anchor.diff:        common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score
         common/scores/score
         double precision score,score_max
  +!$OMP THREADPRIVATE(/stru/,/nres/,/para/,/align/,/nscore/,/scores/)
   
         d_tmp=d
    21   n_cut=0                   !number of residue-pairs dis<d, for iteration
  
positive.code:       rmsd_a=0
        rmsd2_a=0
        n_rmsd=0
        do i=1,n_str
           do j=i,n_str
              do k=1,Lch
                 x1(k)=x(k,i)
                 y1(k)=y(k,i)
                 z1(k)=z(k,i)
                 nn1(k)=k
                 x2(k)=x(k,j)
                 y2(k)=y(k,j)
                 z2(k)=z(k,j)
                 nn2(k)=k
              enddo
              call TMscore(Lch,x1,y1,z1,nn1,Lch,x2,y2,z2,nn2,TM,Rcomm,
       &                    Lcomm)
  !            armsd=dsqrt(rms/Lch) !RMSD12
              if (TM .eq. 0.0) then
                  rmsd = RMSD_max
              else
                  rmsd = 1.0/TM
              endif
  !           Make sure rmsd fits in bounds
              rmsd=min(rmsd,RMSD_max)
              rmsd=max(rmsd,RMSD_min)
  
              amat(i,j)=rmsd
              amat(j,i)=rmsd
              n_rmsd=n_rmsd+1
              rmsd_a=rmsd_a+rmsd
              rmsd2_a=rmsd2_a+rmsd*rmsd
           enddo
        enddo
        rmsd_a=rmsd_a/n_rmsd
        rmsd2_a=rmsd2_a/n_rmsd
        rmsd_delta=sqrt(rmsd2_a-rmsd_a**2) ! 68.2% is in [-d,+d]
  
negative.code:       common/scores/score
        double precision score,score_max
        dimension xa(nmax),ya(nmax),za(nmax)
  !$OMP THREADPRIVATE(/stru/,/nres/,/para/,/align/,/nscore/,/scores/)
  
        dimension x1(nmax),y1(nmax),z1(nmax),n1(nmax)
        dimension x2(nmax),y2(nmax),z2(nmax),n2(nmax)
  