*** ***
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 = 22021417192141187.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 22021417192141187.atom to be opened.
Openam> File opened: 22021417192141187.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 = 1960
First residue number = 1
Last residue number = 478
Number of atoms found = 31430
Mean number per residue = 16.0
Pdbmat> Coordinate statistics:
= 138.065595 +/- 16.806441 From: 92.045000 To: 181.273000
= 138.086755 +/- 16.805236 From: 91.227000 To: 179.312000
= 121.952540 +/- 37.177019 From: 60.000000 To: 214.621000
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 15.3388 % Filled.
Pdbmat> 23066792 non-zero elements.
Pdbmat> 2542473 atom-atom interactions.
Pdbmat> Number per atom= 161.79 +/- 41.93
Maximum number = 246
Minimum number = 19
Pdbmat> Matrix trace = 5.084946E+07
Pdbmat> Larger element = 957.399
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
1960 non-zero elements, NRBL set to 10
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 = 22021417192141187.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 10
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 22021417192141187.atom to be opened.
Openam> file on opening on unit 11:
22021417192141187.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 31430 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 10 residue(s) per block.
Blocpdb> 1960 residues.
Blocpdb> 196 atoms in block 1
Block first atom: 1
Blocpdb> 173 atoms in block 2
Block first atom: 197
Blocpdb> 141 atoms in block 3
Block first atom: 370
Blocpdb> 176 atoms in block 4
Block first atom: 511
Blocpdb> 157 atoms in block 5
Block first atom: 687
Blocpdb> 173 atoms in block 6
Block first atom: 844
Blocpdb> 164 atoms in block 7
Block first atom: 1017
Blocpdb> 168 atoms in block 8
Block first atom: 1181
Blocpdb> 165 atoms in block 9
Block first atom: 1349
Blocpdb> 158 atoms in block 10
Block first atom: 1514
Blocpdb> 151 atoms in block 11
Block first atom: 1672
Blocpdb> 140 atoms in block 12
Block first atom: 1823
Blocpdb> 152 atoms in block 13
Block first atom: 1963
Blocpdb> 179 atoms in block 14
Block first atom: 2115
Blocpdb> 167 atoms in block 15
Block first atom: 2294
Blocpdb> 150 atoms in block 16
Block first atom: 2461
Blocpdb> 142 atoms in block 17
Block first atom: 2611
Blocpdb> 140 atoms in block 18
Block first atom: 2753
Blocpdb> 164 atoms in block 19
Block first atom: 2893
Blocpdb> 162 atoms in block 20
Block first atom: 3057
Blocpdb> 194 atoms in block 21
Block first atom: 3219
Blocpdb> 157 atoms in block 22
Block first atom: 3413
Blocpdb> 162 atoms in block 23
Block first atom: 3570
Blocpdb> 140 atoms in block 24
Block first atom: 3732
Blocpdb> 157 atoms in block 25
Block first atom: 3872
Blocpdb> 168 atoms in block 26
Block first atom: 4029
Blocpdb> 140 atoms in block 27
Block first atom: 4197
Blocpdb> 158 atoms in block 28
Block first atom: 4337
Blocpdb> 150 atoms in block 29
Block first atom: 4495
Blocpdb> 162 atoms in block 30
Block first atom: 4645
Blocpdb> 167 atoms in block 31
Block first atom: 4807
Blocpdb> 179 atoms in block 32
Block first atom: 4974
Blocpdb> 24 atoms in block 33
Block first atom: 5153
Blocpdb> 161 atoms in block 34
Block first atom: 5177
Blocpdb> 184 atoms in block 35
