*** ***
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 = 260812110233605732.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 260812110233605732.atom to be opened.
Openam> File opened: 260812110233605732.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 = 2019
First residue number = 1
Last residue number = 2019
Number of atoms found = 31918
Mean number per residue = 15.8
Pdbmat> Coordinate statistics:
= 69.731504 +/- 24.380272 From: 9.985000 To: 132.166000
= 70.650988 +/- 24.105926 From: 10.895000 To: 139.550000
= 85.609562 +/- 29.483311 From: -0.255000 To: 157.551000
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 7.2652 % Filled.
Pdbmat> 21032430 non-zero elements.
Pdbmat> 2316038 atom-atom interactions.
Pdbmat> Number per atom= 145.12 +/- 43.11
Maximum number = 240
Minimum number = 22
Pdbmat> Matrix trace = 4.632076E+07
Pdbmat> Larger element = 883.556
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2019 non-zero elements, NRBL set to 11
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 = 260812110233605732.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 11
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 260812110233605732.atom to be opened.
Openam> file on opening on unit 11:
260812110233605732.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 31918 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 11 residue(s) per block.
Blocpdb> 2019 residues.
Blocpdb> 170 atoms in block 1
Block first atom: 1
Blocpdb> 192 atoms in block 2
Block first atom: 171
Blocpdb> 181 atoms in block 3
Block first atom: 363
Blocpdb> 151 atoms in block 4
Block first atom: 544
Blocpdb> 165 atoms in block 5
Block first atom: 695
Blocpdb> 182 atoms in block 6
Block first atom: 860
Blocpdb> 178 atoms in block 7
Block first atom: 1042
Blocpdb> 168 atoms in block 8
Block first atom: 1220
Blocpdb> 188 atoms in block 9
Block first atom: 1388
Blocpdb> 175 atoms in block 10
Block first atom: 1576
Blocpdb> 177 atoms in block 11
Block first atom: 1751
Blocpdb> 188 atoms in block 12
Block first atom: 1928
Blocpdb> 185 atoms in block 13
Block first atom: 2116
Blocpdb> 162 atoms in block 14
Block first atom: 2301
Blocpdb> 195 atoms in block 15
Block first atom: 2463
Blocpdb> 181 atoms in block 16
Block first atom: 2658
Blocpdb> 176 atoms in block 17
Block first atom: 2839
Blocpdb> 196 atoms in block 18
Block first atom: 3015
Blocpdb> 173 atoms in block 19
Block first atom: 3211
Blocpdb> 168 atoms in block 20
Block first atom: 3384
Blocpdb> 201 atoms in block 21
Block first atom: 3552
Blocpdb> 161 atoms in block 22
Block first atom: 3753
Blocpdb> 177 atoms in block 23
Block first atom: 3914
Blocpdb> 175 atoms in block 24
Block first atom: 4091
Blocpdb> 174 atoms in block 25
Block first atom: 4266
Blocpdb> 194 atoms in block 26
Block first atom: 4440
Blocpdb> 142 atoms in block 27
Block first atom: 4634
Blocpdb> 171 atoms in block 28
Block first atom: 4776
Blocpdb> 178 atoms in block 29
Block first atom: 4947
Blocpdb> 144 atoms in block 30
Block first atom: 5125
Blocpdb> 145 atoms in block 31
Block first atom: 5269
Blocpdb> 148 atoms in block 32
Block first atom: 5414
Blocpdb> 173 atoms in block 33
Block first atom: 5562
Blocpdb> 182 atoms in block 34
Block first atom: 5735
Blocpdb> 205 atoms in block 35
Block first atom: 5917
Blocpdb> 191 atoms in block 36
Block first atom: 6122
Blocpdb> 182 atoms in block 37
Block first atom: 6313
Blocpdb> 172 atoms in block 38
Block first atom: 6495
Blocpdb> 160 atoms in block 39
Block first atom: 6667
Blocpdb> 192 atoms in block 40
Block first atom: 6827
Blocpdb> 189 atoms in block 41
Block first atom: 7019
Blocpdb> 165 atoms in block 42
Block first atom: 7208
Blocpdb> 161 atoms in block 43
Block first atom: 7373
Blocpdb> 218 atoms in block 44
Block first atom: 7534
Blocpdb> 140 atoms in block 45
Block first atom: 7752
Blocpdb> 152 atoms in block 46
Block first atom: 7892
Blocpdb> 167 atoms in block 47
Block first atom: 8044
Blocpdb> 181 atoms in block 48
