double precision function rmscalc(ishif,i,j,jcon,lprn)
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'DIMENSIONS.COMPAR'
      include 'COMMON.IOUNITS'
      include 'COMMON.COMPAR'
      include 'COMMON.CHAIN' 
      include 'COMMON.INTERACT'
      include 'COMMON.VAR'
      include 'COMMON.CONTROL'
      double precision przes(3),obrot(3,3)
      double precision creff(3,maxres2),cc(3,maxres2)
      logical iadded(maxres)
      integer inumber(2,maxres)
      common /ccc/ creff,cc,iadded,inumber
      logical lprn
      logical non_conv
      integer ishif,i,j
      if (lprn) then
        write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
        write (iout,*) "npiece",npiece(j,i)
        call flush(iout)
      endif
c      write (iout,*) "symetr",symetr
c      call flush(iout)
      nperm=1
      do idup=1,symetr
      nperm=nperm*idup
      enddo
c      write (iout,*) "nperm",nperm
c      call flush(iout)
      do kkk=1,nperm
      idup=0
      do l=1,nres
        iadded(l)=.false.
      enddo
c      write (iout,*) "kkk",kkk
c      call flush(iout)
      do k=1,npiece(j,i)
        if (i.eq.1) then
          if (lprn) then
            write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",
     &         ifrag(1,k,j),ifrag(2,k,j)
            call flush(iout)
          endif
          call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,idup,kkk)
c          write (iout,*) "Exit cprep"
c          call flush(iout)
c          write (iout,*) "ii=",ii
        else
          kk = ipiece(k,j,i)
c          write (iout,*) "kk",kk," npiece",npiece(kk,1)
          do l=1,npiece(kk,1)
            if (lprn) then
              write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,
     &          " l=",l," adding fragment",
     &          ifrag(1,l,kk),ifrag(2,l,kk)
              call flush(iout)
            endif
            call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,idup,kkk)
c            write (iout,*) "After cprep"
c            call flush(iout)
          enddo 
        endif
      enddo
      enddo
      if (lprn) then
        write (iout,*) "tuszukaj"
        do kkk=1,nperm
          do k=1,idup
            write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),
     &        inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
          enddo
        enddo
        call flush(iout)
      endif
      rminrms=1.0d10
      do kkk=1,nperm
      call fitsq(rms,cc(1,1),creff(1,1),idup,przes,obrot,non_conv)
      if (non_conv) then
        print *,'Error: FITSQ non-convergent, jcon',jcon,i
        rms = 1.0d10
      else if (rms.lt.-1.0d-6) then 
        print *,'Error: rms^2 = ',rms,jcon,i
        rms = 1.0d10
      else if (rms.ge.1.0d-6 .and. rms.lt.0) then
        rms = 0.0d0
      endif
c      write (iout,*) "rmsmin", rminrms, "rms", rms
      if (rms.le.rminrms) rminrms=rms
      enddo
      rmscalc = dsqrt(rminrms)
c      write (iout, *) "analysys", rmscalc,anatemp
      return
      end
c-------------------------------------------------------------------------
      subroutine cprep(if1,if2,ishif,idup,kwa)
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'DIMENSIONS.COMPAR'
      include 'COMMON.CONTROL'
      include 'COMMON.IOUNITS'
      include 'COMMON.COMPAR'
      include 'COMMON.CHAIN' 
      include 'COMMON.INTERACT'
      include 'COMMON.VAR'
      double precision przes(3),obrot(3,3)
      double precision creff(3,maxres2),cc(3,maxres2)
      logical iadded(maxres)
      integer inumber(2,maxres),iistrart,kwa,blar
      common /ccc/ creff,cc,iadded,inumber
c      write (iout,*) "Calling cprep symetr",symetr," kwa",kwa
      nperm=1
      do blar=1,symetr
      nperm=nperm*blar
      enddo
c      write (iout,*) "nperm",nperm
      kkk=kwa
c      ii=0
      do l=if1,if2
c        write (iout,*) "l",l," iadded",iadded(l)
c        call flush(iout)
        if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l)) 
     &  then
          idup=idup+1
          iadded(l)=.true.
          inumber(1,idup)=l
          inumber(2,idup)=l+ishif
          do m=1,3
            creff(m,idup)=cref(m,l,kkk)
            cc(m,idup)=c(m,l+ishif)
          enddo
        endif
      enddo
      return
      end
c-------------------------------------------------------------------------
      double precision function rmsnat(jcon)
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'DIMENSIONS.COMPAR'
      include 'COMMON.IOUNITS'
      include 'COMMON.COMPAR'
      include 'COMMON.CHAIN' 
      include 'COMMON.INTERACT'
      include 'COMMON.VAR'
      include 'COMMON.CONTROL'
      double precision przes(3),obrot(3,3),cc(3,2*maxres),
     &   ccref(3,2*maxres)
      logical non_conv
      integer ishif,i,j,resprzesun
      rminrms=10.0d10
      rmsminsing=10d10
      nperm=1
      do i=1,symetr
       nperm=nperm*i
      enddo
      do kkk=1,nperm
       nnsup=0
       do i=1,nres
        if (itype(i).ne.21) then
          nnsup=nnsup+1
          do j=1,3
            cc(j,nnsup)=c(j,i)
            ccref(j,nnsup)=cref(j,i,kkk)
          enddo
        endif
       enddo
       call fitsq(rms,cc(1,1),ccref(1,1),nnsup,przes,obrot,non_conv)
       if (non_conv) then
        print *,'Error: FITSQ non-convergent, jcon',jcon,i
        rms=1.0d10
       else if (rms.lt.-1.0d-6) then 
        print *,'Error: rms^2 = ',rms,jcon,i
        rms = 1.0d10
       else if (rms.ge.1.0d-6 .and. rms.lt.0) then
        rms=0.0d0
       endif
       if (rms.le.rminrms) rminrms=rms
c       write (iout,*) "kkk",kkk," rmsnat",rms , rminrms
      enddo
      rmsnat = dsqrt(rminrms)
C      write (iout,*)  "analysys",rmsnat, anatemp
C      liczenie rmsdla pojedynczego lancucha
      return
      end
c-----------------------------------------------------------------------------
      double precision function gyrate(jcon)
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'COMMON.INTERACT'
      include 'COMMON.CHAIN'
      double precision cen(3),rg

      do j=1,3
       cen(j)=0.0d0
      enddo

      do i=nnt,nct
          do j=1,3
            cen(j)=cen(j)+c(j,i)
          enddo
      enddo
      do j=1,3
            cen(j)=cen(j)/dble(nct-nnt+1)
      enddo
      rg = 0.0d0
      do i = nnt, nct
        do j=1,3
         rg = rg + (c(j,i)-cen(j))**2
        enddo
      end do
      gyrate = dsqrt(rg/dble(nct-nnt+1))
      return
      end