*** output ***
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 = 2404220252371793331.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 2404220252371793331.atom to be opened.
Openam> File opened: 2404220252371793331.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 = 1
First residue number = 1
Last residue number = 1
Number of atoms found = 49
Mean number per residue = 49.0
Pdbmat> Coordinate statistics:
= 3.010735 +/- 1.991616 From: -1.353000 To: 6.883000
= 66.200735 +/- 3.354920 From: 60.354000 To: 71.340000
= 68.825816 +/- 2.171419 From: 63.362000 To: 71.980000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'UNL ' is not a well known amino-acid.
%Pdbmat-W> 1 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 75.7584 % Filled.
Pdbmat> 8241 non-zero elements.
Pdbmat> 883 atom-atom interactions.
Pdbmat> Number per atom= 36.04 +/- 7.03
Maximum number = 48
Minimum number = 25
Pdbmat> Matrix trace = 17660.0
Pdbmat> Larger element = 267.482
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
1 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 = 2404220252371793331.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 2404220252371793331.atom to be opened.
Openam> file on opening on unit 11:
2404220252371793331.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 49 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> 1 residues.
Blocpdb> 49 atoms in block 1
Block first atom: 0
Blocpdb> 1 blocks.
Blocpdb> At most, 49 atoms in each of them.
Blocpdb> At least, 49 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-Wn> 6 eigenvectors, only, can be determined.
Diagrtb> Memory allocation for RTB_to_modes.
Prepmat> Entering in.
Prepmat> Rewriting of the matrix begins.
Prepmat> 8242 matrix lines read.
Prepmat> Matrix order = 147
Prepmat> Matrix trace = 17660.0000
Prepmat> Last element read: 147 147 31.5270
Prepmat> 2 lines saved.
Prepmat> 0 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: 49
RTB> Total mass = 49.0000
RTB> Number of atoms found in matrix: 49
RTB> Number of blocks = 1
RTB> Projection begins.
RTB> Projected matrix is being saved.
RTB> Projected matrix trace = 0.0000
RTB> 21 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 = 6
Diagstd> Nb of non-zero elements: 21
Diagstd> Projected matrix trace = 0.0000
Openam> file on opening on unit 11:
diagrtb_work.eigenfacs
Diagstd> Diagonalization.
Diagstd> 6 eigenvectors are computed.
Diagstd> 6 of them to be saved.
Diagstd> Sum of eigenvalues = 0.0000
Diagstd> Best zero-eigenvalue found : 0.000000
Diagstd> 6 zero-eigenvalues, that is, below or equal to: 0.0000000
Diagstd> Selected eigenvalues:
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
0.0000000
Diagstd> Frequencies (cm-1, if the input matrix is a hessian in CHARMM units):
0.0034339 0.0034340 0.0034340 0.0034340 0.0034340
0.0034340
Diagstd> Normal end.
Rtb_to_modes> Entering in.
Rtb_to_modes> Number of atoms in temporary block-file = 49
Rtb_to_modes> Number of blocs = 1
Openam> file on opening on unit 10:
diagrtb_work.eigenfacs
Openam> file on opening on unit 11:
matrix.eigenrtb
Rdmodfacs> Entering in.
Rdmodfacs> Old Blzpack file format detected.
Rdmodfacs> Eigenvector number: 1
Rdmodfacs> Corresponding eigenvalue: 9.9999E-10
Rdmodfacs> Eigenvector number: 2
Rdmodfacs> Corresponding eigenvalue: 1.0000E-09
Rdmodfacs> Eigenvector number: 3
Rdmodfacs> Corresponding eigenvalue: 1.0000E-09
Rdmodfacs> Eigenvector number: 4
Rdmodfacs> Corresponding eigenvalue: 1.0000E-09
Rdmodfacs> Eigenvector number: 5
Rdmodfacs> Corresponding eigenvalue: 1.0000E-09
Rdmodfacs> Eigenvector number: 6
Rdmodfacs> Corresponding eigenvalue: 1.0000E-09
Rtb_to_modes> 6 vectors, with 6 coordinates in vector file.
Norm of eigenvectors in projected coordinates (one expected):
0.99998 0.99996 1.00000 0.99999 0.99995
1.00000
Rtb_to_modes> RTB block-file is being read.
Rtb_to_modes> 882 lines found in RTB file.
Norm of eigenvectors in cartesian coordinates (one expected):
0.99998 0.99996 1.00000 0.99999 0.99995
1.00000
Orthogonality of first eigenvectors (zero expected):
Vector 2: 0.000
Vector 3: 0.000 0.000
Vector 4: 0.000 0.000 0.000
Vector 5: 0.000-0.000 0.000-0.000
Vector 6: 0.000-0.000-0.000 0.000 0.000
Rtb_to_modes> 6 eigenvectors saved.
Rtb_to_modes> Normal end.
Diagrtb> Normal end.
