*** 5m3j modes ***
Output from eigenvector calculation:
STDOUT:
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 = 2610161429001563241.atom
Pdbmat> Distance cutoff = 5.00
Force constant = 10.00
Origin of mass values = CONS
Pdbmat> Levelshift = 1.0E-09
PRINTing level = 2
Pdbmat> Coordinate file 2610161429001563241.atom to be opened.
Openam> File opened: 2610161429001563241.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 = 2215
First residue number = 0
Last residue number = 29
Number of atoms found = 18003
Mean number per residue = 8.1
Pdbmat> Coordinate statistics:
= -70.151413 +/- 20.047073 From: -126.059000 To: -18.134000
= 37.729002 +/- 23.349051 From: -14.993000 To: 94.068000
= -21.432004 +/- 26.804473 From: -91.425000 To: 36.843000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'A ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'A ' is not a well known amino-acid.
%Pdbmat-W> residue:'C ' is not a well known amino-acid.
%Pdbmat-W> residue:'C ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'C ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 28 residue(s) not known.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is -0.2894 % Filled.
Pdbmat> 1994082 non-zero elements.
Pdbmat> 209611 atom-atom interactions.
Pdbmat> Number per atom= 23.29 +/- 6.60
Maximum number = 44
Minimum number = 3
Pdbmat> Matrix trace = 4.192220E+06
Pdbmat> Larger element = 168.346
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
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 = 2610161429001563241.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 10
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 2610161429001563241.atom to be opened.
Openam> file on opening on unit 11:
2610161429001563241.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 18003 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 10 residue(s) per block.
Blocpdb> 2215 residues.
Blocpdb> 85 atoms in block 1
Block first atom: 1
Blocpdb> 79 atoms in block 2
Block first atom: 86
Blocpdb> 79 atoms in block 3
Block first atom: 165
Blocpdb> 78 atoms in block 4
Block first atom: 244
Blocpdb> 80 atoms in block 5
Block first atom: 322
Blocpdb> 82 atoms in block 6
Block first atom: 402
Blocpdb> 29 atoms in block 7
Block first atom: 484
Blocpdb> 88 atoms in block 8
Block first atom: 513
Blocpdb> 81 atoms in block 9
Block first atom: 601
Blocpdb> 78 atoms in block 10
Block first atom: 682
Blocpdb> 81 atoms in block 11
Block first atom: 760
Blocpdb> 95 atoms in block 12
Block first atom: 841
Blocpdb> 68 atoms in block 13
Block first atom: 936
Blocpdb> 94 atoms in block 14
Block first atom: 1004
Blocpdb> 84 atoms in block 15
Block first atom: 1098
Blocpdb> 80 atoms in block 16
Block first atom: 1182
Blocpdb> 75 atoms in block 17
Block first atom: 1262
Blocpdb> 80 atoms in block 18
Block first atom: 1337
Blocpdb> 85 atoms in block 19
Block first atom: 1417
Blocpdb> 75 atoms in block 20
Block first atom: 1502
Blocpdb> 81 atoms in block 21
Block first atom: 1577
Blocpdb> 75 atoms in block 22
Block first atom: 1658
Blocpdb> 83 atoms in block 23
Block first atom: 1733
Blocpdb> 74 atoms in block 24
Block first atom: 1816
Blocpdb> 79 atoms in block 25
Block first atom: 1890
Blocpdb> 83 atoms in block 26
Block first atom: 1969
Blocpdb> 83 atoms in block 27
Block first atom: 2052
Blocpdb> 85 atoms in block 28
Block first atom: 2135
Blocpdb> 75 atoms in block 29
Block first atom: 2220
Blocpdb> 73 atoms in block 30
Block first atom: 2295
Blocpdb> 77 atoms in block 31
Block first atom: 2368
Blocpdb> 86 atoms in block 32
Block first atom: 2445
Blocpdb> 80 atoms in block 33
Block first atom: 2531
