***    ***
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 = 2403061340131909106.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 2403061340131909106.atom to be opened.
Openam> File opened: 2403061340131909106.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 = 151
First residue number = 1
Last residue number = 22
Number of atoms found = 1982
Mean number per residue = 13.1
Pdbmat> Coordinate statistics:
= 27.846607 +/- 7.479043 From: 5.908000 To: 51.059000
= 24.874761 +/- 9.603194 From: 3.219000 To: 49.815000
= 0.149987 +/- 7.354852 From: -21.521000 To: 20.990000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'HSD ' is not a well known amino-acid.
%Pdbmat-W> residue:'SOD ' is not a well known amino-acid.
%Pdbmat-W> residue:'SOD ' is not a well known amino-acid.
%Pdbmat-W> residue:'SOD ' is not a well known amino-acid.
%Pdbmat-W> residue:'SOD ' is not a well known amino-acid.
%Pdbmat-W> residue:'SOD ' is not a well known amino-acid.
%Pdbmat-W> residue:'SOD ' is not a well known amino-acid.
%Pdbmat-W> residue:'SOD ' is not a well known amino-acid.
%Pdbmat-W> residue:'CLA ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 23 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 7.7119 % Filled.
Pdbmat> 1363503 non-zero elements.
Pdbmat> 150205 atom-atom interactions.
Pdbmat> Number per atom= 151.57 +/- 50.45
Maximum number = 248
Minimum number = 0
Pdbmat> Matrix trace = 3.004100E+06
Pdbmat> Larger element = 901.121
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
151 non-zero elements, NRBL set to 1
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 = 2403061340131909106.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 1
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 2403061340131909106.atom to be opened.
Openam> file on opening on unit 11:
2403061340131909106.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 1982 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 1 residue(s) per block.
Blocpdb> 151 residues.
Blocpdb> 24 atoms in block 1
Block first atom: 1
Blocpdb> 16 atoms in block 2
Block first atom: 25
Blocpdb> 20 atoms in block 3
Block first atom: 41
Blocpdb> 7 atoms in block 4
Block first atom: 61
Blocpdb> 24 atoms in block 5
Block first atom: 68
Blocpdb> 10 atoms in block 6
Block first atom: 92
Blocpdb> 15 atoms in block 7
Block first atom: 102
Blocpdb> 19 atoms in block 8
Block first atom: 117
Blocpdb> 10 atoms in block 9
Block first atom: 136
Blocpdb> 10 atoms in block 10
Block first atom: 146
Blocpdb> 10 atoms in block 11
Block first atom: 156
Blocpdb> 17 atoms in block 12
Block first atom: 166
Blocpdb> 22 atoms in block 13
Block first atom: 183
Blocpdb> 24 atoms in block 14
Block first atom: 205
Blocpdb> 17 atoms in block 15
Block first atom: 229
Blocpdb> 7 atoms in block 16
Block first atom: 246
Blocpdb> 19 atoms in block 17
Block first atom: 253
Blocpdb> 12 atoms in block 18
Block first atom: 272
Blocpdb> 14 atoms in block 19
Block first atom: 284
Blocpdb> 21 atoms in block 20
Block first atom: 298
Blocpdb> 24 atoms in block 21
Block first atom: 319
Blocpdb> 7 atoms in block 22
Block first atom: 343
Blocpdb> 21 atoms in block 23
Block first atom: 350
Blocpdb> 11 atoms in block 24
Block first atom: 371
Blocpdb> 19 atoms in block 25
Block first atom: 382
Blocpdb> 7 atoms in block 26
Block first atom: 401
Blocpdb> 14 atoms in block 27
Block first atom: 408
Blocpdb> 24 atoms in block 28
Block first atom: 422
Blocpdb> 16 atoms in block 29
Block first atom: 446
Blocpdb> 10 atoms in block 30
Block first atom: 462
Blocpdb> 10 atoms in block 31
Block first atom: 472
Blocpdb> 10 atoms in block 32
Block first atom: 482
Blocpdb> 22 atoms in block 33
Block first atom: 492
Blocpdb> 20 atoms in block 34
Block first atom: 514
Blocpdb> 15 atoms in block 35
Block first atom: 534
Blocpdb> 11 atoms in block 36
Block first atom: 549
Blocpdb> 14 atoms in block 37
Block first atom: 560
Blocpdb> 20 atoms in block 38
Block first atom: 574
Blocpdb> 14 atoms in block 39
Block first atom: 594
Blocpdb> 14 atoms in block 40
Block first atom: 608
Blocpdb> 17 atoms in block 41
Block first atom: 622
Blocpdb> 10 atoms in block 42
Block first atom: 639
Blocpdb> 14 atoms in block 43
Block first atom: 649
Blocpdb> 14 atoms in block 44
Block first atom: 663
Blocpdb> 24 atoms in block 45
Block first atom: 677
Blocpdb> 14 atoms in block 46
Block first atom: 701
Blocpdb> 14 atoms in block 47
Block first atom: 715
Blocpdb> 12 atoms in block 48
Block first atom: 729
