*** ***
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 = 240129114322756599.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 240129114322756599.atom to be opened.
Openam> File opened: 240129114322756599.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 = 12
First residue number = 1
Last residue number = 12
Number of atoms found = 200
Mean number per residue = 16.7
Pdbmat> Coordinate statistics:
= 41.790845 +/- 3.847997 From: 33.350000 To: 50.213000
= 42.144835 +/- 3.752962 From: 34.718000 To: 50.921000
= 41.733180 +/- 4.167160 From: 33.445000 To: 49.607000
Pdbmat> Masses are all set to one.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is 46.6406 % Filled.
Pdbmat> 84093 non-zero elements.
Pdbmat> 9212 atom-atom interactions.
Pdbmat> Number per atom= 92.12 +/- 24.92
Maximum number = 141
Minimum number = 37
Pdbmat> Matrix trace = 184240.
Pdbmat> Larger element = 557.041
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
12 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 = 240129114322756599.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 240129114322756599.atom to be opened.
Openam> file on opening on unit 11:
240129114322756599.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 200 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> 12 residues.
Blocpdb> 20 atoms in block 1
Block first atom: 1
Blocpdb> 19 atoms in block 2
Block first atom: 21
Blocpdb> 14 atoms in block 3
Block first atom: 40
Blocpdb> 19 atoms in block 4
Block first atom: 54
Blocpdb> 16 atoms in block 5
Block first atom: 73
Blocpdb> 20 atoms in block 6
Block first atom: 89
Blocpdb> 7 atoms in block 7
Block first atom: 109
Blocpdb> 19 atoms in block 8
Block first atom: 116
Blocpdb> 20 atoms in block 9
Block first atom: 135
Blocpdb> 8 atoms in block 10
Block first atom: 155
Blocpdb> 19 atoms in block 11
Block first atom: 163
Blocpdb> 19 atoms in block 12
Block first atom: 181
Blocpdb> 12 blocks.
Blocpdb> At most, 20 atoms in each of them.
Blocpdb> At least, 7 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> 72 eigenvectors, only, can be determined.
Diagrtb> Memory allocation for RTB_to_modes.
Prepmat> Entering in.
Prepmat> Rewriting of the matrix begins.
Prepmat> 84105 matrix lines read.
Prepmat> Matrix order = 600
Prepmat> Matrix trace = 184240.0000
Prepmat> Last element read: 600 600 225.1793
Prepmat> 79 lines saved.
Prepmat> 9 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: 200
RTB> Total mass = 200.0000
RTB> Number of atoms found in matrix: 200
RTB> Number of blocks = 12
RTB> Projection begins.
RTB> Projected matrix is being saved.
RTB> Projected matrix trace = 18764.2979
RTB> 2304 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 = 72
Diagstd> Nb of non-zero elements: 2304
Diagstd> Projected matrix trace = 18764.2979
Openam> file on opening on unit 11:
diagrtb_work.eigenfacs
Diagstd> Diagonalization.
Diagstd> 72 eigenvectors are computed.
Diagstd> 72 of them to be saved.
