*** ***
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 = 2403061342251916079.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 2403061342251916079.atom to be opened.
Openam> File opened: 2403061342251916079.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 = 2403061342251916079.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 2403061342251916079.atom to be opened.
Openam> file on opening on unit 11:
2403061342251916079.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 0m4.602s
user 0m4.547s
sys 0m0.040s
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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