*** TRANSFERASE, HYDROLASE 26-JAN-21 7LHT ***
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 = 2609101341193111957.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 2609101341193111957.atom to be opened.
Openam> File opened: 2609101341193111957.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 = 3590
First residue number = 558
Last residue number = 2527
Number of atoms found = 28127
Mean number per residue = 7.8
Pdbmat> Coordinate statistics:
= 198.247165 +/- 42.342836 From: 115.711000 To: 280.772000
= 198.249187 +/- 20.812394 From: 142.014000 To: 254.481000
= 212.371389 +/- 32.941463 From: 152.894000 To: 288.361000
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 -1.3928 % Filled.
Pdbmat> 10235276 non-zero elements.
Pdbmat> 1118691 atom-atom interactions.
Pdbmat> Number per atom= 79.55 +/- 21.00
Maximum number = 126
Minimum number = 8
Pdbmat> Matrix trace = 2.237382E+07
Pdbmat> Larger element = 486.017
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3590 non-zero elements, NRBL set to 18
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 = 2609101341193111957.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 18
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 2609101341193111957.atom to be opened.
Openam> file on opening on unit 11:
2609101341193111957.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 28127 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 18 residue(s) per block.
Blocpdb> 3590 residues.
Blocpdb> 132 atoms in block 1
Block first atom: 1
Blocpdb> 13 atoms in block 2
Block first atom: 133
Blocpdb> 125 atoms in block 3
Block first atom: 146
Blocpdb> 77 atoms in block 4
Block first atom: 271
Blocpdb> 138 atoms in block 5
Block first atom: 348
Blocpdb> 134 atoms in block 6
Block first atom: 486
Blocpdb> 149 atoms in block 7
Block first atom: 620
Blocpdb> 147 atoms in block 8
Block first atom: 769
Blocpdb> 132 atoms in block 9
Block first atom: 916
Blocpdb> 136 atoms in block 10
Block first atom: 1048
Blocpdb> 118 atoms in block 11
Block first atom: 1184
Blocpdb> 138 atoms in block 12
Block first atom: 1302
Blocpdb> 135 atoms in block 13
Block first atom: 1440
Blocpdb> 136 atoms in block 14
Block first atom: 1575
Blocpdb> 130 atoms in block 15
Block first atom: 1711
Blocpdb> 142 atoms in block 16
Block first atom: 1841
Blocpdb> 124 atoms in block 17
Block first atom: 1983
Blocpdb> 148 atoms in block 18
Block first atom: 2107
Blocpdb> 141 atoms in block 19
Block first atom: 2255
Blocpdb> 144 atoms in block 20
Block first atom: 2396
Blocpdb> 145 atoms in block 21
Block first atom: 2540
Blocpdb> 142 atoms in block 22
Block first atom: 2685
Blocpdb> 134 atoms in block 23
Block first atom: 2827
Blocpdb> 144 atoms in block 24
Block first atom: 2961
Blocpdb> 136 atoms in block 25
Block first atom: 3105
Blocpdb> 148 atoms in block 26
Block first atom: 3241
Blocpdb> 132 atoms in block 27
Block first atom: 3389
Blocpdb> 141 atoms in block 28
Block first atom: 3521
Blocpdb> 140 atoms in block 29
Block first atom: 3662
Blocpdb> 142 atoms in block 30
Block first atom: 3802
Blocpdb> 156 atoms in block 31
Block first atom: 3944
Blocpdb> 147 atoms in block 32
Block first atom: 4100
Blocpdb> 143 atoms in block 33
Block first atom: 4247
Blocpdb> 146 atoms in block 34
Block first atom: 4390
Blocpdb> 149 atoms in block 35
