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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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[4244, 3078]:
    Comparing 1ngv_A and 1jw9_B, based on their crossing files.
    There are 36 (26 H + 10 S) secondary structure elements in 1ngv_A, of which 32 satisfy the size requirements.
    There are 18 (10 H + 8 S) secondary structure elements in 1jw9_B, of which 17 satisfy the size requirements.
  2.00001 [ 1.06254]   ((1 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (9 . 8) (12 . 10) (13 . 11) (14 . 12) (15 . 13) (16 . 14) (29 . 15) (34 . 16) (35 . 17) (36 . 18))       1.908     {0/84:120}  B:0
  5.33334 [ 2.83335]   ((4 . 3) (5 . 4) (6 . 5) (7 . 6) (9 . 8) (13 . 13))       3.187     {0/9:15}  B:0
  6.63131 [ 4.44293]   ((3 . 1) (6 . 3) (12 . 10) (13 . 11) (14 . 12))       5.900     {2/5:10}  B:0
  8.00002 [ 4.25011]   ((9 . 6) (12 . 8) (14 . 10) (15 . 11))       6.819     {0/2:6}  B:0
  8.00002 [ 4.25016]   ((27 . 1) (34 . 12) (35 . 13) (36 . 14))       7.567     {0/3:6}  B:0
SIMILARITY (1/min{score1}):   0.5000      [and  1/min{score2}:   0.9411]

[4244, 4244]:
    Comparing 1ngv_A and 1ngv_A, based on their crossing files.
    There are 36 (26 H + 10 S) secondary structure elements in 1ngv_A, of which 32 satisfy the size requirements.
    There are 36 (26 H + 10 S) secondary structure elements in 1ngv_A, of which 32 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (35 . 35) (36 . 36))       0.000     {0/415:496}  B:0
  5.33394 [ 5.33394]   ((6 . 4) (16 . 16) (25 . 25) (26 . 26) (27 . 27) (30 . 29))       6.083     {1/13:15}  B:0
  5.34019 [ 5.34019]   ((6 . 4) (15 . 13) (25 . 25) (26 . 26) (27 . 27) (32 . 32))       3.568     {2/14:15}  B:0
  6.40000 [ 6.40000]   ((6 . 4) (15 . 13) (16 . 16) (26 . 26) (27 . 27))       3.823     {0/8:10}  B:0
  6.40003 [ 6.40003]   ((1 . 5) (18 . 23) (20 . 25) (21 . 26) (22 . 27))       6.677     {0/8:10}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[4244, 4245]:
    Comparing 1ngv_A and 1ngv_B, based on their crossing files.
    There are 36 (26 H + 10 S) secondary structure elements in 1ngv_A, of which 32 satisfy the size requirements.
    There are 32 (18 H + 14 S) secondary structure elements in 1ngv_B, of which 23 satisfy the size requirements.
  2.13335 [ 1.53338]   ((3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (9 . 8) (12 . 11) (13 . 12) (14 . 13) (15 . 17) (16 . 18) (29 . 19) (34 . 25) (35 . 26) (36 . 27))       2.010     {1/69:105}  B:0
  2.13354 [ 1.53390]   ((1 . 1) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (9 . 8) (12 . 11) (13 . 12) (14 . 13) (15 . 17) (16 . 18) (29 . 19) (34 . 25) (35 . 26) (36 . 27))       3.153     {2/70:105}  B:0
  6.40001 [ 4.60003]   ((4 . 3) (6 . 5) (7 . 8) (15 . 17) (16 . 18))       5.356     {0/6:10}  B:0
  6.40002 [ 4.60005]   ((29 . 19) (33 . 24) (34 . 25) (35 . 26) (36 . 27))       5.980     {0/4:10}  B:0
  8.00005 [ 5.75013]   ((3 . 8) (4 . 9) (5 . 11) (7 . 13))       9.003     {0/2:6}  B:0
SIMILARITY (1/min{score1}):   0.4687      [and  1/min{score2}:   0.6522]

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