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     = 22121818045850962.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 22121818045850962.atom to be opened.

 Openam> File opened: 22121818045850962.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 =   4084
            First residue number     =      5
            Last  residue number     =    166
            Number of atoms found    =  32038
            Mean number per residue  =      7.8

 Pdbmat> Coordinate statistics: 
 =   146.533569 +/-    16.702193 From:    97.972000 To:   190.265000
 =   147.196863 +/-    21.758019 From:    87.639000 To:   203.101000
 =   133.554071 +/-    69.653081 From:     3.437000 To:   284.593000
 Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'MG  ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG  ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG  ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG  ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG  ' is not a well known amino-acid.
%Pdbmat-W> ........

%Pdbmat-W>     18 residue(s) not known.

 Openam> File opened: pdbmat.xyzm
 Pdbmat> Coordinates and masses considered are saved.

 Openam> File opened: pdbmat.sdijf

 Pdbmat> Matrix statistics:

 Pdbmat> The matrix is   3.7716 % Filled.
 Pdbmat>     12221268  non-zero elements.
 Pdbmat>      1336780 atom-atom interactions.

 Pdbmat> Number per atom=     83.45 +/-     20.14
         Maximum number =    132
         Minimum number =     13

 Pdbmat> Matrix trace   = 2.673560E+07
 Pdbmat> Larger element =  511.071    
 Pdbmat>      0 elements larger than +/-  1.0E+10

 Pdbmat> Normal end.
using diagstd (there are 32038 atoms in your structure)
 
ERROR: number of atoms is too large to use diagstd, that is, over 500
       please choose another option for NRBL (not diagstd)



STDERR:

• 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.