*** ***
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 = 2406101742312107824.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 2406101742312107824.atom to be opened.
Openam> File opened: 2406101742312107824.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 = 2416
First residue number = 1
Last residue number = 35
Number of atoms found = 22586
Mean number per residue = 9.3
Pdbmat> Coordinate statistics:
= -0.783175 +/- 34.256482 From: -96.061000 To: 99.273000
= -0.566368 +/- 31.714810 From: -65.119000 To: 111.054000
= -0.740491 +/- 26.392168 From: -62.623000 To: 63.394000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'DC ' is not a well known amino-acid.
%Pdbmat-W> residue:'DA ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> residue:'DG ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> residue:'DC ' is not a well known amino-acid.
%Pdbmat-W> residue:'DA ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 236 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 5.6913 % Filled.
Pdbmat> 8430186 non-zero elements.
Pdbmat> 921790 atom-atom interactions.
Pdbmat> Number per atom= 81.62 +/- 22.38
Maximum number = 143
Minimum number = 10
Pdbmat> Matrix trace = 1.843580E+07
Pdbmat> Larger element = 537.671
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2416 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 = 2406101742312107824.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 2406101742312107824.atom to be opened.
Openam> file on opening on unit 11:
2406101742312107824.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 22586 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> 2416 residues.
Blocpdb> 106 atoms in block 1
Block first atom: 1
Blocpdb> 112 atoms in block 2
Block first atom: 107
Blocpdb> 108 atoms in block 3
Block first atom: 219
Blocpdb> 105 atoms in block 4
Block first atom: 327
Blocpdb> 101 atoms in block 5
Block first atom: 432
Blocpdb> 103 atoms in block 6
Block first atom: 533
Blocpdb> 102 atoms in block 7
Block first atom: 636
Blocpdb> 101 atoms in block 8
Block first atom: 738
Blocpdb> 103 atoms in block 9
Block first atom: 839
Blocpdb> 111 atoms in block 10
Block first atom: 942
Blocpdb> 114 atoms in block 11
Block first atom: 1053
Blocpdb> 114 atoms in block 12
Block first atom: 1167
Blocpdb> 105 atoms in block 13
Block first atom: 1281
Blocpdb> 102 atoms in block 14
Block first atom: 1386
Blocpdb> 99 atoms in block 15
Block first atom: 1488
Blocpdb> 103 atoms in block 16
Block first atom: 1587
Blocpdb> 103 atoms in block 17
Block first atom: 1690
Blocpdb> 107 atoms in block 18
Block first atom: 1793
Blocpdb> 107 atoms in block 19
Block first atom: 1900
Blocpdb> 111 atoms in block 20
Block first atom: 2007
Blocpdb> 110 atoms in block 21
Block first atom: 2118
Blocpdb> 99 atoms in block 22
Block first atom: 2228
Blocpdb> 108 atoms in block 23
Block first atom: 2327
Blocpdb> 105 atoms in block 24
Block first atom: 2435
Blocpdb> 86 atoms in block 25
Block first atom: 2540
Blocpdb> 113 atoms in block 26
Block first atom: 2626
Blocpdb> 102 atoms in block 27
Block first atom: 2739
Blocpdb> 111 atoms in block 28
Block first atom: 2841
Blocpdb> 101 atoms in block 29
Block first atom: 2952
Blocpdb> 103 atoms in block 30
Block first atom: 3053
Blocpdb> 104 atoms in block 31
Block first atom: 3156
Blocpdb> 108 atoms in block 32
Block first atom: 3260
Blocpdb> 116 atoms in block 33
Block first atom: 3368
Blocpdb> 110 atoms in block 34
Block first atom: 3484
Blocpdb> 110 atoms in block 35
Block first atom: 3594
Blocpdb> 100 atoms in block 36
Block first atom: 3704
Blocpdb> 103 atoms in block 37
Block first atom: 3804
Blocpdb> 107 atoms in block 38
Block first atom: 3907
Blocpdb> 111 atoms in block 39
Block first atom: 4014
Blocpdb> 102 atoms in block 40
Block first atom: 4125
Blocpdb> 109 atoms in block 41
Block first atom: 4227
Blocpdb> 101 atoms in block 42
Block first atom: 4336
Blocpdb> 106 atoms in block 43
Block first atom: 4437
Blocpdb> 112 atoms in block 44
Block first atom: 4543
Blocpdb> 108 atoms in block 45
Block first atom: 4655
Blocpdb> 105 atoms in block 46
Block first atom: 4763
