*** ***
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 = 240417171237899484.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 240417171237899484.atom to be opened.
Openam> File opened: 240417171237899484.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 = 1598
First residue number = 1
Last residue number = 335
Number of atoms found = 24329
Mean number per residue = 15.2
Pdbmat> Coordinate statistics:
= 3.891074 +/- 24.397760 From: -56.978000 To: 53.964000
= 7.771729 +/- 32.297416 From: -50.752000 To: 93.600000
= 2.154984 +/- 19.535431 From: -44.436000 To: 67.091000
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 3.0200 % Filled.
Pdbmat> 15586097 non-zero elements.
Pdbmat> 1715872 atom-atom interactions.
Pdbmat> Number per atom= 141.06 +/- 50.84
Maximum number = 251
Minimum number = 17
Pdbmat> Matrix trace = 3.431744E+07
Pdbmat> Larger element = 874.059
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
1598 non-zero elements, NRBL set to 8
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 = 240417171237899484.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 8
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 240417171237899484.atom to be opened.
Openam> file on opening on unit 11:
240417171237899484.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 24329 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 8 residue(s) per block.
Blocpdb> 1598 residues.
Blocpdb> 114 atoms in block 1
Block first atom: 1
Blocpdb> 105 atoms in block 2
Block first atom: 115
Blocpdb> 113 atoms in block 3
Block first atom: 220
Blocpdb> 103 atoms in block 4
Block first atom: 333
Blocpdb> 105 atoms in block 5
Block first atom: 436
Blocpdb> 128 atoms in block 6
Block first atom: 541
Blocpdb> 106 atoms in block 7
Block first atom: 669
Blocpdb> 118 atoms in block 8
Block first atom: 775
Blocpdb> 93 atoms in block 9
Block first atom: 893
Blocpdb> 118 atoms in block 10
Block first atom: 986
Blocpdb> 110 atoms in block 11
Block first atom: 1104
Blocpdb> 102 atoms in block 12
Block first atom: 1214
Blocpdb> 124 atoms in block 13
Block first atom: 1316
Blocpdb> 105 atoms in block 14
Block first atom: 1440
Blocpdb> 115 atoms in block 15
Block first atom: 1545
Blocpdb> 111 atoms in block 16
Block first atom: 1660
Blocpdb> 101 atoms in block 17
Block first atom: 1771
Blocpdb> 136 atoms in block 18
Block first atom: 1872
Blocpdb> 114 atoms in block 19
Block first atom: 2008
Blocpdb> 119 atoms in block 20
Block first atom: 2122
Blocpdb> 98 atoms in block 21
Block first atom: 2241
Blocpdb> 129 atoms in block 22
Block first atom: 2339
Blocpdb> 104 atoms in block 23
Block first atom: 2468
Blocpdb> 94 atoms in block 24
Block first atom: 2572
Blocpdb> 108 atoms in block 25
Block first atom: 2666
Blocpdb> 117 atoms in block 26
Block first atom: 2774
Blocpdb> 131 atoms in block 27
Block first atom: 2891
Blocpdb> 102 atoms in block 28
Block first atom: 3022
Blocpdb> 92 atoms in block 29
Block first atom: 3124
Blocpdb> 116 atoms in block 30
Block first atom: 3216
Blocpdb> 119 atoms in block 31
Block first atom: 3332
Blocpdb> 111 atoms in block 32
Block first atom: 3451
Blocpdb> 126 atoms in block 33
Block first atom: 3562
Blocpdb> 113 atoms in block 34
Block first atom: 3688
Blocpdb> 111 atoms in block 35
Block first atom: 3801
Blocpdb> 113 atoms in block 36
Block first atom: 3912
Blocpdb> 118 atoms in block 37
Block first atom: 4025
Blocpdb> 105 atoms in block 38
Block first atom: 4143
Blocpdb> 115 atoms in block 39
Block first atom: 4248
Blocpdb> 125 atoms in block 40
Block first atom: 4363
Blocpdb> 112 atoms in block 41
Block first atom: 4488
Blocpdb> 130 atoms in block 42
Block first atom: 4600
Blocpdb> 122 atoms in block 43
Block first atom: 4730
Blocpdb> 114 atoms in block 44
Block first atom: 4852
Blocpdb> 132 atoms in block 45
Block first atom: 4966
Blocpdb> 111 atoms in block 46
Block first atom: 5098
Blocpdb> 111 atoms in block 47
Block first atom: 5209
Blocpdb> 131 atoms in block 48
Block first atom: 5320
Blocpdb> 141 atoms in block 49
Block first atom: 5451
Blocpdb> 120 atoms in block 50
Block first atom: 5592
Blocpdb> 117 atoms in block 51
Block first atom: 5712
Blocpdb> 151 atoms in block 52
Block first atom: 5829
Blocpdb> 131 atoms in block 53
Block first atom: 5980
