remarks file: nmr_relaxation/rfactor.inp
remarks
remarks Author: Michael Nilges and Axel T. Brunger

!
! Please cite the following papers when using this protocol:
! 1. Nilges, M., Habazettl, J., Brunger, A.T., and  Holak, T.A. (1991).  
!    Relaxation Matrix Refinement of the Solution Structure of Squash 
!    Trypsin-Inhibitor, J. Mol. Biol. 219, 499-510.
! 2. Yip, P. and  Case, D. A. (1989).  A New Method for 
!    Refinement of Macromolecular Structures based on Nuclear 
!    Overhauser Effect Spectra, J. Magn. Reson. 83, 643-648.
!

structure @c2.psf end                                {*Read structure file.*}
coor @c2_01_ref.pdb                                     {*Read coordinates.*}

relaxation
    nrestraints 200                        {*Expected number of restraints.*}

{*========================== Specify the physical parameters of the system.*}

    group      DMSO                 {*A group of spectra, DMSO, is defined.*}
    unresolved DMSO                      
        methyl                             {*Methyl protons are unresolved.*}
    end
    average 3                               {*R-3 average to methyl groups.*}
    omega      DMSO 500.0e6                {*Spectrometer frequency, in Hz.*}
    taucorrel  DMSO                              {*Correlation times, in s.*}
        model lipari                                    {*Order parameters.*}
        vector (name hn or name ha) 
               (name hn or name ha)                     0.75e-9 0.85 
        vector (name hn or name ha) 
               (name h* and not (name hn or name ha))   0.75e-9 0.80 
        vector (name h* and not (name hn or name ha)) 
               (name h* and not (name hn or name ha))   0.75e-9 0.65
    end 

    classification D300                    {*Define a classification, D300,*}
    @c2_300.int 

    clgroup     D300 DMSO                  {*which belongs to group DMSO.  *}
    taumix      D300 0.30                              {*Mixing time, in s.*}
    minint      D300 0.05                   {*Minimum measurable intensity.*}

    cutoff                             
        mode all  value 4.5
    end

{*============================================  Calculation of R-6 R value.*}

    set print c2_r6.disp end             {*Open output file for deviations.*}

    potential parabola                      {*Error estimates are not used.*}
    iexp 0.1666666667                     {*Dev = I_calc^iexp - I_obs^iexp.*}

    calibrate
        quality 0.33  automatic off  reference all  group class  
    end

    print threshold -0.1 end   {*List all deviations and calculate R value.*} 

{*==========================================  Calculation of X-ray R value.*}

    set print c2_X.disp end              {*Open output file for deviations.*}

    potential parabola                      {*Error estimates are not used.*}
    iexp 0.1666666667                     {*Dev = I_calc^iexp - I_obs^iexp.*}

    calibrate
        quality 0.33  automatic off  reference all  group class  
    end

    print threshold -0.1 end        {*List all peaks and calculate R value.*} 
end

stop