*** SARS-CoV-1 5 proximal stem-loop 5 ***
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 = 2502181845352492591.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 2502181845352492591.atom to be opened.
Openam> File opened: 2502181845352492591.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 = 2860
First residue number = 150
Last residue number = 292
Number of atoms found = 91400
Mean number per residue = 32.0
Pdbmat> Coordinate statistics:
= 163.318753 +/- 8.566149 From: 135.210000 To: 183.233000
= 162.992780 +/- 17.775493 From: 113.892000 To: 215.777000
= 164.459702 +/- 34.025596 From: 85.737000 To: 216.026000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'G ' is not a well known amino-acid.
%Pdbmat-W> residue:'G ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'G ' 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:'A ' is not a well known amino-acid.
%Pdbmat-W> residue:'A ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 2860 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 -77.3245 % Filled.
Pdbmat> 820992127 non-zero elements.
Pdbmat> 91177427 atom-atom interactions.
Pdbmat> Number per atom= 1995.13 +/- 553.40
Maximum number = 3185
Minimum number = 31
Pdbmat> Matrix trace = 1.823549E+09
Pdbmat> Larger element = 13346.8
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2860 non-zero elements, NRBL set to 15
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 = 2502181845352492591.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 15
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 2502181845352492591.atom to be opened.
Openam> file on opening on unit 11:
2502181845352492591.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 91400 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 15 residue(s) per block.
Blocpdb> 2860 residues.
Blocpdb> 490 atoms in block 1
Block first atom: 1
Blocpdb> 473 atoms in block 2
Block first atom: 491
Blocpdb> 472 atoms in block 3
Block first atom: 964
Blocpdb> 477 atoms in block 4
Block first atom: 1436
Blocpdb> 475 atoms in block 5
Block first atom: 1913
Blocpdb> 477 atoms in block 6
Block first atom: 2388
Blocpdb> 482 atoms in block 7
Block first atom: 2865
Blocpdb> 495 atoms in block 8
Block first atom: 3347
Blocpdb> 476 atoms in block 9
Block first atom: 3842
Blocpdb> 253 atoms in block 10
Block first atom: 4318
Blocpdb> 490 atoms in block 11
Block first atom: 4571
Blocpdb> 473 atoms in block 12
Block first atom: 5061
Blocpdb> 472 atoms in block 13
Block first atom: 5534
Blocpdb> 477 atoms in block 14
Block first atom: 6006
Blocpdb> 475 atoms in block 15
Block first atom: 6483
Blocpdb> 477 atoms in block 16
Block first atom: 6958
Blocpdb> 482 atoms in block 17
Block first atom: 7435
Blocpdb> 495 atoms in block 18
Block first atom: 7917
Blocpdb> 476 atoms in block 19
Block first atom: 8412
Blocpdb> 253 atoms in block 20
Block first atom: 8888
Blocpdb> 490 atoms in block 21
Block first atom: 9141
Blocpdb> 473 atoms in block 22
Block first atom: 9631
Blocpdb> 472 atoms in block 23
Block first atom: 10104
Blocpdb> 477 atoms in block 24
Block first atom: 10576
Blocpdb> 475 atoms in block 25
Block first atom: 11053
Blocpdb> 477 atoms in block 26
Block first atom: 11528
Blocpdb> 482 atoms in block 27
Block first atom: 12005
Blocpdb> 495 atoms in block 28
