*** ***
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 = 2602241108571321913.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 2602241108571321913.atom to be opened.
Openam> File opened: 2602241108571321913.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 = 926
First residue number = 1
Last residue number = 215
Number of atoms found = 60342
Mean number per residue = 65.2
Pdbmat> Coordinate statistics:
= -14.319443 +/- 35.398184 From: -77.547000 To: 48.727000
= -32.522992 +/- 34.672554 From: -95.083000 To: 30.676000
= -1.502140 +/- 14.903465 From: -86.877000 To: 83.086000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'HIE ' is not a well known amino-acid.
%Pdbmat-W> residue:'HIE ' is not a well known amino-acid.
%Pdbmat-W> residue:'HIE ' is not a well known amino-acid.
%Pdbmat-W> residue:'HIE ' is not a well known amino-acid.
%Pdbmat-W> residue:'Na+ ' is not a well known amino-acid.
%Pdbmat-W> residue:'Na+ ' is not a well known amino-acid.
%Pdbmat-W> residue:'Na+ ' is not a well known amino-acid.
%Pdbmat-W> residue:'Na+ ' is not a well known amino-acid.
%Pdbmat-W> residue:'Na+ ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 743 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 -6.2326 % Filled.
Pdbmat> 49522165 non-zero elements.
Pdbmat> 5463164 atom-atom interactions.
Pdbmat> Number per atom= 181.07 +/- 51.42
Maximum number = 353
Minimum number = 0
Pdbmat> Matrix trace = 1.092633E+08
Pdbmat> Larger element = 1345.24
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
926 non-zero elements, NRBL set to 5
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 = 2602241108571321913.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 5
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 2602241108571321913.atom to be opened.
Openam> file on opening on unit 11:
2602241108571321913.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 60342 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 5 residue(s) per block.
Blocpdb> 926 residues.
Blocpdb> 68 atoms in block 1
Block first atom: 1
Blocpdb> 81 atoms in block 2
Block first atom: 69
Blocpdb> 77 atoms in block 3
Block first atom: 150
Blocpdb> 83 atoms in block 4
Block first atom: 227
Blocpdb> 78 atoms in block 5
Block first atom: 310
Blocpdb> 69 atoms in block 6
Block first atom: 388
Blocpdb> 84 atoms in block 7
Block first atom: 457
Blocpdb> 91 atoms in block 8
Block first atom: 541
Blocpdb> 69 atoms in block 9
Block first atom: 632
Blocpdb> 87 atoms in block 10
Block first atom: 701
Blocpdb> 78 atoms in block 11
Block first atom: 788
Blocpdb> 66 atoms in block 12
Block first atom: 866
Blocpdb> 83 atoms in block 13
Block first atom: 932
Blocpdb> 87 atoms in block 14
Block first atom: 1015
Blocpdb> 68 atoms in block 15
Block first atom: 1102
Blocpdb> 77 atoms in block 16
Block first atom: 1170
Blocpdb> 86 atoms in block 17
Block first atom: 1247
Blocpdb> 71 atoms in block 18
Block first atom: 1333
Blocpdb> 69 atoms in block 19
Block first atom: 1404
Blocpdb> 80 atoms in block 20
Block first atom: 1473
Blocpdb> 100 atoms in block 21
Block first atom: 1553
Blocpdb> 93 atoms in block 22