Block first atom: 5338
Blocpdb> 132 atoms in block 36
Block first atom: 5522
Blocpdb> 160 atoms in block 37
Block first atom: 5654
Blocpdb> 157 atoms in block 38
Block first atom: 5814
Blocpdb> 146 atoms in block 39
Block first atom: 5971
Blocpdb> 150 atoms in block 40
Block first atom: 6117
Blocpdb> 20 atoms in block 41
Block first atom: 6267
Blocpdb> 196 atoms in block 42
Block first atom: 6287
Blocpdb> 173 atoms in block 43
Block first atom: 6483
Blocpdb> 141 atoms in block 44
Block first atom: 6656
Blocpdb> 176 atoms in block 45
Block first atom: 6797
Blocpdb> 157 atoms in block 46
Block first atom: 6973
Blocpdb> 173 atoms in block 47
Block first atom: 7130
Blocpdb> 164 atoms in block 48
Block first atom: 7303
Blocpdb> 168 atoms in block 49
Block first atom: 7467
Blocpdb> 165 atoms in block 50
Block first atom: 7635
Blocpdb> 158 atoms in block 51
Block first atom: 7800
Blocpdb> 151 atoms in block 52
Block first atom: 7958
Blocpdb> 140 atoms in block 53
Block first atom: 8109
Blocpdb> 152 atoms in block 54
Block first atom: 8249
Blocpdb> 179 atoms in block 55
Block first atom: 8401
Blocpdb> 167 atoms in block 56
Block first atom: 8580
Blocpdb> 150 atoms in block 57
Block first atom: 8747
Blocpdb> 142 atoms in block 58
Block first atom: 8897
Blocpdb> 140 atoms in block 59
Block first atom: 9039
Blocpdb> 164 atoms in block 60
Block first atom: 9179
Blocpdb> 162 atoms in block 61
Block first atom: 9343
Blocpdb> 194 atoms in block 62
Block first atom: 9505
Blocpdb> 157 atoms in block 63
Block first atom: 9699
Blocpdb> 162 atoms in block 64
Block first atom: 9856
Blocpdb> 140 atoms in block 65
Block first atom: 10018
Blocpdb> 157 atoms in block 66
Block first atom: 10158
Blocpdb> 168 atoms in block 67
Block first atom: 10315
Blocpdb> 140 atoms in block 68
Block first atom: 10483
Blocpdb> 158 atoms in block 69
Block first atom: 10623
Blocpdb> 150 atoms in block 70
Block first atom: 10781
Blocpdb> 162 atoms in block 71
Block first atom: 10931
Blocpdb> 167 atoms in block 72
Block first atom: 11093
Blocpdb> 179 atoms in block 73
Block first atom: 11260
Blocpdb> 24 atoms in block 74
Block first atom: 11439
Blocpdb> 161 atoms in block 75
Block first atom: 11463
Blocpdb> 184 atoms in block 76
Block first atom: 11624
Blocpdb> 132 atoms in block 77
Block first atom: 11808
Blocpdb> 160 atoms in block 78
Block first atom: 11940
Blocpdb> 157 atoms in block 79
Block first atom: 12100
Blocpdb> 146 atoms in block 80
Block first atom: 12257
Blocpdb> 150 atoms in block 81
Block first atom: 12403
Blocpdb> 20 atoms in block 82
Block first atom: 12553
Blocpdb> 196 atoms in block 83
Block first atom: 12573
Blocpdb> 173 atoms in block 84
Block first atom: 12769
Blocpdb> 141 atoms in block 85
Block first atom: 12942
Blocpdb> 176 atoms in block 86
Block first atom: 13083
Blocpdb> 157 atoms in block 87
Block first atom: 13259
Blocpdb> 173 atoms in block 88
Block first atom: 13416
Blocpdb> 164 atoms in block 89
Block first atom: 13589
Blocpdb> 168 atoms in block 90
Block first atom: 13753
Blocpdb> 165 atoms in block 91
Block first atom: 13921
Blocpdb> 158 atoms in block 92
Block first atom: 14086
Blocpdb> 151 atoms in block 93
Block first atom: 14244
Blocpdb> 140 atoms in block 94
Block first atom: 14395
Blocpdb> 152 atoms in block 95
