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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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[2904, 2904]:
    Comparing 1jj2_E and 1jj2_E, based on their crossing files.
    There are 16 (3 H + 13 S) secondary structure elements in 1jj2_E, of which 7 satisfy the size requirements.
    There are 16 (3 H + 13 S) secondary structure elements in 1jj2_E, of which 7 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7))       0.000     {0/9:21}  B:0
  2.24470 [ 2.24470]   ((1 . 4) (2 . 5) (3 . 6) (4 . 1) (5 . 2) (6 . 3) (7 . 7))       3.294     {2/9:21}  B:1
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[2904, 2905]:
    Comparing 1jj2_E and 1jj2_E, based on their crossing files.
    There are 16 (3 H + 13 S) secondary structure elements in 1jj2_E, of which 7 satisfy the size requirements.
    There are 16 (3 H + 13 S) secondary structure elements in 1jj2_E, of which 8 satisfy the size requirements.
  1.75987 [ 2.00663]   ((1 . 10) (3 . 12) (5 . 14) (7 . 15))      10.874     {0/0:6}  B:0
  2.24467 [ 2.26012]   ((1 . 8) (2 . 9) (3 . 10) (4 . 12) (5 . 13) (6 . 14) (7 . 15))       2.515     {2/9:21}  B:0
  5.01873 [ 5.03177]   ((1 . 12) (2 . 13) (3 . 14) (6 . 16))       7.128     {1/2:6}  B:0
 10.00236 [10.00401]   ((1 . 9) (2 . 10) (3 . 12) (5 . 14))       7.501     {1/1:6}  B:0
 10.00236 [10.00401]   ((2 . 10) (3 . 12) (4 . 13) (5 . 14))       7.839     {1/1:6}  B:0
SIMILARITY (1/min{score1}):   0.7119      [and  1/min{score2}:   0.6238]

[2904, 5670]:
    Comparing 1jj2_E and 1rl6_A, based on their crossing files.
    There are 16 (3 H + 13 S) secondary structure elements in 1jj2_E, of which 7 satisfy the size requirements.
    There are 15 (2 H + 13 S) secondary structure elements in 1rl6_A, of which 6 satisfy the size requirements.
  1.16667 [ 1.00000]   ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7))       0.630     {0/6:15}  B:0
  3.34579 [ 3.34008]   ((1 . 4) (2 . 5) (3 . 6) (5 . 2) (6 . 3) (7 . 7))       3.691     {2/6:15}  B:1
SIMILARITY (1/min{score1}):   0.8571      [and  1/min{score2}:   0.9999]

[2904, 5671]:
    Comparing 1jj2_E and 1rl6_A, based on their crossing files.
    There are 16 (3 H + 13 S) secondary structure elements in 1jj2_E, of which 7 satisfy the size requirements.
    There are 15 (2 H + 13 S) secondary structure elements in 1rl6_A, of which 8 satisfy the size requirements.
  1.26059 [ 1.34073]   ((1 . 8) (2 . 9) (3 . 10) (4 . 11) (5 . 12) (6 . 13) (7 . 14))       2.890     {1/9:21}  B:0
  1.75155 [ 2.00104]   ((1 . 11) (2 . 12) (3 . 13) (6 . 15))       6.829     {0/2:6}  B:0
 10.00235 [10.00401]   ((1 . 9) (2 . 10) (3 . 11) (5 . 13))       7.120     {1/1:6}  B:0
 10.00236 [10.00401]   ((2 . 10) (3 . 11) (4 . 12) (5 . 13))       7.661     {1/1:6}  B:0
  1.75415 [ 2.00278]   ((1 . 10) (3 . 13) (4 . 12) (7 . 14))       8.744     {0/0:6}  B:1
SIMILARITY (1/min{score1}):   0.7933      [and  1/min{score2}:   0.7459]

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