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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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[878, 878]:
    Comparing 1dm9_A and 1dm9_A, based on their crossing files.
    There are 10 (4 H + 6 S) secondary structure elements in 1dm9_A, of which 9 satisfy the size requirements.
    There are 10 (4 H + 6 S) secondary structure elements in 1dm9_A, of which 9 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10))       0.000     {0/31:36}  B:0
  1.29695 [ 1.29695]   ((1 . 1) (2 . 2) (3 . 3) (7 . 6) (8 . 8) (9 . 9) (10 . 10))       6.022     {1/19:21}  B:0
  1.50185 [ 1.50185]   ((1 . 1) (2 . 2) (3 . 3) (6 . 7) (8 . 8) (10 . 10))       6.360     {0/13:15}  B:0
  2.25005 [ 2.25005]   ((3 . 3) (5 . 6) (8 . 8) (10 . 10))       3.469     {0/3:6}  B:0
  2.25076 [ 2.25076]   ((5 . 3) (6 . 5) (9 . 6) (10 . 8))       6.902     {0/2:6}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[878, 1519]:
    Comparing 1dm9_A and 1fjg_D, based on their crossing files.
    There are 10 (4 H + 6 S) secondary structure elements in 1dm9_A, of which 9 satisfy the size requirements.
    There are 15 (11 H + 4 S) secondary structure elements in 1fjg_D, of which 15 satisfy the size requirements.
  1.80001 [ 3.00000]   ((1 . 7) (2 . 8) (3 . 9) (5 . 10) (9 . 13))       2.053     {0/8:10}  B:0
  2.25159 [ 3.75034]   ((1 . 8) (7 . 13) (9 . 14) (10 . 15))       8.309     {0/5:6}  B:0
  2.25305 [ 3.75066]   ((1 . 8) (2 . 11) (7 . 13) (10 . 15))       9.774     {0/6:6}  B:0
  2.40873 [ 3.78752]   ((2 . 7) (5 . 9) (7 . 10) (8 . 12))      12.015     {1/6:6}  B:0
  2.43044 [ 3.20410]   ((1 . 7) (2 . 8) (3 . 9) (5 . 10) (8 . 12))       4.933     {2/9:10}  B:0
SIMILARITY (1/min{score1}):   0.6666      [and  1/min{score2}:   0.4000]

[878, 2060]:
    Comparing 1dm9_A and 1h3f_A, based on their crossing files.
    There are 10 (4 H + 6 S) secondary structure elements in 1dm9_A, of which 9 satisfy the size requirements.
    There are 34 (21 H + 13 S) secondary structure elements in 1h3f_A, of which 8 satisfy the size requirements.
  1.80003 [ 1.60005]   ((1 . 28) (2 . 29) (3 . 30) (5 . 33) (6 . 34))       2.640     {0/8:10}  B:0
  2.25154 [ 2.00219]   ((2 . 28) (5 . 30) (6 . 33) (9 . 34))       8.234     {0/4:6}  B:0
  3.86821 [ 3.85997]   ((1 . 28) (2 . 29) (3 . 30) (5 . 33) (6 . 34) (9 . 25))       3.108     {5/13:15}  B:1
SIMILARITY (1/min{score1}):   0.5555      [and  1/min{score2}:   0.6250]

[878, 2865]:
    Comparing 1dm9_A and 1jh3_A, based on their crossing files.
    There are 10 (4 H + 6 S) secondary structure elements in 1dm9_A, of which 9 satisfy the size requirements.
    There are 8 (3 H + 5 S) secondary structure elements in 1jh3_A, of which 7 satisfy the size requirements.
  2.25011 [ 1.75023]   ((1 . 3) (2 . 4) (3 . 5) (7 . 8))       4.217     {0/6:6}  B:0
  2.54296 [ 2.24865]   ((1 . 1) (2 . 3) (5 . 5) (9 . 8))      10.545     {1/5:6}  B:0
  2.83623 [ 2.63842]   ((1 . 1) (3 . 2) (6 . 5) (9 . 7))       5.822     {1/4:6}  B:0
  2.83635 [ 2.63857]   ((2 . 1) (3 . 2) (6 . 5) (9 . 7))       6.572     {1/4:6}  B:0
  2.57745 [ 2.52925]   ((1 . 3) (2 . 4) (3 . 5) (5 . 7) (7 . 2) (9 . 8))       4.752     {3/12:15}  B:1
SIMILARITY (1/min{score1}):   0.4444      [and  1/min{score2}:   0.5714]

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