*** nompc ***
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 = 2601231139483643062.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 2601231139483643062.atom to be opened.
Openam> File opened: 2601231139483643062.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 = 5996
First residue number = 124
Last residue number = 1689
Number of atoms found = 40868
Mean number per residue = 6.8
Pdbmat> Coordinate statistics:
= 243.093212 +/- 30.554307 From: 161.437000 To: 324.636000
= 243.131842 +/- 30.563441 From: 161.524000 To: 325.020000
= 258.904071 +/- 65.018647 From: 130.778000 To: 378.057000
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 1.3465 % Filled.
Pdbmat> 14454450 non-zero elements.
Pdbmat> 1579078 atom-atom interactions.
Pdbmat> Number per atom= 77.28 +/- 21.29
Maximum number = 122
Minimum number = 11
Pdbmat> Matrix trace = 3.158156E+07
Pdbmat> Larger element = 495.870
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
5996 non-zero elements, NRBL set to 30
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 = 2601231139483643062.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 30
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 2601231139483643062.atom to be opened.
Openam> file on opening on unit 11:
2601231139483643062.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 40868 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 30 residue(s) per block.
Blocpdb> 5996 residues.
Blocpdb> 148 atoms in block 1
Block first atom: 1
Blocpdb> 149 atoms in block 2
Block first atom: 149
Blocpdb> 146 atoms in block 3
Block first atom: 298
Blocpdb> 147 atoms in block 4
Block first atom: 444
Blocpdb> 148 atoms in block 5
Block first atom: 591
Blocpdb> 147 atoms in block 6
Block first atom: 739
Blocpdb> 148 atoms in block 7
Block first atom: 886
Blocpdb> 149 atoms in block 8
Block first atom: 1034
Blocpdb> 197 atoms in block 9
Block first atom: 1183
Blocpdb> 207 atoms in block 10
Block first atom: 1380
Blocpdb> 197 atoms in block 11
Block first atom: 1587
Blocpdb> 201 atoms in block 12
Block first atom: 1784
Blocpdb> 193 atoms in block 13
Block first atom: 1985
Blocpdb> 203 atoms in block 14
Block first atom: 2178
Blocpdb> 228 atoms in block 15
Block first atom: 2381
Blocpdb> 203 atoms in block 16
Block first atom: 2609
Blocpdb> 205 atoms in block 17
Block first atom: 2812
Blocpdb> 217 atoms in block 18
Block first atom: 3017
Blocpdb> 210 atoms in block 19
Block first atom: 3234
Blocpdb> 216 atoms in block 20
Block first atom: 3444
Blocpdb> 225 atoms in block 21
Block first atom: 3660
Blocpdb> 201 atoms in block 22
Block first atom: 3885
Blocpdb> 195 atoms in block 23
Block first atom: 4086
Blocpdb> 181 atoms in block 24
Block first atom: 4281
Blocpdb> 180 atoms in block 25
Block first atom: 4462
Blocpdb> 192 atoms in block 26
Block first atom: 4642
Blocpdb> 184 atoms in block 27
Block first atom: 4834
Blocpdb> 210 atoms in block 28
Block first atom: 5018
Blocpdb> 198 atoms in block 29
Block first atom: 5228
Blocpdb> 205 atoms in block 30
Block first atom: 5426
Blocpdb> 218 atoms in block 31
Block first atom: 5631
Blocpdb> 223 atoms in block 32
Block first atom: 5849
Blocpdb> 199 atoms in block 33
Block first atom: 6072
Blocpdb> 252 atoms in block 34
Block first atom: 6271
