*** 2xnd_full ***
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 = 240323233842347054.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 240323233842347054.atom to be opened.
Openam> File opened: 240323233842347054.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 = 3892
First residue number = 19
Last residue number = 73
Number of atoms found = 28025
Mean number per residue = 7.2
Pdbmat> Coordinate statistics:
= 27.738083 +/- 36.942107 From: -81.524000 To: 107.403000
= 1.114286 +/- 22.828785 From: -53.761000 To: 62.148000
= 64.530963 +/- 31.731080 From: -1.459000 To: 156.077000
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 -1.4088 % Filled.
Pdbmat> 10715773 non-zero elements.
Pdbmat> 1172137 atom-atom interactions.
Pdbmat> Number per atom= 83.65 +/- 21.34
Maximum number = 131
Minimum number = 9
Pdbmat> Matrix trace = 2.344274E+07
Pdbmat> Larger element = 492.426
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3892 non-zero elements, NRBL set to 20
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 = 240323233842347054.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 20
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 240323233842347054.atom to be opened.
Openam> file on opening on unit 11:
240323233842347054.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 28025 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 20 residue(s) per block.
Blocpdb> 3892 residues.
Blocpdb> 142 atoms in block 1
Block first atom: 1
Blocpdb> 154 atoms in block 2
Block first atom: 143
Blocpdb> 146 atoms in block 3
Block first atom: 297
Blocpdb> 151 atoms in block 4
Block first atom: 443
Blocpdb> 141 atoms in block 5
Block first atom: 594
Blocpdb> 143 atoms in block 6
Block first atom: 735
Blocpdb> 152 atoms in block 7
Block first atom: 878
Blocpdb> 153 atoms in block 8
Block first atom: 1030
Blocpdb> 163 atoms in block 9
Block first atom: 1183
Blocpdb> 157 atoms in block 10
Block first atom: 1346
Blocpdb> 147 atoms in block 11
Block first atom: 1503
Blocpdb> 155 atoms in block 12
Block first atom: 1650
Blocpdb> 157 atoms in block 13
Block first atom: 1805
Blocpdb> 161 atoms in block 14
Block first atom: 1962
Blocpdb> 161 atoms in block 15
Block first atom: 2123
Blocpdb> 140 atoms in block 16
Block first atom: 2284
Blocpdb> 162 atoms in block 17
Block first atom: 2424
Blocpdb> 136 atoms in block 18
Block first atom: 2586
Blocpdb> 160 atoms in block 19
Block first atom: 2722
Blocpdb> 147 atoms in block 20
Block first atom: 2882
Blocpdb> 156 atoms in block 21
Block first atom: 3029
Blocpdb> 158 atoms in block 22
Block first atom: 3185
Blocpdb> 161 atoms in block 23
Block first atom: 3343
Blocpdb> 153 atoms in block 24
Block first atom: 3504
Blocpdb> 92 atoms in block 25
Block first atom: 3657
Blocpdb> 142 atoms in block 26
Block first atom: 3749
Blocpdb> 154 atoms in block 27
Block first atom: 3891
Blocpdb> 146 atoms in block 28
Block first atom: 4045
Blocpdb> 151 atoms in block 29
Block first atom: 4191
Blocpdb> 141 atoms in block 30
Block first atom: 4342
Blocpdb> 143 atoms in block 31
Block first atom: 4483
Blocpdb> 152 atoms in block 32
Block first atom: 4626
Blocpdb> 153 atoms in block 33
Block first atom: 4778
Blocpdb> 163 atoms in block 34