Blocpdb> 7 atoms in block 49
Block first atom: 741
Blocpdb> 11 atoms in block 50
Block first atom: 748
Blocpdb> 14 atoms in block 51
Block first atom: 759
Blocpdb> 12 atoms in block 52
Block first atom: 773
Blocpdb> 21 atoms in block 53
Block first atom: 785
Blocpdb> 7 atoms in block 54
Block first atom: 806
Blocpdb> 19 atoms in block 55
Block first atom: 813
Blocpdb> 19 atoms in block 56
Block first atom: 832
Blocpdb> 17 atoms in block 57
Block first atom: 851
Blocpdb> 19 atoms in block 58
Block first atom: 868
Blocpdb> 14 atoms in block 59
Block first atom: 887
Blocpdb> 11 atoms in block 60
Block first atom: 901
Blocpdb> 24 atoms in block 61
Block first atom: 912
Blocpdb> 24 atoms in block 62
Block first atom: 936
Blocpdb> 24 atoms in block 63
Block first atom: 960
Blocpdb> 10 atoms in block 64
Block first atom: 984
Blocpdb> 14 atoms in block 65
Block first atom: 994
Blocpdb> 12 atoms in block 66
Block first atom: 1008
Blocpdb> 7 atoms in block 67
Block first atom: 1020
Blocpdb> 24 atoms in block 68
Block first atom: 1027
Blocpdb> 14 atoms in block 69
Block first atom: 1051
Blocpdb> 14 atoms in block 70
Block first atom: 1065
Blocpdb> 7 atoms in block 71
Block first atom: 1079
Blocpdb> 11 atoms in block 72
Block first atom: 1086
Blocpdb> 24 atoms in block 73
Block first atom: 1097
Blocpdb> 14 atoms in block 74
Block first atom: 1121
Blocpdb> 19 atoms in block 75
Block first atom: 1135
Blocpdb> 10 atoms in block 76
Block first atom: 1154
Blocpdb> 14 atoms in block 77
Block first atom: 1164
Blocpdb> 19 atoms in block 78
Block first atom: 1178
Blocpdb> 14 atoms in block 79
Block first atom: 1197
Blocpdb> 10 atoms in block 80
Block first atom: 1211
Blocpdb> 11 atoms in block 81
Block first atom: 1221
Blocpdb> 10 atoms in block 82
Block first atom: 1232
Blocpdb> 19 atoms in block 83
Block first atom: 1242
Blocpdb> 19 atoms in block 84
Block first atom: 1261
Blocpdb> 11 atoms in block 85
Block first atom: 1280
Blocpdb> 11 atoms in block 86
Block first atom: 1291
Blocpdb> 12 atoms in block 87
Block first atom: 1302
Blocpdb> 19 atoms in block 88
Block first atom: 1314
Blocpdb> 14 atoms in block 89
Block first atom: 1333
Blocpdb> 10 atoms in block 90
Block first atom: 1347
Blocpdb> 11 atoms in block 91
Block first atom: 1357
Blocpdb> 16 atoms in block 92
Block first atom: 1368
Blocpdb> 14 atoms in block 93
Block first atom: 1384
Blocpdb> 10 atoms in block 94
Block first atom: 1398
Blocpdb> 10 atoms in block 95
Block first atom: 1408
Blocpdb> 22 atoms in block 96
Block first atom: 1418
Blocpdb> 22 atoms in block 97
Block first atom: 1440
Blocpdb> 19 atoms in block 98
Block first atom: 1462
Blocpdb> 16 atoms in block 99
Block first atom: 1481
Blocpdb> 11 atoms in block 100
Block first atom: 1497
Blocpdb> 12 atoms in block 101
Block first atom: 1508
Blocpdb> 7 atoms in block 102
Block first atom: 1520
Blocpdb> 14 atoms in block 103
Block first atom: 1527
Blocpdb> 7 atoms in block 104
Block first atom: 1541
Blocpdb> 17 atoms in block 105
Block first atom: 1548
Blocpdb> 14 atoms in block 106
Block first atom: 1565
Blocpdb> 10 atoms in block 107
Block first atom: 1579
Blocpdb> 24 atoms in block 108
Block first atom: 1589
Blocpdb> 16 atoms in block 109
Block first atom: 1613
Blocpdb> 10 atoms in block 110
Block first atom: 1629
Blocpdb> 24 atoms in block 111
Block first atom: 1639
Blocpdb> 24 atoms in block 112
Block first atom: 1663
Blocpdb> 14 atoms in block 113
Block first atom: 1687
Blocpdb> 24 atoms in block 114
Block first atom: 1701
Blocpdb> 10 atoms in block 115
Block first atom: 1725
Blocpdb> 22 atoms in block 116
Block first atom: 1735
Blocpdb> 7 atoms in block 117
Block first atom: 1757
Blocpdb> 14 atoms in block 118
Block first atom: 1764
Blocpdb> 12 atoms in block 119
Block first atom: 1778
Blocpdb> 16 atoms in block 120
Block first atom: 1790
Blocpdb> 17 atoms in block 121
Block first atom: 1806
Blocpdb> 10 atoms in block 122
Block first atom: 1823
Blocpdb> 24 atoms in block 123
Block first atom: 1833
Blocpdb> 19 atoms in block 124
Block first atom: 1857
Blocpdb> 24 atoms in block 125
Block first atom: 1876
Blocpdb> 7 atoms in block 126
Block first atom: 1900
Blocpdb> 10 atoms in block 127
Block first atom: 1907
Blocpdb> 24 atoms in block 128
Block first atom: 1917
Blocpdb> 20 atoms in block 129
Block first atom: 1941
%Blocpdb-Wn> 1 atoms in block 130 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1961th, in residue I 1
%Blocpdb-Wn> It will be merged with next block.