Blocpdb> 243 atoms in block 35
Block first atom: 6523
Blocpdb> 214 atoms in block 36
Block first atom: 6766
Blocpdb> 179 atoms in block 37
Block first atom: 6980
Blocpdb> 254 atoms in block 38
Block first atom: 7159
Blocpdb> 241 atoms in block 39
Block first atom: 7413
Blocpdb> 248 atoms in block 40
Block first atom: 7654
Blocpdb> 252 atoms in block 41
Block first atom: 7902
Blocpdb> 206 atoms in block 42
Block first atom: 8154
Blocpdb> 229 atoms in block 43
Block first atom: 8360
Blocpdb> 249 atoms in block 44
Block first atom: 8589
Blocpdb> 225 atoms in block 45
Block first atom: 8838
Blocpdb> 230 atoms in block 46
Block first atom: 9063
Blocpdb> 246 atoms in block 47
Block first atom: 9293
Blocpdb> 243 atoms in block 48
Block first atom: 9539
Blocpdb> 230 atoms in block 49
Block first atom: 9782
Blocpdb> 47 atoms in block 50
Block first atom: 10012
Blocpdb> 159 atoms in block 51
Block first atom: 10059
Blocpdb> 148 atoms in block 52
Block first atom: 10218
Blocpdb> 149 atoms in block 53
Block first atom: 10366
Blocpdb> 146 atoms in block 54
Block first atom: 10515
Blocpdb> 147 atoms in block 55
Block first atom: 10661
Blocpdb> 148 atoms in block 56
Block first atom: 10808
Blocpdb> 147 atoms in block 57
Block first atom: 10956
Blocpdb> 148 atoms in block 58
Block first atom: 11103
Blocpdb> 149 atoms in block 59
Block first atom: 11251
Blocpdb> 197 atoms in block 60
Block first atom: 11400
Blocpdb> 207 atoms in block 61
Block first atom: 11597
Blocpdb> 197 atoms in block 62
Block first atom: 11804
Blocpdb> 201 atoms in block 63
Block first atom: 12001
Blocpdb> 193 atoms in block 64
Block first atom: 12202
Blocpdb> 203 atoms in block 65
Block first atom: 12395
Blocpdb> 228 atoms in block 66
Block first atom: 12598
Blocpdb> 203 atoms in block 67
Block first atom: 12826
Blocpdb> 205 atoms in block 68
Block first atom: 13029
Blocpdb> 217 atoms in block 69
Block first atom: 13234
Blocpdb> 210 atoms in block 70
Block first atom: 13451
Blocpdb> 216 atoms in block 71
Block first atom: 13661
Blocpdb> 225 atoms in block 72
Block first atom: 13877
Blocpdb> 201 atoms in block 73
Block first atom: 14102
Blocpdb> 195 atoms in block 74
Block first atom: 14303
Blocpdb> 181 atoms in block 75
Block first atom: 14498
Blocpdb> 180 atoms in block 76
Block first atom: 14679
Blocpdb> 192 atoms in block 77
Block first atom: 14859
Blocpdb> 184 atoms in block 78
Block first atom: 15051
Blocpdb> 210 atoms in block 79
Block first atom: 15235
Blocpdb> 198 atoms in block 80
Block first atom: 15445
Blocpdb> 205 atoms in block 81
Block first atom: 15643
Blocpdb> 218 atoms in block 82
Block first atom: 15848
Blocpdb> 223 atoms in block 83
Block first atom: 16066
Blocpdb> 199 atoms in block 84
Block first atom: 16289
Blocpdb> 252 atoms in block 85
Block first atom: 16488
Blocpdb> 243 atoms in block 86
Block first atom: 16740
Blocpdb> 214 atoms in block 87
Block first atom: 16983
Blocpdb> 179 atoms in block 88
Block first atom: 17197
Blocpdb> 254 atoms in block 89
Block first atom: 17376
Blocpdb> 241 atoms in block 90
Block first atom: 17630
Blocpdb> 248 atoms in block 91
Block first atom: 17871
Blocpdb> 252 atoms in block 92
Block first atom: 18119
Blocpdb> 206 atoms in block 93
Block first atom: 18371
Blocpdb> 229 atoms in block 94
Block first atom: 18577
