*** Model_31 ***
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 = 2401050415323912417.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 2401050415323912417.atom to be opened.
Openam> File opened: 2401050415323912417.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 = 1708
First residue number = 1
Last residue number = 427
Number of atoms found = 26937
Mean number per residue = 15.8
Pdbmat> Coordinate statistics:
= 0.391741 +/- 20.519301 From: -50.281000 To: 58.172000
= -0.163011 +/- 19.039817 From: -50.282000 To: 54.508000
= -7.912332 +/- 26.963263 From: -77.943000 To: 63.636000
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 -1.9119 % Filled.
Pdbmat> 19686918 non-zero elements.
Pdbmat> 2169849 atom-atom interactions.
Pdbmat> Number per atom= 161.11 +/- 46.74
Maximum number = 258
Minimum number = 20
Pdbmat> Matrix trace = 4.339698E+07
Pdbmat> Larger element = 894.151
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
1708 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 = 2401050415323912417.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 2401050415323912417.atom to be opened.
Openam> file on opening on unit 11:
2401050415323912417.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 26937 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> 1708 residues.
Blocpdb> 150 atoms in block 1
Block first atom: 1
Blocpdb> 117 atoms in block 2
Block first atom: 151
Blocpdb> 135 atoms in block 3
Block first atom: 268
Blocpdb> 124 atoms in block 4
Block first atom: 403
Blocpdb> 150 atoms in block 5
Block first atom: 527
Blocpdb> 151 atoms in block 6
Block first atom: 677
Blocpdb> 138 atoms in block 7
Block first atom: 828
Blocpdb> 151 atoms in block 8
Block first atom: 966
Blocpdb> 154 atoms in block 9
Block first atom: 1117
Blocpdb> 169 atoms in block 10
Block first atom: 1271
Blocpdb> 159 atoms in block 11
Block first atom: 1440
Blocpdb> 145 atoms in block 12
Block first atom: 1599
Blocpdb> 130 atoms in block 13
Block first atom: 1744
Blocpdb> 122 atoms in block 14
Block first atom: 1874
Blocpdb> 138 atoms in block 15
Block first atom: 1996
Blocpdb> 129 atoms in block 16
Block first atom: 2134
Blocpdb> 137 atoms in block 17
Block first atom: 2263
Blocpdb> 138 atoms in block 18
Block first atom: 2400
Blocpdb> 139 atoms in block 19
Block first atom: 2538
Blocpdb> 131 atoms in block 20
Block first atom: 2677
Blocpdb> 163 atoms in block 21
Block first atom: 2808
Blocpdb> 140 atoms in block 22
Block first atom: 2971
Blocpdb> 137 atoms in block 23
Block first atom: 3111
Blocpdb> 151 atoms in block 24
Block first atom: 3248
Blocpdb> 153 atoms in block 25
Block first atom: 3399
Blocpdb> 156 atoms in block 26
Block first atom: 3552
Blocpdb> 145 atoms in block 27
Block first atom: 3708
Blocpdb> 142 atoms in block 28
Block first atom: 3853
Blocpdb> 131 atoms in block 29
Block first atom: 3995
Blocpdb> 148 atoms in block 30
Block first atom: 4126
Blocpdb> 134 atoms in block 31
Block first atom: 4274
Blocpdb> 145 atoms in block 32
Block first atom: 4408
Blocpdb> 141 atoms in block 33
Block first atom: 4553
Blocpdb> 123 atoms in block 34
Block first atom: 4694
Blocpdb> 140 atoms in block 35
Block first atom: 4817
Blocpdb> 144 atoms in block 36
Block first atom: 4957
Blocpdb> 159 atoms in block 37
Block first atom: 5101
Blocpdb> 163 atoms in block 38
Block first atom: 5260
Blocpdb> 163 atoms in block 39
Block first atom: 5423
Blocpdb> 129 atoms in block 40
Block first atom: 5586
Blocpdb> 158 atoms in block 41
Block first atom: 5715
Blocpdb> 130 atoms in block 42
Block first atom: 5873
Blocpdb> 137 atoms in block 43
Block first atom: 6003
Blocpdb> 116 atoms in block 44
Block first atom: 6140
Blocpdb> 116 atoms in block 45
Block first atom: 6256
Blocpdb> 135 atoms in block 46
Block first atom: 6372
Blocpdb> 167 atoms in block 47
Block first atom: 6507
Blocpdb> 61 atoms in block 48
Block first atom: 6674
Blocpdb> 150 atoms in block 49
Block first atom: 6735
Blocpdb> 117 atoms in block 50
Block first atom: 6885
Blocpdb> 135 atoms in block 51
Block first atom: 7002
Blocpdb> 124 atoms in block 52