Diagstd> Sum of eigenvalues = 18764.2979
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 20.5409941 26.9472727 42.2869877 72.8294225
81.0135969 96.9657773 104.5768946 112.5807536 118.8526987
130.7760613 142.2662134 149.1279675 159.4393292 163.8203125
164.6711069 185.0081043 188.7275219 190.4822457 202.5295652
203.9983921 215.2669322 226.1546662 230.3552835 231.1001787
236.9617737 240.1298915 244.7758322 250.8857821 254.0368409
266.2354491 267.8103477 277.6852255 280.5690736 284.0025250
291.9061332 294.8425198 298.8490680 300.3034170 305.3935350
315.0058828 320.1336726 324.2049137 329.3009250 331.7467501
336.3622360 343.4195454 349.8770737 350.5332779 357.6167494
361.9434941 363.8476478 372.6860885 382.4293136 385.2423311
391.9581279 405.2332599 411.0243961 424.6047332 444.2523709
472.2274242 500.7263555 525.6877972 548.2885834 567.3366963
623.6281914 670.2743376
Diagstd> Frequencies (cm-1, if the input matrix is a hessian in CHARMM units):
0.0034318 0.0034332 0.0034337 0.0034339 0.0034340
0.0034341 492.1596549 563.7060410 706.1527506 926.7203790
977.4042824 1069.3122002 1110.4861615 1152.1986341 1183.8585200
1241.8221640 1295.2278273 1326.0955866 1371.1753890 1389.8859195
1393.4904051 1477.0345589 1491.8078872 1498.7270009 1545.3949737
1550.9887668 1593.2500514 1633.0446405 1648.1410226 1650.8036517
1671.6079436 1682.7453248 1698.9458937 1720.0192417 1730.7870297
1771.8551727 1777.0880928 1809.5544967 1818.9266220 1830.0222956
1855.3117294 1864.6199964 1877.2461967 1881.8084625 1897.6896973
1927.3234807 1942.9470212 1955.2625254 1970.5694955 1977.8739876
1991.5852250 2012.3697703 2031.2015676 2033.1054629 2053.5449140
2065.9303110 2071.3575233 2096.3648596 2123.5909569 2131.3868468
2149.8844457 2185.9882435 2201.5526712 2237.6270106 2288.8121877
2359.7765587 2429.9397513 2489.7699913 2542.7278614 2586.5192677
2711.8030820 2811.3931111
Diagstd> Normal end.
Rtb_to_modes> Entering in.
Rtb_to_modes> Number of atoms in temporary block-file = 200
Rtb_to_modes> Number of blocs = 12
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: 9.9875E-10
Rdmodfacs> Eigenvector number: 2
Rdmodfacs> Corresponding eigenvalue: 9.9958E-10
Rdmodfacs> Eigenvector number: 3
Rdmodfacs> Corresponding eigenvalue: 9.9984E-10
Rdmodfacs> Eigenvector number: 4
Rdmodfacs> Corresponding eigenvalue: 9.9995E-10
Rdmodfacs> Eigenvector number: 5
Rdmodfacs> Corresponding eigenvalue: 1.0000E-09
Rdmodfacs> Eigenvector number: 6
Rdmodfacs> Corresponding eigenvalue: 1.0001E-09
Rdmodfacs> Eigenvector number: 7
Rdmodfacs> Corresponding eigenvalue: 20.54
Rdmodfacs> Eigenvector number: 8
Rdmodfacs> Corresponding eigenvalue: 26.95
Rdmodfacs> Eigenvector number: 9
Rdmodfacs> Corresponding eigenvalue: 42.29
Rdmodfacs> Eigenvector number: 10
Rdmodfacs> Corresponding eigenvalue: 72.83
Rdmodfacs> Eigenvector number: 11
Rdmodfacs> Corresponding eigenvalue: 81.01
Rdmodfacs> Eigenvector number: 12
Rdmodfacs> Corresponding eigenvalue: 96.97
Rdmodfacs> Eigenvector number: 13
Rdmodfacs> Corresponding eigenvalue: 104.6
Rdmodfacs> Eigenvector number: 14
Rdmodfacs> Corresponding eigenvalue: 112.6
