*** ApoB ***
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 = 251228183124576648.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 251228183124576648.atom to be opened.
Openam> File opened: 251228183124576648.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 = 4526
First residue number = 38
Last residue number = 4563
Number of atoms found = 36083
Mean number per residue = 8.0
Pdbmat> Coordinate statistics:
= 249.661647 +/- 42.063888 From: 159.699000 To: 333.073000
= 248.523480 +/- 56.448228 From: 138.169000 To: 361.451000
= 260.137039 +/- 66.578223 From: 141.333000 To: 388.458000
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 -2.0816 % Filled.
Pdbmat> 12145487 non-zero elements.
Pdbmat> 1325666 atom-atom interactions.
Pdbmat> Number per atom= 73.48 +/- 16.34
Maximum number = 126
Minimum number = 12
Pdbmat> Matrix trace = 2.651332E+07
Pdbmat> Larger element = 482.995
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
4526 non-zero elements, NRBL set to 23
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 = 251228183124576648.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 23
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 251228183124576648.atom to be opened.
Openam> file on opening on unit 11:
251228183124576648.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 36083 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 23 residue(s) per block.
Blocpdb> 4526 residues.
Blocpdb> 198 atoms in block 1
Block first atom: 1
Blocpdb> 164 atoms in block 2
Block first atom: 199
Blocpdb> 182 atoms in block 3
Block first atom: 363
Blocpdb> 179 atoms in block 4
Block first atom: 545
Blocpdb> 191 atoms in block 5
Block first atom: 724
Blocpdb> 177 atoms in block 6
Block first atom: 915
Blocpdb> 182 atoms in block 7
Block first atom: 1092
Blocpdb> 180 atoms in block 8
Block first atom: 1274
Blocpdb> 166 atoms in block 9
Block first atom: 1454
Blocpdb> 190 atoms in block 10
Block first atom: 1620
Blocpdb> 187 atoms in block 11
Block first atom: 1810
Blocpdb> 178 atoms in block 12
Block first atom: 1997
Blocpdb> 177 atoms in block 13
Block first atom: 2175
Blocpdb> 185 atoms in block 14
Block first atom: 2352
Blocpdb> 170 atoms in block 15
Block first atom: 2537
Blocpdb> 184 atoms in block 16
Block first atom: 2707
Blocpdb> 181 atoms in block 17
Block first atom: 2891
Blocpdb> 185 atoms in block 18
Block first atom: 3072
Blocpdb> 188 atoms in block 19
Block first atom: 3257
Blocpdb> 181 atoms in block 20
Block first atom: 3445
Blocpdb> 175 atoms in block 21
Block first atom: 3626
Blocpdb> 185 atoms in block 22
Block first atom: 3801
Blocpdb> 179 atoms in block 23
Block first atom: 3986
Blocpdb> 189 atoms in block 24
Block first atom: 4165
Blocpdb> 183 atoms in block 25
Block first atom: 4354
Blocpdb> 192 atoms in block 26
Block first atom: 4537
Blocpdb> 175 atoms in block 27
Block first atom: 4729
Blocpdb> 183 atoms in block 28
Block first atom: 4904
Blocpdb> 170 atoms in block 29
Block first atom: 5087
Blocpdb> 185 atoms in block 30
Block first atom: 5257
Blocpdb> 186 atoms in block 31
Block first atom: 5442
Blocpdb> 176 atoms in block 32
Block first atom: 5628
Blocpdb> 182 atoms in block 33
Block first atom: 5804
Blocpdb> 177 atoms in block 34
Block first atom: 5986
Blocpdb> 187 atoms in block 35
Block first atom: 6163
Blocpdb> 155 atoms in block 36
Block first atom: 6350
Blocpdb> 167 atoms in block 37
Block first atom: 6505
Blocpdb> 182 atoms in block 38
Block first atom: 6672
Blocpdb> 178 atoms in block 39
Block first atom: 6854
Blocpdb> 168 atoms in block 40
Block first atom: 7032
Blocpdb> 179 atoms in block 41
Block first atom: 7200
Blocpdb> 176 atoms in block 42
Block first atom: 7379
Blocpdb> 190 atoms in block 43
Block first atom: 7555
Blocpdb> 174 atoms in block 44
Block first atom: 7745
Blocpdb> 190 atoms in block 45
Block first atom: 7919
Blocpdb> 180 atoms in block 46
Block first atom: 8109
Blocpdb> 182 atoms in block 47
Block first atom: 8289
Blocpdb> 184 atoms in block 48
Block first atom: 8471
Blocpdb> 167 atoms in block 49
Block first atom: 8655
Blocpdb> 199 atoms in block 50
Block first atom: 8822
Blocpdb> 189 atoms in block 51
Block first atom: 9021
Blocpdb> 184 atoms in block 52
