Should you encounter any unexpected behaviour,
please let us know.

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

• K. Suhre & Y.H. Sanejouand, ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research, 32, W610-W614, 2004.
• K. Suhre & Y.H. Sanejouand, On the potential of normal mode analysis for solving difficult molecular replacement problems. Acta Cryst. D vol.60, p796-799, 2004 © International Union of Crystallography.