Blocpdb> 94 atoms in block 34
Block first atom: 2611
Blocpdb> 78 atoms in block 35
Block first atom: 2705
Blocpdb> 81 atoms in block 36
Block first atom: 2783
Blocpdb> 76 atoms in block 37
Block first atom: 2864
Blocpdb> 83 atoms in block 38
Block first atom: 2940
Blocpdb> 81 atoms in block 39
Block first atom: 3023
Blocpdb> 77 atoms in block 40
Block first atom: 3104
Blocpdb> 83 atoms in block 41
Block first atom: 3181
Blocpdb> 75 atoms in block 42
Block first atom: 3264
Blocpdb> 70 atoms in block 43
Block first atom: 3339
Blocpdb> 83 atoms in block 44
Block first atom: 3409
Blocpdb> 90 atoms in block 45
Block first atom: 3492
Blocpdb> 77 atoms in block 46
Block first atom: 3582
Blocpdb> 81 atoms in block 47
Block first atom: 3659
Blocpdb> 75 atoms in block 48
Block first atom: 3740
Blocpdb> 78 atoms in block 49
Block first atom: 3815
Blocpdb> 79 atoms in block 50
Block first atom: 3893
Blocpdb> 76 atoms in block 51
Block first atom: 3972
Blocpdb> 77 atoms in block 52
Block first atom: 4048
Blocpdb> 77 atoms in block 53
Block first atom: 4125
Blocpdb> 91 atoms in block 54
Block first atom: 4202
Blocpdb> 74 atoms in block 55
Block first atom: 4293
Blocpdb> 86 atoms in block 56
Block first atom: 4367
Blocpdb> 80 atoms in block 57
Block first atom: 4453
Blocpdb> 81 atoms in block 58
Block first atom: 4533
Blocpdb> 81 atoms in block 59
Block first atom: 4614
Blocpdb> 77 atoms in block 60
Block first atom: 4695
Blocpdb> 78 atoms in block 61
Block first atom: 4772
Blocpdb> 74 atoms in block 62
Block first atom: 4850
Blocpdb> 71 atoms in block 63
Block first atom: 4924
Blocpdb> 81 atoms in block 64
Block first atom: 4995
Blocpdb> 82 atoms in block 65
Block first atom: 5076
Blocpdb> 80 atoms in block 66
Block first atom: 5158
Blocpdb> 79 atoms in block 67
Block first atom: 5238
Blocpdb> 88 atoms in block 68
Block first atom: 5317
Blocpdb> 74 atoms in block 69
Block first atom: 5405
Blocpdb> 78 atoms in block 70
Block first atom: 5479
Blocpdb> 100 atoms in block 71
Block first atom: 5557
Blocpdb> 74 atoms in block 72
Block first atom: 5657
Blocpdb> 17 atoms in block 73
Block first atom: 5731
Blocpdb> 89 atoms in block 74
Block first atom: 5748
Blocpdb> 70 atoms in block 75
Block first atom: 5837
Blocpdb> 81 atoms in block 76
Block first atom: 5907
Blocpdb> 69 atoms in block 77
Block first atom: 5988
Blocpdb> 85 atoms in block 78
Block first atom: 6057
Blocpdb> 80 atoms in block 79
Block first atom: 6142
Blocpdb> 69 atoms in block 80
Block first atom: 6222
Blocpdb> 73 atoms in block 81
Block first atom: 6291
Blocpdb> 77 atoms in block 82
Block first atom: 6364
Blocpdb> 83 atoms in block 83
Block first atom: 6441
Blocpdb> 70 atoms in block 84
Block first atom: 6524
Blocpdb> 76 atoms in block 85
Block first atom: 6594
Blocpdb> 83 atoms in block 86
Block first atom: 6670
Blocpdb> 79 atoms in block 87
Block first atom: 6753
Blocpdb> 74 atoms in block 88
Block first atom: 6832
Blocpdb> 77 atoms in block 89
Block first atom: 6906
Blocpdb> 73 atoms in block 90
Block first atom: 6983
Blocpdb> 80 atoms in block 91
Block first atom: 7056
Blocpdb> 87 atoms in block 92
Block first atom: 7136
Blocpdb> 80 atoms in block 93
Block first atom: 7223
Blocpdb> 84 atoms in block 94
Block first atom: 7303
Blocpdb> 89 atoms in block 95
Block first atom: 7387
Blocpdb> 74 atoms in block 96
Block first atom: 7476
Blocpdb> 82 atoms in block 97
Block first atom: 7550
Blocpdb> 69 atoms in block 98
Block first atom: 7632
Blocpdb> 79 atoms in block 99
Block first atom: 7701
Blocpdb> 75 atoms in block 100
Block first atom: 7780
Blocpdb> 70 atoms in block 101
Block first atom: 7855
