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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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[796, 289]:
    Comparing 1dcp_A and 1b4b_A, based on their crossing files.
    There are 7 (3 H + 4 S) secondary structure elements in 1dcp_A, of which 6 satisfy the size requirements.
    There are 7 (3 H + 4 S) secondary structure elements in 1b4b_A, of which 6 satisfy the size requirements.
  1.20040 [ 1.20040]   ((3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7))       3.658     {0/2:10}  B:0
  1.50010 [ 1.50010]   ((3 . 3) (4 . 4) (5 . 5) (6 . 6))       3.090     {0/1:6}  B:0
SIMILARITY (1/min{score1}):   0.8331      [and  1/min{score2}:   0.8331]

[796, 353]:
    Comparing 1dcp_A and 1bdf_A, based on their crossing files.
    There are 7 (3 H + 4 S) secondary structure elements in 1dcp_A, of which 6 satisfy the size requirements.
    There are 18 (5 H + 13 S) secondary structure elements in 1bdf_A, of which 6 satisfy the size requirements.
 NO SIMILARITY!

[796, 500]:
    Comparing 1dcp_A and 1c0a_A, based on their crossing files.
    There are 7 (3 H + 4 S) secondary structure elements in 1dcp_A, of which 6 satisfy the size requirements.
    There are 48 (24 H + 24 S) secondary structure elements in 1c0a_A, of which 12 satisfy the size requirements.
  1.20071 [ 2.40009]   ((3 . 26) (4 . 28) (5 . 29) (6 . 34) (7 . 35))       4.237     {0/2:10}  B:0
  1.50024 [ 3.00003]   ((3 . 26) (5 . 29) (6 . 34) (7 . 35))       3.828     {0/0:6}  B:0
  1.50272 [ 3.00034]   ((1 . 25) (3 . 26) (4 . 28) (5 . 29))       7.007     {0/1:6}  B:0
  1.51111 [ 3.00140]   ((3 . 26) (4 . 28) (5 . 29) (7 . 33))       9.986     {0/2:6}  B:0
  1.50213 [ 3.00027]   ((3 . 26) (4 . 35) (5 . 29) (6 . 34))       6.592     {0/0:6}  B:1
SIMILARITY (1/min{score1}):   0.8328      [and  1/min{score2}:   0.4167]

[796, 796]:
    Comparing 1dcp_A and 1dcp_A, based on their crossing files.
    There are 7 (3 H + 4 S) secondary structure elements in 1dcp_A, of which 6 satisfy the size requirements.
    There are 7 (3 H + 4 S) secondary structure elements in 1dcp_A, of which 6 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7))       0.000     {0/2:15}  B:0
  1.20108 [ 1.20108]   ((1 . 1) (3 . 3) (4 . 4) (5 . 6) (7 . 7))       4.701     {0/2:10}  B:0
  1.20108 [ 1.20108]   ((1 . 1) (3 . 3) (4 . 4) (6 . 5) (7 . 7))       4.701     {0/2:10}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[796, 2393]:
    Comparing 1dcp_A and 1i50_C, based on their crossing files.
    There are 7 (3 H + 4 S) secondary structure elements in 1dcp_A, of which 6 satisfy the size requirements.
    There are 19 (8 H + 11 S) secondary structure elements in 1i50_C, of which 6 satisfy the size requirements.
 NO SIMILARITY!

[796, 2400]:
    Comparing 1dcp_A and 1i50_K, based on their crossing files.
    There are 7 (3 H + 4 S) secondary structure elements in 1dcp_A, of which 6 satisfy the size requirements.
    There are 7 (3 H + 4 S) secondary structure elements in 1i50_K, of which 7 satisfy the size requirements.
  1.20589 [ 1.40372]   ((3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7))       7.199     {0/1:10}  B:0
  1.51195 [ 1.75757]   ((4 . 1) (5 . 2) (6 . 3) (7 . 4))      10.171     {0/0:6}  B:0
  1.20448 [ 1.40283]   ((3 . 6) (4 . 7) (5 . 2) (6 . 3) (7 . 4))       6.720     {0/2:10}  B:1
SIMILARITY (1/min{score1}):   0.8302      [and  1/min{score2}:   0.7128]

[796, 3511]:
    Comparing 1dcp_A and 1l0w_A, based on their crossing files.
    There are 7 (3 H + 4 S) secondary structure elements in 1dcp_A, of which 6 satisfy the size requirements.
    There are 48 (24 H + 24 S) secondary structure elements in 1l0w_A, of which 9 satisfy the size requirements.
  1.20041 [ 1.80012]   ((3 . 27) (4 . 28) (5 . 29) (6 . 33) (7 . 34))       3.697     {0/2:10}  B:0
  1.50006 [ 2.25002]   ((3 . 27) (4 . 28) (6 . 33) (7 . 34))       2.750     {0/2:6}  B:0
  1.50013 [ 2.25004]   ((3 . 27) (5 . 29) (6 . 33) (7 . 34))       3.253     {0/0:6}  B:0
  1.50021 [ 2.25006]   ((3 . 27) (4 . 28) (5 . 29) (6 . 33))       3.704     {0/1:6}  B:0
  1.50487 [ 2.25145]   ((1 . 26) (3 . 27) (4 . 28) (7 . 34))       8.112     {0/2:6}  B:0
SIMILARITY (1/min{score1}):   0.8330      [and  1/min{score2}:   0.5555]

[796, 6353]:
    Comparing 1dcp_A and 1xxa_A, based on their crossing files.
    There are 7 (3 H + 4 S) secondary structure elements in 1dcp_A, of which 6 satisfy the size requirements.
    There are 6 (2 H + 4 S) secondary structure elements in 1xxa_A, of which 6 satisfy the size requirements.
  1.20107 [ 1.20107]   ((3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6))       4.692     {0/2:10}  B:0
  1.50025 [ 1.50025]   ((3 . 2) (4 . 3) (5 . 4) (6 . 5))       3.865     {0/1:6}  B:0
SIMILARITY (1/min{score1}):   0.8326      [and  1/min{score2}:   0.8326]

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