subroutine proc_cont
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'DIMENSIONS.FREE'
      include 'DIMENSIONS.COMPAR'
      include 'COMMON.IOUNITS'
      include 'COMMON.TIME1'
      include 'COMMON.SBRIDGE'
      include 'COMMON.CONTROL'
      include 'COMMON.COMPAR'
      include 'COMMON.CHAIN'
      include 'COMMON.HEADER'
      include 'COMMON.CONTACTS1'
      include 'COMMON.PEPTCONT'
      include 'COMMON.GEO'
      write (iout,*) "proc_cont: nlevel",nlevel
      if (nlevel.lt.0) then
        write (iout,*) "call define_fragments"
        call define_fragments
      else
        write (iout,*) "call secondary2"
        call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,
     &     isec_ref)
      endif
      write (iout,'(80(1h=))')
      write (iout,*) "Electrostatic contacts"
      call contacts_between_fragments(.true.,0,ncont_pept_ref,
     & icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
      write (iout,'(80(1h=))')
      write (iout,*) "Side chain contacts"
      call contacts_between_fragments(.true.,0,ncont_ref,
     & icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
      if (nlevel.lt.0) then
        do i=1,nfrag(1)
          ind=icant(i,i)
          len_cut=1000
          if (istruct(i).le.1) then
            len_cut=max0(len_frag(i,1)*4/5,3)
          else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
            len_cut=max0(len_frag(i,1)*2/5,3)
          endif
          write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",
     &      ncont_frag_ref(ind)," len_cut",len_cut,
     &      " icont_single",icont_single," iloc_single",iloc_single
          iloc(i)=iloc_single
          if (iloc(i).gt.0) write (iout,*) 
     &     "Local structure used to compare structure of fragment",i,
     &     " to native."
          if (istruct(i).ne.3 .and. istruct(i).ne.0 
     &        .and. icont_single.gt.0 .and. 
     &        ncont_frag_ref(ind).ge.len_cut) then
            write (iout,*) "Electrostatic contacts used to compare",
     &       " structure of fragment",i," to native."
            ielecont(i,1)=1
            isccont(i,1)=0
          else if (icont_single.gt.0 .and. nsccont_frag_ref(ind)
     &      .ge.len_cut) then
            write (iout,*) "Side chain contacts used to compare",
     &       " structure of fragment",i," to native."
            isccont(i,1)=1
            ielecont(i,1)=0
          else
            write (iout,*) "Contacts not used to compare",
     &       " structure of fragment",i," to native."
            ielecont(i,1)=0
            isccont(i,1)=0
            nc_req_setf(i,1)=0
          endif
          if (irms_single.gt.0 .or. isccont(i,1).eq.0 
     &         .and. ielecont(i,1).eq.0) then
            write (iout,*) "RMSD used to compare",
     &       " structure of fragment",i," to native."
            irms(i,1)=1
          else
            write (iout,*) "RMSD not used to compare",
     &       " structure of fragment",i," to native."
            irms(i,1)=0
          endif
        enddo
      endif
      if (nlevel.lt.-1) then
        call define_pairs
        nlevel = -nlevel
        if (nlevel.gt.3) nlevel=3
        if (nlevel.eq.3) then
          nfrag(3)=1
          npiece(1,3)=nfrag(1)
          do i=1,nfrag(1)
            ipiece(i,1,3)=i
          enddo
          ielecont(1,3)=0
          isccont(1,3)=0
          irms(1,3)=1
          n_shift(1,1,3)=0
          n_shift(2,1,3)=0
        endif 
      else if (nlevel.eq.-1) then
        nlevel=1
      endif
      isnfrag(1)=0
      do i=1,nlevel
        isnfrag(i+1)=isnfrag(i)+nfrag(i)
      enddo
      ndigit=3*nfrag(1)
      do i=2,nlevel
        ndigit=ndigit+2*nfrag(i)
      enddo
      write (iout,*) "ndigit",ndigit
      if (.not.binary .and. ndigit.gt.30) then
        write (iout,*) "Highest class too large; switching to",
     &    " binary representation."
        binary=.true.
      endif
      write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
      write(iout,*) "rmscut_base_up",rmscut_base_up,
     & " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
      do i=1,nlevel
        do j=1,nfrag(i)
          length_frag = 0
          if (i.eq.1) then
            do k=1,npiece(j,i)
              length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
            enddo
          else
            do k=1,npiece(j,i)
              length_frag=length_frag+len_frag(ipiece(k,j,i),1)
            enddo
          endif
          len_frag(j,i)=length_frag
          rmscutfrag(1,j,i)=rmscut_base_up*length_frag
          rmscutfrag(2,j,i)=rmscut_base_low*length_frag 
          if (rmscutfrag(1,j,i).lt.rmsup_lim) 
     &      rmscutfrag(1,j,i)=rmsup_lim
          if (rmscutfrag(1,j,i).gt.rmsupup_lim) 
     &      rmscutfrag(1,j,i)=rmsupup_lim
        enddo
      enddo
      write (iout,*) "Level",1," number of fragments:",nfrag(1)
      do j=1,nfrag(1)
        write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),
     &    k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),
     &    rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),
     &    ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),
     &    nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
      enddo
      do i=2,nlevel
        write (iout,*) "Level",i," number of fragments:",nfrag(i)
        do j=1,nfrag(i)
          write (iout,*) npiece(j,i),(ipiece(k,j,i),
     &      k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),
     &      rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),
     &      nc_fragm(j,i),nc_req_setf(j,i) 
        enddo
      enddo
      return
      end