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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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[6552, 2747]:
    Comparing 2uag_A and 1j6u_A, based on their crossing files.
    There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 9 satisfy the size requirements.
    There are 37 (16 H + 21 S) secondary structure elements in 1j6u_A, of which 7 satisfy the size requirements.
  1.33910 [ 1.10351]   ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 6) (8 . 7) (9 . 8))       2.536     {1/12:21}  B:0
  1.50018 [ 1.16705]   ((1 . 1) (2 . 2) (5 . 3) (7 . 6) (8 . 7) (9 . 8))       3.554     {0/9:15}  B:0
  1.60204 [ 1.35563]   ((1 . 1) (2 . 2) (3 . 3) (7 . 6) (8 . 7) (9 . 8))       2.381     {1/9:15}  B:0
  1.80096 [ 1.40205]   ((2 . 2) (4 . 4) (5 . 6) (6 . 7) (7 . 8))       6.197     {0/7:10}  B:0
  1.80418 [ 1.40882]   ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (8 . 7))       8.946     {0/4:10}  B:0
SIMILARITY (1/min{score1}):   0.7773      [and  1/min{score2}:   0.9982]

[6552, 4878]:
    Comparing 2uag_A and 1p3d_A, based on their crossing files.
    There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 9 satisfy the size requirements.
    There are 40 (18 H + 22 S) secondary structure elements in 1p3d_A, of which 9 satisfy the size requirements.
  1.01547 [ 1.01547]   ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9))       2.730     {1/20:36}  B:0
  1.15095 [ 1.15095]   ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9))       2.301     {1/16:28}  B:0
  1.50348 [ 1.50348]   ((1 . 1) (2 . 2) (3 . 3) (6 . 4) (8 . 8) (9 . 9))       7.457     {0/8:15}  B:0
  1.80025 [ 1.80025]   ((1 . 5) (2 . 6) (3 . 7) (4 . 8) (5 . 9))       4.438     {0/5:10}  B:0
  1.80290 [ 1.80290]   ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (7 . 5))       8.164     {0/1:10}  B:0
SIMILARITY (1/min{score1}):   0.9848      [and  1/min{score2}:   0.9848]

[6552, 6552]:
    Comparing 2uag_A and 2uag_A, based on their crossing files.
    There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 9 satisfy the size requirements.
    There are 40 (20 H + 20 S) secondary structure elements in 2uag_A, of which 9 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9))       0.000     {0/28:36}  B:0
  1.80070 [ 1.80070]   ((1 . 1) (2 . 2) (5 . 7) (6 . 8) (7 . 9))       5.723     {0/5:10}  B:0
  2.83619 [ 2.83619]   ((1 . 3) (3 . 5) (4 . 6) (5 . 7))       5.479     {1/4:6}  B:0
  2.83619 [ 2.83619]   ((3 . 1) (5 . 3) (6 . 4) (7 . 5))       5.479     {1/4:6}  B:0
  1.74364 [ 1.74364]   ((1 . 1) (2 . 2) (3 . 3) (5 . 7) (7 . 9) (8 . 8))       5.684     {1/7:15}  B:1
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

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