Block first atom: 14535
Blocpdb> 179 atoms in block 96
Block first atom: 14687
Blocpdb> 167 atoms in block 97
Block first atom: 14866
Blocpdb> 150 atoms in block 98
Block first atom: 15033
Blocpdb> 142 atoms in block 99
Block first atom: 15183
Blocpdb> 140 atoms in block 100
Block first atom: 15325
Blocpdb> 164 atoms in block 101
Block first atom: 15465
Blocpdb> 162 atoms in block 102
Block first atom: 15629
Blocpdb> 194 atoms in block 103
Block first atom: 15791
Blocpdb> 157 atoms in block 104
Block first atom: 15985
Blocpdb> 162 atoms in block 105
Block first atom: 16142
Blocpdb> 140 atoms in block 106
Block first atom: 16304
Blocpdb> 157 atoms in block 107
Block first atom: 16444
Blocpdb> 168 atoms in block 108
Block first atom: 16601
Blocpdb> 140 atoms in block 109
Block first atom: 16769
Blocpdb> 158 atoms in block 110
Block first atom: 16909
Blocpdb> 150 atoms in block 111
Block first atom: 17067
Blocpdb> 162 atoms in block 112
Block first atom: 17217
Blocpdb> 167 atoms in block 113
Block first atom: 17379
Blocpdb> 179 atoms in block 114
Block first atom: 17546
Blocpdb> 24 atoms in block 115
Block first atom: 17725
Blocpdb> 161 atoms in block 116
Block first atom: 17749
Blocpdb> 184 atoms in block 117
Block first atom: 17910
Blocpdb> 132 atoms in block 118
Block first atom: 18094
Blocpdb> 160 atoms in block 119
Block first atom: 18226
Blocpdb> 157 atoms in block 120
Block first atom: 18386
Blocpdb> 146 atoms in block 121
Block first atom: 18543
Blocpdb> 150 atoms in block 122
Block first atom: 18689
Blocpdb> 20 atoms in block 123
Block first atom: 18839
Blocpdb> 196 atoms in block 124
Block first atom: 18859
Blocpdb> 173 atoms in block 125
Block first atom: 19055
Blocpdb> 141 atoms in block 126
Block first atom: 19228
Blocpdb> 176 atoms in block 127
Block first atom: 19369
Blocpdb> 157 atoms in block 128
Block first atom: 19545
Blocpdb> 173 atoms in block 129
Block first atom: 19702
Blocpdb> 164 atoms in block 130
Block first atom: 19875
Blocpdb> 168 atoms in block 131
Block first atom: 20039
Blocpdb> 165 atoms in block 132
Block first atom: 20207
Blocpdb> 158 atoms in block 133
Block first atom: 20372
Blocpdb> 151 atoms in block 134
Block first atom: 20530
Blocpdb> 140 atoms in block 135
Block first atom: 20681
Blocpdb> 152 atoms in block 136
Block first atom: 20821
Blocpdb> 179 atoms in block 137
Block first atom: 20973
Blocpdb> 167 atoms in block 138
Block first atom: 21152
Blocpdb> 150 atoms in block 139
Block first atom: 21319
Blocpdb> 142 atoms in block 140
Block first atom: 21469
Blocpdb> 140 atoms in block 141
Block first atom: 21611
Blocpdb> 164 atoms in block 142
Block first atom: 21751
Blocpdb> 162 atoms in block 143
Block first atom: 21915
Blocpdb> 194 atoms in block 144
Block first atom: 22077
Blocpdb> 157 atoms in block 145
Block first atom: 22271
Blocpdb> 162 atoms in block 146
Block first atom: 22428
Blocpdb> 140 atoms in block 147
Block first atom: 22590
Blocpdb> 157 atoms in block 148
Block first atom: 22730
Blocpdb> 168 atoms in block 149
Block first atom: 22887
Blocpdb> 140 atoms in block 150
Block first atom: 23055
Blocpdb> 158 atoms in block 151
Block first atom: 23195
Blocpdb> 150 atoms in block 152
Block first atom: 23353
Blocpdb> 162 atoms in block 153
Block first atom: 23503