Blocpdb> 101 atoms in block 47
Block first atom: 4868
Blocpdb> 103 atoms in block 48
Block first atom: 4969
Blocpdb> 102 atoms in block 49
Block first atom: 5072
Blocpdb> 101 atoms in block 50
Block first atom: 5174
Blocpdb> 103 atoms in block 51
Block first atom: 5275
Blocpdb> 111 atoms in block 52
Block first atom: 5378
Blocpdb> 114 atoms in block 53
Block first atom: 5489
Blocpdb> 114 atoms in block 54
Block first atom: 5603
Blocpdb> 105 atoms in block 55
Block first atom: 5717
Blocpdb> 102 atoms in block 56
Block first atom: 5822
Blocpdb> 99 atoms in block 57
Block first atom: 5924
Blocpdb> 103 atoms in block 58
Block first atom: 6023
Blocpdb> 103 atoms in block 59
Block first atom: 6126
Blocpdb> 107 atoms in block 60
Block first atom: 6229
Blocpdb> 107 atoms in block 61
Block first atom: 6336
Blocpdb> 111 atoms in block 62
Block first atom: 6443
Blocpdb> 110 atoms in block 63
Block first atom: 6554
Blocpdb> 99 atoms in block 64
Block first atom: 6664
Blocpdb> 108 atoms in block 65
Block first atom: 6763
Blocpdb> 105 atoms in block 66
Block first atom: 6871
Blocpdb> 86 atoms in block 67
Block first atom: 6976
Blocpdb> 113 atoms in block 68
Block first atom: 7062
Blocpdb> 102 atoms in block 69
Block first atom: 7175
Blocpdb> 111 atoms in block 70
Block first atom: 7277
Blocpdb> 101 atoms in block 71
Block first atom: 7388
Blocpdb> 103 atoms in block 72
Block first atom: 7489
Blocpdb> 104 atoms in block 73
Block first atom: 7592
Blocpdb> 108 atoms in block 74
Block first atom: 7696
Blocpdb> 116 atoms in block 75
Block first atom: 7804
Blocpdb> 110 atoms in block 76
Block first atom: 7920
Blocpdb> 110 atoms in block 77
Block first atom: 8030
Blocpdb> 100 atoms in block 78
Block first atom: 8140
Blocpdb> 103 atoms in block 79
Block first atom: 8240
Blocpdb> 107 atoms in block 80
Block first atom: 8343
Blocpdb> 111 atoms in block 81
Block first atom: 8450
Blocpdb> 102 atoms in block 82
Block first atom: 8561
Blocpdb> 109 atoms in block 83
Block first atom: 8663
Blocpdb> 101 atoms in block 84
Block first atom: 8772
Blocpdb> 106 atoms in block 85
Block first atom: 8873
Blocpdb> 112 atoms in block 86
Block first atom: 8979
Blocpdb> 108 atoms in block 87
Block first atom: 9091
Blocpdb> 105 atoms in block 88
Block first atom: 9199
Blocpdb> 101 atoms in block 89
Block first atom: 9304
Blocpdb> 103 atoms in block 90
Block first atom: 9405
Blocpdb> 102 atoms in block 91
Block first atom: 9508
Blocpdb> 101 atoms in block 92
Block first atom: 9610
Blocpdb> 103 atoms in block 93
Block first atom: 9711
Blocpdb> 111 atoms in block 94
Block first atom: 9814
Blocpdb> 114 atoms in block 95
Block first atom: 9925
Blocpdb> 114 atoms in block 96
Block first atom: 10039
Blocpdb> 105 atoms in block 97
Block first atom: 10153
Blocpdb> 102 atoms in block 98
Block first atom: 10258
Blocpdb> 99 atoms in block 99
Block first atom: 10360
Blocpdb> 103 atoms in block 100
Block first atom: 10459
Blocpdb> 103 atoms in block 101
Block first atom: 10562
Blocpdb> 107 atoms in block 102
Block first atom: 10665
Blocpdb> 107 atoms in block 103
Block first atom: 10772
Blocpdb> 111 atoms in block 104
Block first atom: 10879
Blocpdb> 110 atoms in block 105
Block first atom: 10990
Blocpdb> 99 atoms in block 106
Block first atom: 11100
Blocpdb> 108 atoms in block 107
Block first atom: 11199
Blocpdb> 105 atoms in block 108
Block first atom: 11307
Blocpdb> 86 atoms in block 109
Block first atom: 11412
Blocpdb> 113 atoms in block 110
Block first atom: 11498
Blocpdb> 102 atoms in block 111
Block first atom: 11611
Blocpdb> 111 atoms in block 112
Block first atom: 11713
Blocpdb> 101 atoms in block 113
Block first atom: 11824
Blocpdb> 103 atoms in block 114
Block first atom: 11925
Blocpdb> 104 atoms in block 115
Block first atom: 12028
Blocpdb> 108 atoms in block 116
Block first atom: 12132
Blocpdb> 116 atoms in block 117
Block first atom: 12240
Blocpdb> 110 atoms in block 118
Block first atom: 12356
Blocpdb> 110 atoms in block 119
Block first atom: 12466
Blocpdb> 100 atoms in block 120
Block first atom: 12576
Blocpdb> 103 atoms in block 121
Block first atom: 12676
Blocpdb> 107 atoms in block 122