Block first atom: 4536
Blocpdb> 149 atoms in block 36
Block first atom: 4685
Blocpdb> 153 atoms in block 37
Block first atom: 4834
Blocpdb> 131 atoms in block 38
Block first atom: 4987
Blocpdb> 135 atoms in block 39
Block first atom: 5118
Blocpdb> 156 atoms in block 40
Block first atom: 5253
Blocpdb> 154 atoms in block 41
Block first atom: 5409
Blocpdb> 135 atoms in block 42
Block first atom: 5563
Blocpdb> 143 atoms in block 43
Block first atom: 5698
Blocpdb> 59 atoms in block 44
Block first atom: 5841
Blocpdb> 120 atoms in block 45
Block first atom: 5900
Blocpdb> 142 atoms in block 46
Block first atom: 6020
Blocpdb> 152 atoms in block 47
Block first atom: 6162
Blocpdb> 142 atoms in block 48
Block first atom: 6314
Blocpdb> 147 atoms in block 49
Block first atom: 6456
Blocpdb> 147 atoms in block 50
Block first atom: 6603
Blocpdb> 146 atoms in block 51
Block first atom: 6750
Blocpdb> 145 atoms in block 52
Block first atom: 6896
Blocpdb> 133 atoms in block 53
Block first atom: 7041
Blocpdb> 49 atoms in block 54
Block first atom: 7174
Blocpdb> 155 atoms in block 55
Block first atom: 7223
Blocpdb> 130 atoms in block 56
Block first atom: 7378
Blocpdb> 145 atoms in block 57
Block first atom: 7508
Blocpdb> 151 atoms in block 58
Block first atom: 7653
Blocpdb> 152 atoms in block 59
Block first atom: 7804
Blocpdb> 129 atoms in block 60
Block first atom: 7956
Blocpdb> 136 atoms in block 61
Block first atom: 8085
Blocpdb> 149 atoms in block 62
Block first atom: 8221
Blocpdb> 142 atoms in block 63
Block first atom: 8370
Blocpdb> 131 atoms in block 64
Block first atom: 8512
Blocpdb> 138 atoms in block 65
Block first atom: 8643
Blocpdb> 138 atoms in block 66
Block first atom: 8781
Blocpdb> 147 atoms in block 67
Block first atom: 8919
Blocpdb> 133 atoms in block 68
Block first atom: 9066
Blocpdb> 154 atoms in block 69
Block first atom: 9199
Blocpdb> 136 atoms in block 70
Block first atom: 9353
Blocpdb> 139 atoms in block 71
Block first atom: 9489
Blocpdb> 148 atoms in block 72
Block first atom: 9628
Blocpdb> 147 atoms in block 73
Block first atom: 9776
Blocpdb> 141 atoms in block 74
Block first atom: 9923
Blocpdb> 111 atoms in block 75
Block first atom: 10064
Blocpdb> 125 atoms in block 76
Block first atom: 10175
Blocpdb> 151 atoms in block 77
Block first atom: 10300
Blocpdb> 140 atoms in block 78
Block first atom: 10451
Blocpdb> 138 atoms in block 79
Block first atom: 10591
Blocpdb> 148 atoms in block 80
Block first atom: 10729
Blocpdb> 135 atoms in block 81
Block first atom: 10877
Blocpdb> 143 atoms in block 82
Block first atom: 11012
Blocpdb> 137 atoms in block 83
Block first atom: 11155
Blocpdb> 139 atoms in block 84
Block first atom: 11292
Blocpdb> 130 atoms in block 85
Block first atom: 11431
Blocpdb> 135 atoms in block 86
Block first atom: 11561
Blocpdb> 143 atoms in block 87
Block first atom: 11696
Blocpdb> 149 atoms in block 88
Block first atom: 11839
Blocpdb> 133 atoms in block 89
Block first atom: 11988
Blocpdb> 126 atoms in block 90
Block first atom: 12121
Blocpdb> 136 atoms in block 91
Block first atom: 12247
Blocpdb> 144 atoms in block 92
Block first atom: 12383
Blocpdb> 143 atoms in block 93
Block first atom: 12527
Blocpdb> 135 atoms in block 94
Block first atom: 12670
Blocpdb> 143 atoms in block 95
Block first atom: 12805