Block first atom: 1653
Blocpdb> 84 atoms in block 23
Block first atom: 1746
Blocpdb> 78 atoms in block 24
Block first atom: 1830
Blocpdb> 73 atoms in block 25
Block first atom: 1908
Blocpdb> 66 atoms in block 26
Block first atom: 1981
Blocpdb> 90 atoms in block 27
Block first atom: 2047
Blocpdb> 63 atoms in block 28
Block first atom: 2137
Blocpdb> 50 atoms in block 29
Block first atom: 2200
Blocpdb> 75 atoms in block 30
Block first atom: 2250
Blocpdb> 44 atoms in block 31
Block first atom: 2325
Blocpdb> 5 atoms in block 32
Block first atom: 2369
Blocpdb> 5 atoms in block 33
Block first atom: 2374
Blocpdb> 5 atoms in block 34
Block first atom: 2379
Blocpdb> 5 atoms in block 35
Block first atom: 2384
Blocpdb> 5 atoms in block 36
Block first atom: 2389
Blocpdb> 5 atoms in block 37
Block first atom: 2394
Blocpdb> 5 atoms in block 38
Block first atom: 2399
Blocpdb> 5 atoms in block 39
Block first atom: 2404
Blocpdb> 5 atoms in block 40
Block first atom: 2409
Blocpdb> 5 atoms in block 41
Block first atom: 2414
Blocpdb> 5 atoms in block 42
Block first atom: 2419
Blocpdb> 5 atoms in block 43
Block first atom: 2424
Blocpdb> 5 atoms in block 44
Block first atom: 2429
Blocpdb> 5 atoms in block 45
Block first atom: 2434
Blocpdb> 5 atoms in block 46
Block first atom: 2439
Blocpdb> 4 atoms in block 47
Block first atom: 2444
Blocpdb> 5 atoms in block 48
Block first atom: 2448
Blocpdb> 5 atoms in block 49
Block first atom: 2453
Blocpdb> 5 atoms in block 50
Block first atom: 2458
Blocpdb> 5 atoms in block 51
Block first atom: 2463
Blocpdb> 5 atoms in block 52
Block first atom: 2468
Blocpdb> 5 atoms in block 53
Block first atom: 2473
Blocpdb> 5 atoms in block 54
Block first atom: 2478
Blocpdb> 5 atoms in block 55
Block first atom: 2483
Blocpdb> 5 atoms in block 56
Block first atom: 2488
Blocpdb> 5 atoms in block 57
Block first atom: 2493
Blocpdb> 5 atoms in block 58
Block first atom: 2498
Blocpdb> 5 atoms in block 59
Block first atom: 2503
Blocpdb> 5 atoms in block 60
Block first atom: 2508
Blocpdb> 5 atoms in block 61
Block first atom: 2513
Blocpdb> 5 atoms in block 62
Block first atom: 2518
Blocpdb> 5 atoms in block 63
Block first atom: 2523
Blocpdb> 5 atoms in block 64
Block first atom: 2528
Blocpdb> 5 atoms in block 65
Block first atom: 2533
Blocpdb> 5 atoms in block 66
Block first atom: 2538
Blocpdb> 5 atoms in block 67
Block first atom: 2543
Blocpdb> 5 atoms in block 68
Block first atom: 2548
Blocpdb> 5 atoms in block 69
Block first atom: 2553
Blocpdb> 5 atoms in block 70
Block first atom: 2558
Blocpdb> 5 atoms in block 71
Block first atom: 2563
Blocpdb> 5 atoms in block 72
Block first atom: 2568
Blocpdb> 5 atoms in block 73
Block first atom: 2573
Blocpdb> 5 atoms in block 74
Block first atom: 2578
Blocpdb> 5 atoms in block 75
Block first atom: 2583
Blocpdb> 5 atoms in block 76
Block first atom: 2588
Blocpdb> 5 atoms in block 77
Block first atom: 2593
Blocpdb> 5 atoms in block 78
Block first atom: 2598
%Blocpdb-Wn> 2 atoms in block 79 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 2604th, in residue L 82
%Blocpdb-Wn> It is merged with the previous one.