Block first atom: 8211
Blocpdb> 192 atoms in block 49
Block first atom: 8392
Blocpdb> 142 atoms in block 50
Block first atom: 8584
Blocpdb> 149 atoms in block 51
Block first atom: 8726
Blocpdb> 191 atoms in block 52
Block first atom: 8875
Blocpdb> 124 atoms in block 53
Block first atom: 9066
Blocpdb> 169 atoms in block 54
Block first atom: 9190
Blocpdb> 155 atoms in block 55
Block first atom: 9359
Blocpdb> 117 atoms in block 56
Block first atom: 9514
Blocpdb> 196 atoms in block 57
Block first atom: 9631
Blocpdb> 151 atoms in block 58
Block first atom: 9827
Blocpdb> 150 atoms in block 59
Block first atom: 9978
Blocpdb> 145 atoms in block 60
Block first atom: 10128
Blocpdb> 167 atoms in block 61
Block first atom: 10273
Blocpdb> 171 atoms in block 62
Block first atom: 10440
Blocpdb> 181 atoms in block 63
Block first atom: 10611
Blocpdb> 194 atoms in block 64
Block first atom: 10792
Blocpdb> 198 atoms in block 65
Block first atom: 10986
Blocpdb> 168 atoms in block 66
Block first atom: 11184
Blocpdb> 178 atoms in block 67
Block first atom: 11352
Blocpdb> 173 atoms in block 68
Block first atom: 11530
Blocpdb> 166 atoms in block 69
Block first atom: 11703
Blocpdb> 189 atoms in block 70
Block first atom: 11869
Blocpdb> 179 atoms in block 71
Block first atom: 12058
Blocpdb> 192 atoms in block 72
Block first atom: 12237
Blocpdb> 166 atoms in block 73
Block first atom: 12429
Blocpdb> 196 atoms in block 74
Block first atom: 12595
Blocpdb> 196 atoms in block 75
Block first atom: 12791
Blocpdb> 177 atoms in block 76
Block first atom: 12987
Blocpdb> 160 atoms in block 77
Block first atom: 13164
Blocpdb> 172 atoms in block 78
Block first atom: 13324
Blocpdb> 182 atoms in block 79
Block first atom: 13496
Blocpdb> 177 atoms in block 80
Block first atom: 13678
Blocpdb> 199 atoms in block 81
Block first atom: 13855
Blocpdb> 196 atoms in block 82
Block first atom: 14054
Blocpdb> 170 atoms in block 83
Block first atom: 14250
Blocpdb> 176 atoms in block 84
Block first atom: 14420
Blocpdb> 173 atoms in block 85
Block first atom: 14596
Blocpdb> 178 atoms in block 86
Block first atom: 14769
Blocpdb> 139 atoms in block 87
Block first atom: 14947
Blocpdb> 178 atoms in block 88
Block first atom: 15086
Blocpdb> 206 atoms in block 89
Block first atom: 15264
Blocpdb> 185 atoms in block 90
Block first atom: 15470
Blocpdb> 176 atoms in block 91
Block first atom: 15655
Blocpdb> 164 atoms in block 92
Block first atom: 15831
Blocpdb> 165 atoms in block 93
Block first atom: 15995
Blocpdb> 185 atoms in block 94
Block first atom: 16160
Blocpdb> 149 atoms in block 95
Block first atom: 16345
Blocpdb> 156 atoms in block 96
Block first atom: 16494
Blocpdb> 153 atoms in block 97
Block first atom: 16650
Blocpdb> 154 atoms in block 98
Block first atom: 16803
Blocpdb> 149 atoms in block 99
Block first atom: 16957
Blocpdb> 183 atoms in block 100
Block first atom: 17106
Blocpdb> 129 atoms in block 101
Block first atom: 17289
Blocpdb> 176 atoms in block 102
Block first atom: 17418
Blocpdb> 138 atoms in block 103
Block first atom: 17594
Blocpdb> 141 atoms in block 104
Block first atom: 17732
Blocpdb> 163 atoms in block 105
Block first atom: 17873
Blocpdb> 162 atoms in block 106
Block first atom: 18036
Blocpdb> 169 atoms in block 107
Block first atom: 18198
Blocpdb> 148 atoms in block 108
Block first atom: 18367
Blocpdb> 210 atoms in block 109
Block first atom: 18515
Blocpdb> 193 atoms in block 110
Block first atom: 18725
Blocpdb> 188 atoms in block 111
Block first atom: 18918
Blocpdb> 167 atoms in block 112
Block first atom: 19106
Blocpdb> 206 atoms in block 113
Block first atom: 19273
Blocpdb> 187 atoms in block 114
Block first atom: 19479
Blocpdb> 190 atoms in block 115
Block first atom: 19666
Blocpdb> 201 atoms in block 116
Block first atom: 19856
Blocpdb> 171 atoms in block 117
Block first atom: 20057
Blocpdb> 161 atoms in block 118
Block first atom: 20228
Blocpdb> 183 atoms in block 119
Block first atom: 20389
Blocpdb> 199 atoms in block 120