Blocpdb> 156 atoms in block 96
Block first atom: 12948
Blocpdb> 144 atoms in block 97
Block first atom: 13104
Blocpdb> 132 atoms in block 98
Block first atom: 13248
Blocpdb> 147 atoms in block 99
Block first atom: 13380
Blocpdb> 140 atoms in block 100
Block first atom: 13527
Blocpdb> 146 atoms in block 101
Block first atom: 13667
Blocpdb> 155 atoms in block 102
Block first atom: 13813
Blocpdb> 90 atoms in block 103
Block first atom: 13968
Blocpdb> 132 atoms in block 104
Block first atom: 14058
Blocpdb> 13 atoms in block 105
Block first atom: 14190
Blocpdb> 125 atoms in block 106
Block first atom: 14203
Blocpdb> 77 atoms in block 107
Block first atom: 14328
Blocpdb> 138 atoms in block 108
Block first atom: 14405
Blocpdb> 134 atoms in block 109
Block first atom: 14543
Blocpdb> 149 atoms in block 110
Block first atom: 14677
Blocpdb> 147 atoms in block 111
Block first atom: 14826
Blocpdb> 132 atoms in block 112
Block first atom: 14973
Blocpdb> 136 atoms in block 113
Block first atom: 15105
Blocpdb> 118 atoms in block 114
Block first atom: 15241
Blocpdb> 138 atoms in block 115
Block first atom: 15359
Blocpdb> 135 atoms in block 116
Block first atom: 15497
Blocpdb> 136 atoms in block 117
Block first atom: 15632
Blocpdb> 130 atoms in block 118
Block first atom: 15768
Blocpdb> 142 atoms in block 119
Block first atom: 15898
Blocpdb> 124 atoms in block 120
Block first atom: 16040
Blocpdb> 148 atoms in block 121
Block first atom: 16164
Blocpdb> 141 atoms in block 122
Block first atom: 16312
Blocpdb> 144 atoms in block 123
Block first atom: 16453
Blocpdb> 145 atoms in block 124
Block first atom: 16597
Blocpdb> 142 atoms in block 125
Block first atom: 16742
Blocpdb> 134 atoms in block 126
Block first atom: 16884
Blocpdb> 144 atoms in block 127
Block first atom: 17018
Blocpdb> 136 atoms in block 128
Block first atom: 17162
Blocpdb> 148 atoms in block 129
Block first atom: 17298
Blocpdb> 132 atoms in block 130
Block first atom: 17446
Blocpdb> 141 atoms in block 131
Block first atom: 17578
Blocpdb> 140 atoms in block 132
Block first atom: 17719
Blocpdb> 142 atoms in block 133
Block first atom: 17859
Blocpdb> 156 atoms in block 134
Block first atom: 18001
Blocpdb> 147 atoms in block 135
Block first atom: 18157
Blocpdb> 143 atoms in block 136
Block first atom: 18304
Blocpdb> 146 atoms in block 137
Block first atom: 18447
Blocpdb> 149 atoms in block 138
Block first atom: 18593
Blocpdb> 149 atoms in block 139
Block first atom: 18742
Blocpdb> 153 atoms in block 140
Block first atom: 18891
Blocpdb> 131 atoms in block 141
Block first atom: 19044
Blocpdb> 135 atoms in block 142
Block first atom: 19175
Blocpdb> 156 atoms in block 143
Block first atom: 19310
Blocpdb> 154 atoms in block 144
Block first atom: 19466
Blocpdb> 131 atoms in block 145
Block first atom: 19620
Blocpdb> 143 atoms in block 146
Block first atom: 19751
Blocpdb> 59 atoms in block 147
Block first atom: 19894
Blocpdb> 120 atoms in block 148
Block first atom: 19953
Blocpdb> 142 atoms in block 149
Block first atom: 20073
Blocpdb> 152 atoms in block 150
Block first atom: 20215
Blocpdb> 142 atoms in block 151
Block first atom: 20367
Blocpdb> 147 atoms in block 152
Block first atom: 20509
Blocpdb> 147 atoms in block 153
Block first atom: 20656
Blocpdb> 146 atoms in block 154
Block first atom: 20803
Blocpdb> 145 atoms in block 155