Blocpdb> 249 atoms in block 95
Block first atom: 18806
Blocpdb> 225 atoms in block 96
Block first atom: 19055
Blocpdb> 230 atoms in block 97
Block first atom: 19280
Blocpdb> 246 atoms in block 98
Block first atom: 19510
Blocpdb> 243 atoms in block 99
Block first atom: 19756
Blocpdb> 230 atoms in block 100
Block first atom: 19999
Blocpdb> 47 atoms in block 101
Block first atom: 20229
Blocpdb> 159 atoms in block 102
Block first atom: 20276
Blocpdb> 148 atoms in block 103
Block first atom: 20435
Blocpdb> 149 atoms in block 104
Block first atom: 20583
Blocpdb> 146 atoms in block 105
Block first atom: 20732
Blocpdb> 147 atoms in block 106
Block first atom: 20878
Blocpdb> 148 atoms in block 107
Block first atom: 21025
Blocpdb> 147 atoms in block 108
Block first atom: 21173
Blocpdb> 148 atoms in block 109
Block first atom: 21320
Blocpdb> 149 atoms in block 110
Block first atom: 21468
Blocpdb> 197 atoms in block 111
Block first atom: 21617
Blocpdb> 207 atoms in block 112
Block first atom: 21814
Blocpdb> 197 atoms in block 113
Block first atom: 22021
Blocpdb> 201 atoms in block 114
Block first atom: 22218
Blocpdb> 193 atoms in block 115
Block first atom: 22419
Blocpdb> 203 atoms in block 116
Block first atom: 22612
Blocpdb> 228 atoms in block 117
Block first atom: 22815
Blocpdb> 203 atoms in block 118
Block first atom: 23043
Blocpdb> 205 atoms in block 119
Block first atom: 23246
Blocpdb> 217 atoms in block 120
Block first atom: 23451
Blocpdb> 210 atoms in block 121
Block first atom: 23668
Blocpdb> 216 atoms in block 122
Block first atom: 23878
Blocpdb> 225 atoms in block 123
Block first atom: 24094
Blocpdb> 201 atoms in block 124
Block first atom: 24319
Blocpdb> 195 atoms in block 125
Block first atom: 24520
Blocpdb> 181 atoms in block 126
Block first atom: 24715
Blocpdb> 180 atoms in block 127
Block first atom: 24896
Blocpdb> 192 atoms in block 128
Block first atom: 25076
Blocpdb> 184 atoms in block 129
Block first atom: 25268
Blocpdb> 210 atoms in block 130
Block first atom: 25452
Blocpdb> 198 atoms in block 131
Block first atom: 25662
Blocpdb> 205 atoms in block 132
Block first atom: 25860
Blocpdb> 218 atoms in block 133
Block first atom: 26065
Blocpdb> 223 atoms in block 134
Block first atom: 26283
Blocpdb> 199 atoms in block 135
Block first atom: 26506
Blocpdb> 252 atoms in block 136
Block first atom: 26705
Blocpdb> 243 atoms in block 137
Block first atom: 26957
Blocpdb> 214 atoms in block 138
Block first atom: 27200
Blocpdb> 179 atoms in block 139
Block first atom: 27414
Blocpdb> 254 atoms in block 140
Block first atom: 27593
Blocpdb> 241 atoms in block 141
Block first atom: 27847
Blocpdb> 248 atoms in block 142
Block first atom: 28088
Blocpdb> 252 atoms in block 143
Block first atom: 28336
Blocpdb> 206 atoms in block 144
Block first atom: 28588
Blocpdb> 229 atoms in block 145
Block first atom: 28794
Blocpdb> 249 atoms in block 146
Block first atom: 29023
Blocpdb> 225 atoms in block 147
Block first atom: 29272
Blocpdb> 230 atoms in block 148
Block first atom: 29497
Blocpdb> 246 atoms in block 149
Block first atom: 29727
Blocpdb> 243 atoms in block 150
Block first atom: 29973
Blocpdb> 230 atoms in block 151
Block first atom: 30216
Blocpdb> 47 atoms in block 152
Block first atom: 30446
