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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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[5938, 1424]:
    Comparing 1tx4_A and 1f7c_A, based on their crossing files.
    There are 11 (11 H + 0 S) secondary structure elements in 1tx4_A, of which 10 satisfy the size requirements.
    There are 9 (9 H + 0 S) secondary structure elements in 1f7c_A, of which 9 satisfy the size requirements.
  1.25466 [ 1.13137]   ((2 . 1) (3 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7) (11 . 8))       2.748     {1/23:28}  B:0
  2.50097 [ 2.25133]   ((7 . 3) (8 . 4) (9 . 5) (10 . 6))       7.941     {0/4:6}  B:0
  2.97412 [ 2.83731]   ((1 . 2) (6 . 6) (7 . 7) (9 . 9))       9.339     {1/4:6}  B:0
  3.57091 [ 3.49475]   ((1 . 5) (2 . 6) (3 . 7) (5 . 8))       8.477     {2/6:6}  B:0
  6.69947 [ 6.68827]   ((5 . 1) (8 . 3) (9 . 4) (10 . 5))       9.060     {2/3:6}  B:0
SIMILARITY (1/min{score1}):   0.7970      [and  1/min{score2}:   0.8839]

[5938, 4225]:
    Comparing 1tx4_A and 1nf1_A, based on their crossing files.
    There are 11 (11 H + 0 S) secondary structure elements in 1tx4_A, of which 10 satisfy the size requirements.
    There are 15 (15 H + 0 S) secondary structure elements in 1nf1_A, of which 13 satisfy the size requirements.
  2.50070 [ 3.25032]   ((5 . 5) (7 . 7) (8 . 8) (11 . 11))       7.313     {0/5:6}  B:0
  2.50093 [ 3.25042]   ((5 . 7) (6 . 8) (7 . 9) (8 . 11))       7.856     {0/4:6}  B:0
  2.50145 [ 3.25066]   ((5 . 5) (8 . 8) (9 . 9) (11 . 11))       8.776     {0/3:6}  B:0
  2.50502 [ 3.25229]   ((1 . 3) (5 . 7) (6 . 8) (9 . 11))      11.984     {0/6:6}  B:0
  2.72569 [ 3.36161]   ((1 . 7) (2 . 8) (3 . 10) (5 . 11))       9.665     {1/5:6}  B:0
SIMILARITY (1/min{score1}):   0.5987      [and  1/min{score2}:   0.4612]

[5938, 4963]:
    Comparing 1tx4_A and 1pbw_A, based on their crossing files.
    There are 11 (11 H + 0 S) secondary structure elements in 1tx4_A, of which 10 satisfy the size requirements.
    There are 10 (10 H + 0 S) secondary structure elements in 1pbw_A, of which 8 satisfy the size requirements.
  1.30774 [ 1.10359]   ((2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10))       2.871     {2/24:28}  B:0
  1.43674 [ 1.15862]   ((2 . 2) (3 . 3) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (11 . 10))       2.731     {1/18:21}  B:0
  2.50414 [ 2.00806]   ((1 . 3) (2 . 5) (5 . 8) (8 . 10))      11.419     {0/5:6}  B:0
  2.52183 [ 2.35958]   ((2 . 2) (3 . 3) (5 . 5) (8 . 7) (11 . 10))       7.853     {2/9:10}  B:0
  2.73242 [ 2.39096]   ((5 . 3) (8 . 6) (9 . 7) (11 . 8))      14.533     {1/5:6}  B:0
SIMILARITY (1/min{score1}):   0.7647      [and  1/min{score2}:   0.9061]

[5938, 5938]:
    Comparing 1tx4_A and 1tx4_A, based on their crossing files.
    There are 11 (11 H + 0 S) secondary structure elements in 1tx4_A, of which 10 satisfy the size requirements.
    There are 11 (11 H + 0 S) secondary structure elements in 1tx4_A, of which 10 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11))       0.000     {0/40:45}  B:0
  2.50434 [ 2.50434]   ((1 . 3) (2 . 5) (5 . 8) (7 . 9))      11.557     {0/5:6}  B:0
  2.50434 [ 2.50434]   ((3 . 1) (5 . 2) (8 . 5) (9 . 7))      11.557     {0/5:6}  B:0
  2.72812 [ 2.72812]   ((3 . 1) (8 . 6) (9 . 7) (11 . 8))      12.127     {1/5:6}  B:0
  2.72812 [ 2.72812]   ((1 . 3) (6 . 8) (7 . 9) (8 . 11))      12.127     {1/5:6}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[5938, 6329]:
    Comparing 1tx4_A and 1wer, based on their crossing files.
    There are 11 (11 H + 0 S) secondary structure elements in 1tx4_A, of which 10 satisfy the size requirements.
    There are 20 (20 H + 0 S) secondary structure elements in 1wer, of which 18 satisfy the size requirements.
  2.50190 [ 4.50033]   ((7 . 9) (8 . 11) (9 . 12) (11 . 15))       9.400     {0/4:6}  B:0
  2.50223 [ 4.50038]   ((2 . 3) (3 . 4) (9 . 11) (10 . 12))       9.776     {0/3:6}  B:0
  2.50446 [ 4.50077]   ((7 . 1) (8 . 3) (9 . 4) (10 . 5))      11.635     {0/3:6}  B:0
  2.62305 [ 4.52254]   ((3 . 1) (5 . 3) (8 . 7) (11 . 11))      13.848     {1/6:6}  B:0
  2.72570 [ 4.54362]   ((1 . 5) (2 . 6) (5 . 9) (9 . 15))       9.680     {1/5:6}  B:0
SIMILARITY (1/min{score1}):   0.5871      [and  1/min{score2}:   0.3800]

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