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***  HYDROLASE 23-OCT-17 6BDF  ***

LOGs for ID: 21091408552152716

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 = 21091408552152716.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 21091408552152716.atom to be opened. Openam> File opened: 21091408552152716.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 = 5908 First residue number = 13 Last residue number = 201 Number of atoms found = 45654 Mean number per residue = 7.7 Pdbmat> Coordinate statistics: = 144.650846 +/- 28.100868 From: 84.018000 To: 205.283000 = 144.656432 +/- 28.100866 From: 85.318000 To: 205.050000 = 143.992417 +/- 43.943037 From: 61.550000 To: 226.435000 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 2.2517 % Filled. Pdbmat> 17775423 non-zero elements. Pdbmat> 1944991 atom-atom interactions. Pdbmat> Number per atom= 85.21 +/- 20.42 Maximum number = 129 Minimum number = 12 Pdbmat> Matrix trace = 3.889982E+07 Pdbmat> Larger element = 507.322 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. 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 = 21091408552152716.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 200 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 21091408552152716.atom to be opened. Openam> file on opening on unit 11: 21091408552152716.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 45654 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 200 residue(s) per block. Blocpdb> 5908 residues. Blocpdb> 1543 atoms in block 1 Block first atom: 1 Blocpdb> 177 atoms in block 2 Block first atom: 1544 Blocpdb> 1533 atoms in block 3 Block first atom: 1721 Blocpdb> 8 atoms in block 4 Block first atom: 3254 Blocpdb> 1543 atoms in block 5 Block first atom: 3262 Blocpdb> 177 atoms in block 6 Block first atom: 4805 Blocpdb> 1533 atoms in block 7 Block first atom: 4982 Blocpdb> 8 atoms in block 8 Block first atom: 6515 Blocpdb> 1543 atoms in block 9 Block first atom: 6523 Blocpdb> 177 atoms in block 10 Block first atom: 8066 Blocpdb> 1533 atoms in block 11 Block first atom: 8243 Blocpdb> 8 atoms in block 12 Block first atom: 9776 Blocpdb> 1543 atoms in block 13 Block first atom: 9784 Blocpdb> 177 atoms in block 14 Block first atom: 11327 Blocpdb> 1533 atoms in block 15 Block first atom: 11504 Blocpdb> 8 atoms in block 16 Block first atom: 13037 Blocpdb> 1543 atoms in block 17 Block first atom: 13045 Blocpdb> 177 atoms in block 18 Block first atom: 14588 Blocpdb> 1533 atoms in block 19 Block first atom: 14765 Blocpdb> 8 atoms in block 20 Block first atom: 16298 Blocpdb> 1543 atoms in block 21 Block first atom: 16306 Blocpdb> 177 atoms in block 22 Block first atom: 17849 Blocpdb> 1533 atoms in block 23 Block first atom: 18026 Blocpdb> 8 atoms in block 24 Block first atom: 19559 Blocpdb> 1543 atoms in block 25 Block first atom: 19567 Blocpdb> 177 atoms in block 26 Block first atom: 21110 Blocpdb> 1533 atoms in block 27 Block first atom: 21287 Blocpdb> 8 atoms in block 28 Block first atom: 22820 Blocpdb> 1543 atoms in block 29 Block first atom: 22828 Blocpdb> 177 atoms in block 30 Block first atom: 24371 Blocpdb> 1533 atoms in block 31 Block first atom: 24548 Blocpdb> 8 atoms in block 32 Block first atom: 26081 Blocpdb> 1543 atoms in block 33 Block first atom: 26089 Blocpdb> 177 atoms in block 34 Block first atom: 27632 Blocpdb> 1533 atoms in block 35 Block first atom: 27809 Blocpdb> 8 atoms in block 36 Block first atom: 29342 Blocpdb> 1543 atoms in block 37 Block first atom: 29350 Blocpdb> 177 atoms in block 38 Block first atom: 30893 Blocpdb> 1533 atoms in block 39 Block first atom: 31070 Blocpdb> 8 atoms in block 40 Block first atom: 32603 Blocpdb> 1543 atoms in block 41 Block first atom: 32611 Blocpdb> 177 atoms in block 42 Block first atom: 34154 Blocpdb> 1533 atoms in block 43 Block first atom: 34331 Blocpdb> 8 atoms in block 44 Block first atom: 35864 Blocpdb> 1543 atoms in block 45 Block first atom: 35872 Blocpdb> 177 atoms in block 46 Block first atom: 37415 Blocpdb> 1533 atoms in block 47 Block first atom: 37592 Blocpdb> 8 atoms in block 48 Block first atom: 39125 Blocpdb> 1543 atoms in block 49 Block first atom: 39133 Blocpdb> 177 atoms in block 50 Block first atom: 40676 Blocpdb> 1533 atoms in block 51 Block first atom: 40853 Blocpdb> 8 atoms in block 52 Block first atom: 42386 Blocpdb> 1543 atoms in block 53 Block first atom: 42394 Blocpdb> 177 atoms in block 54 Block first atom: 43937 Blocpdb> 1533 atoms in block 55 Block first atom: 44114 Blocpdb> 8 atoms in block 56 Block first atom: 45646 Blocpdb> 56 blocks. Blocpdb> At most, 1543 atoms in each of them. Blocpdb> At least, 8 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> IIWKMX up to: 42955283 Maximum allowed is LIWORK= 5000000 %Diagrtb-Er> IRWKMX up to: 655424740 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 0m0.242s user 0m0.236s sys 0m0.004s




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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: October 18th, 2018.