-------------------------------------------------------------------------------------------------------------------------

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.

-------------------------------------------------------------------------------------------------------------------------

[2870, 264]:
    Comparing 1jhf_A and 1b12_A, based on their crossing files.
    There are 18 (6 H + 12 S) secondary structure elements in 1jhf_A, of which 11 satisfy the size requirements.
    There are 24 (6 H + 18 S) secondary structure elements in 1b12_A, of which 17 satisfy the size requirements.
  2.75011 [ 4.25003]   ((6 . 1) (8 . 2) (12 . 6) (15 . 8))       4.906     {0/4:6}  B:0
  2.75011 [ 4.25003]   ((6 . 1) (8 . 2) (12 . 6) (14 . 7))       4.936     {0/6:6}  B:0
  2.75014 [ 4.25004]   ((6 . 1) (8 . 2) (12 . 6) (16 . 9))       5.286     {0/4:6}  B:0
  2.75019 [ 4.25005]   ((8 . 6) (10 . 7) (16 . 12) (17 . 14))       5.665     {0/5:6}  B:0
  2.75022 [ 4.25006]   ((6 . 6) (8 . 7) (13 . 12) (14 . 14))       5.885     {0/4:6}  B:0
SIMILARITY (1/min{score1}):   0.4787      [and  1/min{score2}:   0.3431]

[2870, 1382]:
    Comparing 1jhf_A and 1f39_A, based on their crossing files.
    There are 18 (6 H + 12 S) secondary structure elements in 1jhf_A, of which 11 satisfy the size requirements.
    There are 8 (1 H + 7 S) secondary structure elements in 1f39_A, of which 6 satisfy the size requirements.
  1.84753 [ 1.07869]   ((10 . 1) (12 . 2) (13 . 3) (14 . 4) (16 . 5) (18 . 7))       3.968     {1/13:15}  B:0
  2.23495 [ 1.37725]   ((10 . 1) (12 . 2) (13 . 3) (16 . 5) (18 . 7))       1.713     {1/9:10}  B:0
  2.66395 [ 2.51589]   ((10 . 1) (12 . 2) (13 . 3) (15 . 4) (16 . 5) (18 . 7))       3.616     {3/12:15}  B:0
  2.75011 [ 1.50066]   ((10 . 1) (12 . 2) (16 . 4) (18 . 7))       4.917     {0/5:6}  B:0
  2.92527 [ 2.14315]   ((6 . 1) (8 . 2) (10 . 4) (12 . 5))       6.877     {1/5:6}  B:0
SIMILARITY (1/min{score1}):   0.5413      [and  1/min{score2}:   0.9270]

[2870, 2870]:
    Comparing 1jhf_A and 1jhf_A, based on their crossing files.
    There are 18 (6 H + 12 S) secondary structure elements in 1jhf_A, of which 11 satisfy the size requirements.
    There are 18 (6 H + 12 S) secondary structure elements in 1jhf_A, of which 11 satisfy the size requirements.
  1.00000 [ 1.00000]   ((6 . 6) (8 . 8) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18))       0.000     {0/45:55}  B:0
  2.75043 [ 2.75043]   ((8 . 6) (10 . 8) (12 . 10) (14 . 12))       6.944     {0/5:6}  B:0
  2.75043 [ 2.75043]   ((6 . 8) (8 . 10) (10 . 12) (12 . 14))       6.944     {0/5:6}  B:0
  2.75045 [ 2.75045]   ((8 . 10) (10 . 12) (13 . 16) (14 . 17))       7.046     {0/4:6}  B:0
  2.75045 [ 2.75045]   ((10 . 8) (12 . 10) (16 . 13) (17 . 14))       7.046     {0/4:6}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[2870, 6053]:
    Comparing 1jhf_A and 1umu_A, based on their crossing files.
    There are 18 (6 H + 12 S) secondary structure elements in 1jhf_A, of which 11 satisfy the size requirements.
    There are 10 (3 H + 7 S) secondary structure elements in 1umu_A, of which 8 satisfy the size requirements.
  1.57147 [ 1.14296]   ((10 . 3) (11 . 4) (12 . 5) (13 . 6) (14 . 7) (16 . 8) (18 . 10))       2.517     {0/17:21}  B:0
  2.46217 [ 2.38506]   ((10 . 3) (11 . 4) (12 . 5) (13 . 6) (14 . 7) (17 . 8) (18 . 10))       3.567     {4/17:21}  B:0
  2.75281 [ 2.00727]   ((8 . 3) (10 . 5) (13 . 8) (17 . 10))      11.129     {0/4:6}  B:0
  2.92660 [ 2.38152]   ((8 . 3) (10 . 5) (13 . 7) (17 . 10))      10.232     {1/5:6}  B:0
  3.48134 [ 3.37675]   ((10 . 3) (11 . 4) (12 . 5) (13 . 7) (18 . 10))       4.320     {3/9:10}  B:0
SIMILARITY (1/min{score1}):   0.6363      [and  1/min{score2}:   0.8749]

-------------------------------------------------------------------------------------------------------------------------