*** naniav ***
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 = 2601240651053769005.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 2601240651053769005.atom to be opened.
Openam> File opened: 2601240651053769005.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 = 2500
First residue number = 1
Last residue number = 647
Number of atoms found = 39782
Mean number per residue = 15.9
Pdbmat> Coordinate statistics:
= 71.197726 +/- 25.420880 From: 9.130000 To: 127.200000
= 71.049098 +/- 24.452700 From: 14.280000 To: 126.420000
= 96.699324 +/- 32.312519 From: 24.940000 To: 172.170000
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 4.0720 % Filled.
Pdbmat> 27662744 non-zero elements.
Pdbmat> 3052022 atom-atom interactions.
Pdbmat> Number per atom= 153.44 +/- 44.91
Maximum number = 256
Minimum number = 20
Pdbmat> Matrix trace = 6.104044E+07
Pdbmat> Larger element = 913.598
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2500 non-zero elements, NRBL set to 13
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 = 2601240651053769005.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 13
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 2601240651053769005.atom to be opened.
Openam> file on opening on unit 11:
2601240651053769005.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 39782 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 13 residue(s) per block.
Blocpdb> 2500 residues.
Blocpdb> 205 atoms in block 1
Block first atom: 1
Blocpdb> 242 atoms in block 2
Block first atom: 206
Blocpdb> 196 atoms in block 3
Block first atom: 448
Blocpdb> 187 atoms in block 4
Block first atom: 644
Blocpdb> 189 atoms in block 5
Block first atom: 831
Blocpdb> 197 atoms in block 6
Block first atom: 1020
Blocpdb> 211 atoms in block 7
Block first atom: 1217
Blocpdb> 195 atoms in block 8
Block first atom: 1428
Blocpdb> 182 atoms in block 9
Block first atom: 1623
Blocpdb> 181 atoms in block 10
Block first atom: 1805
Blocpdb> 201 atoms in block 11
Block first atom: 1986
Blocpdb> 211 atoms in block 12
Block first atom: 2187
Blocpdb> 198 atoms in block 13
Block first atom: 2398
Blocpdb> 201 atoms in block 14
Block first atom: 2596
Blocpdb> 217 atoms in block 15
Block first atom: 2797
Blocpdb> 212 atoms in block 16
Block first atom: 3014
Blocpdb> 185 atoms in block 17
Block first atom: 3226
Blocpdb> 204 atoms in block 18
Block first atom: 3411
Blocpdb> 197 atoms in block 19
Block first atom: 3615
Blocpdb> 232 atoms in block 20
Block first atom: 3812
Blocpdb> 245 atoms in block 21
Block first atom: 4044
Blocpdb> 213 atoms in block 22
Block first atom: 4289
Blocpdb> 199 atoms in block 23
Block first atom: 4502
Blocpdb> 139 atoms in block 24
Block first atom: 4701
Blocpdb> 209 atoms in block 25
Block first atom: 4840
Blocpdb> 192 atoms in block 26
Block first atom: 5049
Blocpdb> 212 atoms in block 27
Block first atom: 5241
Blocpdb> 192 atoms in block 28
Block first atom: 5453
Blocpdb> 218 atoms in block 29
Block first atom: 5645
Blocpdb> 199 atoms in block 30
Block first atom: 5863
Blocpdb> 199 atoms in block 31
Block first atom: 6062
Blocpdb> 201 atoms in block 32
Block first atom: 6261
Blocpdb> 195 atoms in block 33
Block first atom: 6462
Blocpdb> 220 atoms in block 34
Block first atom: 6657
Blocpdb> 215 atoms in block 35
Block first atom: 6877
Blocpdb> 187 atoms in block 36
Block first atom: 7092
Blocpdb> 191 atoms in block 37
Block first atom: 7279
Blocpdb> 205 atoms in block 38
Block first atom: 7470
Blocpdb> 231 atoms in block 39
Block first atom: 7675
Blocpdb> 210 atoms in block 40
Block first atom: 7906
Blocpdb> 209 atoms in block 41
Block first atom: 8116
Blocpdb> 218 atoms in block 42
Block first atom: 8325
Blocpdb> 225 atoms in block 43
Block first atom: 8543
Blocpdb> 186 atoms in block 44
Block first atom: 8768
Blocpdb> 220 atoms in block 45
Block first atom: 8954
Blocpdb> 215 atoms in block 46
Block first atom: 9174
Blocpdb> 235 atoms in block 47
Block first atom: 9389
Blocpdb> 231 atoms in block 48
Block first atom: 9624
Blocpdb> 197 atoms in block 49
Block first atom: 9855
Blocpdb> 186 atoms in block 50
Block first atom: 10052
Blocpdb> 201 atoms in block 51