Blocpdb> 7 atoms in block 78
Blocpdb> 5 atoms in block 79
Block first atom: 2605
Blocpdb> 5 atoms in block 80
Block first atom: 2610
Blocpdb> 5 atoms in block 81
Block first atom: 2615
Blocpdb> 5 atoms in block 82
Block first atom: 2620
Blocpdb> 5 atoms in block 83
Block first atom: 2625
Blocpdb> 5 atoms in block 84
Block first atom: 2630
Blocpdb> 5 atoms in block 85
Block first atom: 2635
Blocpdb> 5 atoms in block 86
Block first atom: 2640
Blocpdb> 5 atoms in block 87
Block first atom: 2645
Blocpdb> 5 atoms in block 88
Block first atom: 2650
Blocpdb> 5 atoms in block 89
Block first atom: 2655
Blocpdb> 5 atoms in block 90
Block first atom: 2660
Blocpdb> 5 atoms in block 91
Block first atom: 2665
Blocpdb> 5 atoms in block 92
Block first atom: 2670
Blocpdb> 5 atoms in block 93
Block first atom: 2675
%Blocpdb-Wn> 2 atoms in block 94 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 2681th, in residue M 77
%Blocpdb-Wn> It is merged with the previous one.
Blocpdb> 7 atoms in block 93
Blocpdb> 82 atoms in block 94
Block first atom: 2682
Blocpdb> 71 atoms in block 95
Block first atom: 2764
Blocpdb> 87 atoms in block 96
Block first atom: 2835
Blocpdb> 97 atoms in block 97
Block first atom: 2922
Blocpdb> 89 atoms in block 98
Block first atom: 3019
Blocpdb> 88 atoms in block 99
Block first atom: 3108
Blocpdb> 63 atoms in block 100
Block first atom: 3196
Blocpdb> 670 atoms in block 101
Block first atom: 3259
Blocpdb> 670 atoms in block 102
Block first atom: 3929
Blocpdb> 670 atoms in block 103
Block first atom: 4599
Blocpdb> 670 atoms in block 104
Block first atom: 5269
Blocpdb> 670 atoms in block 105
Block first atom: 5939
Blocpdb> 670 atoms in block 106
Block first atom: 6609
Blocpdb> 670 atoms in block 107
Block first atom: 7279
Blocpdb> 670 atoms in block 108
Block first atom: 7949
Blocpdb> 670 atoms in block 109
Block first atom: 8619
Blocpdb> 670 atoms in block 110
Block first atom: 9289
Blocpdb> 670 atoms in block 111
Block first atom: 9959
Blocpdb> 670 atoms in block 112
Block first atom: 10629
Blocpdb> 670 atoms in block 113
Block first atom: 11299
Blocpdb> 670 atoms in block 114
Block first atom: 11969
Blocpdb> 670 atoms in block 115
Block first atom: 12639
Blocpdb> 670 atoms in block 116
Block first atom: 13309
Blocpdb> 670 atoms in block 117
Block first atom: 13979
Blocpdb> 670 atoms in block 118
Block first atom: 14649
Blocpdb> 670 atoms in block 119
Block first atom: 15319
Blocpdb> 670 atoms in block 120
Block first atom: 15989
Blocpdb> 670 atoms in block 121
Block first atom: 16659
Blocpdb> 670 atoms in block 122
Block first atom: 17329
Blocpdb> 670 atoms in block 123
Block first atom: 17999
Blocpdb> 670 atoms in block 124
Block first atom: 18669
Blocpdb> 670 atoms in block 125
Block first atom: 19339
Blocpdb> 670 atoms in block 126
Block first atom: 20009
Blocpdb> 670 atoms in block 127
Block first atom: 20679
Blocpdb> 670 atoms in block 128
Block first atom: 21349
Blocpdb> 670 atoms in block 129
Block first atom: 22019
Blocpdb> 670 atoms in block 130
Block first atom: 22689
Blocpdb> 670 atoms in block 131
Block first atom: 23359
Blocpdb> 670 atoms in block 132
Block first atom: 24029
Blocpdb> 670 atoms in block 133
Block first atom: 24699
Blocpdb> 670 atoms in block 134
Block first atom: 25369
Blocpdb> 670 atoms in block 135
