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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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[4983, 915]:
    Comparing 1pda and 1dq3_A, based on their crossing files.
    There are 25 (12 H + 13 S) secondary structure elements in 1pda, of which 6 satisfy the size requirements.
    There are 44 (14 H + 30 S) secondary structure elements in 1dq3_A, of which 7 satisfy the size requirements.
  1.20131 [ 1.40083]   ((20 . 33) (21 . 34) (22 . 35) (23 . 36) (24 . 39))       4.938     {0/2:10}  B:0
  1.50059 [ 1.75037]   ((20 . 33) (21 . 34) (22 . 35) (23 . 36))       4.777     {0/1:6}  B:0
SIMILARITY (1/min{score1}):   0.8324      [and  1/min{score2}:   0.7139]

[4983, 3359]:
    Comparing 1pda and 1kn0_A, based on their crossing files.
    There are 25 (12 H + 13 S) secondary structure elements in 1pda, of which 6 satisfy the size requirements.
    There are 12 (7 H + 5 S) secondary structure elements in 1kn0_A, of which 10 satisfy the size requirements.
  5.00430 [ 5.03185]   ((20 . 4) (21 . 5) (22 . 6) (23 . 7) (24 . 8))       8.476     {1/2:10}  B:0
SIMILARITY (1/min{score1}):   0.1998      [and  1/min{score2}:   0.1987]

[4983, 4983]:
    Comparing 1pda and 1pda, based on their crossing files.
    There are 25 (12 H + 13 S) secondary structure elements in 1pda, of which 6 satisfy the size requirements.
    There are 25 (12 H + 13 S) secondary structure elements in 1pda, of which 6 satisfy the size requirements.
  1.00000 [ 1.00000]   ((20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25))       0.000     {0/10:15}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

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