Block first atom: 12779
Blocpdb> 111 atoms in block 123
Block first atom: 12886
Blocpdb> 102 atoms in block 124
Block first atom: 12997
Blocpdb> 109 atoms in block 125
Block first atom: 13099
Blocpdb> 101 atoms in block 126
Block first atom: 13208
Blocpdb> 106 atoms in block 127
Block first atom: 13309
Blocpdb> 112 atoms in block 128
Block first atom: 13415
Blocpdb> 108 atoms in block 129
Block first atom: 13527
Blocpdb> 105 atoms in block 130
Block first atom: 13635
Blocpdb> 101 atoms in block 131
Block first atom: 13740
Blocpdb> 103 atoms in block 132
Block first atom: 13841
Blocpdb> 102 atoms in block 133
Block first atom: 13944
Blocpdb> 101 atoms in block 134
Block first atom: 14046
Blocpdb> 103 atoms in block 135
Block first atom: 14147
Blocpdb> 111 atoms in block 136
Block first atom: 14250
Blocpdb> 114 atoms in block 137
Block first atom: 14361
Blocpdb> 114 atoms in block 138
Block first atom: 14475
Blocpdb> 105 atoms in block 139
Block first atom: 14589
Blocpdb> 102 atoms in block 140
Block first atom: 14694
Blocpdb> 99 atoms in block 141
Block first atom: 14796
Blocpdb> 103 atoms in block 142
Block first atom: 14895
Blocpdb> 103 atoms in block 143
Block first atom: 14998
Blocpdb> 107 atoms in block 144
Block first atom: 15101
Blocpdb> 107 atoms in block 145
Block first atom: 15208
Blocpdb> 111 atoms in block 146
Block first atom: 15315
Blocpdb> 110 atoms in block 147
Block first atom: 15426
Blocpdb> 99 atoms in block 148
Block first atom: 15536
Blocpdb> 108 atoms in block 149
Block first atom: 15635
Blocpdb> 105 atoms in block 150
Block first atom: 15743
Blocpdb> 86 atoms in block 151
Block first atom: 15848
Blocpdb> 113 atoms in block 152
Block first atom: 15934
Blocpdb> 102 atoms in block 153
Block first atom: 16047
Blocpdb> 111 atoms in block 154
Block first atom: 16149
Blocpdb> 101 atoms in block 155
Block first atom: 16260
Blocpdb> 103 atoms in block 156
Block first atom: 16361
Blocpdb> 104 atoms in block 157
Block first atom: 16464
Blocpdb> 108 atoms in block 158
Block first atom: 16568
Blocpdb> 116 atoms in block 159
Block first atom: 16676
Blocpdb> 110 atoms in block 160
Block first atom: 16792
Blocpdb> 110 atoms in block 161
Block first atom: 16902
Blocpdb> 100 atoms in block 162
Block first atom: 17012
Blocpdb> 103 atoms in block 163
Block first atom: 17112
Blocpdb> 107 atoms in block 164
Block first atom: 17215
Blocpdb> 111 atoms in block 165
Block first atom: 17322
Blocpdb> 102 atoms in block 166
Block first atom: 17433
Blocpdb> 109 atoms in block 167
Block first atom: 17535
Blocpdb> 101 atoms in block 168
Block first atom: 17644
Blocpdb> 266 atoms in block 169
Block first atom: 17745
Blocpdb> 266 atoms in block 170
Block first atom: 18011
Blocpdb> 266 atoms in block 171
Block first atom: 18277
Blocpdb> 266 atoms in block 172
Block first atom: 18543
Blocpdb> 267 atoms in block 173
Block first atom: 18809
Blocpdb> 227 atoms in block 174
Block first atom: 19076
Blocpdb> 267 atoms in block 175
Block first atom: 19303
Blocpdb> 227 atoms in block 176
Block first atom: 19570
Blocpdb> 269 atoms in block 177
Block first atom: 19797
Blocpdb> 264 atoms in block 178
Block first atom: 20066
Blocpdb> 147 atoms in block 179
Block first atom: 20330
Blocpdb> 269 atoms in block 180
Block first atom: 20477
Blocpdb> 264 atoms in block 181
Block first atom: 20746
Blocpdb> 147 atoms in block 182
Block first atom: 21010
Blocpdb> 266 atoms in block 183
Block first atom: 21157
Blocpdb> 267 atoms in block 184
Block first atom: 21423
Blocpdb> 182 atoms in block 185
Block first atom: 21690
Blocpdb> 266 atoms in block 186
Block first atom: 21872
Blocpdb> 267 atoms in block 187
Block first atom: 22138
Blocpdb> 182 atoms in block 188
Block first atom: 22404
Blocpdb> 188 blocks.
Blocpdb> At most, 269 atoms in each of them.
Blocpdb> At least, 86 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: 55331956 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 0m0.116s
user 0m0.112s
sys 0m0.004s
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).
Last modification: April 25th, 2023.
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