B-factor analysis
Bfactors> Version 1.22, Bordeaux.
Getnam> Eigenvector filename ?
Getnam> 2404220252371793331.eigenfacs
Openam> file on opening on unit 10:
2404220252371793331.eigenfacs
Getnam> Corresponding pdb filename ?
Getnam> 2404220252371793331.atom
Openam> file on opening on unit 11:
2404220252371793331.atom
Getnum> Number of skipped eigenvectors ?
Getnum> 0
Getnum> Number of usefull eigenvectors ?
Getnum> 10000
%Getnum-Err: number larger than 106 This is not allowed. Sorry.
Rdatompdb> Reading pdb file.
Rdatompdb> End of file reached.
Rdatompdb> Number of I/O errors: 0
Rdatompdb> Number of residues found = 1
First residue number = 1
Last residue number = 1
Number of atoms found = 49
Mean number per residue = 49.0
Rdmodfacs> Old Blzpack file format detected.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 1
Rdmodfacs> Valeur propre du vecteur en lecture: 9.9999E-10
Rdmodfacs> Numero du vecteur CERFACS en lecture: 2
Rdmodfacs> Valeur propre du vecteur en lecture: 1.0000E-09
Rdmodfacs> Numero du vecteur CERFACS en lecture: 3
Rdmodfacs> Valeur propre du vecteur en lecture: 1.0000E-09
Rdmodfacs> Numero du vecteur CERFACS en lecture: 4
Rdmodfacs> Valeur propre du vecteur en lecture: 1.0000E-09
Rdmodfacs> Numero du vecteur CERFACS en lecture: 5
Rdmodfacs> Valeur propre du vecteur en lecture: 1.0000E-09
Rdmodfacs> Numero du vecteur CERFACS en lecture: 6
Rdmodfacs> Valeur propre du vecteur en lecture: 1.0000E-09
Bfactors> 6 vectors, 147 coordinates in file.
%Bfactors-Wn> All vectors required were not found in vector file.
Openam> file on opening on unit 12:
bfactors.pred
Bfactors> Best zero-eigenvalue found : 0.000000
Bfactors> 6 eigenvalues less than : 0.000000
Bfactors> 0 eigenvectors will be considered.
%Bfactors-Wn> 0 negative values found in the B-factors column of pdb file.
%Bfactors-Wn> So, only mass-weighted predicted B-factors will be saved.
(CHARMM units assumed for eigenvalues)
Bfactors> Normal end.
check_modes
getting mode 7
running: ../../bin/get_modes.sh 2404220252371793331 7 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 7
calculating perturbed structure for DQ=-100
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=0
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=100
2404220252371793331.eigenfacs
2404220252371793331.atom
making animated gifs
11 models are in 2404220252371793331.7.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.7.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.7.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
getting mode 8
running: ../../bin/get_modes.sh 2404220252371793331 8 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 8
calculating perturbed structure for DQ=-100
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=0
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=100
2404220252371793331.eigenfacs
2404220252371793331.atom
making animated gifs
11 models are in 2404220252371793331.8.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.8.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.8.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
getting mode 9
running: ../../bin/get_modes.sh 2404220252371793331 9 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 9
calculating perturbed structure for DQ=-100
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=0
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=100
2404220252371793331.eigenfacs
2404220252371793331.atom
making animated gifs
11 models are in 2404220252371793331.9.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.9.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.9.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
getting mode 10
running: ../../bin/get_modes.sh 2404220252371793331 10 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 10
calculating perturbed structure for DQ=-100
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=0
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=100
2404220252371793331.eigenfacs
2404220252371793331.atom
making animated gifs
11 models are in 2404220252371793331.10.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.10.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.10.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
getting mode 11
running: ../../bin/get_modes.sh 2404220252371793331 11 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 11
calculating perturbed structure for DQ=-100
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=-20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=0
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=20
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=40
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=60
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=80
2404220252371793331.eigenfacs
2404220252371793331.atom
calculating perturbed structure for DQ=100
2404220252371793331.eigenfacs
2404220252371793331.atom
making animated gifs
11 models are in 2404220252371793331.11.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.11.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
11 models are in 2404220252371793331.11.pdb, 1 models will be skipped
MODEL 1 will be plotted
MODEL 3 will be plotted
MODEL 5 will be plotted
MODEL 7 will be plotted
MODEL 9 will be plotted
MODEL 11 will be plotted
making thumbnail 100x100
making small animated gif 100x100
making animated gif 300x300
2404220252371793331.10.pdb
2404220252371793331.11.pdb
2404220252371793331.7.pdb
2404220252371793331.8.pdb
2404220252371793331.9.pdb
STDERR:
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
real 0m0.013s
user 0m0.008s
sys 0m0.004s
../../bin/check_modes: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
mv: cannot stat 'Chkmod.res': No such file or directory
cat: 2404220252371793331.Chkmod.res: No such file or directory
pstopnm: Writing ppmraw format
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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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