Block first atom: 26039
Blocpdb> 670 atoms in block 136
Block first atom: 26709
Blocpdb> 670 atoms in block 137
Block first atom: 27379
Blocpdb> 670 atoms in block 138
Block first atom: 28049
Blocpdb> 670 atoms in block 139
Block first atom: 28719
Blocpdb> 670 atoms in block 140
Block first atom: 29389
Blocpdb> 670 atoms in block 141
Block first atom: 30059
Blocpdb> 670 atoms in block 142
Block first atom: 30729
Blocpdb> 134 atoms in block 143
Block first atom: 31399
Blocpdb> 670 atoms in block 144
Block first atom: 31533
Blocpdb> 670 atoms in block 145
Block first atom: 32203
Blocpdb> 670 atoms in block 146
Block first atom: 32873
Blocpdb> 670 atoms in block 147
Block first atom: 33543
Blocpdb> 670 atoms in block 148
Block first atom: 34213
Blocpdb> 670 atoms in block 149
Block first atom: 34883
Blocpdb> 670 atoms in block 150
Block first atom: 35553
Blocpdb> 670 atoms in block 151
Block first atom: 36223
Blocpdb> 670 atoms in block 152
Block first atom: 36893
Blocpdb> 670 atoms in block 153
Block first atom: 37563
Blocpdb> 670 atoms in block 154
Block first atom: 38233
Blocpdb> 670 atoms in block 155
Block first atom: 38903
Blocpdb> 670 atoms in block 156
Block first atom: 39573
Blocpdb> 670 atoms in block 157
Block first atom: 40243
Blocpdb> 670 atoms in block 158
Block first atom: 40913
Blocpdb> 670 atoms in block 159
Block first atom: 41583
Blocpdb> 670 atoms in block 160
Block first atom: 42253
Blocpdb> 670 atoms in block 161
Block first atom: 42923
Blocpdb> 670 atoms in block 162
Block first atom: 43593
Blocpdb> 670 atoms in block 163
Block first atom: 44263
Blocpdb> 670 atoms in block 164
Block first atom: 44933
Blocpdb> 670 atoms in block 165
Block first atom: 45603
Blocpdb> 670 atoms in block 166
Block first atom: 46273
Blocpdb> 670 atoms in block 167
Block first atom: 46943
Blocpdb> 670 atoms in block 168
Block first atom: 47613
Blocpdb> 670 atoms in block 169
Block first atom: 48283
Blocpdb> 670 atoms in block 170
Block first atom: 48953
Blocpdb> 670 atoms in block 171
Block first atom: 49623
Blocpdb> 670 atoms in block 172
Block first atom: 50293
Blocpdb> 670 atoms in block 173
Block first atom: 50963
Blocpdb> 670 atoms in block 174
Block first atom: 51633
Blocpdb> 670 atoms in block 175
Block first atom: 52303
Blocpdb> 670 atoms in block 176
Block first atom: 52973
Blocpdb> 670 atoms in block 177
Block first atom: 53643
Blocpdb> 670 atoms in block 178
Block first atom: 54313
Blocpdb> 670 atoms in block 179
Block first atom: 54983
Blocpdb> 670 atoms in block 180
Block first atom: 55653
Blocpdb> 670 atoms in block 181
Block first atom: 56323
Blocpdb> 670 atoms in block 182
Block first atom: 56993
Blocpdb> 670 atoms in block 183
Block first atom: 57663
Blocpdb> 670 atoms in block 184
Block first atom: 58333
Blocpdb> 670 atoms in block 185
Block first atom: 59003
Blocpdb> 670 atoms in block 186
Block first atom: 59672
Blocpdb> 186 blocks.
Blocpdb> At most, 670 atoms in each of them.
Blocpdb> At least, 4 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> IIWKMX up to: 8180201 Maximum allowed is LIWORK= 5000000
%Diagrtb-Er> IRWKMX up to: 367902361 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 0m0.259s
user 0m0.246s
sys 0m0.013s
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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