Blocpdb> 167 atoms in block 154
Block first atom: 23665
Blocpdb> 179 atoms in block 155
Block first atom: 23832
Blocpdb> 24 atoms in block 156
Block first atom: 24011
Blocpdb> 161 atoms in block 157
Block first atom: 24035
Blocpdb> 184 atoms in block 158
Block first atom: 24196
Blocpdb> 132 atoms in block 159
Block first atom: 24380
Blocpdb> 160 atoms in block 160
Block first atom: 24512
Blocpdb> 157 atoms in block 161
Block first atom: 24672
Blocpdb> 146 atoms in block 162
Block first atom: 24829
Blocpdb> 150 atoms in block 163
Block first atom: 24975
Blocpdb> 20 atoms in block 164
Block first atom: 25125
Blocpdb> 196 atoms in block 165
Block first atom: 25145
Blocpdb> 173 atoms in block 166
Block first atom: 25341
Blocpdb> 141 atoms in block 167
Block first atom: 25514
Blocpdb> 176 atoms in block 168
Block first atom: 25655
Blocpdb> 157 atoms in block 169
Block first atom: 25831
Blocpdb> 173 atoms in block 170
Block first atom: 25988
Blocpdb> 164 atoms in block 171
Block first atom: 26161
Blocpdb> 168 atoms in block 172
Block first atom: 26325
Blocpdb> 165 atoms in block 173
Block first atom: 26493
Blocpdb> 158 atoms in block 174
Block first atom: 26658
Blocpdb> 151 atoms in block 175
Block first atom: 26816
Blocpdb> 140 atoms in block 176
Block first atom: 26967
Blocpdb> 152 atoms in block 177
Block first atom: 27107
Blocpdb> 179 atoms in block 178
Block first atom: 27259
Blocpdb> 167 atoms in block 179
Block first atom: 27438
Blocpdb> 150 atoms in block 180
Block first atom: 27605
Blocpdb> 142 atoms in block 181
Block first atom: 27755
Blocpdb> 140 atoms in block 182
Block first atom: 27897
Blocpdb> 164 atoms in block 183
Block first atom: 28037
Blocpdb> 162 atoms in block 184
Block first atom: 28201
Blocpdb> 194 atoms in block 185
Block first atom: 28363
Blocpdb> 157 atoms in block 186
Block first atom: 28557
Blocpdb> 162 atoms in block 187
Block first atom: 28714
Blocpdb> 140 atoms in block 188
Block first atom: 28876
Blocpdb> 157 atoms in block 189
Block first atom: 29016
Blocpdb> 168 atoms in block 190
Block first atom: 29173
Blocpdb> 140 atoms in block 191
Block first atom: 29341
Blocpdb> 158 atoms in block 192
Block first atom: 29481
Blocpdb> 150 atoms in block 193
Block first atom: 29639
Blocpdb> 162 atoms in block 194
Block first atom: 29789
Blocpdb> 167 atoms in block 195
Block first atom: 29951
Blocpdb> 179 atoms in block 196
Block first atom: 30118
Blocpdb> 24 atoms in block 197
Block first atom: 30297
Blocpdb> 161 atoms in block 198
Block first atom: 30321
Blocpdb> 184 atoms in block 199
Block first atom: 30482
Blocpdb> 132 atoms in block 200
Block first atom: 30666
Blocpdb> 160 atoms in block 201
Block first atom: 30798
Blocpdb> 157 atoms in block 202
Block first atom: 30958
Blocpdb> 146 atoms in block 203
Block first atom: 31115
Blocpdb> 150 atoms in block 204
Block first atom: 31261
Blocpdb> 20 atoms in block 205
Block first atom: 31410
Blocpdb> 205 blocks.
Blocpdb> At most, 196 atoms in each of them.
Blocpdb> At least, 20 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: 55788265 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 0m0.190s
user 0m0.180s
sys 0m0.008s
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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