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Will print the top 5 alignments (based on backbone shifts) for each pairing of chains, as measured by a combination of score and contiguity.
Some relevant parameters:  
        HELIX min length: 5     STRAND min length: 3
        shift-tolerance = -10    permissible-violations = 4   max-breaks = NIL   retain-m = 100   best-n = 100
        anglethresh = 0.5    septhresh = 5   min_length = 4   rmsd-tol = 9.9999999999999E12

Legend:
 score1 [score2]   pairings     L2ERR        {Xbad/Xsig:Xtot}  Breaks

(score2 is the score from protein2's perspective, not the minimum of the two perspectives as in some earlier printouts.)

Recall that "SIMILARITY" refers to similarities over all alignments not just the top ones.

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[61, 61]:
    Comparing 1a79_A and 1a79_A, based on their crossing files.
    There are 17 (6 H + 11 S) secondary structure elements in 1a79_A, of which 7 satisfy the size requirements.
    There are 17 (6 H + 11 S) secondary structure elements in 1a79_A, of which 7 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8))       0.000     {0/19:21}  B:0
  2.24460 [ 2.24460]   ((1 . 2) (3 . 3) (6 . 6) (8 . 8))       4.192     {1/5:6}  B:0
  2.24460 [ 2.24460]   ((2 . 1) (3 . 3) (6 . 6) (8 . 8))       4.192     {1/5:6}  B:0
  4.03651 [ 4.03651]   ((5 . 1) (6 . 3) (7 . 2) (8 . 6))       8.929     {2/5:6}  B:1
  4.03651 [ 4.03651]   ((1 . 5) (2 . 7) (3 . 6) (6 . 8))       8.929     {2/5:6}  B:1
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[61, 1020]:
    Comparing 1a79_A and 1e3m_A, based on their crossing files.
    There are 17 (6 H + 11 S) secondary structure elements in 1a79_A, of which 7 satisfy the size requirements.
    There are 60 (33 H + 27 S) secondary structure elements in 1e3m_A, of which 9 satisfy the size requirements.
  1.16686 [ 1.50009]   ((1 . 3) (2 . 4) (3 . 5) (5 . 7) (6 . 8) (7 . 9))       3.011     {0/11:15}  B:0
  1.40067 [ 1.80031]   ((2 . 3) (3 . 5) (5 . 7) (6 . 8) (7 . 9))       4.678     {0/6:10}  B:0
  2.89757 [ 2.96368]   ((1 . 3) (2 . 4) (3 . 5) (5 . 6) (6 . 8))       5.213     {2/7:10}  B:0
  4.03634 [ 4.09675]   ((3 . 2) (5 . 4) (6 . 5) (7 . 6))       7.615     {2/5:6}  B:0
  1.75362 [ 2.25171]   ((3 . 2) (6 . 5) (7 . 4) (8 . 8))       8.450     {0/5:6}  B:1
SIMILARITY (1/min{score1}):   0.8570      [and  1/min{score2}:   0.6666]

[61, 1288]:
    Comparing 1a79_A and 1ewq_A, based on their crossing files.
    There are 17 (6 H + 11 S) secondary structure elements in 1a79_A, of which 7 satisfy the size requirements.
    There are 56 (30 H + 26 S) secondary structure elements in 1ewq_A, of which 9 satisfy the size requirements.
  1.16703 [ 1.50017]   ((1 . 2) (2 . 3) (3 . 4) (5 . 6) (6 . 7) (7 . 8))       3.504     {0/11:15}  B:0
  4.03632 [ 4.09673]   ((3 . 1) (5 . 3) (6 . 4) (7 . 5))       7.414     {2/5:6}  B:0
  1.75344 [ 2.25162]   ((3 . 1) (6 . 4) (7 . 3) (8 . 7))       8.344     {0/5:6}  B:1
  1.75383 [ 2.25181]   ((1 . 3) (2 . 2) (3 . 4) (5 . 5))       8.573     {0/4:6}  B:1
SIMILARITY (1/min{score1}):   0.8569      [and  1/min{score2}:   0.6666]

[61, 5515]:
    Comparing 1a79_A and 1r0v_A, based on their crossing files.
    There are 17 (6 H + 11 S) secondary structure elements in 1a79_A, of which 7 satisfy the size requirements.
    There are 24 (9 H + 15 S) secondary structure elements in 1r0v_A, of which 8 satisfy the size requirements.
  1.26049 [ 1.34064]   ((1 . 8) (2 . 9) (3 . 10) (5 . 12) (6 . 13) (7 . 14) (8 . 15))       1.972     {2/18:21}  B:0
  2.55937 [ 2.59889]   ((2 . 8) (3 . 10) (6 . 13) (7 . 14) (8 . 15))       3.837     {2/8:10}  B:0
  2.24672 [ 2.38029]   ((1 . 12) (2 . 14) (3 . 13) (6 . 15))       9.020     {1/5:6}  B:1
  3.35900 [ 3.37674]   ((1 . 9) (2 . 8) (3 . 10) (6 . 13) (8 . 15))       4.140     {3/9:10}  B:1
SIMILARITY (1/min{score1}):   0.7933      [and  1/min{score2}:   0.7459]

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