Block first atom: 9210
Blocpdb> 182 atoms in block 53
Block first atom: 9394
Blocpdb> 191 atoms in block 54
Block first atom: 9576
Blocpdb> 187 atoms in block 55
Block first atom: 9767
Blocpdb> 178 atoms in block 56
Block first atom: 9954
Blocpdb> 193 atoms in block 57
Block first atom: 10132
Blocpdb> 181 atoms in block 58
Block first atom: 10325
Blocpdb> 182 atoms in block 59
Block first atom: 10506
Blocpdb> 177 atoms in block 60
Block first atom: 10688
Blocpdb> 186 atoms in block 61
Block first atom: 10865
Blocpdb> 170 atoms in block 62
Block first atom: 11051
Blocpdb> 187 atoms in block 63
Block first atom: 11221
Blocpdb> 181 atoms in block 64
Block first atom: 11408
Blocpdb> 180 atoms in block 65
Block first atom: 11589
Blocpdb> 169 atoms in block 66
Block first atom: 11769
Blocpdb> 188 atoms in block 67
Block first atom: 11938
Blocpdb> 184 atoms in block 68
Block first atom: 12126
Blocpdb> 184 atoms in block 69
Block first atom: 12310
Blocpdb> 171 atoms in block 70
Block first atom: 12494
Blocpdb> 165 atoms in block 71
Block first atom: 12665
Blocpdb> 174 atoms in block 72
Block first atom: 12830
Blocpdb> 165 atoms in block 73
Block first atom: 13004
Blocpdb> 179 atoms in block 74
Block first atom: 13169
Blocpdb> 176 atoms in block 75
Block first atom: 13348
Blocpdb> 190 atoms in block 76
Block first atom: 13524
Blocpdb> 184 atoms in block 77
Block first atom: 13714
Blocpdb> 176 atoms in block 78
Block first atom: 13898
Blocpdb> 175 atoms in block 79
Block first atom: 14074
Blocpdb> 169 atoms in block 80
Block first atom: 14249
Blocpdb> 183 atoms in block 81
Block first atom: 14418
Blocpdb> 174 atoms in block 82
Block first atom: 14601
Blocpdb> 190 atoms in block 83
Block first atom: 14775
Blocpdb> 172 atoms in block 84
Block first atom: 14965
Blocpdb> 188 atoms in block 85
Block first atom: 15137
Blocpdb> 175 atoms in block 86
Block first atom: 15325
Blocpdb> 177 atoms in block 87
Block first atom: 15500
Blocpdb> 189 atoms in block 88
Block first atom: 15677
Blocpdb> 203 atoms in block 89
Block first atom: 15866
Blocpdb> 196 atoms in block 90
Block first atom: 16069
Blocpdb> 188 atoms in block 91
Block first atom: 16265
Blocpdb> 198 atoms in block 92
Block first atom: 16453
Blocpdb> 184 atoms in block 93
Block first atom: 16651
Blocpdb> 197 atoms in block 94
Block first atom: 16835
Blocpdb> 197 atoms in block 95
Block first atom: 17032
Blocpdb> 184 atoms in block 96
Block first atom: 17229
Blocpdb> 199 atoms in block 97
Block first atom: 17413
Blocpdb> 190 atoms in block 98
Block first atom: 17612
Blocpdb> 185 atoms in block 99
Block first atom: 17802
Blocpdb> 189 atoms in block 100
Block first atom: 17987
Blocpdb> 198 atoms in block 101
Block first atom: 18176
Blocpdb> 191 atoms in block 102
Block first atom: 18374
Blocpdb> 191 atoms in block 103
Block first atom: 18565
Blocpdb> 193 atoms in block 104
Block first atom: 18756
Blocpdb> 199 atoms in block 105
Block first atom: 18949
Blocpdb> 183 atoms in block 106
Block first atom: 19148
Blocpdb> 189 atoms in block 107
Block first atom: 19331
Blocpdb> 179 atoms in block 108
Block first atom: 19520
Blocpdb> 198 atoms in block 109
Block first atom: 19699
Blocpdb> 190 atoms in block 110
Block first atom: 19897
Blocpdb> 190 atoms in block 111
Block first atom: 20087
Blocpdb> 176 atoms in block 112
Block first atom: 20277
Blocpdb> 186 atoms in block 113
Block first atom: 20453
Blocpdb> 191 atoms in block 114
Block first atom: 20639
Blocpdb> 189 atoms in block 115
Block first atom: 20830
Blocpdb> 196 atoms in block 116
Block first atom: 21019
Blocpdb> 186 atoms in block 117
Block first atom: 21215
Blocpdb> 193 atoms in block 118
Block first atom: 21401
Blocpdb> 181 atoms in block 119
Block first atom: 21594
Blocpdb> 145 atoms in block 120
Block first atom: 21775
Blocpdb> 184 atoms in block 121
Block first atom: 21920
Blocpdb> 184 atoms in block 122
Block first atom: 22104
Blocpdb> 174 atoms in block 123
Block first atom: 22288
Blocpdb> 180 atoms in block 124
Block first atom: 22462
Blocpdb> 191 atoms in block 125
Block first atom: 22642
Blocpdb> 179 atoms in block 126
Block first atom: 22833
Blocpdb> 175 atoms in block 127
Block first atom: 23012
Blocpdb> 183 atoms in block 128
Block first atom: 23187