Block first atom: 12487
Blocpdb> 476 atoms in block 29
Block first atom: 12982
Blocpdb> 253 atoms in block 30
Block first atom: 13458
Blocpdb> 490 atoms in block 31
Block first atom: 13711
Blocpdb> 473 atoms in block 32
Block first atom: 14201
Blocpdb> 472 atoms in block 33
Block first atom: 14674
Blocpdb> 477 atoms in block 34
Block first atom: 15146
Blocpdb> 475 atoms in block 35
Block first atom: 15623
Blocpdb> 477 atoms in block 36
Block first atom: 16098
Blocpdb> 482 atoms in block 37
Block first atom: 16575
Blocpdb> 495 atoms in block 38
Block first atom: 17057
Blocpdb> 476 atoms in block 39
Block first atom: 17552
Blocpdb> 253 atoms in block 40
Block first atom: 18028
Blocpdb> 490 atoms in block 41
Block first atom: 18281
Blocpdb> 473 atoms in block 42
Block first atom: 18771
Blocpdb> 472 atoms in block 43
Block first atom: 19244
Blocpdb> 477 atoms in block 44
Block first atom: 19716
Blocpdb> 475 atoms in block 45
Block first atom: 20193
Blocpdb> 477 atoms in block 46
Block first atom: 20668
Blocpdb> 482 atoms in block 47
Block first atom: 21145
Blocpdb> 495 atoms in block 48
Block first atom: 21627
Blocpdb> 476 atoms in block 49
Block first atom: 22122
Blocpdb> 253 atoms in block 50
Block first atom: 22598
Blocpdb> 490 atoms in block 51
Block first atom: 22851
Blocpdb> 473 atoms in block 52
Block first atom: 23341
Blocpdb> 472 atoms in block 53
Block first atom: 23814
Blocpdb> 477 atoms in block 54
Block first atom: 24286
Blocpdb> 475 atoms in block 55
Block first atom: 24763
Blocpdb> 477 atoms in block 56
Block first atom: 25238
Blocpdb> 482 atoms in block 57
Block first atom: 25715
Blocpdb> 495 atoms in block 58
Block first atom: 26197
Blocpdb> 476 atoms in block 59
Block first atom: 26692
Blocpdb> 253 atoms in block 60
Block first atom: 27168
Blocpdb> 490 atoms in block 61
Block first atom: 27421
Blocpdb> 473 atoms in block 62
Block first atom: 27911
Blocpdb> 472 atoms in block 63
Block first atom: 28384
Blocpdb> 477 atoms in block 64
Block first atom: 28856
Blocpdb> 475 atoms in block 65
Block first atom: 29333
Blocpdb> 477 atoms in block 66
Block first atom: 29808
Blocpdb> 482 atoms in block 67
Block first atom: 30285
Blocpdb> 495 atoms in block 68
Block first atom: 30767
Blocpdb> 476 atoms in block 69
Block first atom: 31262
Blocpdb> 253 atoms in block 70
Block first atom: 31738
Blocpdb> 490 atoms in block 71
Block first atom: 31991
Blocpdb> 473 atoms in block 72
Block first atom: 32481
Blocpdb> 472 atoms in block 73
Block first atom: 32954
Blocpdb> 477 atoms in block 74
Block first atom: 33426
Blocpdb> 475 atoms in block 75
Block first atom: 33903
Blocpdb> 477 atoms in block 76
Block first atom: 34378
Blocpdb> 482 atoms in block 77
Block first atom: 34855
Blocpdb> 495 atoms in block 78
Block first atom: 35337
Blocpdb> 476 atoms in block 79
Block first atom: 35832
Blocpdb> 253 atoms in block 80
Block first atom: 36308
Blocpdb> 490 atoms in block 81
Block first atom: 36561
Blocpdb> 473 atoms in block 82
Block first atom: 37051
Blocpdb> 472 atoms in block 83
Block first atom: 37524
Blocpdb> 477 atoms in block 84
Block first atom: 37996
Blocpdb> 475 atoms in block 85
Block first atom: 38473
Blocpdb> 477 atoms in block 86
Block first atom: 38948
Blocpdb> 482 atoms in block 87
Block first atom: 39425
Blocpdb> 495 atoms in block 88
Block first atom: 39907
