double precision function rmsnat(ib,jcon,iref,iprot)
      implicit none
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.IOUNITS'
      include 'COMMON.COMPAR'
      include 'COMMON.CHAIN' 
      include 'COMMON.INTERACT'
      include 'COMMON.VAR'
      double precision creff(3,maxres2),cc(3,maxres2)
      integer jcon,ib,iref,iprot
      double precision rmscalc
      rmsnat=rmscalc(c(1,1),cref(1,1,iref,ib,iprot),jcon,iref,iprot)
      return
      end
c------------------------------------------------------------------------
      double precision function rmscalc(ccc,cccref,jcon,iref,iprot)
      implicit none
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.IOUNITS'
      include 'COMMON.COMPAR'
      include 'COMMON.CHAIN' 
      include 'COMMON.INTERACT'
      include 'COMMON.VAR'
      double precision cccref(3,maxres2),creff(3,maxres2),
     &  ccc(3,maxres2),cc(3,maxres2)
      double precision przes(3),obrot(3,3)
      logical non_conv
      integer ishif,i,ii,j,jcon,ib,iref,iprot
      double precision rms
      ii=0
      if (.not.sconly(iprot)) then
        do i=nstart_sup(iprot),nend_sup(iprot)
          if (itype(i).ne.ntyp1) then
            ii=ii+1
            do j=1,3
              cc(j,ii)=ccc(j,i)
              creff(j,ii)=cccref(j,i)
            enddo
          endif
        enddo
      endif
      do i=nstart_sup(iprot),nend_sup(iprot)
        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
          ii=ii+1
          do j=1,3
            cc(j,ii)=ccc(j,i+nres)
            creff(j,ii)=cccref(j,i+nres)
          enddo
        endif
      enddo
      write (iout,*) "rmscalc: iprot",iprot," nsup",nsup(iprot)," ii",ii
      call fitsq(rms,cc(1,1),creff(1,1),ii,przes,obrot,non_conv)
      if (non_conv) then
        write (iout,*) 'Error: FITSQ non-convergent, iprot',iprot,
     &   ' jcon',jcon,' iref',iref
        rmscalc=1.0d2
      else if (rms.lt.-1.0d-6) then 
        print *,'Error: rms^2 = ',rms,jcon
        rmscalc = 1.0d2
      else if (rms.ge.1.0d-6 .and. rms.lt.0) then
        rmscalc=0.0d0
      else 
        rmscalc = dsqrt(rms)
      endif
      return
      end