Blocpdb> 159 atoms in block 153
Block first atom: 30493
Blocpdb> 148 atoms in block 154
Block first atom: 30652
Blocpdb> 149 atoms in block 155
Block first atom: 30800
Blocpdb> 146 atoms in block 156
Block first atom: 30949
Blocpdb> 147 atoms in block 157
Block first atom: 31095
Blocpdb> 148 atoms in block 158
Block first atom: 31242
Blocpdb> 147 atoms in block 159
Block first atom: 31390
Blocpdb> 148 atoms in block 160
Block first atom: 31537
Blocpdb> 149 atoms in block 161
Block first atom: 31685
Blocpdb> 197 atoms in block 162
Block first atom: 31834
Blocpdb> 207 atoms in block 163
Block first atom: 32031
Blocpdb> 197 atoms in block 164
Block first atom: 32238
Blocpdb> 201 atoms in block 165
Block first atom: 32435
Blocpdb> 193 atoms in block 166
Block first atom: 32636
Blocpdb> 203 atoms in block 167
Block first atom: 32829
Blocpdb> 228 atoms in block 168
Block first atom: 33032
Blocpdb> 203 atoms in block 169
Block first atom: 33260
Blocpdb> 205 atoms in block 170
Block first atom: 33463
Blocpdb> 217 atoms in block 171
Block first atom: 33668
Blocpdb> 210 atoms in block 172
Block first atom: 33885
Blocpdb> 216 atoms in block 173
Block first atom: 34095
Blocpdb> 225 atoms in block 174
Block first atom: 34311
Blocpdb> 201 atoms in block 175
Block first atom: 34536
Blocpdb> 195 atoms in block 176
Block first atom: 34737
Blocpdb> 181 atoms in block 177
Block first atom: 34932
Blocpdb> 180 atoms in block 178
Block first atom: 35113
Blocpdb> 192 atoms in block 179
Block first atom: 35293
Blocpdb> 184 atoms in block 180
Block first atom: 35485
Blocpdb> 210 atoms in block 181
Block first atom: 35669
Blocpdb> 198 atoms in block 182
Block first atom: 35879
Blocpdb> 205 atoms in block 183
Block first atom: 36077
Blocpdb> 218 atoms in block 184
Block first atom: 36282
Blocpdb> 223 atoms in block 185
Block first atom: 36500
Blocpdb> 199 atoms in block 186
Block first atom: 36723
Blocpdb> 252 atoms in block 187
Block first atom: 36922
Blocpdb> 243 atoms in block 188
Block first atom: 37174
Blocpdb> 214 atoms in block 189
Block first atom: 37417
Blocpdb> 179 atoms in block 190
Block first atom: 37631
Blocpdb> 254 atoms in block 191
Block first atom: 37810
Blocpdb> 241 atoms in block 192
Block first atom: 38064
Blocpdb> 248 atoms in block 193
Block first atom: 38305
Blocpdb> 252 atoms in block 194
Block first atom: 38553
Blocpdb> 206 atoms in block 195
Block first atom: 38805
Blocpdb> 229 atoms in block 196
Block first atom: 39011
Blocpdb> 249 atoms in block 197
Block first atom: 39240
Blocpdb> 225 atoms in block 198
Block first atom: 39489
Blocpdb> 230 atoms in block 199
Block first atom: 39714
Blocpdb> 246 atoms in block 200
Block first atom: 39944
Blocpdb> 243 atoms in block 201
Block first atom: 40190
Blocpdb> 230 atoms in block 202
Block first atom: 40433
Blocpdb> 47 atoms in block 203
Block first atom: 40663
Blocpdb> 159 atoms in block 204
Block first atom: 40709
Blocpdb> 204 blocks.
Blocpdb> At most, 254 atoms in each of them.
Blocpdb> At least, 47 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: 94004893 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 0m0.155s
user 0m0.149s
sys 0m0.005s
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: december 26th, 2025.
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