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***  HYDROLASE/PROTEIN BINDING 16-JUL-21 7FD4  ***

LOGs for ID: 220323143810135347

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 = 220323143810135347.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 220323143810135347.atom to be opened. Openam> File opened: 220323143810135347.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 = 4696 First residue number = 2 Last residue number = 22 Number of atoms found = 36818 Mean number per residue = 7.8 Pdbmat> Coordinate statistics: = 138.169869 +/- 32.921268 From: 63.565000 To: 235.204000 = 137.718619 +/- 33.303693 From: 66.185000 To: 243.919000 = 139.276596 +/- 43.677774 From: 53.732000 To: 244.046000 Pdbmat> Masses are all set to one. %Pdbmat-W> residue:'UNK ' is not a well known amino-acid. %Pdbmat-W> residue:'UNK ' is not a well known amino-acid. %Pdbmat-W> residue:'UNK ' is not a well known amino-acid. %Pdbmat-W> residue:'UNK ' is not a well known amino-acid. %Pdbmat-W> residue:'UNK ' is not a well known amino-acid. %Pdbmat-W> residue:'UNK ' is not a well known amino-acid. %Pdbmat-W> residue:'UNK ' is not a well known amino-acid. %Pdbmat-W> residue:'UNK ' is not a well known amino-acid. %Pdbmat-W> residue:'UNK ' is not a well known amino-acid. %Pdbmat-W> ........ %Pdbmat-W> 22 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 -3.8133 % Filled. Pdbmat> 13054927 non-zero elements. Pdbmat> 1426236 atom-atom interactions. Pdbmat> Number per atom= 77.47 +/- 18.41 Maximum number = 126 Minimum number = 10 Pdbmat> Matrix trace = 2.852472E+07 Pdbmat> Larger element = 500.331 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 = 220323143810135347.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 500 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 220323143810135347.atom to be opened. Openam> file on opening on unit 11: 220323143810135347.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 36818 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 500 residue(s) per block. Blocpdb> 4696 residues. Blocpdb> 3991 atoms in block 1 Block first atom: 1 Blocpdb> 2127 atoms in block 2 Block first atom: 3992 Blocpdb> 3991 atoms in block 3 Block first atom: 6119 Blocpdb> 2127 atoms in block 4 Block first atom: 10110 Blocpdb> 3991 atoms in block 5 Block first atom: 12237 Blocpdb> 2127 atoms in block 6 Block first atom: 16228 Blocpdb> 3991 atoms in block 7 Block first atom: 18355 Blocpdb> 2127 atoms in block 8 Block first atom: 22346 Blocpdb> 3991 atoms in block 9 Block first atom: 24473 Blocpdb> 2127 atoms in block 10 Block first atom: 28464 Blocpdb> 3991 atoms in block 11 Block first atom: 30591 Blocpdb> 2127 atoms in block 12 Block first atom: 34582 Blocpdb> 110 atoms in block 13 Block first atom: 36708 Blocpdb> 13 blocks. Blocpdb> At most, 3991 atoms in each of them. Blocpdb> At least, 110 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> 78 eigenvectors, only, can be determined. Diagrtb> Memory allocation for RTB_to_modes. %Diagrtb-Er> IIWKMX up to: 286805459 Maximum allowed is LIWORK= 5000000 %Diagrtb-Er> IRWKMX up to: 1465818472 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 0m0.209s user 0m0.204s 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.