Blocpdb> 73 atoms in block 102
Block first atom: 7925
Blocpdb> 64 atoms in block 103
Block first atom: 7998
Blocpdb> 79 atoms in block 104
Block first atom: 8062
Blocpdb> 81 atoms in block 105
Block first atom: 8141
Blocpdb> 82 atoms in block 106
Block first atom: 8222
Blocpdb> 88 atoms in block 107
Block first atom: 8304
Blocpdb> 80 atoms in block 108
Block first atom: 8392
Blocpdb> 74 atoms in block 109
Block first atom: 8472
Blocpdb> 79 atoms in block 110
Block first atom: 8546
Blocpdb> 83 atoms in block 111
Block first atom: 8625
Blocpdb> 87 atoms in block 112
Block first atom: 8708
Blocpdb> 85 atoms in block 113
Block first atom: 8795
Blocpdb> 67 atoms in block 114
Block first atom: 8880
Blocpdb> 75 atoms in block 115
Block first atom: 8947
Blocpdb> 66 atoms in block 116
Block first atom: 9022
Blocpdb> 84 atoms in block 117
Block first atom: 9088
Blocpdb> 79 atoms in block 118
Block first atom: 9172
Blocpdb> 78 atoms in block 119
Block first atom: 9251
Blocpdb> 84 atoms in block 120
Block first atom: 9329
Blocpdb> 77 atoms in block 121
Block first atom: 9413
Blocpdb> 80 atoms in block 122
Block first atom: 9490
Blocpdb> 89 atoms in block 123
Block first atom: 9570
Blocpdb> 75 atoms in block 124
Block first atom: 9659
Blocpdb> 66 atoms in block 125
Block first atom: 9734
Blocpdb> 73 atoms in block 126
Block first atom: 9800
Blocpdb> 71 atoms in block 127
Block first atom: 9873
Blocpdb> 74 atoms in block 128
Block first atom: 9944
Blocpdb> 90 atoms in block 129
Block first atom: 10018
Blocpdb> 77 atoms in block 130
Block first atom: 10108
Blocpdb> 93 atoms in block 131
Block first atom: 10185
Blocpdb> 74 atoms in block 132
Block first atom: 10278
Blocpdb> 72 atoms in block 133
Block first atom: 10352
Blocpdb> 84 atoms in block 134
Block first atom: 10424
Blocpdb> 90 atoms in block 135
Block first atom: 10508
Blocpdb> 83 atoms in block 136
Block first atom: 10598
Blocpdb> 43 atoms in block 137
Block first atom: 10681
Blocpdb> 74 atoms in block 138
Block first atom: 10724
Blocpdb> 93 atoms in block 139
Block first atom: 10798
Blocpdb> 83 atoms in block 140
Block first atom: 10891
Blocpdb> 79 atoms in block 141
Block first atom: 10974
Blocpdb> 77 atoms in block 142
Block first atom: 11053
Blocpdb> 81 atoms in block 143
Block first atom: 11130
Blocpdb> 83 atoms in block 144
Block first atom: 11211
Blocpdb> 79 atoms in block 145
Block first atom: 11294
Blocpdb> 84 atoms in block 146
Block first atom: 11373
Blocpdb> 52 atoms in block 147
Block first atom: 11457
Blocpdb> 79 atoms in block 148
Block first atom: 11509
Blocpdb> 82 atoms in block 149
Block first atom: 11588
Blocpdb> 83 atoms in block 150
Block first atom: 11670
Blocpdb> 87 atoms in block 151
Block first atom: 11753
Blocpdb> 83 atoms in block 152
Block first atom: 11840
Blocpdb> 78 atoms in block 153
Block first atom: 11923
Blocpdb> 76 atoms in block 154
Block first atom: 12001
Blocpdb> 83 atoms in block 155
Block first atom: 12077
Blocpdb> 69 atoms in block 156
Block first atom: 12160
Blocpdb> 75 atoms in block 157
Block first atom: 12229
Blocpdb> 79 atoms in block 158
Block first atom: 12304
Blocpdb> 89 atoms in block 159
Block first atom: 12383
Blocpdb> 87 atoms in block 160
Block first atom: 12472
Blocpdb> 80 atoms in block 161
Block first atom: 12559
Blocpdb> 89 atoms in block 162
Block first atom: 12639
Blocpdb> 79 atoms in block 163
Block first atom: 12728
Blocpdb> 78 atoms in block 164
Block first atom: 12807
Blocpdb> 75 atoms in block 165
Block first atom: 12885
Blocpdb> 93 atoms in block 166
Block first atom: 12960
Blocpdb> 82 atoms in block 167
Block first atom: 13053
Blocpdb> 79 atoms in block 168