Blocpdb> 112 atoms in block 54
Block first atom: 6111
Blocpdb> 127 atoms in block 55
Block first atom: 6223
Blocpdb> 117 atoms in block 56
Block first atom: 6350
Blocpdb> 137 atoms in block 57
Block first atom: 6467
Blocpdb> 137 atoms in block 58
Block first atom: 6604
Blocpdb> 133 atoms in block 59
Block first atom: 6741
Blocpdb> 131 atoms in block 60
Block first atom: 6874
Blocpdb> 124 atoms in block 61
Block first atom: 7005
Blocpdb> 108 atoms in block 62
Block first atom: 7129
Blocpdb> 134 atoms in block 63
Block first atom: 7237
Blocpdb> 114 atoms in block 64
Block first atom: 7371
Blocpdb> 124 atoms in block 65
Block first atom: 7485
Blocpdb> 140 atoms in block 66
Block first atom: 7609
Blocpdb> 117 atoms in block 67
Block first atom: 7749
Blocpdb> 130 atoms in block 68
Block first atom: 7866
Blocpdb> 148 atoms in block 69
Block first atom: 7996
Blocpdb> 131 atoms in block 70
Block first atom: 8144
Blocpdb> 136 atoms in block 71
Block first atom: 8275
Blocpdb> 112 atoms in block 72
Block first atom: 8411
Blocpdb> 118 atoms in block 73
Block first atom: 8523
Blocpdb> 129 atoms in block 74
Block first atom: 8641
Blocpdb> 134 atoms in block 75
Block first atom: 8770
Blocpdb> 131 atoms in block 76
Block first atom: 8904
Blocpdb> 130 atoms in block 77
Block first atom: 9035
Blocpdb> 126 atoms in block 78
Block first atom: 9165
Blocpdb> 139 atoms in block 79
Block first atom: 9291
Blocpdb> 117 atoms in block 80
Block first atom: 9430
Blocpdb> 100 atoms in block 81
Block first atom: 9547
Blocpdb> 123 atoms in block 82
Block first atom: 9647
Blocpdb> 113 atoms in block 83
Block first atom: 9770
Blocpdb> 129 atoms in block 84
Block first atom: 9883
Blocpdb> 123 atoms in block 85
Block first atom: 10012
Blocpdb> 135 atoms in block 86
Block first atom: 10135
Blocpdb> 115 atoms in block 87
Block first atom: 10270
Blocpdb> 128 atoms in block 88
Block first atom: 10385
Blocpdb> 117 atoms in block 89
Block first atom: 10513
Blocpdb> 109 atoms in block 90
Block first atom: 10630
Blocpdb> 113 atoms in block 91
Block first atom: 10739
Blocpdb> 124 atoms in block 92
Block first atom: 10852
Blocpdb> 156 atoms in block 93
Block first atom: 10976
Blocpdb> 117 atoms in block 94
Block first atom: 11132
Blocpdb> 122 atoms in block 95
Block first atom: 11249
Blocpdb> 127 atoms in block 96
Block first atom: 11371
Blocpdb> 144 atoms in block 97
Block first atom: 11498
Blocpdb> 124 atoms in block 98
Block first atom: 11642
Blocpdb> 134 atoms in block 99
Block first atom: 11766
Blocpdb> 151 atoms in block 100
Block first atom: 11900
Blocpdb> 125 atoms in block 101
Block first atom: 12051
Blocpdb> 128 atoms in block 102
Block first atom: 12176
Blocpdb> 138 atoms in block 103
Block first atom: 12304
Blocpdb> 139 atoms in block 104
Block first atom: 12442
Blocpdb> 122 atoms in block 105
Block first atom: 12581
Blocpdb> 120 atoms in block 106
Block first atom: 12703
Blocpdb> 111 atoms in block 107
Block first atom: 12823
Blocpdb> 137 atoms in block 108
Block first atom: 12934
Blocpdb> 137 atoms in block 109
Block first atom: 13071
Blocpdb> 132 atoms in block 110
Block first atom: 13208
Blocpdb> 135 atoms in block 111
Block first atom: 13340
Blocpdb> 120 atoms in block 112
Block first atom: 13475
Blocpdb> 132 atoms in block 113
Block first atom: 13595
Blocpdb> 134 atoms in block 114
Block first atom: 13727
Blocpdb> 122 atoms in block 115
Block first atom: 13861
Blocpdb> 123 atoms in block 116
Block first atom: 13983
Blocpdb> 146 atoms in block 117
Block first atom: 14106
Blocpdb> 124 atoms in block 118
Block first atom: 14252
Blocpdb> 97 atoms in block 119
Block first atom: 14376
Blocpdb> 99 atoms in block 120
Block first atom: 14473
Blocpdb> 125 atoms in block 121
Block first atom: 14572
Blocpdb> 118 atoms in block 122
Block first atom: 14697
Blocpdb> 123 atoms in block 123
Block first atom: 14815
Blocpdb> 108 atoms in block 124
Block first atom: 14938
Blocpdb> 117 atoms in block 125
Block first atom: 15046
Blocpdb> 111 atoms in block 126
Block first atom: 15163
Blocpdb> 121 atoms in block 127
Block first atom: 15274
Blocpdb> 118 atoms in block 128
Block first atom: 15395
Blocpdb> 103 atoms in block 129
Block first atom: 15513
Blocpdb> 114 atoms in block 130
Block first atom: 15616
Blocpdb> 101 atoms in block 131