Block first atom: 7137
Blocpdb> 150 atoms in block 53
Block first atom: 7261
Blocpdb> 151 atoms in block 54
Block first atom: 7411
Blocpdb> 138 atoms in block 55
Block first atom: 7562
Blocpdb> 151 atoms in block 56
Block first atom: 7700
Blocpdb> 154 atoms in block 57
Block first atom: 7851
Blocpdb> 169 atoms in block 58
Block first atom: 8005
Blocpdb> 159 atoms in block 59
Block first atom: 8174
Blocpdb> 145 atoms in block 60
Block first atom: 8333
Blocpdb> 130 atoms in block 61
Block first atom: 8478
Blocpdb> 122 atoms in block 62
Block first atom: 8608
Blocpdb> 138 atoms in block 63
Block first atom: 8730
Blocpdb> 130 atoms in block 64
Block first atom: 8868
Blocpdb> 137 atoms in block 65
Block first atom: 8998
Blocpdb> 138 atoms in block 66
Block first atom: 9135
Blocpdb> 139 atoms in block 67
Block first atom: 9273
Blocpdb> 131 atoms in block 68
Block first atom: 9412
Blocpdb> 163 atoms in block 69
Block first atom: 9543
Blocpdb> 140 atoms in block 70
Block first atom: 9706
Blocpdb> 137 atoms in block 71
Block first atom: 9846
Blocpdb> 151 atoms in block 72
Block first atom: 9983
Blocpdb> 153 atoms in block 73
Block first atom: 10134
Blocpdb> 156 atoms in block 74
Block first atom: 10287
Blocpdb> 145 atoms in block 75
Block first atom: 10443
Blocpdb> 142 atoms in block 76
Block first atom: 10588
Blocpdb> 131 atoms in block 77
Block first atom: 10730
Blocpdb> 148 atoms in block 78
Block first atom: 10861
Blocpdb> 134 atoms in block 79
Block first atom: 11009
Blocpdb> 145 atoms in block 80
Block first atom: 11143
Blocpdb> 141 atoms in block 81
Block first atom: 11288
Blocpdb> 123 atoms in block 82
Block first atom: 11429
Blocpdb> 140 atoms in block 83
Block first atom: 11552
Blocpdb> 144 atoms in block 84
Block first atom: 11692
Blocpdb> 159 atoms in block 85
Block first atom: 11836
Blocpdb> 163 atoms in block 86
Block first atom: 11995
Blocpdb> 163 atoms in block 87
Block first atom: 12158
Blocpdb> 129 atoms in block 88
Block first atom: 12321
Blocpdb> 158 atoms in block 89
Block first atom: 12450
Blocpdb> 130 atoms in block 90
Block first atom: 12608
Blocpdb> 137 atoms in block 91
Block first atom: 12738
Blocpdb> 116 atoms in block 92
Block first atom: 12875
Blocpdb> 116 atoms in block 93
Block first atom: 12991
Blocpdb> 135 atoms in block 94
Block first atom: 13107
Blocpdb> 167 atoms in block 95
Block first atom: 13242
Blocpdb> 61 atoms in block 96
Block first atom: 13409
Blocpdb> 150 atoms in block 97
Block first atom: 13470
Blocpdb> 117 atoms in block 98
Block first atom: 13620
Blocpdb> 135 atoms in block 99
Block first atom: 13737
Blocpdb> 124 atoms in block 100
Block first atom: 13872
Blocpdb> 150 atoms in block 101
Block first atom: 13996
Blocpdb> 151 atoms in block 102
Block first atom: 14146
Blocpdb> 138 atoms in block 103
Block first atom: 14297
Blocpdb> 151 atoms in block 104
Block first atom: 14435
Blocpdb> 154 atoms in block 105
Block first atom: 14586
Blocpdb> 169 atoms in block 106
Block first atom: 14740
Blocpdb> 159 atoms in block 107
Block first atom: 14909
Blocpdb> 145 atoms in block 108
Block first atom: 15068
Blocpdb> 130 atoms in block 109
Block first atom: 15213
Blocpdb> 122 atoms in block 110
Block first atom: 15343
Blocpdb> 138 atoms in block 111
Block first atom: 15465
Blocpdb> 129 atoms in block 112
Block first atom: 15603
Blocpdb> 137 atoms in block 113
Block first atom: 15732
Blocpdb> 138 atoms in block 114
Block first atom: 15869
Blocpdb> 139 atoms in block 115
Block first atom: 16007
Blocpdb> 131 atoms in block 116
Block first atom: 16146
Blocpdb> 163 atoms in block 117
Block first atom: 16277
Blocpdb> 140 atoms in block 118
Block first atom: 16440
Blocpdb> 137 atoms in block 119
Block first atom: 16580
Blocpdb> 151 atoms in block 120
Block first atom: 16717
Blocpdb> 153 atoms in block 121
Block first atom: 16868
Blocpdb> 156 atoms in block 122
Block first atom: 17021
Blocpdb> 145 atoms in block 123
Block first atom: 17177
Blocpdb> 142 atoms in block 124
Block first atom: 17322
Blocpdb> 131 atoms in block 125
Block first atom: 17464
Blocpdb> 148 atoms in block 126
