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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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[2777, 1301]:
    Comparing 1j9i_A and 1exj_A, based on their crossing files.
    There are 6 (4 H + 2 S) secondary structure elements in 1j9i_A, of which 6 satisfy the size requirements.
    There are 19 (7 H + 12 S) secondary structure elements in 1exj_A, of which 7 satisfy the size requirements.
  1.20025 [ 1.40016]   ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (6 . 6))       3.255     {0/9:10}  B:0
  2.06192 [ 2.11059]   ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (5 . 6))       3.256     {2/10:10}  B:0
  1.89257 [ 2.03488]   ((1 . 1) (4 . 5) (5 . 3) (6 . 6))       7.595     {1/6:6}  B:1
  1.89301 [ 2.03524]   ((1 . 5) (2 . 3) (3 . 6) (5 . 7))       8.010     {1/6:6}  B:1
SIMILARITY (1/min{score1}):   0.8332      [and  1/min{score2}:   0.7142]

[2777, 2777]:
    Comparing 1j9i_A and 1j9i_A, based on their crossing files.
    There are 6 (4 H + 2 S) secondary structure elements in 1j9i_A, of which 6 satisfy the size requirements.
    There are 6 (4 H + 2 S) secondary structure elements in 1j9i_A, of which 6 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6))       0.000     {0/14:15}  B:0
  4.01968 [ 4.01968]   ((1 . 4) (3 . 5) (4 . 1) (6 . 3))       5.393     {2/5:6}  B:1
  4.01968 [ 4.01968]   ((1 . 4) (3 . 6) (4 . 1) (5 . 3))       5.393     {2/5:6}  B:1
  4.01982 [ 4.01982]   ((3 . 2) (4 . 1) (5 . 3) (6 . 5))       7.523     {2/5:6}  B:1
  4.01982 [ 4.01982]   ((1 . 4) (2 . 3) (3 . 5) (5 . 6))       7.523     {2/5:6}  B:1
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[2777, 2810]:
    Comparing 1j9i_A and 1jbg_A, based on their crossing files.
    There are 6 (4 H + 2 S) secondary structure elements in 1j9i_A, of which 6 satisfy the size requirements.
    There are 8 (5 H + 3 S) secondary structure elements in 1jbg_A, of which 6 satisfy the size requirements.
  1.89079 [ 1.89079]   ((2 . 2) (3 . 3) (4 . 5) (5 . 6))       3.686     {1/6:6}  B:0
  1.89278 [ 1.89278]   ((1 . 5) (2 . 3) (3 . 6) (5 . 7))       7.800     {1/6:6}  B:1
SIMILARITY (1/min{score1}):   0.5289      [and  1/min{score2}:   0.5289]

[2777, 2926]:
    Comparing 1j9i_A and 1jjc_B, based on their crossing files.
    There are 6 (4 H + 2 S) secondary structure elements in 1j9i_A, of which 6 satisfy the size requirements.
    There are 66 (25 H + 41 S) secondary structure elements in 1jjc_B, of which 6 satisfy the size requirements.
 NO SIMILARITY!

[2777, 2929]:
    Comparing 1j9i_A and 1jjc_B, based on their crossing files.
    There are 6 (4 H + 2 S) secondary structure elements in 1j9i_A, of which 6 satisfy the size requirements.
    There are 66 (25 H + 41 S) secondary structure elements in 1jjc_B, of which 6 satisfy the size requirements.
  1.45798 [ 1.45798]   ((1 . 36) (2 . 37) (3 . 38) (4 . 40) (5 . 41))       3.936     {1/8:10}  B:0
  2.57737 [ 2.57737]   ((1 . 36) (2 . 37) (3 . 38) (4 . 40))       3.437     {1/4:6}  B:0
  2.57751 [ 2.57751]   ((1 . 36) (2 . 37) (3 . 38) (6 . 41))       5.265     {1/4:6}  B:0
  5.01012 [ 5.01012]   ((2 . 37) (3 . 38) (4 . 40) (6 . 41))       5.317     {2/4:6}  B:0
  1.50117 [ 1.50117]   ((2 . 37) (3 . 38) (4 . 36) (6 . 41))       5.671     {0/4:6}  B:1
SIMILARITY (1/min{score1}):   0.6859      [and  1/min{score2}:   0.6859]

[2777, 3573]:
    Comparing 1j9i_A and 1l8r_A, based on their crossing files.
    There are 6 (4 H + 2 S) secondary structure elements in 1j9i_A, of which 6 satisfy the size requirements.
    There are 10 (5 H + 5 S) secondary structure elements in 1l8r_A, of which 8 satisfy the size requirements.
 NO SIMILARITY!

[2777, 5164]:
    Comparing 1j9i_A and 1q06_A, based on their crossing files.
    There are 6 (4 H + 2 S) secondary structure elements in 1j9i_A, of which 6 satisfy the size requirements.
    There are 8 (6 H + 2 S) secondary structure elements in 1q06_A, of which 6 satisfy the size requirements.
 NO SIMILARITY!

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