Block first atom: 15730
Blocpdb> 99 atoms in block 132
Block first atom: 15831
Blocpdb> 143 atoms in block 133
Block first atom: 15930
Blocpdb> 94 atoms in block 134
Block first atom: 16073
Blocpdb> 111 atoms in block 135
Block first atom: 16167
Blocpdb> 107 atoms in block 136
Block first atom: 16278
Blocpdb> 115 atoms in block 137
Block first atom: 16385
Blocpdb> 128 atoms in block 138
Block first atom: 16500
Blocpdb> 88 atoms in block 139
Block first atom: 16628
Blocpdb> 109 atoms in block 140
Block first atom: 16716
Blocpdb> 112 atoms in block 141
Block first atom: 16825
Blocpdb> 123 atoms in block 142
Block first atom: 16937
Blocpdb> 119 atoms in block 143
Block first atom: 17060
Blocpdb> 98 atoms in block 144
Block first atom: 17179
Blocpdb> 106 atoms in block 145
Block first atom: 17277
Blocpdb> 118 atoms in block 146
Block first atom: 17383
Blocpdb> 101 atoms in block 147
Block first atom: 17501
Blocpdb> 104 atoms in block 148
Block first atom: 17602
Blocpdb> 106 atoms in block 149
Block first atom: 17706
Blocpdb> 106 atoms in block 150
Block first atom: 17812
Blocpdb> 102 atoms in block 151
Block first atom: 17918
Blocpdb> 113 atoms in block 152
Block first atom: 18020
Blocpdb> 135 atoms in block 153
Block first atom: 18133
Blocpdb> 101 atoms in block 154
Block first atom: 18268
Blocpdb> 107 atoms in block 155
Block first atom: 18369
Blocpdb> 111 atoms in block 156
Block first atom: 18476
Blocpdb> 113 atoms in block 157
Block first atom: 18587
Blocpdb> 119 atoms in block 158
Block first atom: 18700
Blocpdb> 115 atoms in block 159
Block first atom: 18819
Blocpdb> 142 atoms in block 160
Block first atom: 18934
Blocpdb> 119 atoms in block 161
Block first atom: 19076
Blocpdb> 146 atoms in block 162
Block first atom: 19195
Blocpdb> 148 atoms in block 163
Block first atom: 19341
Blocpdb> 142 atoms in block 164
Block first atom: 19489
Blocpdb> 124 atoms in block 165
Block first atom: 19631
Blocpdb> 131 atoms in block 166
Block first atom: 19755
Blocpdb> 147 atoms in block 167
Block first atom: 19886
Blocpdb> 117 atoms in block 168
Block first atom: 20033
Blocpdb> 143 atoms in block 169
Block first atom: 20150
Blocpdb> 133 atoms in block 170
Block first atom: 20293
Blocpdb> 126 atoms in block 171
Block first atom: 20426
Blocpdb> 103 atoms in block 172
Block first atom: 20552
Blocpdb> 108 atoms in block 173
Block first atom: 20655
Blocpdb> 154 atoms in block 174
Block first atom: 20763
Blocpdb> 128 atoms in block 175
Block first atom: 20917
Blocpdb> 120 atoms in block 176
Block first atom: 21045
Blocpdb> 158 atoms in block 177
Block first atom: 21165
Blocpdb> 136 atoms in block 178
Block first atom: 21323
Blocpdb> 135 atoms in block 179
Block first atom: 21459
Blocpdb> 130 atoms in block 180
Block first atom: 21594
Blocpdb> 109 atoms in block 181
Block first atom: 21724
Blocpdb> 127 atoms in block 182
Block first atom: 21833
Blocpdb> 143 atoms in block 183
Block first atom: 21960
Blocpdb> 123 atoms in block 184
Block first atom: 22103
Blocpdb> 152 atoms in block 185
Block first atom: 22226
Blocpdb> 113 atoms in block 186
Block first atom: 22378
Blocpdb> 134 atoms in block 187
Block first atom: 22491
Blocpdb> 117 atoms in block 188
Block first atom: 22625
Blocpdb> 126 atoms in block 189
Block first atom: 22742
Blocpdb> 152 atoms in block 190
Block first atom: 22868
Blocpdb> 134 atoms in block 191
Block first atom: 23020
Blocpdb> 147 atoms in block 192
Block first atom: 23154
Blocpdb> 134 atoms in block 193
Block first atom: 23301
Blocpdb> 107 atoms in block 194
Block first atom: 23435
Blocpdb> 140 atoms in block 195
Block first atom: 23542
Blocpdb> 130 atoms in block 196
Block first atom: 23682
Blocpdb> 136 atoms in block 197
Block first atom: 23812
Blocpdb> 126 atoms in block 198
Block first atom: 23948
Blocpdb> 134 atoms in block 199
Block first atom: 24074
Blocpdb> 122 atoms in block 200
Block first atom: 24207
Blocpdb> 200 blocks.
Blocpdb> At most, 158 atoms in each of them.
Blocpdb> At least, 88 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: 34820515 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 0m0.120s
user 0m0.111s
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: April 25th, 2023.
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