Block first atom: 20572
Blocpdb> 162 atoms in block 121
Block first atom: 20771
Blocpdb> 174 atoms in block 122
Block first atom: 20933
Blocpdb> 198 atoms in block 123
Block first atom: 21107
Blocpdb> 166 atoms in block 124
Block first atom: 21305
Blocpdb> 161 atoms in block 125
Block first atom: 21471
Blocpdb> 171 atoms in block 126
Block first atom: 21632
Blocpdb> 176 atoms in block 127
Block first atom: 21803
Blocpdb> 173 atoms in block 128
Block first atom: 21979
Blocpdb> 162 atoms in block 129
Block first atom: 22152
Blocpdb> 179 atoms in block 130
Block first atom: 22314
Blocpdb> 169 atoms in block 131
Block first atom: 22493
Blocpdb> 203 atoms in block 132
Block first atom: 22662
Blocpdb> 182 atoms in block 133
Block first atom: 22865
Blocpdb> 178 atoms in block 134
Block first atom: 23047
Blocpdb> 184 atoms in block 135
Block first atom: 23225
Blocpdb> 194 atoms in block 136
Block first atom: 23409
Blocpdb> 187 atoms in block 137
Block first atom: 23603
Blocpdb> 193 atoms in block 138
Block first atom: 23790
Blocpdb> 187 atoms in block 139
Block first atom: 23983
Blocpdb> 183 atoms in block 140
Block first atom: 24170
Blocpdb> 170 atoms in block 141
Block first atom: 24353
Blocpdb> 171 atoms in block 142
Block first atom: 24523
Blocpdb> 188 atoms in block 143
Block first atom: 24694
Blocpdb> 160 atoms in block 144
Block first atom: 24882
Blocpdb> 199 atoms in block 145
Block first atom: 25042
Blocpdb> 184 atoms in block 146
Block first atom: 25241
Blocpdb> 177 atoms in block 147
Block first atom: 25425
Blocpdb> 201 atoms in block 148
Block first atom: 25602
Blocpdb> 203 atoms in block 149
Block first atom: 25803
Blocpdb> 185 atoms in block 150
Block first atom: 26006
Blocpdb> 170 atoms in block 151
Block first atom: 26191
Blocpdb> 194 atoms in block 152
Block first atom: 26361
Blocpdb> 170 atoms in block 153
Block first atom: 26555
Blocpdb> 174 atoms in block 154
Block first atom: 26725
Blocpdb> 167 atoms in block 155
Block first atom: 26899
Blocpdb> 167 atoms in block 156
Block first atom: 27066
Blocpdb> 157 atoms in block 157
Block first atom: 27233
Blocpdb> 158 atoms in block 158
Block first atom: 27390
Blocpdb> 132 atoms in block 159
Block first atom: 27548
Blocpdb> 191 atoms in block 160
Block first atom: 27680
Blocpdb> 182 atoms in block 161
Block first atom: 27871
Blocpdb> 172 atoms in block 162
Block first atom: 28053
Blocpdb> 158 atoms in block 163
Block first atom: 28225
Blocpdb> 197 atoms in block 164
Block first atom: 28383
Blocpdb> 174 atoms in block 165
Block first atom: 28580
Blocpdb> 153 atoms in block 166
Block first atom: 28754
Blocpdb> 188 atoms in block 167
Block first atom: 28907
Blocpdb> 158 atoms in block 168
Block first atom: 29095
Blocpdb> 188 atoms in block 169
Block first atom: 29253
Blocpdb> 167 atoms in block 170
Block first atom: 29441
Blocpdb> 188 atoms in block 171
Block first atom: 29608
Blocpdb> 164 atoms in block 172
Block first atom: 29796
Blocpdb> 196 atoms in block 173
Block first atom: 29960
Blocpdb> 172 atoms in block 174
Block first atom: 30156
Blocpdb> 210 atoms in block 175
Block first atom: 30328
Blocpdb> 162 atoms in block 176
Block first atom: 30538
Blocpdb> 150 atoms in block 177
Block first atom: 30700
Blocpdb> 160 atoms in block 178
Block first atom: 30850
Blocpdb> 166 atoms in block 179
Block first atom: 31010
Blocpdb> 157 atoms in block 180
Block first atom: 31176
Blocpdb> 157 atoms in block 181
Block first atom: 31333
Blocpdb> 169 atoms in block 182
Block first atom: 31490
Blocpdb> 162 atoms in block 183
Block first atom: 31659
Blocpdb> 98 atoms in block 184
Block first atom: 31820
Blocpdb> 184 blocks.
Blocpdb> At most, 218 atoms in each of them.
Blocpdb> At least, 98 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: 63050833 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 0m0.146s
user 0m0.135s
sys 0m0.010s
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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