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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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[5346, 2131]:
    Comparing 1qhv_A and 1h7z_A, based on their crossing files.
    There are 16 (6 H + 10 S) secondary structure elements in 1qhv_A, of which 9 satisfy the size requirements.
    There are 12 (3 H + 9 S) secondary structure elements in 1h7z_A, of which 9 satisfy the size requirements.
  1.12505 [ 1.12505]   ((2 . 1) (3 . 2) (4 . 3) (6 . 5) (11 . 9) (13 . 10) (15 . 11) (16 . 12))       2.113     {0/19:28}  B:0
  1.80198 [ 1.80198]   ((4 . 2) (6 . 3) (13 . 9) (15 . 10) (16 . 11))       7.425     {0/4:10}  B:0
  1.80260 [ 1.80260]   ((3 . 1) (4 . 2) (6 . 3) (13 . 9) (15 . 10))       7.946     {0/4:10}  B:0
  2.25104 [ 2.25104]   ((3 . 3) (11 . 10) (13 . 11) (15 . 12))       7.470     {0/3:6}  B:0
  2.25188 [ 2.25188]   ((11 . 1) (13 . 2) (15 . 3) (16 . 5))       8.661     {0/1:6}  B:0
SIMILARITY (1/min{score1}):   0.8888      [and  1/min{score2}:   0.8888]

[5346, 3332]:
    Comparing 1qhv_A and 1kke_A, based on their crossing files.
    There are 16 (6 H + 10 S) secondary structure elements in 1qhv_A, of which 9 satisfy the size requirements.
    There are 20 (2 H + 18 S) secondary structure elements in 1kke_A, of which 6 satisfy the size requirements.
 NO SIMILARITY!

[5346, 5346]:
    Comparing 1qhv_A and 1qhv_A, based on their crossing files.
    There are 16 (6 H + 10 S) secondary structure elements in 1qhv_A, of which 9 satisfy the size requirements.
    There are 16 (6 H + 10 S) secondary structure elements in 1qhv_A, of which 9 satisfy the size requirements.
  1.00000 [ 1.00000]   ((2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (11 . 11) (13 . 13) (15 . 15) (16 . 16))       0.000     {0/27:36}  B:0
  1.80160 [ 1.80160]   ((4 . 3) (6 . 4) (13 . 11) (15 . 13) (16 . 15))       7.030     {0/4:10}  B:0
  1.80160 [ 1.80160]   ((3 . 4) (4 . 6) (11 . 13) (13 . 15) (15 . 16))       7.030     {0/4:10}  B:0
  2.25108 [ 2.25108]   ((2 . 11) (3 . 13) (4 . 15) (6 . 16))       7.539     {0/1:6}  B:0
  2.25108 [ 2.25108]   ((11 . 2) (13 . 3) (15 . 4) (16 . 6))       7.539     {0/1:6}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

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