Blocpdb> 177 atoms in block 129
Block first atom: 23370
Blocpdb> 171 atoms in block 130
Block first atom: 23547
Blocpdb> 176 atoms in block 131
Block first atom: 23718
Blocpdb> 188 atoms in block 132
Block first atom: 23894
Blocpdb> 189 atoms in block 133
Block first atom: 24082
Blocpdb> 176 atoms in block 134
Block first atom: 24271
Blocpdb> 188 atoms in block 135
Block first atom: 24447
Blocpdb> 189 atoms in block 136
Block first atom: 24635
Blocpdb> 194 atoms in block 137
Block first atom: 24824
Blocpdb> 190 atoms in block 138
Block first atom: 25018
Blocpdb> 199 atoms in block 139
Block first atom: 25208
Blocpdb> 183 atoms in block 140
Block first atom: 25407
Blocpdb> 177 atoms in block 141
Block first atom: 25590
Blocpdb> 175 atoms in block 142
Block first atom: 25767
Blocpdb> 185 atoms in block 143
Block first atom: 25942
Blocpdb> 181 atoms in block 144
Block first atom: 26127
Blocpdb> 171 atoms in block 145
Block first atom: 26308
Blocpdb> 187 atoms in block 146
Block first atom: 26479
Blocpdb> 165 atoms in block 147
Block first atom: 26666
Blocpdb> 181 atoms in block 148
Block first atom: 26831
Blocpdb> 184 atoms in block 149
Block first atom: 27012
Blocpdb> 170 atoms in block 150
Block first atom: 27196
Blocpdb> 177 atoms in block 151
Block first atom: 27366
Blocpdb> 171 atoms in block 152
Block first atom: 27543
Blocpdb> 179 atoms in block 153
Block first atom: 27714
Blocpdb> 202 atoms in block 154
Block first atom: 27893
Blocpdb> 176 atoms in block 155
Block first atom: 28095
Blocpdb> 175 atoms in block 156
Block first atom: 28271
Blocpdb> 195 atoms in block 157
Block first atom: 28446
Blocpdb> 181 atoms in block 158
Block first atom: 28641
Blocpdb> 193 atoms in block 159
Block first atom: 28822
Blocpdb> 188 atoms in block 160
Block first atom: 29015
Blocpdb> 178 atoms in block 161
Block first atom: 29203
Blocpdb> 179 atoms in block 162
Block first atom: 29381
Blocpdb> 194 atoms in block 163
Block first atom: 29560
Blocpdb> 185 atoms in block 164
Block first atom: 29754
Blocpdb> 182 atoms in block 165
Block first atom: 29939
Blocpdb> 167 atoms in block 166
Block first atom: 30121
Blocpdb> 172 atoms in block 167
Block first atom: 30288
Blocpdb> 180 atoms in block 168
Block first atom: 30460
Blocpdb> 178 atoms in block 169
Block first atom: 30640
Blocpdb> 175 atoms in block 170
Block first atom: 30818
Blocpdb> 199 atoms in block 171
Block first atom: 30993
Blocpdb> 189 atoms in block 172
Block first atom: 31192
Blocpdb> 155 atoms in block 173
Block first atom: 31381
Blocpdb> 200 atoms in block 174
Block first atom: 31536
Blocpdb> 197 atoms in block 175
Block first atom: 31736
Blocpdb> 170 atoms in block 176
Block first atom: 31933
Blocpdb> 200 atoms in block 177
Block first atom: 32103
Blocpdb> 196 atoms in block 178
Block first atom: 32303
Blocpdb> 184 atoms in block 179
Block first atom: 32499
Blocpdb> 178 atoms in block 180
Block first atom: 32683
Blocpdb> 195 atoms in block 181
Block first atom: 32861
Blocpdb> 197 atoms in block 182
Block first atom: 33056
Blocpdb> 182 atoms in block 183
Block first atom: 33253
Blocpdb> 194 atoms in block 184
Block first atom: 33435
Blocpdb> 187 atoms in block 185
Block first atom: 33629
Blocpdb> 197 atoms in block 186
Block first atom: 33816
Blocpdb> 200 atoms in block 187
Block first atom: 34013
Blocpdb> 201 atoms in block 188
Block first atom: 34213
Blocpdb> 194 atoms in block 189
Block first atom: 34414
Blocpdb> 205 atoms in block 190
Block first atom: 34608
Blocpdb> 179 atoms in block 191
Block first atom: 34813
Blocpdb> 195 atoms in block 192
Block first atom: 34992
Blocpdb> 169 atoms in block 193
Block first atom: 35187
Blocpdb> 196 atoms in block 194
Block first atom: 35356
Blocpdb> 198 atoms in block 195
Block first atom: 35552
Blocpdb> 195 atoms in block 196
Block first atom: 35750
Blocpdb> 139 atoms in block 197
Block first atom: 35944
Blocpdb> 197 blocks.
Blocpdb> At most, 205 atoms in each of them.
Blocpdb> At least, 139 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: 66951361 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 0m0.204s
user 0m0.197s
sys 0m0.006s
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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