Rdmodfacs> Eigenvector number: 15
Rdmodfacs> Corresponding eigenvalue: 118.9
Rdmodfacs> Eigenvector number: 16
Rdmodfacs> Corresponding eigenvalue: 130.8
Rdmodfacs> Eigenvector number: 17
Rdmodfacs> Corresponding eigenvalue: 142.3
Rdmodfacs> Eigenvector number: 18
Rdmodfacs> Corresponding eigenvalue: 149.1
Rdmodfacs> Eigenvector number: 19
Rdmodfacs> Corresponding eigenvalue: 159.4
Rdmodfacs> Eigenvector number: 20
Rdmodfacs> Corresponding eigenvalue: 163.8
Rdmodfacs> Eigenvector number: 21
Rdmodfacs> Corresponding eigenvalue: 164.7
Rdmodfacs> Eigenvector number: 22
Rdmodfacs> Corresponding eigenvalue: 185.0
Rdmodfacs> Eigenvector number: 23
Rdmodfacs> Corresponding eigenvalue: 188.7
Rdmodfacs> Eigenvector number: 24
Rdmodfacs> Corresponding eigenvalue: 190.5
Rdmodfacs> Eigenvector number: 25
Rdmodfacs> Corresponding eigenvalue: 202.5
Rdmodfacs> Eigenvector number: 26
Rdmodfacs> Corresponding eigenvalue: 204.0
Rdmodfacs> Eigenvector number: 27
Rdmodfacs> Corresponding eigenvalue: 215.3
Rdmodfacs> Eigenvector number: 28
Rdmodfacs> Corresponding eigenvalue: 226.2
Rdmodfacs> Eigenvector number: 29
Rdmodfacs> Corresponding eigenvalue: 230.4
Rdmodfacs> Eigenvector number: 30
Rdmodfacs> Corresponding eigenvalue: 231.1
Rdmodfacs> Eigenvector number: 31
Rdmodfacs> Corresponding eigenvalue: 237.0
Rdmodfacs> Eigenvector number: 32
Rdmodfacs> Corresponding eigenvalue: 240.1
Rdmodfacs> Eigenvector number: 33
Rdmodfacs> Corresponding eigenvalue: 244.8
Rdmodfacs> Eigenvector number: 34
Rdmodfacs> Corresponding eigenvalue: 250.9
Rdmodfacs> Eigenvector number: 35
Rdmodfacs> Corresponding eigenvalue: 254.0
Rdmodfacs> Eigenvector number: 36
Rdmodfacs> Corresponding eigenvalue: 266.2
Rdmodfacs> Eigenvector number: 37
Rdmodfacs> Corresponding eigenvalue: 267.8
Rdmodfacs> Eigenvector number: 38
Rdmodfacs> Corresponding eigenvalue: 277.7
Rdmodfacs> Eigenvector number: 39
Rdmodfacs> Corresponding eigenvalue: 280.6
Rdmodfacs> Eigenvector number: 40
Rdmodfacs> Corresponding eigenvalue: 284.0
Rdmodfacs> Eigenvector number: 41
Rdmodfacs> Corresponding eigenvalue: 291.9
Rdmodfacs> Eigenvector number: 42
Rdmodfacs> Corresponding eigenvalue: 294.8
Rdmodfacs> Eigenvector number: 43
Rdmodfacs> Corresponding eigenvalue: 298.8
Rdmodfacs> Eigenvector number: 44
Rdmodfacs> Corresponding eigenvalue: 300.3
Rdmodfacs> Eigenvector number: 45
Rdmodfacs> Corresponding eigenvalue: 305.4
Rdmodfacs> Eigenvector number: 46
Rdmodfacs> Corresponding eigenvalue: 315.0
Rdmodfacs> Eigenvector number: 47
Rdmodfacs> Corresponding eigenvalue: 320.1
Rdmodfacs> Eigenvector number: 48
Rdmodfacs> Corresponding eigenvalue: 324.2
Rdmodfacs> Eigenvector number: 49
Rdmodfacs> Corresponding eigenvalue: 329.3
Rdmodfacs> Eigenvector number: 50
Rdmodfacs> Corresponding eigenvalue: 331.7
Rdmodfacs> Eigenvector number: 51
Rdmodfacs> Corresponding eigenvalue: 336.4
Rdmodfacs> Eigenvector number: 52
Rdmodfacs> Corresponding eigenvalue: 343.4
Rdmodfacs> Eigenvector number: 53
Rdmodfacs> Corresponding eigenvalue: 349.9
Rdmodfacs> Eigenvector number: 54
Rdmodfacs> Corresponding eigenvalue: 350.5
Rdmodfacs> Eigenvector number: 55
