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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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[4819, 614]:
    Comparing 1oxw_A and 1cjy_A, based on their crossing files.
    There are 27 (19 H + 8 S) secondary structure elements in 1oxw_A, of which 21 satisfy the size requirements.
    There are 53 (28 H + 25 S) secondary structure elements in 1cjy_A, of which 34 satisfy the size requirements.
  1.32890 [ 2.12893]   ((1 . 14) (2 . 15) (4 . 17) (5 . 18) (6 . 19) (7 . 22) (9 . 25) (10 . 27) (12 . 33) (13 . 38) (14 . 39) (19 . 43) (22 . 44) (24 . 47) (26 . 52) (27 . 53))       5.391     {5/82:120}  B:0
  2.32033 [ 2.67941]   ((1 . 14) (2 . 15) (4 . 17) (5 . 18) (6 . 19) (7 . 24) (9 . 25) (10 . 27) (12 . 33) (14 . 38) (19 . 43) (22 . 44) (24 . 47) (26 . 52) (27 . 53))       6.180     {15/67:105}  B:0
  4.20036 [ 6.80008]   ((6 . 30) (13 . 38) (14 . 39) (19 . 43) (24 . 47))       9.116     {0/9:10}  B:0
  4.22584 [ 6.80614]   ((1 . 14) (2 . 15) (9 . 25) (10 . 27) (15 . 33))       5.431     {1/6:10}  B:0
  4.56600 [ 6.89612]   ((2 . 15) (4 . 17) (5 . 18) (6 . 19) (13 . 27))       6.487     {2/6:10}  B:0
SIMILARITY (1/min{score1}):   0.7540      [and  1/min{score2}:   0.4699]

[4819, 3972]:
    Comparing 1oxw_A and 1mla, based on their crossing files.
    There are 27 (19 H + 8 S) secondary structure elements in 1oxw_A, of which 21 satisfy the size requirements.
    There are 23 (14 H + 9 S) secondary structure elements in 1mla, of which 8 satisfy the size requirements.
  5.25012 [ 2.00223]   ((4 . 1) (5 . 2) (7 . 6) (9 . 7))       8.273     {0/2:6}  B:0
  5.25019 [ 2.00349]   ((4 . 1) (6 . 3) (7 . 6) (12 . 9))       9.255     {0/3:6}  B:0
  5.25019 [ 2.00350]   ((4 . 1) (5 . 3) (6 . 4) (9 . 7))       9.263     {0/3:6}  B:0
  5.25218 [ 2.03838]   ((16 . 4) (17 . 6) (20 . 8) (22 . 9))      16.965     {0/4:6}  B:0
  5.45160 [ 3.43725]   ((5 . 2) (6 . 3) (7 . 6) (12 . 9))       9.607     {1/3:6}  B:0
SIMILARITY (1/min{score1}):   0.2606      [and  1/min{score2}:   0.4999]

[4819, 4308]:
    Comparing 1oxw_A and 1nm2_A, based on their crossing files.
    There are 27 (19 H + 8 S) secondary structure elements in 1oxw_A, of which 21 satisfy the size requirements.
    There are 24 (14 H + 10 S) secondary structure elements in 1nm2_A, of which 15 satisfy the size requirements.
  2.00195 [ 1.58031]   ((1 . 1) (2 . 6) (4 . 7) (5 . 8) (6 . 9) (7 . 16) (12 . 18) (16 . 20) (19 . 21) (24 . 23) (27 . 24))       4.654     {4/31:55}  B:0
  2.69017 [ 2.55401]   ((1 . 1) (2 . 2) (4 . 7) (5 . 8) (6 . 9) (7 . 16) (12 . 18) (15 . 20) (19 . 21) (24 . 23) (27 . 24))       6.586     {8/32:55}  B:0
  4.20020 [ 3.00054]   ((4 . 7) (5 . 8) (6 . 9) (19 . 21) (22 . 24))       7.852     {0/4:10}  B:0
  4.21446 [ 3.03911]   ((1 . 1) (5 . 6) (16 . 16) (22 . 22) (24 . 23))       9.820     {1/7:10}  B:0
  4.22613 [ 3.06989]   ((2 . 6) (4 . 7) (5 . 8) (19 . 21) (22 . 24))       8.986     {1/6:10}  B:0
SIMILARITY (1/min{score1}):   0.5313      [and  1/min{score2}:   0.6496]

[4819, 4819]:
    Comparing 1oxw_A and 1oxw_A, based on their crossing files.
    There are 27 (19 H + 8 S) secondary structure elements in 1oxw_A, of which 21 satisfy the size requirements.
    There are 27 (19 H + 8 S) secondary structure elements in 1oxw_A, of which 21 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (24 . 24) (26 . 26) (27 . 27))       0.000     {0/171:210}  B:0
  5.25010 [ 5.25010]   ((2 . 7) (7 . 16) (14 . 24) (16 . 26))       7.858     {0/5:6}  B:0
  5.25010 [ 5.25010]   ((7 . 2) (16 . 7) (24 . 14) (26 . 16))       7.858     {0/5:6}  B:0
  5.25015 [ 5.25015]   ((1 . 19) (2 . 22) (4 . 24) (6 . 26))       8.742     {0/0:6}  B:0
  5.25015 [ 5.25015]   ((19 . 1) (22 . 2) (24 . 4) (26 . 6))       8.742     {0/0:6}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

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