Block first atom: 4931
Blocpdb> 157 atoms in block 35
Block first atom: 5094
Blocpdb> 147 atoms in block 36
Block first atom: 5251
Blocpdb> 155 atoms in block 37
Block first atom: 5398
Blocpdb> 157 atoms in block 38
Block first atom: 5553
Blocpdb> 161 atoms in block 39
Block first atom: 5710
Blocpdb> 161 atoms in block 40
Block first atom: 5871
Blocpdb> 140 atoms in block 41
Block first atom: 6032
Blocpdb> 162 atoms in block 42
Block first atom: 6172
Blocpdb> 136 atoms in block 43
Block first atom: 6334
Blocpdb> 160 atoms in block 44
Block first atom: 6470
Blocpdb> 147 atoms in block 45
Block first atom: 6630
Blocpdb> 156 atoms in block 46
Block first atom: 6777
Blocpdb> 158 atoms in block 47
Block first atom: 6933
Blocpdb> 161 atoms in block 48
Block first atom: 7091
Blocpdb> 153 atoms in block 49
Block first atom: 7252
Blocpdb> 92 atoms in block 50
Block first atom: 7405
Blocpdb> 142 atoms in block 51
Block first atom: 7497
Blocpdb> 154 atoms in block 52
Block first atom: 7639
Blocpdb> 146 atoms in block 53
Block first atom: 7793
Blocpdb> 151 atoms in block 54
Block first atom: 7939
Blocpdb> 141 atoms in block 55
Block first atom: 8090
Blocpdb> 143 atoms in block 56
Block first atom: 8231
Blocpdb> 152 atoms in block 57
Block first atom: 8374
Blocpdb> 153 atoms in block 58
Block first atom: 8526
Blocpdb> 163 atoms in block 59
Block first atom: 8679
Blocpdb> 157 atoms in block 60
Block first atom: 8842
Blocpdb> 147 atoms in block 61
Block first atom: 8999
Blocpdb> 155 atoms in block 62
Block first atom: 9146
Blocpdb> 157 atoms in block 63
Block first atom: 9301
Blocpdb> 161 atoms in block 64
Block first atom: 9458
Blocpdb> 161 atoms in block 65
Block first atom: 9619
Blocpdb> 140 atoms in block 66
Block first atom: 9780
Blocpdb> 162 atoms in block 67
Block first atom: 9920
Blocpdb> 136 atoms in block 68
Block first atom: 10082
Blocpdb> 160 atoms in block 69
Block first atom: 10218
Blocpdb> 147 atoms in block 70
Block first atom: 10378
Blocpdb> 156 atoms in block 71
Block first atom: 10525
Blocpdb> 158 atoms in block 72
Block first atom: 10681
Blocpdb> 161 atoms in block 73
Block first atom: 10839
Blocpdb> 153 atoms in block 74
Block first atom: 11000
Blocpdb> 92 atoms in block 75
Block first atom: 11153
Blocpdb> 143 atoms in block 76
Block first atom: 11245
Blocpdb> 158 atoms in block 77
Block first atom: 11388
Blocpdb> 143 atoms in block 78
Block first atom: 11546
Blocpdb> 145 atoms in block 79
Block first atom: 11689
Blocpdb> 153 atoms in block 80
Block first atom: 11834
Blocpdb> 156 atoms in block 81
Block first atom: 11987
Blocpdb> 154 atoms in block 82
Block first atom: 12143
Blocpdb> 132 atoms in block 83
Block first atom: 12297
Blocpdb> 141 atoms in block 84
Block first atom: 12429
Blocpdb> 163 atoms in block 85
Block first atom: 12570
Blocpdb> 144 atoms in block 86
Block first atom: 12733
Blocpdb> 158 atoms in block 87
Block first atom: 12877
Blocpdb> 163 atoms in block 88
Block first atom: 13035
Blocpdb> 142 atoms in block 89
Block first atom: 13198
Blocpdb> 150 atoms in block 90
Block first atom: 13340
Blocpdb> 147 atoms in block 91
Block first atom: 13490
Blocpdb> 145 atoms in block 92
Block first atom: 13637
Blocpdb> 156 atoms in block 93
Block first atom: 13782