Block first atom: 10238
Blocpdb> 220 atoms in block 52
Block first atom: 10439
Blocpdb> 221 atoms in block 53
Block first atom: 10659
Blocpdb> 203 atoms in block 54
Block first atom: 10880
Blocpdb> 202 atoms in block 55
Block first atom: 11083
Blocpdb> 177 atoms in block 56
Block first atom: 11285
Blocpdb> 202 atoms in block 57
Block first atom: 11462
Blocpdb> 208 atoms in block 58
Block first atom: 11664
Blocpdb> 208 atoms in block 59
Block first atom: 11872
Blocpdb> 195 atoms in block 60
Block first atom: 12080
Blocpdb> 176 atoms in block 61
Block first atom: 12275
Blocpdb> 216 atoms in block 62
Block first atom: 12451
Blocpdb> 184 atoms in block 63
Block first atom: 12667
Blocpdb> 218 atoms in block 64
Block first atom: 12851
Blocpdb> 216 atoms in block 65
Block first atom: 13069
Blocpdb> 230 atoms in block 66
Block first atom: 13285
Blocpdb> 188 atoms in block 67
Block first atom: 13515
Blocpdb> 192 atoms in block 68
Block first atom: 13703
Blocpdb> 197 atoms in block 69
Block first atom: 13895
Blocpdb> 217 atoms in block 70
Block first atom: 14092
Blocpdb> 242 atoms in block 71
Block first atom: 14309
Blocpdb> 235 atoms in block 72
Block first atom: 14551
Blocpdb> 214 atoms in block 73
Block first atom: 14786
Blocpdb> 189 atoms in block 74
Block first atom: 15000
Blocpdb> 194 atoms in block 75
Block first atom: 15189
Blocpdb> 192 atoms in block 76
Block first atom: 15383
Blocpdb> 200 atoms in block 77
Block first atom: 15575
Blocpdb> 197 atoms in block 78
Block first atom: 15775
Blocpdb> 222 atoms in block 79
Block first atom: 15972
Blocpdb> 218 atoms in block 80
Block first atom: 16194
Blocpdb> 227 atoms in block 81
Block first atom: 16412
Blocpdb> 217 atoms in block 82
Block first atom: 16639
Blocpdb> 211 atoms in block 83
Block first atom: 16856
Blocpdb> 223 atoms in block 84
Block first atom: 17067
Blocpdb> 204 atoms in block 85
Block first atom: 17290
Blocpdb> 214 atoms in block 86
Block first atom: 17494
Blocpdb> 220 atoms in block 87
Block first atom: 17708
Blocpdb> 231 atoms in block 88
Block first atom: 17928
Blocpdb> 214 atoms in block 89
Block first atom: 18159
Blocpdb> 180 atoms in block 90
Block first atom: 18373
Blocpdb> 202 atoms in block 91
Block first atom: 18553
Blocpdb> 200 atoms in block 92
Block first atom: 18755
Blocpdb> 208 atoms in block 93
Block first atom: 18955
Blocpdb> 213 atoms in block 94
Block first atom: 19163
Blocpdb> 198 atoms in block 95
Block first atom: 19376
Blocpdb> 241 atoms in block 96
Block first atom: 19574
Blocpdb> 77 atoms in block 97
Block first atom: 19815
Blocpdb> 201 atoms in block 98
Block first atom: 19892
Blocpdb> 220 atoms in block 99
Block first atom: 20093
Blocpdb> 221 atoms in block 100
Block first atom: 20313
Blocpdb> 203 atoms in block 101
Block first atom: 20534
Blocpdb> 202 atoms in block 102
Block first atom: 20737
Blocpdb> 177 atoms in block 103
Block first atom: 20939
Blocpdb> 202 atoms in block 104
Block first atom: 21116
Blocpdb> 208 atoms in block 105
Block first atom: 21318
Blocpdb> 208 atoms in block 106
Block first atom: 21526
Blocpdb> 195 atoms in block 107
Block first atom: 21734
Blocpdb> 176 atoms in block 108
Block first atom: 21929
Blocpdb> 216 atoms in block 109
Block first atom: 22105
Blocpdb> 184 atoms in block 110
Block first atom: 22321
Blocpdb> 218 atoms in block 111
Block first atom: 22505
Blocpdb> 216 atoms in block 112
Block first atom: 22723
Blocpdb> 230 atoms in block 113
Block first atom: 22939
Blocpdb> 188 atoms in block 114
Block first atom: 23169
Blocpdb> 192 atoms in block 115
Block first atom: 23357
Blocpdb> 197 atoms in block 116
Block first atom: 23549
Blocpdb> 217 atoms in block 117
Block first atom: 23746
Blocpdb> 242 atoms in block 118
Block first atom: 23963
Blocpdb> 235 atoms in block 119
Block first atom: 24205
Blocpdb> 214 atoms in block 120
Block first atom: 24440
Blocpdb> 189 atoms in block 121
Block first atom: 24654
Blocpdb> 194 atoms in block 122
Block first atom: 24843
Blocpdb> 192 atoms in block 123
Block first atom: 25037
Blocpdb> 200 atoms in block 124
Block first atom: 25229
Blocpdb> 197 atoms in block 125
Block first atom: 25429
Blocpdb> 222 atoms in block 126
Block first atom: 25626
