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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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[556, 556]:
    Comparing 1cbf and 1cbf, based on their crossing files.
    There are 21 (11 H + 10 S) secondary structure elements in 1cbf, of which 18 satisfy the size requirements.
    There are 21 (11 H + 10 S) secondary structure elements in 1cbf, of which 18 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20))       0.000     {0/124:153}  B:0
  1.80000 [ 1.80000]   ((1 . 1) (6 . 4) (7 . 7) (8 . 8) (10 . 10) (12 . 12) (14 . 14) (15 . 15) (16 . 16) (19 . 19))       1.434     {0/37:45}  B:0
  1.80000 [ 1.80000]   ((1 . 1) (4 . 6) (7 . 7) (8 . 8) (10 . 10) (12 . 12) (14 . 14) (15 . 15) (16 . 16) (19 . 19))       1.434     {0/37:45}  B:0
  3.60001 [ 3.60001]   ((12 . 6) (14 . 7) (15 . 8) (16 . 9) (17 . 10))       3.609     {0/6:10}  B:0
  3.60001 [ 3.60001]   ((6 . 12) (7 . 14) (8 . 15) (9 . 16) (10 . 17))       3.609     {0/6:10}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[556, 5031]:
    Comparing 1cbf and 1pjq_A, based on their crossing files.
    There are 21 (11 H + 10 S) secondary structure elements in 1cbf, of which 18 satisfy the size requirements.
    There are 38 (19 H + 19 S) secondary structure elements in 1pjq_A, of which 19 satisfy the size requirements.
  1.00803 [ 1.06240]   ((1 . 19) (3 . 21) (4 . 22) (5 . 23) (6 . 24) (7 . 25) (8 . 26) (9 . 27) (10 . 28) (11 . 29) (12 . 30) (14 . 31) (15 . 32) (16 . 33) (17 . 34) (18 . 35) (19 . 36) (20 . 37))       2.051     {5/118:153}  B:0
  2.00070 [ 2.11171]   ((1 . 19) (6 . 22) (7 . 25) (8 . 26) (12 . 30) (15 . 32) (16 . 33) (19 . 36) (20 . 37))       2.421     {1/26:36}  B:0
  2.25114 [ 2.37597]   ((1 . 19) (6 . 22) (7 . 25) (14 . 31) (15 . 32) (16 . 33) (19 . 36) (20 . 37))       2.466     {1/21:28}  B:0
  3.00006 [ 3.16672]   ((6 . 22) (10 . 26) (14 . 31) (16 . 33) (19 . 36) (20 . 37))       4.503     {0/11:15}  B:0
  3.06905 [ 3.22576]   ((1 . 19) (7 . 25) (8 . 26) (10 . 28) (12 . 32) (14 . 33))       3.787     {2/12:15}  B:0
SIMILARITY (1/min{score1}):   0.9920      [and  1/min{score2}:   0.9413]

[556, 6247]:
    Comparing 1cbf and 1vhv_A, based on their crossing files.
    There are 21 (11 H + 10 S) secondary structure elements in 1cbf, of which 18 satisfy the size requirements.
    There are 24 (14 H + 10 S) secondary structure elements in 1vhv_A, of which 22 satisfy the size requirements.
  1.06946 [ 1.29999]   ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (12 . 14) (14 . 15) (15 . 16) (16 . 17) (17 . 19) (18 . 20) (19 . 21) (20 . 22))       3.920     {5/107:136}  B:0
  1.10409 [ 1.28394]   ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (12 . 14) (14 . 15) (15 . 16) (16 . 17) (17 . 19) (18 . 20) (19 . 21) (20 . 22))       3.964     {10/120:153}  B:0
  1.12409 [ 1.33164]   ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 8) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (14 . 15) (15 . 16) (16 . 17) (17 . 19) (18 . 20) (19 . 21) (20 . 22))       3.665     {8/105:136}  B:0
  1.20260 [ 1.46810]   ((1 . 1) (3 . 3) (4 . 4) (7 . 5) (8 . 9) (10 . 11) (11 . 12) (12 . 14) (14 . 15) (15 . 16) (16 . 17) (17 . 19) (18 . 20) (19 . 21) (20 . 22))       5.554     {2/82:105}  B:0
  2.57349 [ 3.14399]   ((1 . 1) (7 . 5) (10 . 9) (12 . 14) (14 . 15) (15 . 16) (19 . 21))       6.054     {1/17:21}  B:0
SIMILARITY (1/min{score1}):   0.9350      [and  1/min{score2}:   0.7789]

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