Blocpdb> 161 atoms in block 94
Block first atom: 13938
Blocpdb> 154 atoms in block 95
Block first atom: 14099
Blocpdb> 166 atoms in block 96
Block first atom: 14253
Blocpdb> 152 atoms in block 97
Block first atom: 14419
Blocpdb> 160 atoms in block 98
Block first atom: 14571
Blocpdb> 53 atoms in block 99
Block first atom: 14731
Blocpdb> 143 atoms in block 100
Block first atom: 14784
Blocpdb> 158 atoms in block 101
Block first atom: 14927
Blocpdb> 143 atoms in block 102
Block first atom: 15085
Blocpdb> 145 atoms in block 103
Block first atom: 15228
Blocpdb> 153 atoms in block 104
Block first atom: 15373
Blocpdb> 156 atoms in block 105
Block first atom: 15526
Blocpdb> 154 atoms in block 106
Block first atom: 15682
Blocpdb> 132 atoms in block 107
Block first atom: 15836
Blocpdb> 141 atoms in block 108
Block first atom: 15968
Blocpdb> 163 atoms in block 109
Block first atom: 16109
Blocpdb> 144 atoms in block 110
Block first atom: 16272
Blocpdb> 158 atoms in block 111
Block first atom: 16416
Blocpdb> 163 atoms in block 112
Block first atom: 16574
Blocpdb> 142 atoms in block 113
Block first atom: 16737
Blocpdb> 150 atoms in block 114
Block first atom: 16879
Blocpdb> 147 atoms in block 115
Block first atom: 17029
Blocpdb> 145 atoms in block 116
Block first atom: 17176
Blocpdb> 156 atoms in block 117
Block first atom: 17321
Blocpdb> 161 atoms in block 118
Block first atom: 17477
Blocpdb> 154 atoms in block 119
Block first atom: 17638
Blocpdb> 166 atoms in block 120
Block first atom: 17792
Blocpdb> 152 atoms in block 121
Block first atom: 17958
Blocpdb> 160 atoms in block 122
Block first atom: 18110
Blocpdb> 44 atoms in block 123
Block first atom: 18270
Blocpdb> 143 atoms in block 124
Block first atom: 18314
Blocpdb> 158 atoms in block 125
Block first atom: 18457
Blocpdb> 143 atoms in block 126
Block first atom: 18615
Blocpdb> 145 atoms in block 127
Block first atom: 18758
Blocpdb> 153 atoms in block 128
Block first atom: 18903
Blocpdb> 156 atoms in block 129
Block first atom: 19056
Blocpdb> 154 atoms in block 130
Block first atom: 19212
Blocpdb> 132 atoms in block 131
Block first atom: 19366
Blocpdb> 141 atoms in block 132
Block first atom: 19498
Blocpdb> 163 atoms in block 133
Block first atom: 19639
Blocpdb> 144 atoms in block 134
Block first atom: 19802
Blocpdb> 158 atoms in block 135
Block first atom: 19946
Blocpdb> 163 atoms in block 136
Block first atom: 20104
Blocpdb> 142 atoms in block 137
Block first atom: 20267
Blocpdb> 150 atoms in block 138
Block first atom: 20409
Blocpdb> 147 atoms in block 139
Block first atom: 20559
Blocpdb> 145 atoms in block 140
Block first atom: 20706
Blocpdb> 156 atoms in block 141
Block first atom: 20851
Blocpdb> 161 atoms in block 142
Block first atom: 21007
Blocpdb> 154 atoms in block 143
Block first atom: 21168
Blocpdb> 166 atoms in block 144
Block first atom: 21322
Blocpdb> 152 atoms in block 145
Block first atom: 21488
Blocpdb> 160 atoms in block 146
Block first atom: 21640
Blocpdb> 44 atoms in block 147
Block first atom: 21800
Blocpdb> 163 atoms in block 148
Block first atom: 21844
Blocpdb> 157 atoms in block 149
Block first atom: 22007
Blocpdb> 151 atoms in block 150
Block first atom: 22164
Blocpdb> 9 atoms in block 151
Block first atom: 22315