Blocpdb> 476 atoms in block 89
Block first atom: 40402
Blocpdb> 253 atoms in block 90
Block first atom: 40878
Blocpdb> 490 atoms in block 91
Block first atom: 41131
Blocpdb> 473 atoms in block 92
Block first atom: 41621
Blocpdb> 472 atoms in block 93
Block first atom: 42094
Blocpdb> 477 atoms in block 94
Block first atom: 42566
Blocpdb> 475 atoms in block 95
Block first atom: 43043
Blocpdb> 477 atoms in block 96
Block first atom: 43518
Blocpdb> 482 atoms in block 97
Block first atom: 43995
Blocpdb> 495 atoms in block 98
Block first atom: 44477
Blocpdb> 476 atoms in block 99
Block first atom: 44972
Blocpdb> 253 atoms in block 100
Block first atom: 45448
Blocpdb> 490 atoms in block 101
Block first atom: 45701
Blocpdb> 473 atoms in block 102
Block first atom: 46191
Blocpdb> 472 atoms in block 103
Block first atom: 46664
Blocpdb> 477 atoms in block 104
Block first atom: 47136
Blocpdb> 475 atoms in block 105
Block first atom: 47613
Blocpdb> 477 atoms in block 106
Block first atom: 48088
Blocpdb> 482 atoms in block 107
Block first atom: 48565
Blocpdb> 495 atoms in block 108
Block first atom: 49047
Blocpdb> 476 atoms in block 109
Block first atom: 49542
Blocpdb> 253 atoms in block 110
Block first atom: 50018
Blocpdb> 490 atoms in block 111
Block first atom: 50271
Blocpdb> 473 atoms in block 112
Block first atom: 50761
Blocpdb> 472 atoms in block 113
Block first atom: 51234
Blocpdb> 477 atoms in block 114
Block first atom: 51706
Blocpdb> 475 atoms in block 115
Block first atom: 52183
Blocpdb> 477 atoms in block 116
Block first atom: 52658
Blocpdb> 482 atoms in block 117
Block first atom: 53135
Blocpdb> 495 atoms in block 118
Block first atom: 53617
Blocpdb> 476 atoms in block 119
Block first atom: 54112
Blocpdb> 253 atoms in block 120
Block first atom: 54588
Blocpdb> 490 atoms in block 121
Block first atom: 54841
Blocpdb> 473 atoms in block 122
Block first atom: 55331
Blocpdb> 472 atoms in block 123
Block first atom: 55804
Blocpdb> 477 atoms in block 124
Block first atom: 56276
Blocpdb> 475 atoms in block 125
Block first atom: 56753
Blocpdb> 477 atoms in block 126
Block first atom: 57228
Blocpdb> 482 atoms in block 127
Block first atom: 57705
Blocpdb> 495 atoms in block 128
Block first atom: 58187
Blocpdb> 476 atoms in block 129
Block first atom: 58682
Blocpdb> 253 atoms in block 130
Block first atom: 59158
Blocpdb> 490 atoms in block 131
Block first atom: 59411
Blocpdb> 473 atoms in block 132
Block first atom: 59901
Blocpdb> 472 atoms in block 133
Block first atom: 60374
Blocpdb> 477 atoms in block 134
Block first atom: 60846
Blocpdb> 475 atoms in block 135
Block first atom: 61323
Blocpdb> 477 atoms in block 136
Block first atom: 61798
Blocpdb> 482 atoms in block 137
Block first atom: 62275
Blocpdb> 495 atoms in block 138
Block first atom: 62757
Blocpdb> 476 atoms in block 139
Block first atom: 63252
Blocpdb> 253 atoms in block 140
Block first atom: 63728
Blocpdb> 490 atoms in block 141
Block first atom: 63981
Blocpdb> 473 atoms in block 142
Block first atom: 64471
Blocpdb> 472 atoms in block 143
Block first atom: 64944
Blocpdb> 477 atoms in block 144
Block first atom: 65416
Blocpdb> 475 atoms in block 145
Block first atom: 65893
Blocpdb> 477 atoms in block 146
Block first atom: 66368
Blocpdb> 482 atoms in block 147
Block first atom: 66845
