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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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[2108, 2108]:
    Comparing 1h6q_A and 1h6q_A, based on their crossing files.
    There are 14 (3 H + 11 S) secondary structure elements in 1h6q_A, of which 11 satisfy the size requirements.
    There are 14 (3 H + 11 S) secondary structure elements in 1h6q_A, of which 11 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (12 . 12) (13 . 13) (14 . 14))       0.000     {0/51:55}  B:0
  1.84478 [ 1.84478]   ((1 . 1) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (13 . 14))       6.328     {1/14:15}  B:0
  1.84478 [ 1.84478]   ((1 . 1) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (14 . 13))       6.328     {1/14:15}  B:0
  1.84843 [ 1.84843]   ((4 . 4) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (14 . 13))       6.465     {1/13:15}  B:0
  1.84843 [ 1.84843]   ((4 . 4) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (13 . 14))       6.465     {1/13:15}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[2108, 2323]:
    Comparing 1h6q_A and 1hxr_A, based on their crossing files.
    There are 14 (3 H + 11 S) secondary structure elements in 1h6q_A, of which 11 satisfy the size requirements.
    There are 13 (2 H + 11 S) secondary structure elements in 1hxr_A, of which 10 satisfy the size requirements.
 NO SIMILARITY!

[2108, 3512]:
    Comparing 1h6q_A and 1l1d_A, based on their crossing files.
    There are 14 (3 H + 11 S) secondary structure elements in 1h6q_A, of which 11 satisfy the size requirements.
    There are 17 (8 H + 9 S) secondary structure elements in 1l1d_A, of which 11 satisfy the size requirements.
  2.75053 [ 2.75053]   ((7 . 2) (12 . 10) (13 . 11) (14 . 13))       7.336     {0/5:6}  B:0
  2.84231 [ 2.84231]   ((3 . 9) (6 . 15) (7 . 16) (9 . 17))      12.376     {1/6:6}  B:0
  3.13259 [ 3.13259]   ((3 . 9) (4 . 10) (6 . 15) (7 . 16))       7.314     {1/4:6}  B:0
  3.66647 [ 3.66647]   ((3 . 4) (4 . 5) (9 . 16) (10 . 17))       8.099     {1/3:6}  B:0
  3.66825 [ 3.66825]   ((7 . 1) (9 . 2) (13 . 9) (14 . 10))      12.854     {2/6:6}  B:0
SIMILARITY (1/min{score1}):   0.3636      [and  1/min{score2}:   0.3636]

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