%Blocpdb-Wn> 2 atoms in block 130 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1962th, in residue I 2
%Blocpdb-Wn> It will be merged with next block.
Blocpdb> 3 atoms in block 130
Block first atom: 1961
%Blocpdb-Wn> 1 atoms in block 131 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1964th, in residue I 4
%Blocpdb-Wn> It will be merged with next block.
%Blocpdb-Wn> 2 atoms in block 131 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1965th, in residue I 5
%Blocpdb-Wn> It will be merged with next block.
Blocpdb> 3 atoms in block 131
Block first atom: 1964
%Blocpdb-Wn> 1 atoms in block 132 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1967th, in residue I 7
%Blocpdb-Wn> It will be merged with next block.
%Blocpdb-Wn> 2 atoms in block 132 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1968th, in residue I 8
%Blocpdb-Wn> It will be merged with next block.
Blocpdb> 3 atoms in block 132
Block first atom: 1967
%Blocpdb-Wn> 1 atoms in block 133 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1970th, in residue I 10
%Blocpdb-Wn> It will be merged with next block.
%Blocpdb-Wn> 2 atoms in block 133 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1971th, in residue I 11
%Blocpdb-Wn> It will be merged with next block.
Blocpdb> 3 atoms in block 133
Block first atom: 1970
%Blocpdb-Wn> 1 atoms in block 134 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1973th, in residue I 13
%Blocpdb-Wn> It will be merged with next block.
%Blocpdb-Wn> 2 atoms in block 134 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1974th, in residue I 14
%Blocpdb-Wn> It will be merged with next block.
Blocpdb> 3 atoms in block 134
Block first atom: 1973
%Blocpdb-Wn> 1 atoms in block 135 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1976th, in residue I 16
%Blocpdb-Wn> It will be merged with next block.
%Blocpdb-Wn> 2 atoms in block 135 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1977th, in residue I 17
%Blocpdb-Wn> It will be merged with next block.
Blocpdb> 3 atoms in block 135
Block first atom: 1976
%Blocpdb-Wn> 1 atoms in block 136 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1979th, in residue I 19
%Blocpdb-Wn> It will be merged with next block.
%Blocpdb-Wn> 2 atoms in block 136 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 1980th, in residue I 20
%Blocpdb-Wn> It will be merged with next block.
Blocpdb> 4 atoms in block 136
Block first atom: 1978
Blocpdb> 136 blocks.
Blocpdb> At most, 24 atoms in each of them.
Blocpdb> At least, 3 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.
Prepmat> Entering in.
Prepmat> Rewriting of the matrix begins.
Prepmat> 1363639 matrix lines read.
Prepmat> Matrix order = 5946
Prepmat> Matrix trace = 3004100.0000
Prepmat> Last element read: 5946 5946 0.0000
Prepmat> 9317 lines saved.
Prepmat> 7395 empty lines.
Prepmat> Number of lines on output is as expected.
Prepmat> Normal end of Prepmat.
RTB> Entering in.
RTB> Number of atoms found in temporary coordinate file: 1982
RTB> Total mass = 1982.0000
RTB> Number of atoms found in matrix: 1982
RTB> Number of blocks = 136
RTB> Projection begins.
RTB> Projected matrix is being saved.
RTB> Projected matrix trace = 362991.9998
RTB> 67110 non-zero elements.
RTB> Normal end of RTB.
Diagstd> Entering in.
Openam> file on opening on unit 10:
diagrtb_work.sdijb
Diagstd> Projected matrix to be read from file: diagrtb_work.sdijb
Diagstd> CERFACS matrix format.
Diagstd> Projected matrix order = 816
Diagstd> Nb of non-zero elements: 67110
Diagstd> Projected matrix trace = 362991.9998
Openam> file on opening on unit 11:
diagrtb_work.eigenfacs
Diagstd> Diagonalization.
Diagstd> 816 eigenvectors are computed.
Diagstd> 106 of them to be saved.
STDERR:
PAUSE too many iterations
To resume execution, type go. Other input will terminate the job.
real 0m4.567s
user 0m4.539s
sys 0m0.028s
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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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