Blocpdb> 495 atoms in block 148
Block first atom: 67327
Blocpdb> 476 atoms in block 149
Block first atom: 67822
Blocpdb> 253 atoms in block 150
Block first atom: 68298
Blocpdb> 490 atoms in block 151
Block first atom: 68551
Blocpdb> 473 atoms in block 152
Block first atom: 69041
Blocpdb> 472 atoms in block 153
Block first atom: 69514
Blocpdb> 477 atoms in block 154
Block first atom: 69986
Blocpdb> 475 atoms in block 155
Block first atom: 70463
Blocpdb> 477 atoms in block 156
Block first atom: 70938
Blocpdb> 482 atoms in block 157
Block first atom: 71415
Blocpdb> 495 atoms in block 158
Block first atom: 71897
Blocpdb> 476 atoms in block 159
Block first atom: 72392
Blocpdb> 253 atoms in block 160
Block first atom: 72868
Blocpdb> 490 atoms in block 161
Block first atom: 73121
Blocpdb> 473 atoms in block 162
Block first atom: 73611
Blocpdb> 472 atoms in block 163
Block first atom: 74084
Blocpdb> 477 atoms in block 164
Block first atom: 74556
Blocpdb> 475 atoms in block 165
Block first atom: 75033
Blocpdb> 477 atoms in block 166
Block first atom: 75508
Blocpdb> 482 atoms in block 167
Block first atom: 75985
Blocpdb> 495 atoms in block 168
Block first atom: 76467
Blocpdb> 476 atoms in block 169
Block first atom: 76962
Blocpdb> 253 atoms in block 170
Block first atom: 77438
Blocpdb> 490 atoms in block 171
Block first atom: 77691
Blocpdb> 473 atoms in block 172
Block first atom: 78181
Blocpdb> 472 atoms in block 173
Block first atom: 78654
Blocpdb> 477 atoms in block 174
Block first atom: 79126
Blocpdb> 475 atoms in block 175
Block first atom: 79603
Blocpdb> 477 atoms in block 176
Block first atom: 80078
Blocpdb> 482 atoms in block 177
Block first atom: 80555
Blocpdb> 495 atoms in block 178
Block first atom: 81037
Blocpdb> 476 atoms in block 179
Block first atom: 81532
Blocpdb> 253 atoms in block 180
Block first atom: 82008
Blocpdb> 490 atoms in block 181
Block first atom: 82261
Blocpdb> 473 atoms in block 182
Block first atom: 82751
Blocpdb> 472 atoms in block 183
Block first atom: 83224
Blocpdb> 477 atoms in block 184
Block first atom: 83696
Blocpdb> 475 atoms in block 185
Block first atom: 84173
Blocpdb> 477 atoms in block 186
Block first atom: 84648
Blocpdb> 482 atoms in block 187
Block first atom: 85125
Blocpdb> 495 atoms in block 188
Block first atom: 85607
Blocpdb> 476 atoms in block 189
Block first atom: 86102
Blocpdb> 253 atoms in block 190
Block first atom: 86578
Blocpdb> 490 atoms in block 191
Block first atom: 86831
Blocpdb> 473 atoms in block 192
Block first atom: 87321
Blocpdb> 472 atoms in block 193
Block first atom: 87794
Blocpdb> 477 atoms in block 194
Block first atom: 88266
Blocpdb> 475 atoms in block 195
Block first atom: 88743
Blocpdb> 477 atoms in block 196
Block first atom: 89218
Blocpdb> 482 atoms in block 197
Block first atom: 89695
Blocpdb> 495 atoms in block 198
Block first atom: 90177
Blocpdb> 476 atoms in block 199
Block first atom: 90672
Blocpdb> 253 atoms in block 200
Block first atom: 91147
Blocpdb> 200 blocks.
Blocpdb> At most, 495 atoms in each of them.
Blocpdb> At least, 253 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: 409392226 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 0m0.461s
user 0m0.431s
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 8th, 2025.
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