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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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[595, 595]:
    Comparing 1chu_A and 1chu_A, based on their crossing files.
    There are 36 (19 H + 17 S) secondary structure elements in 1chu_A, of which 8 satisfy the size requirements.
    There are 36 (19 H + 17 S) secondary structure elements in 1chu_A, of which 8 satisfy the size requirements.
  1.00000 [ 1.00000]   ((18 . 18) (19 . 19) (20 . 20) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27))       0.000     {0/23:28}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[595, 2995]:
    Comparing 1chu_A and 1jnr_A, based on their crossing files.
    There are 36 (19 H + 17 S) secondary structure elements in 1chu_A, of which 8 satisfy the size requirements.
    There are 46 (25 H + 21 S) secondary structure elements in 1jnr_A, of which 9 satisfy the size requirements.
  1.14422 [ 1.28667]   ((18 . 20) (19 . 21) (23 . 26) (24 . 27) (25 . 29) (26 . 30) (27 . 31))       4.811     {0/18:21}  B:0
  1.73275 [ 1.89731]   ((18 . 20) (19 . 21) (23 . 26) (24 . 27) (26 . 28))       5.977     {1/8:10}  B:0
  5.03199 [ 5.05078]   ((23 . 28) (25 . 29) (26 . 30) (27 . 31))       9.984     {2/4:6}  B:0
SIMILARITY (1/min{score1}):   0.8740      [and  1/min{score2}:   0.7772]

[595, 5263]:
    Comparing 1chu_A and 1q9i_A, based on their crossing files.
    There are 36 (19 H + 17 S) secondary structure elements in 1chu_A, of which 8 satisfy the size requirements.
    There are 47 (25 H + 22 S) secondary structure elements in 1q9i_A, of which 10 satisfy the size requirements.
  1.00043 [ 1.25022]   ((18 . 30) (19 . 31) (20 . 32) (23 . 33) (24 . 35) (25 . 36) (26 . 37) (27 . 41))       3.262     {0/23:28}  B:0
  1.14301 [ 1.42865]   ((18 . 30) (19 . 31) (20 . 32) (23 . 33) (24 . 35) (25 . 36) (26 . 37))       2.764     {0/18:21}  B:0
  1.14314 [ 1.42872]   ((18 . 30) (19 . 31) (20 . 32) (23 . 33) (24 . 35) (25 . 36) (27 . 41))       3.246     {0/17:21}  B:0
  2.92512 [ 3.01523]   ((18 . 30) (19 . 31) (20 . 32) (24 . 35) (26 . 39))       5.914     {2/7:10}  B:0
  6.01856 [ 6.04483]   ((24 . 30) (25 . 31) (26 . 33) (27 . 35))       9.162     {3/5:6}  B:0
SIMILARITY (1/min{score1}):   0.9996      [and  1/min{score2}:   0.7999]

[595, 5371]:
    Comparing 1chu_A and 1qla_A, based on their crossing files.
    There are 36 (19 H + 17 S) secondary structure elements in 1chu_A, of which 8 satisfy the size requirements.
    There are 51 (25 H + 26 S) secondary structure elements in 1qla_A, of which 7 satisfy the size requirements.
  1.42842 [ 1.29991]   ((18 . 24) (20 . 25) (23 . 28) (24 . 29) (26 . 31) (27 . 33))       3.643     {1/10:15}  B:0
  1.80943 [ 1.68217]   ((18 . 24) (20 . 25) (23 . 28) (24 . 29) (26 . 31))       2.590     {1/7:10}  B:0
  3.43671 [ 3.39519]   ((18 . 25) (20 . 29) (23 . 31) (24 . 32))       7.280     {1/3:6}  B:0
SIMILARITY (1/min{score1}):   0.7001      [and  1/min{score2}:   0.7693]

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