Rdmodfacs> Corresponding eigenvalue: 357.6
Rdmodfacs> Eigenvector number: 56
Rdmodfacs> Corresponding eigenvalue: 361.9
Rdmodfacs> Eigenvector number: 57
Rdmodfacs> Corresponding eigenvalue: 363.8
Rdmodfacs> Eigenvector number: 58
Rdmodfacs> Corresponding eigenvalue: 372.7
Rdmodfacs> Eigenvector number: 59
Rdmodfacs> Corresponding eigenvalue: 382.4
Rdmodfacs> Eigenvector number: 60
Rdmodfacs> Corresponding eigenvalue: 385.2
Rdmodfacs> Eigenvector number: 61
Rdmodfacs> Corresponding eigenvalue: 392.0
Rdmodfacs> Eigenvector number: 62
Rdmodfacs> Corresponding eigenvalue: 405.2
Rdmodfacs> Eigenvector number: 63
Rdmodfacs> Corresponding eigenvalue: 411.0
Rdmodfacs> Eigenvector number: 64
Rdmodfacs> Corresponding eigenvalue: 424.6
Rdmodfacs> Eigenvector number: 65
Rdmodfacs> Corresponding eigenvalue: 444.3
Rdmodfacs> Eigenvector number: 66
Rdmodfacs> Corresponding eigenvalue: 472.2
Rdmodfacs> Eigenvector number: 67
Rdmodfacs> Corresponding eigenvalue: 500.7
Rdmodfacs> Eigenvector number: 68
Rdmodfacs> Corresponding eigenvalue: 525.7
Rdmodfacs> Eigenvector number: 69
Rdmodfacs> Corresponding eigenvalue: 548.3
Rdmodfacs> Eigenvector number: 70
Rdmodfacs> Corresponding eigenvalue: 567.3
Rdmodfacs> Eigenvector number: 71
Rdmodfacs> Corresponding eigenvalue: 623.6
Rdmodfacs> Eigenvector number: 72
Rdmodfacs> Corresponding eigenvalue: 670.3
Rtb_to_modes> 72 vectors, with 72 coordinates in vector file.
Norm of eigenvectors in projected coordinates (one expected):
0.99998 1.00003 0.99999 0.99997 1.00005
1.00003 0.99996 1.00005 0.99999 0.99999
1.00001 0.99997 1.00001 0.99999 1.00004
1.00005 0.99997 1.00003 0.99998 0.99998
1.00000 1.00002 1.00001 0.99997 0.99999
1.00003 1.00003 0.99997 1.00003 1.00002
1.00006 1.00002 1.00000 0.99996 0.99996
1.00004 0.99999 1.00002 1.00000 1.00003
1.00003 0.99996 1.00001 1.00002 1.00000
0.99995 0.99997 0.99997 1.00001 1.00004
1.00002 1.00000 1.00001 1.00002 1.00003
0.99995 1.00005 1.00001 1.00001 0.99997
0.99996 0.99997 1.00005 0.99999 0.99998
1.00003 1.00003 0.99998 0.99998 0.99999
0.99999 1.00000
Rtb_to_modes> RTB block-file is being read.
Rtb_to_modes> 3600 lines found in RTB file.
Norm of eigenvectors in cartesian coordinates (one expected):
0.99998 1.00003 0.99999 0.99997 1.00005
1.00003 0.99996 1.00005 0.99999 0.99999
1.00001 0.99997 1.00001 0.99999 1.00004
1.00005 0.99997 1.00003 0.99998 0.99998
1.00000 1.00002 1.00001 0.99997 0.99999
1.00003 1.00003 0.99997 1.00003 1.00002
1.00006 1.00002 1.00000 0.99996 0.99996
1.00004 0.99999 1.00002 1.00000 1.00003
1.00003 0.99996 1.00001 1.00002 1.00000
0.99995 0.99997 0.99997 1.00001 1.00004
1.00002 1.00000 1.00001 1.00002 1.00003
0.99995 1.00005 1.00001 1.00001 0.99997
0.99996 0.99997 1.00005 0.99999 0.99998
1.00003 1.00003 0.99998 0.99998 0.99999
0.99999 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
Vector 7:-0.000-0.000-0.000-0.000-0.000-0.000
Vector 8: 0.000-0.000 0.000 0.000-0.000 0.000 0.000
Vector 9:-0.000 0.000-0.000 0.000-0.000-0.000-0.000 0.000
Vector 10:-0.000-0.000-0.000-0.000-0.000 0.000-0.000-0.000-0.000
Rtb_to_modes> 72 eigenvectors saved.
