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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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[3092, 443]:
    Comparing 1jyh_A and 1bow_A, based on their crossing files.
    There are 13 (4 H + 9 S) secondary structure elements in 1jyh_A, of which 11 satisfy the size requirements.
    There are 11 (3 H + 8 S) secondary structure elements in 1bow_A, of which 11 satisfy the size requirements.
  1.10174 [ 1.10174]   ((1 . 1) (2 . 2) (3 . 4) (4 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (13 . 11))       3.841     {1/36:45}  B:0
  1.10425 [ 1.10425]   ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (13 . 11))       5.697     {1/35:45}  B:0
  1.22237 [ 1.22237]   ((1 . 1) (2 . 2) (4 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (13 . 11))       2.901     {0/29:36}  B:0
  2.17247 [ 2.17247]   ((1 . 1) (2 . 2) (4 . 5) (6 . 6) (9 . 9) (10 . 10))       7.547     {2/11:15}  B:0
  2.29256 [ 2.29256]   ((7 . 1) (8 . 2) (9 . 3) (11 . 5) (13 . 6))       6.832     {1/7:10}  B:0
SIMILARITY (1/min{score1}):   0.9077      [and  1/min{score2}:   0.9077]

[3092, 760]:
    Comparing 1jyh_A and 1d5y_A, based on their crossing files.
    There are 13 (4 H + 9 S) secondary structure elements in 1jyh_A, of which 11 satisfy the size requirements.
    There are 22 (12 H + 10 S) secondary structure elements in 1d5y_A, of which 12 satisfy the size requirements.
  1.10077 [ 1.20059]   ((1 . 9) (2 . 10) (3 . 11) (4 . 12) (6 . 13) (7 . 15) (8 . 16) (9 . 18) (11 . 20) (13 . 22))       4.049     {0/38:45}  B:0
  1.10133 [ 1.20102]   ((1 . 9) (2 . 10) (3 . 11) (4 . 12) (6 . 13) (7 . 15) (8 . 16) (9 . 17) (11 . 20) (13 . 22))       4.641     {0/37:45}  B:0
  2.22384 [ 2.41845]   ((1 . 9) (2 . 10) (3 . 11) (7 . 13) (9 . 17))       6.773     {1/10:10}  B:0
  2.75056 [ 3.00043]   ((8 . 13) (9 . 14) (10 . 15) (11 . 16))       7.438     {0/5:6}  B:0
  2.75061 [ 3.00047]   ((2 . 9) (8 . 13) (10 . 15) (11 . 16))       7.595     {0/6:6}  B:0
SIMILARITY (1/min{score1}):   0.9085      [and  1/min{score2}:   0.8329]

[3092, 3092]:
    Comparing 1jyh_A and 1jyh_A, based on their crossing files.
    There are 13 (4 H + 9 S) secondary structure elements in 1jyh_A, of which 11 satisfy the size requirements.
    There are 13 (4 H + 9 S) secondary structure elements in 1jyh_A, of which 11 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13))       0.000     {0/47:55}  B:0
  2.36308 [ 2.36308]   ((1 . 7) (2 . 8) (3 . 9) (4 . 10) (6 . 13))       7.212     {1/6:10}  B:0
  2.36308 [ 2.36308]   ((7 . 1) (8 . 2) (9 . 3) (10 . 4) (13 . 6))       7.212     {1/6:10}  B:0
  2.75278 [ 2.75278]   ((8 . 1) (9 . 3) (11 . 4) (13 . 6))      11.104     {0/3:6}  B:0
  2.75278 [ 2.75278]   ((1 . 8) (3 . 9) (4 . 11) (6 . 13))      11.104     {0/3:6}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

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