Block first atom: 20949
Blocpdb> 133 atoms in block 156
Block first atom: 21094
Blocpdb> 49 atoms in block 157
Block first atom: 21227
Blocpdb> 155 atoms in block 158
Block first atom: 21276
Blocpdb> 139 atoms in block 159
Block first atom: 21431
Blocpdb> 149 atoms in block 160
Block first atom: 21570
Blocpdb> 151 atoms in block 161
Block first atom: 21719
Blocpdb> 152 atoms in block 162
Block first atom: 21870
Blocpdb> 133 atoms in block 163
Block first atom: 22022
Blocpdb> 136 atoms in block 164
Block first atom: 22155
Blocpdb> 149 atoms in block 165
Block first atom: 22291
Blocpdb> 142 atoms in block 166
Block first atom: 22440
Blocpdb> 131 atoms in block 167
Block first atom: 22582
Blocpdb> 138 atoms in block 168
Block first atom: 22713
Blocpdb> 138 atoms in block 169
Block first atom: 22851
Blocpdb> 147 atoms in block 170
Block first atom: 22989
Blocpdb> 133 atoms in block 171
Block first atom: 23136
Blocpdb> 154 atoms in block 172
Block first atom: 23269
Blocpdb> 136 atoms in block 173
Block first atom: 23423
Blocpdb> 139 atoms in block 174
Block first atom: 23559
Blocpdb> 148 atoms in block 175
Block first atom: 23698
Blocpdb> 147 atoms in block 176
Block first atom: 23846
Blocpdb> 141 atoms in block 177
Block first atom: 23993
Blocpdb> 111 atoms in block 178
Block first atom: 24134
Blocpdb> 125 atoms in block 179
Block first atom: 24245
Blocpdb> 151 atoms in block 180
Block first atom: 24370
Blocpdb> 140 atoms in block 181
Block first atom: 24521
Blocpdb> 138 atoms in block 182
Block first atom: 24661
Blocpdb> 148 atoms in block 183
Block first atom: 24799
Blocpdb> 135 atoms in block 184
Block first atom: 24947
Blocpdb> 143 atoms in block 185
Block first atom: 25082
Blocpdb> 137 atoms in block 186
Block first atom: 25225
Blocpdb> 139 atoms in block 187
Block first atom: 25362
Blocpdb> 130 atoms in block 188
Block first atom: 25501
Blocpdb> 135 atoms in block 189
Block first atom: 25631
Blocpdb> 143 atoms in block 190
Block first atom: 25766
Blocpdb> 149 atoms in block 191
Block first atom: 25909
Blocpdb> 133 atoms in block 192
Block first atom: 26058
Blocpdb> 126 atoms in block 193
Block first atom: 26191
Blocpdb> 136 atoms in block 194
Block first atom: 26317
Blocpdb> 144 atoms in block 195
Block first atom: 26453
Blocpdb> 143 atoms in block 196
Block first atom: 26597
Blocpdb> 135 atoms in block 197
Block first atom: 26740
Blocpdb> 143 atoms in block 198
Block first atom: 26875
Blocpdb> 156 atoms in block 199
Block first atom: 27018
Blocpdb> 144 atoms in block 200
Block first atom: 27174
Blocpdb> 132 atoms in block 201
Block first atom: 27318
Blocpdb> 147 atoms in block 202
Block first atom: 27450
Blocpdb> 140 atoms in block 203
Block first atom: 27597
Blocpdb> 146 atoms in block 204
Block first atom: 27737
Blocpdb> 155 atoms in block 205
Block first atom: 27883
Blocpdb> 90 atoms in block 206
Block first atom: 28037
Blocpdb> 206 blocks.
Blocpdb> At most, 156 atoms in each of them.
Blocpdb> At least, 13 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: 39709333 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 0m0.120s
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).
Between 2015 and 2025, it was hosted by US2B (Nantes).
Last modification: april 24th, 2026.
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