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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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[37, 37]:
    Comparing 1a44 and 1a44, based on their crossing files.
    There are 15 (5 H + 10 S) secondary structure elements in 1a44, of which 11 satisfy the size requirements.
    There are 15 (5 H + 10 S) secondary structure elements in 1a44, of which 11 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15))       0.000     {0/41:55}  B:0
  2.20007 [ 2.20007]   ((1 . 1) (5 . 7) (13 . 13) (14 . 14) (15 . 15))       3.716     {0/9:10}  B:0
  2.20007 [ 2.20007]   ((1 . 1) (7 . 5) (13 . 13) (14 . 14) (15 . 15))       3.716     {0/9:10}  B:0
  4.20689 [ 4.20689]   ((1 . 1) (5 . 7) (9 . 11) (14 . 14))       6.445     {2/5:6}  B:0
  4.20689 [ 4.20689]   ((1 . 1) (7 . 5) (11 . 9) (14 . 14))       6.445     {2/5:6}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[37, 1532]:
    Comparing 1a44 and 1fjj_A, based on their crossing files.
    There are 15 (5 H + 10 S) secondary structure elements in 1a44, of which 11 satisfy the size requirements.
    There are 11 (3 H + 8 S) secondary structure elements in 1fjj_A, of which 8 satisfy the size requirements.
  1.61379 [ 1.24345]   ((4 . 1) (7 . 3) (8 . 4) (9 . 5) (12 . 9) (13 . 10) (14 . 11))       3.233     {1/11:21}  B:0
  1.83336 [ 1.33340]   ((4 . 1) (7 . 3) (8 . 4) (9 . 5) (12 . 9) (14 . 11))       2.548     {0/9:15}  B:0
  2.20222 [ 1.60576]   ((7 . 1) (8 . 3) (9 . 4) (11 . 5) (14 . 9))       8.879     {0/3:10}  B:0
  2.75019 [ 2.00049]   ((5 . 3) (12 . 9) (13 . 10) (14 . 11))       5.651     {0/2:6}  B:0
  2.75200 [ 2.00518]   ((8 . 1) (11 . 3) (12 . 4) (13 . 7))      10.221     {0/2:6}  B:0
SIMILARITY (1/min{score1}):   0.6197      [and  1/min{score2}:   0.8042]

[37, 5407]:
    Comparing 1a44 and 1qou_A, based on their crossing files.
    There are 15 (5 H + 10 S) secondary structure elements in 1a44, of which 11 satisfy the size requirements.
    There are 11 (3 H + 8 S) secondary structure elements in 1qou_A, of which 8 satisfy the size requirements.
  1.37501 [ 1.00001]   ((4 . 1) (7 . 4) (8 . 5) (9 . 6) (11 . 8) (12 . 9) (13 . 10) (14 . 11))       1.367     {0/16:28}  B:0
  2.75024 [ 2.00062]   ((9 . 1) (11 . 4) (12 . 5) (14 . 9))       5.996     {0/3:6}  B:0
  2.75043 [ 2.00111]   ((7 . 1) (9 . 5) (11 . 6) (12 . 8))       6.946     {0/3:6}  B:0
  2.75044 [ 2.00115]   ((8 . 1) (11 . 4) (12 . 5) (14 . 9))       7.017     {0/2:6}  B:0
  2.75205 [ 2.00531]   ((4 . 5) (5 . 6) (7 . 8) (8 . 9))      10.281     {0/1:6}  B:0
SIMILARITY (1/min{score1}):   0.7273      [and  1/min{score2}:   0.9999]

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