Rtb_to_modes> Normal end.
Diagrtb> Normal end.
B-factor analysis
Bfactors> Version 1.22, Bordeaux.
Getnam> Eigenvector filename ?
Getnam> 240129114322756599.eigenfacs
Openam> file on opening on unit 10:
240129114322756599.eigenfacs
Getnam> Corresponding pdb filename ?
Getnam> 240129114322756599.atom
Openam> file on opening on unit 11:
240129114322756599.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 = 12
First residue number = 1
Last residue number = 12
Number of atoms found = 200
Mean number per residue = 16.7
Rdmodfacs> Old Blzpack file format detected.
Rdmodfacs> Numero du vecteur CERFACS en lecture: 1
Rdmodfacs> Valeur propre du vecteur en lecture: 9.9875E-10
Rdmodfacs> Numero du vecteur CERFACS en lecture: 2
Rdmodfacs> Valeur propre du vecteur en lecture: 9.9958E-10
Rdmodfacs> Numero du vecteur CERFACS en lecture: 3
Rdmodfacs> Valeur propre du vecteur en lecture: 9.9984E-10
Rdmodfacs> Numero du vecteur CERFACS en lecture: 4
Rdmodfacs> Valeur propre du vecteur en lecture: 9.9995E-10
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: 1.0001E-09
Rdmodfacs> Numero du vecteur CERFACS en lecture: 7
Rdmodfacs> Valeur propre du vecteur en lecture: 20.54
Rdmodfacs> Numero du vecteur CERFACS en lecture: 8
Rdmodfacs> Valeur propre du vecteur en lecture: 26.95
Rdmodfacs> Numero du vecteur CERFACS en lecture: 9
Rdmodfacs> Valeur propre du vecteur en lecture: 42.29
Rdmodfacs> Numero du vecteur CERFACS en lecture: 10
Rdmodfacs> Valeur propre du vecteur en lecture: 72.83
Rdmodfacs> Numero du vecteur CERFACS en lecture: 11
Rdmodfacs> Valeur propre du vecteur en lecture: 81.01
Rdmodfacs> Numero du vecteur CERFACS en lecture: 12
Rdmodfacs> Valeur propre du vecteur en lecture: 96.97
Rdmodfacs> Numero du vecteur CERFACS en lecture: 13
Rdmodfacs> Valeur propre du vecteur en lecture: 104.6
Rdmodfacs> Numero du vecteur CERFACS en lecture: 14
Rdmodfacs> Valeur propre du vecteur en lecture: 112.6
Rdmodfacs> Numero du vecteur CERFACS en lecture: 15
Rdmodfacs> Valeur propre du vecteur en lecture: 118.9
Rdmodfacs> Numero du vecteur CERFACS en lecture: 16
Rdmodfacs> Valeur propre du vecteur en lecture: 130.8
Rdmodfacs> Numero du vecteur CERFACS en lecture: 17
Rdmodfacs> Valeur propre du vecteur en lecture: 142.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 18
Rdmodfacs> Valeur propre du vecteur en lecture: 149.1
Rdmodfacs> Numero du vecteur CERFACS en lecture: 19
Rdmodfacs> Valeur propre du vecteur en lecture: 159.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 20
Rdmodfacs> Valeur propre du vecteur en lecture: 163.8
Rdmodfacs> Numero du vecteur CERFACS en lecture: 21
Rdmodfacs> Valeur propre du vecteur en lecture: 164.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 22
Rdmodfacs> Valeur propre du vecteur en lecture: 185.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 23
Rdmodfacs> Valeur propre du vecteur en lecture: 188.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 24
Rdmodfacs> Valeur propre du vecteur en lecture: 190.5
Rdmodfacs> Numero du vecteur CERFACS en lecture: 25
Rdmodfacs> Valeur propre du vecteur en lecture: 202.5
Rdmodfacs> Numero du vecteur CERFACS en lecture: 26
Rdmodfacs> Valeur propre du vecteur en lecture: 204.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 27
Rdmodfacs> Valeur propre du vecteur en lecture: 215.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 28
Rdmodfacs> Valeur propre du vecteur en lecture: 226.2
Rdmodfacs> Numero du vecteur CERFACS en lecture: 29
Rdmodfacs> Valeur propre du vecteur en lecture: 230.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 30
Rdmodfacs> Valeur propre du vecteur en lecture: 231.1
Rdmodfacs> Numero du vecteur CERFACS en lecture: 31
Rdmodfacs> Valeur propre du vecteur en lecture: 237.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 32
Rdmodfacs> Valeur propre du vecteur en lecture: 240.1
Rdmodfacs> Numero du vecteur CERFACS en lecture: 33
Rdmodfacs> Valeur propre du vecteur en lecture: 244.8
Rdmodfacs> Numero du vecteur CERFACS en lecture: 34
Rdmodfacs> Valeur propre du vecteur en lecture: 250.9
Rdmodfacs> Numero du vecteur CERFACS en lecture: 35
