006
Blocpdb> 162 atoms in block 151
Block first atom: 25188
Blocpdb> 168 atoms in block 152
Block first atom: 25350
Blocpdb> 162 atoms in block 153
Block first atom: 25518
Blocpdb> 173 atoms in block 154
Block first atom: 25680
Blocpdb> 174 atoms in block 155
Block first atom: 25853
Blocpdb> 162 atoms in block 156
Block first atom: 26027
Blocpdb> 181 atoms in block 157
Block first atom: 26189
Blocpdb> 170 atoms in block 158
Block first atom: 26370
Blocpdb> 168 atoms in block 159
Block first atom: 26540
Blocpdb> 160 atoms in block 160
Block first atom: 26708
Blocpdb> 164 atoms in block 161
Block first atom: 26868
Blocpdb> 172 atoms in block 162
Block first atom: 27032
Blocpdb> 156 atoms in block 163
Block first atom: 27204
Blocpdb> 165 atoms in block 164
Block first atom: 27360
Blocpdb> 173 atoms in block 165
Block first atom: 27525
Blocpdb> 180 atoms in block 166
Block first atom: 27698
Blocpdb> 170 atoms in block 167
Block first atom: 27878
Blocpdb> 173 atoms in block 168
Block first atom: 28048
Blocpdb> 175 atoms in block 169
Block first atom: 28221
Blocpdb> 167 atoms in block 170
Block first atom: 28396
Blocpdb> 152 atoms in block 171
Block first atom: 28563
Blocpdb> 178 atoms in block 172
Block first atom: 28715
Blocpdb> 156 atoms in block 173
Block first atom: 28893
Blocpdb> 178 atoms in block 174
Block first atom: 29049
Blocpdb> 179 atoms in block 175
Block first atom: 29227
Blocpdb> 164 atoms in block 176
Block first atom: 29406
Blocpdb> 177 atoms in block 177
Block first atom: 29570
Blocpdb> 174 atoms in block 178
Block first atom: 29747
Blocpdb> 158 atoms in block 179
Block first atom: 29921
Blocpdb> 154 atoms in block 180
Block first atom: 30079
Blocpdb> 167 atoms in block 181
Block first atom: 30233
Blocpdb> 165 atoms in block 182
Block first atom: 30400
Blocpdb> 167 atoms in block 183
Block first atom: 30565
Blocpdb> 183 atoms in block 184
Block first atom: 30732
Blocpdb> 165 atoms in block 185
Block first atom: 30915
Blocpdb> 173 atoms in block 186
Block first atom: 31080
Blocpdb> 145 atoms in block 187
Block first atom: 31253
Blocpdb> 180 atoms in block 188
Block first atom: 31398
Blocpdb> 151 atoms in block 189
Block first atom: 31578
Blocpdb> 157 atoms in block 190
Block first atom: 31729
Blocpdb> 176 atoms in block 191
Block first atom: 31886
Blocpdb> 170 atoms in block 192
Block first atom: 32062
Blocpdb> 187 atoms in block 193
Block first atom: 32232
Blocpdb> 176 atoms in block 194
Block first atom: 32419
Blocpdb> 154 atoms in block 195
Block first atom: 32595
Blocpdb> 140 atoms in block 196
Block first atom: 32748
Blocpdb> 196 blocks.
Blocpdb> At most, 187 atoms in each of them.
Blocpdb> At least, 140 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: 55665226 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 0m0.164s
user 0m0.164s
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: April 25th, 2023.
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