Blocpdb> 135 atoms in block 152
Block first atom: 22324
Blocpdb> 76 atoms in block 153
Block first atom: 22459
Blocpdb> 161 atoms in block 154
Block first atom: 22535
Blocpdb> 162 atoms in block 155
Block first atom: 22696
Blocpdb> 149 atoms in block 156
Block first atom: 22858
Blocpdb> 174 atoms in block 157
Block first atom: 23007
Blocpdb> 149 atoms in block 158
Block first atom: 23181
Blocpdb> 174 atoms in block 159
Block first atom: 23330
Blocpdb> 143 atoms in block 160
Block first atom: 23504
Blocpdb> 165 atoms in block 161
Block first atom: 23647
Blocpdb> 83 atoms in block 162
Block first atom: 23812
Blocpdb> 160 atoms in block 163
Block first atom: 23895
Blocpdb> 142 atoms in block 164
Block first atom: 24055
Blocpdb> 148 atoms in block 165
Block first atom: 24197
Blocpdb> 143 atoms in block 166
Block first atom: 24345
Blocpdb> 147 atoms in block 167
Block first atom: 24488
Blocpdb> 149 atoms in block 168
Block first atom: 24635
Blocpdb> 81 atoms in block 169
Block first atom: 24784
Blocpdb> 167 atoms in block 170
Block first atom: 24865
Blocpdb> 147 atoms in block 171
Block first atom: 25032
Blocpdb> 55 atoms in block 172
Block first atom: 25179
Blocpdb> 96 atoms in block 173
Block first atom: 25234
Blocpdb> 95 atoms in block 174
Block first atom: 25330
Blocpdb> 98 atoms in block 175
Block first atom: 25425
Blocpdb> 60 atoms in block 176
Block first atom: 25523
Blocpdb> 96 atoms in block 177
Block first atom: 25583
Blocpdb> 95 atoms in block 178
Block first atom: 25679
Blocpdb> 98 atoms in block 179
Block first atom: 25774
Blocpdb> 60 atoms in block 180
Block first atom: 25872
Blocpdb> 96 atoms in block 181
Block first atom: 25932
Blocpdb> 95 atoms in block 182
Block first atom: 26028
Blocpdb> 98 atoms in block 183
Block first atom: 26123
Blocpdb> 60 atoms in block 184
Block first atom: 26221
Blocpdb> 96 atoms in block 185
Block first atom: 26281
Blocpdb> 95 atoms in block 186
Block first atom: 26377
Blocpdb> 98 atoms in block 187
Block first atom: 26472
Blocpdb> 60 atoms in block 188
Block first atom: 26570
Blocpdb> 96 atoms in block 189
Block first atom: 26630
Blocpdb> 95 atoms in block 190
Block first atom: 26726
Blocpdb> 98 atoms in block 191
Block first atom: 26821
Blocpdb> 60 atoms in block 192
Block first atom: 26919
Blocpdb> 96 atoms in block 193
Block first atom: 26979
Blocpdb> 95 atoms in block 194
Block first atom: 27075
Blocpdb> 98 atoms in block 195
Block first atom: 27170
Blocpdb> 60 atoms in block 196
Block first atom: 27268
Blocpdb> 96 atoms in block 197
Block first atom: 27328
Blocpdb> 95 atoms in block 198
Block first atom: 27424
Blocpdb> 98 atoms in block 199
Block first atom: 27519
Blocpdb> 60 atoms in block 200
Block first atom: 27617
Blocpdb> 96 atoms in block 201
Block first atom: 27677
Blocpdb> 95 atoms in block 202
Block first atom: 27773
Blocpdb> 98 atoms in block 203
Block first atom: 27868
Blocpdb> 60 atoms in block 204
Block first atom: 27965
Blocpdb> 204 blocks.
Blocpdb> At most, 174 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: 44159635 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 0m0.128s
user 0m0.128s
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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