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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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[1075, 1075]:
    Comparing 1e8c_A and 1e8c_A, based on their crossing files.
    There are 43 (19 H + 24 S) secondary structure elements in 1e8c_A, of which 7 satisfy the size requirements.
    There are 43 (19 H + 24 S) secondary structure elements in 1e8c_A, of which 7 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9))       0.000     {0/12:21}  B:0
  3.39501 [ 3.39501]   ((1 . 1) (5 . 5) (7 . 6) (9 . 9))       5.608     {1/3:6}  B:0
  3.39501 [ 3.39501]   ((1 . 1) (5 . 5) (6 . 7) (9 . 9))       5.608     {1/3:6}  B:0
  4.01493 [ 4.01493]   ((1 . 1) (4 . 4) (5 . 5) (8 . 7) (9 . 9))       3.486     {2/5:10}  B:0
  4.01493 [ 4.01493]   ((1 . 1) (4 . 4) (5 . 5) (7 . 8) (9 . 9))       3.486     {2/5:10}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[1075, 1818]:
    Comparing 1e8c_A and 1gg4_A, based on their crossing files.
    There are 43 (19 H + 24 S) secondary structure elements in 1e8c_A, of which 7 satisfy the size requirements.
    There are 39 (17 H + 22 S) secondary structure elements in 1gg4_A, of which 7 satisfy the size requirements.
  1.16679 [ 1.16679]   ((1 . 2) (4 . 7) (5 . 8) (6 . 9) (8 . 10) (9 . 11))       2.679     {0/5:15}  B:0
  1.75008 [ 1.75008]   ((1 . 2) (4 . 9) (6 . 10) (9 . 11))       3.299     {0/2:6}  B:0
  3.39570 [ 3.39570]   ((5 . 2) (6 . 3) (7 . 7) (9 . 8))       9.485     {1/3:6}  B:0
  1.00063 [ 1.00063]   ((1 . 2) (4 . 7) (5 . 8) (6 . 9) (7 . 3) (8 . 10) (9 . 11))       3.592     {0/9:21}  B:1
  2.55935 [ 2.55935]   ((1 . 2) (5 . 8) (6 . 7) (8 . 10) (9 . 11))       3.354     {1/4:10}  B:1
SIMILARITY (1/min{score1}):   0.9994      [and  1/min{score2}:   0.9994]

[1075, 3368]:
    Comparing 1e8c_A and 1knx_A, based on their crossing files.
    There are 43 (19 H + 24 S) secondary structure elements in 1e8c_A, of which 7 satisfy the size requirements.
    There are 27 (13 H + 14 S) secondary structure elements in 1knx_A, of which 11 satisfy the size requirements.
  1.16726 [ 1.83349]   ((1 . 1) (4 . 3) (5 . 6) (6 . 7) (8 . 9) (9 . 10))       3.970     {0/5:15}  B:0
  1.16744 [ 1.83353]   ((1 . 1) (4 . 3) (5 . 6) (6 . 7) (8 . 9) (9 . 11))       4.241     {0/5:15}  B:0
  1.40016 [ 2.20004]   ((4 . 3) (5 . 6) (6 . 7) (8 . 9) (9 . 10))       3.298     {0/3:10}  B:0
  1.40057 [ 2.20015]   ((4 . 3) (5 . 6) (6 . 7) (8 . 9) (9 . 11))       4.491     {0/3:10}  B:0
  1.75028 [ 2.75007]   ((4 . 7) (5 . 8) (6 . 9) (9 . 11))       4.448     {0/1:6}  B:0
SIMILARITY (1/min{score1}):   0.8567      [and  1/min{score2}:   0.5454]

[1075, 3376]:
    Comparing 1e8c_A and 1ko7_A, based on their crossing files.
    There are 43 (19 H + 24 S) secondary structure elements in 1e8c_A, of which 7 satisfy the size requirements.
    There are 31 (14 H + 17 S) secondary structure elements in 1ko7_A, of which 11 satisfy the size requirements.
  1.75012 [ 2.75003]   ((4 . 10) (5 . 11) (6 . 12) (9 . 13))       3.622     {0/1:6}  B:0
  1.75330 [ 2.75085]   ((4 . 2) (5 . 3) (7 . 6) (9 . 9))       8.255     {0/3:6}  B:0
  3.39585 [ 3.66688]   ((1 . 1) (4 . 6) (5 . 7) (9 . 11))       9.914     {1/3:6}  B:0
  1.00043 [ 1.57154]   ((1 . 1) (4 . 6) (5 . 9) (6 . 10) (7 . 2) (8 . 12) (9 . 13))       3.262     {0/10:21}  B:1
  1.75705 [ 2.75183]   ((5 . 5) (6 . 6) (8 . 10) (9 . 9))       9.992     {0/2:6}  B:1
SIMILARITY (1/min{score1}):   0.9996      [and  1/min{score2}:   0.6363]

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