Rdmodfacs> Valeur propre du vecteur en lecture: 254.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 36
Rdmodfacs> Valeur propre du vecteur en lecture: 266.2
Rdmodfacs> Numero du vecteur CERFACS en lecture: 37
Rdmodfacs> Valeur propre du vecteur en lecture: 267.8
Rdmodfacs> Numero du vecteur CERFACS en lecture: 38
Rdmodfacs> Valeur propre du vecteur en lecture: 277.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 39
Rdmodfacs> Valeur propre du vecteur en lecture: 280.6
Rdmodfacs> Numero du vecteur CERFACS en lecture: 40
Rdmodfacs> Valeur propre du vecteur en lecture: 284.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 41
Rdmodfacs> Valeur propre du vecteur en lecture: 291.9
Rdmodfacs> Numero du vecteur CERFACS en lecture: 42
Rdmodfacs> Valeur propre du vecteur en lecture: 294.8
Rdmodfacs> Numero du vecteur CERFACS en lecture: 43
Rdmodfacs> Valeur propre du vecteur en lecture: 298.8
Rdmodfacs> Numero du vecteur CERFACS en lecture: 44
Rdmodfacs> Valeur propre du vecteur en lecture: 300.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 45
Rdmodfacs> Valeur propre du vecteur en lecture: 305.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 46
Rdmodfacs> Valeur propre du vecteur en lecture: 315.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 47
Rdmodfacs> Valeur propre du vecteur en lecture: 320.1
Rdmodfacs> Numero du vecteur CERFACS en lecture: 48
Rdmodfacs> Valeur propre du vecteur en lecture: 324.2
Rdmodfacs> Numero du vecteur CERFACS en lecture: 49
Rdmodfacs> Valeur propre du vecteur en lecture: 329.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 50
Rdmodfacs> Valeur propre du vecteur en lecture: 331.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 51
Rdmodfacs> Valeur propre du vecteur en lecture: 336.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 52
Rdmodfacs> Valeur propre du vecteur en lecture: 343.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 53
Rdmodfacs> Valeur propre du vecteur en lecture: 349.9
Rdmodfacs> Numero du vecteur CERFACS en lecture: 54
Rdmodfacs> Valeur propre du vecteur en lecture: 350.5
Rdmodfacs> Numero du vecteur CERFACS en lecture: 55
Rdmodfacs> Valeur propre du vecteur en lecture: 357.6
Rdmodfacs> Numero du vecteur CERFACS en lecture: 56
Rdmodfacs> Valeur propre du vecteur en lecture: 361.9
Rdmodfacs> Numero du vecteur CERFACS en lecture: 57
Rdmodfacs> Valeur propre du vecteur en lecture: 363.8
Rdmodfacs> Numero du vecteur CERFACS en lecture: 58
Rdmodfacs> Valeur propre du vecteur en lecture: 372.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 59
Rdmodfacs> Valeur propre du vecteur en lecture: 382.4
Rdmodfacs> Numero du vecteur CERFACS en lecture: 60
Rdmodfacs> Valeur propre du vecteur en lecture: 385.2
Rdmodfacs> Numero du vecteur CERFACS en lecture: 61
Rdmodfacs> Valeur propre du vecteur en lecture: 392.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 62
Rdmodfacs> Valeur propre du vecteur en lecture: 405.2
Rdmodfacs> Numero du vecteur CERFACS en lecture: 63
Rdmodfacs> Valeur propre du vecteur en lecture: 411.0
Rdmodfacs> Numero du vecteur CERFACS en lecture: 64
Rdmodfacs> Valeur propre du vecteur en lecture: 424.6
Rdmodfacs> Numero du vecteur CERFACS en lecture: 65
Rdmodfacs> Valeur propre du vecteur en lecture: 444.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 66
Rdmodfacs> Valeur propre du vecteur en lecture: 472.2
Rdmodfacs> Numero du vecteur CERFACS en lecture: 67
Rdmodfacs> Valeur propre du vecteur en lecture: 500.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 68
Rdmodfacs> Valeur propre du vecteur en lecture: 525.7
Rdmodfacs> Numero du vecteur CERFACS en lecture: 69
Rdmodfacs> Valeur propre du vecteur en lecture: 548.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 70
Rdmodfacs> Valeur propre du vecteur en lecture: 567.3
Rdmodfacs> Numero du vecteur CERFACS en lecture: 71
Rdmodfacs> Valeur propre du vecteur en lecture: 623.6
Rdmodfacs> Numero du vecteur CERFACS en lecture: 72
Rdmodfacs> Valeur propre du vecteur en lecture: 670.3