Block first atom: 13135
Blocpdb> 92 atoms in block 169
Block first atom: 13214
Blocpdb> 66 atoms in block 170
Block first atom: 13306
Blocpdb> 79 atoms in block 171
Block first atom: 13372
Blocpdb> 87 atoms in block 172
Block first atom: 13451
Blocpdb> 79 atoms in block 173
Block first atom: 13538
Blocpdb> 81 atoms in block 174
Block first atom: 13617
Blocpdb> 75 atoms in block 175
Block first atom: 13698
Blocpdb> 73 atoms in block 176
Block first atom: 13773
Blocpdb> 76 atoms in block 177
Block first atom: 13846
Blocpdb> 60 atoms in block 178
Block first atom: 13922
Blocpdb> 74 atoms in block 179
Block first atom: 13982
Blocpdb> 93 atoms in block 180
Block first atom: 14056
Blocpdb> 81 atoms in block 181
Block first atom: 14149
Blocpdb> 79 atoms in block 182
Block first atom: 14230
Blocpdb> 79 atoms in block 183
Block first atom: 14309
Blocpdb> 80 atoms in block 184
Block first atom: 14388
Blocpdb> 79 atoms in block 185
Block first atom: 14468
Blocpdb> 81 atoms in block 186
Block first atom: 14547
Blocpdb> 83 atoms in block 187
Block first atom: 14628
Blocpdb> 78 atoms in block 188
Block first atom: 14711
Blocpdb> 82 atoms in block 189
Block first atom: 14789
Blocpdb> 80 atoms in block 190
Block first atom: 14871
Blocpdb> 93 atoms in block 191
Block first atom: 14951
Blocpdb> 85 atoms in block 192
Block first atom: 15044
Blocpdb> 81 atoms in block 193
Block first atom: 15129
Blocpdb> 78 atoms in block 194
Block first atom: 15210
Blocpdb> 73 atoms in block 195
Block first atom: 15288
Blocpdb> 40 atoms in block 196
Block first atom: 15361
Blocpdb> 76 atoms in block 197
Block first atom: 15401
Blocpdb> 75 atoms in block 198
Block first atom: 15477
Blocpdb> 75 atoms in block 199
Block first atom: 15552
Blocpdb> 79 atoms in block 200
Block first atom: 15627
Blocpdb> 84 atoms in block 201
Block first atom: 15706
Blocpdb> 89 atoms in block 202
Block first atom: 15790
Blocpdb> 81 atoms in block 203
Block first atom: 15879
Blocpdb> 88 atoms in block 204
Block first atom: 15960
Blocpdb> 80 atoms in block 205
Block first atom: 16048
Blocpdb> 73 atoms in block 206
Block first atom: 16128
Blocpdb> 84 atoms in block 207
Block first atom: 16201
Blocpdb> 85 atoms in block 208
Block first atom: 16285
Blocpdb> 81 atoms in block 209
Block first atom: 16370
Blocpdb> 81 atoms in block 210
Block first atom: 16451
Blocpdb> 77 atoms in block 211
Block first atom: 16532
Blocpdb> 80 atoms in block 212
Block first atom: 16609
Blocpdb> 81 atoms in block 213
Block first atom: 16689
Blocpdb> 76 atoms in block 214
Block first atom: 16770
Blocpdb> 79 atoms in block 215
Block first atom: 16846
Blocpdb> 76 atoms in block 216
Block first atom: 16925
Blocpdb> 74 atoms in block 217
Block first atom: 17001
Blocpdb> 79 atoms in block 218
Block first atom: 17075
Blocpdb> 81 atoms in block 219
Block first atom: 17154
Blocpdb> 78 atoms in block 220
Block first atom: 17235
Blocpdb> 39 atoms in block 221
Block first atom: 17313
Blocpdb> 202 atoms in block 222
Block first atom: 17352
Blocpdb> 80 atoms in block 223
Block first atom: 17554
Blocpdb> 217 atoms in block 224
Block first atom: 17634
Blocpdb> 90 atoms in block 225
Block first atom: 17851
Blocpdb> 38 atoms in block 226
Block first atom: 17941
Blocpdb> 25 atoms in block 227
Block first atom: 17978
Blocpdb> 227 blocks.
Blocpdb> At most, 217 atoms in each of them.
Blocpdb> At least, 17 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: 35583661 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 0m0.102s
user 0m0.096s
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: april 24th, 2026.
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