Blocpdb> 218 atoms in block 127
Block first atom: 25848
Blocpdb> 227 atoms in block 128
Block first atom: 26066
Blocpdb> 217 atoms in block 129
Block first atom: 26293
Blocpdb> 211 atoms in block 130
Block first atom: 26510
Blocpdb> 223 atoms in block 131
Block first atom: 26721
Blocpdb> 204 atoms in block 132
Block first atom: 26944
Blocpdb> 214 atoms in block 133
Block first atom: 27148
Blocpdb> 220 atoms in block 134
Block first atom: 27362
Blocpdb> 231 atoms in block 135
Block first atom: 27582
Blocpdb> 214 atoms in block 136
Block first atom: 27813
Blocpdb> 180 atoms in block 137
Block first atom: 28027
Blocpdb> 202 atoms in block 138
Block first atom: 28207
Blocpdb> 200 atoms in block 139
Block first atom: 28409
Blocpdb> 208 atoms in block 140
Block first atom: 28609
Blocpdb> 213 atoms in block 141
Block first atom: 28817
Blocpdb> 198 atoms in block 142
Block first atom: 29030
Blocpdb> 241 atoms in block 143
Block first atom: 29228
Blocpdb> 77 atoms in block 144
Block first atom: 29469
Blocpdb> 205 atoms in block 145
Block first atom: 29546
Blocpdb> 242 atoms in block 146
Block first atom: 29751
Blocpdb> 196 atoms in block 147
Block first atom: 29993
Blocpdb> 187 atoms in block 148
Block first atom: 30189
Blocpdb> 189 atoms in block 149
Block first atom: 30376
Blocpdb> 197 atoms in block 150
Block first atom: 30565
Blocpdb> 211 atoms in block 151
Block first atom: 30762
Blocpdb> 195 atoms in block 152
Block first atom: 30973
Blocpdb> 182 atoms in block 153
Block first atom: 31168
Blocpdb> 181 atoms in block 154
Block first atom: 31350
Blocpdb> 201 atoms in block 155
Block first atom: 31531
Blocpdb> 211 atoms in block 156
Block first atom: 31732
Blocpdb> 198 atoms in block 157
Block first atom: 31943
Blocpdb> 201 atoms in block 158
Block first atom: 32141
Blocpdb> 217 atoms in block 159
Block first atom: 32342
Blocpdb> 212 atoms in block 160
Block first atom: 32559
Blocpdb> 185 atoms in block 161
Block first atom: 32771
Blocpdb> 204 atoms in block 162
Block first atom: 32956
Blocpdb> 197 atoms in block 163
Block first atom: 33160
Blocpdb> 232 atoms in block 164
Block first atom: 33357
Blocpdb> 245 atoms in block 165
Block first atom: 33589
Blocpdb> 213 atoms in block 166
Block first atom: 33834
Blocpdb> 199 atoms in block 167
Block first atom: 34047
Blocpdb> 139 atoms in block 168
Block first atom: 34246
Blocpdb> 209 atoms in block 169
Block first atom: 34385
Blocpdb> 192 atoms in block 170
Block first atom: 34594
Blocpdb> 212 atoms in block 171
Block first atom: 34786
Blocpdb> 192 atoms in block 172
Block first atom: 34998
Blocpdb> 218 atoms in block 173
Block first atom: 35190
Blocpdb> 199 atoms in block 174
Block first atom: 35408
Blocpdb> 199 atoms in block 175
Block first atom: 35607
Blocpdb> 201 atoms in block 176
Block first atom: 35806
Blocpdb> 195 atoms in block 177
Block first atom: 36007
Blocpdb> 220 atoms in block 178
Block first atom: 36202
Blocpdb> 215 atoms in block 179
Block first atom: 36422
Blocpdb> 187 atoms in block 180
Block first atom: 36637
Blocpdb> 191 atoms in block 181
Block first atom: 36824
Blocpdb> 205 atoms in block 182
Block first atom: 37015
Blocpdb> 231 atoms in block 183
Block first atom: 37220
Blocpdb> 210 atoms in block 184
Block first atom: 37451
Blocpdb> 209 atoms in block 185
Block first atom: 37661
Blocpdb> 218 atoms in block 186
Block first atom: 37870
Blocpdb> 225 atoms in block 187
Block first atom: 38088
Blocpdb> 186 atoms in block 188
Block first atom: 38313
Blocpdb> 220 atoms in block 189
Block first atom: 38499
Blocpdb> 215 atoms in block 190
Block first atom: 38719
Blocpdb> 235 atoms in block 191
Block first atom: 38934
Blocpdb> 231 atoms in block 192
Block first atom: 39169
Blocpdb> 197 atoms in block 193
Block first atom: 39400
Blocpdb> 186 atoms in block 194
Block first atom: 39596
Blocpdb> 194 blocks.
Blocpdb> At most, 245 atoms in each of them.
Blocpdb> At least, 77 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: 88259536 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 0m0.231s
user 0m0.197s
sys 0m0.034s
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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