Bfactors> 72 vectors, 600 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> Lowest non-zero eigenvalue : 20.540000
Bfactors> 66 eigenvectors will be considered.
Bfactors> Rotation-Tranlation modes are skipped.
Bfactors> Mass-weighted B-factors are computed.
(CHARMM units assumed for eigenvalues)
Bfactors> Correlation= 0.335 for 12 C-alpha atoms.
Bfactors> = 0.017 +/- 0.00
Bfactors> = 0.500 +/- 0.20
Bfactors> Shiftng-fct= 0.483
Bfactors> Scaling-fct= 43.395
Bfactors> Predicted, Scaled and Experimental B-factors are saved.
Bfactors> Normal end.
check_modes
getting mode 7
running: ../../bin/get_modes.sh 240129114322756599 7 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 7
calculating perturbed structure for DQ=-100
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=0
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=100
240129114322756599.eigenfacs
240129114322756599.atom
making animated gifs
11 models are in 240129114322756599.7.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 240129114322756599.7.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 240129114322756599.7.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 240129114322756599 8 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 8
calculating perturbed structure for DQ=-100
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=0
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=100
240129114322756599.eigenfacs
240129114322756599.atom
making animated gifs
11 models are in 240129114322756599.8.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 240129114322756599.8.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 240129114322756599.8.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 240129114322756599 9 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 9
calculating perturbed structure for DQ=-100
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=0
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=100
240129114322756599.eigenfacs
240129114322756599.atom
making animated gifs
11 models are in 240129114322756599.9.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 240129114322756599.9.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 240129114322756599.9.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 240129114322756599 10 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 10
calculating perturbed structure for DQ=-100
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=0
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=100
240129114322756599.eigenfacs
240129114322756599.atom
making animated gifs
11 models are in 240129114322756599.10.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 240129114322756599.10.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 240129114322756599.10.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 240129114322756599 11 -100 100 20 on 0
normal mode computation
generate a series of perturbations for mode 11
calculating perturbed structure for DQ=-100
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=-20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=0
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=20
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=40
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=60
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=80
240129114322756599.eigenfacs
240129114322756599.atom
calculating perturbed structure for DQ=100
240129114322756599.eigenfacs
240129114322756599.atom
making animated gifs
11 models are in 240129114322756599.11.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 240129114322756599.11.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 240129114322756599.11.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
240129114322756599.10.pdb
240129114322756599.11.pdb
240129114322756599.7.pdb
240129114322756599.8.pdb
240129114322756599.9.pdb
STDERR:
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
real 0m0.146s
user 0m0.116s
sys 0m0.008s
../../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: 240129114322756599.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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