Block first atom: 17595
Blocpdb> 134 atoms in block 127
Block first atom: 17743
Blocpdb> 145 atoms in block 128
Block first atom: 17877
Blocpdb> 141 atoms in block 129
Block first atom: 18022
Blocpdb> 123 atoms in block 130
Block first atom: 18163
Blocpdb> 140 atoms in block 131
Block first atom: 18286
Blocpdb> 144 atoms in block 132
Block first atom: 18426
Blocpdb> 159 atoms in block 133
Block first atom: 18570
Blocpdb> 163 atoms in block 134
Block first atom: 18729
Blocpdb> 163 atoms in block 135
Block first atom: 18892
Blocpdb> 129 atoms in block 136
Block first atom: 19055
Blocpdb> 158 atoms in block 137
Block first atom: 19184
Blocpdb> 130 atoms in block 138
Block first atom: 19342
Blocpdb> 137 atoms in block 139
Block first atom: 19472
Blocpdb> 116 atoms in block 140
Block first atom: 19609
Blocpdb> 116 atoms in block 141
Block first atom: 19725
Blocpdb> 135 atoms in block 142
Block first atom: 19841
Blocpdb> 167 atoms in block 143
Block first atom: 19976
Blocpdb> 61 atoms in block 144
Block first atom: 20143
Blocpdb> 150 atoms in block 145
Block first atom: 20204
Blocpdb> 117 atoms in block 146
Block first atom: 20354
Blocpdb> 135 atoms in block 147
Block first atom: 20471
Blocpdb> 124 atoms in block 148
Block first atom: 20606
Blocpdb> 150 atoms in block 149
Block first atom: 20730
Blocpdb> 151 atoms in block 150
Block first atom: 20880
Blocpdb> 138 atoms in block 151
Block first atom: 21031
Blocpdb> 151 atoms in block 152
Block first atom: 21169
Blocpdb> 154 atoms in block 153
Block first atom: 21320
Blocpdb> 169 atoms in block 154
Block first atom: 21474
Blocpdb> 159 atoms in block 155
Block first atom: 21643
Blocpdb> 145 atoms in block 156
Block first atom: 21802
Blocpdb> 130 atoms in block 157
Block first atom: 21947
Blocpdb> 122 atoms in block 158
Block first atom: 22077
Blocpdb> 138 atoms in block 159
Block first atom: 22199
Blocpdb> 129 atoms in block 160
Block first atom: 22337
Blocpdb> 137 atoms in block 161
Block first atom: 22466
Blocpdb> 138 atoms in block 162
Block first atom: 22603
Blocpdb> 139 atoms in block 163
Block first atom: 22741
Blocpdb> 131 atoms in block 164
Block first atom: 22880
Blocpdb> 163 atoms in block 165
Block first atom: 23011
Blocpdb> 140 atoms in block 166
Block first atom: 23174
Blocpdb> 137 atoms in block 167
Block first atom: 23314
Blocpdb> 151 atoms in block 168
Block first atom: 23451
Blocpdb> 153 atoms in block 169
Block first atom: 23602
Blocpdb> 156 atoms in block 170
Block first atom: 23755
Blocpdb> 145 atoms in block 171
Block first atom: 23911
Blocpdb> 142 atoms in block 172
Block first atom: 24056
Blocpdb> 131 atoms in block 173
Block first atom: 24198
Blocpdb> 148 atoms in block 174
Block first atom: 24329
Blocpdb> 134 atoms in block 175
Block first atom: 24477
Blocpdb> 145 atoms in block 176
Block first atom: 24611
Blocpdb> 141 atoms in block 177
Block first atom: 24756
Blocpdb> 123 atoms in block 178
Block first atom: 24897
Blocpdb> 140 atoms in block 179
Block first atom: 25020
Blocpdb> 144 atoms in block 180
Block first atom: 25160
Blocpdb> 159 atoms in block 181
Block first atom: 25304
Blocpdb> 163 atoms in block 182
Block first atom: 25463
Blocpdb> 163 atoms in block 183
Block first atom: 25626
Blocpdb> 129 atoms in block 184
Block first atom: 25789
Blocpdb> 158 atoms in block 185
Block first atom: 25918
Blocpdb> 130 atoms in block 186
Block first atom: 26076
Blocpdb> 137 atoms in block 187
Block first atom: 26206
Blocpdb> 116 atoms in block 188
Block first atom: 26343
Blocpdb> 116 atoms in block 189
Block first atom: 26459
Blocpdb> 135 atoms in block 190
Block first atom: 26575
Blocpdb> 167 atoms in block 191
Block first atom: 26710
Blocpdb> 61 atoms in block 192
Block first atom: 26876
Blocpdb> 192 blocks.
Blocpdb> At most, 169 atoms in each of them.
Blocpdb> At least, 61 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: 41228227 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 0m0.125s
user 0m0.121s
sys 0m0.004s
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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