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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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[2843, 2843]:
    Comparing 1jey_A and 1jey_A, based on their crossing files.
    There are 37 (18 H + 19 S) secondary structure elements in 1jey_A, of which 18 satisfy the size requirements.
    There are 37 (18 H + 19 S) secondary structure elements in 1jey_A, of which 18 satisfy the size requirements.
  1.00000 [ 1.00000]   ((14 . 14) (15 . 15) (16 . 16) (17 . 17) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (25 . 25) (27 . 27) (28 . 28) (29 . 29) (31 . 31) (32 . 32) (34 . 34) (35 . 35) (36 . 36) (37 . 37))       0.000     {0/135:153}  B:0
  3.62213 [ 3.62213]   ((20 . 19) (21 . 21) (27 . 27) (34 . 34) (35 . 35))       3.812     {1/7:10}  B:0
  3.62213 [ 3.62213]   ((19 . 20) (21 . 21) (27 . 27) (34 . 34) (35 . 35))       3.812     {1/7:10}  B:0
  3.79708 [ 3.79708]   ((15 . 14) (19 . 17) (28 . 25) (32 . 29) (36 . 35))      15.361     {2/8:10}  B:0
  3.79708 [ 3.79708]   ((14 . 15) (17 . 19) (25 . 28) (29 . 32) (35 . 36))      15.361     {2/8:10}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

[2843, 2845]:
    Comparing 1jey_A and 1jey_B, based on their crossing files.
    There are 37 (18 H + 19 S) secondary structure elements in 1jey_A, of which 18 satisfy the size requirements.
    There are 41 (20 H + 21 S) secondary structure elements in 1jey_B, of which 17 satisfy the size requirements.
  1.27133 [ 1.22948]   ((14 . 16) (15 . 17) (16 . 18) (17 . 19) (19 . 22) (20 . 23) (21 . 24) (22 . 25) (25 . 28) (27 . 29) (28 . 30) (29 . 31) (32 . 32) (34 . 34) (35 . 38) (37 . 40))       5.128     {10/100:120}  B:0
  1.31002 [ 1.24294]   ((14 . 16) (15 . 17) (19 . 22) (20 . 23) (21 . 24) (22 . 25) (25 . 28) (27 . 29) (28 . 30) (29 . 31) (32 . 32) (34 . 34) (35 . 38) (37 . 40))       4.067     {5/74:91}  B:0
  1.35145 [ 1.30632]   ((14 . 16) (15 . 17) (16 . 18) (19 . 22) (20 . 23) (21 . 24) (22 . 25) (25 . 28) (27 . 29) (28 . 30) (29 . 31) (32 . 32) (34 . 34) (35 . 38) (37 . 40))       4.324     {9/85:105}  B:0
  1.80328 [ 1.78494]   ((14 . 16) (15 . 17) (16 . 18) (19 . 22) (20 . 23) (21 . 24) (22 . 25) (25 . 28) (27 . 29) (28 . 30) (29 . 31) (32 . 32) (34 . 34) (35 . 38) (36 . 40))       4.027     {14/82:105}  B:0
  2.72411 [ 2.68274]   ((14 . 16) (15 . 17) (22 . 25) (25 . 28) (27 . 29) (28 . 30) (29 . 31) (32 . 32) (34 . 40))       4.392     {8/32:36}  B:0
SIMILARITY (1/min{score1}):   0.7866      [and  1/min{score2}:   0.8134]

[2843, 4801]:
    Comparing 1jey_A and 1ow1_A, based on their crossing files.
    There are 37 (18 H + 19 S) secondary structure elements in 1jey_A, of which 18 satisfy the size requirements.
    There are 15 (7 H + 8 S) secondary structure elements in 1ow1_A, of which 14 satisfy the size requirements.
  2.25088 [ 1.75188]   ((14 . 2) (15 . 3) (22 . 5) (25 . 8) (27 . 10) (28 . 11) (29 . 12) (32 . 15))       4.152     {1/23:28}  B:0
  2.25089 [ 1.75188]   ((14 . 2) (15 . 3) (22 . 6) (25 . 8) (27 . 10) (28 . 11) (29 . 12) (32 . 15))       4.194     {1/23:28}  B:0
  2.25108 [ 1.75230]   ((14 . 2) (15 . 3) (22 . 6) (25 . 8) (27 . 9) (28 . 11) (29 . 12) (32 . 15))       5.460     {1/23:28}  B:0
  3.60040 [ 2.80085]   ((21 . 4) (22 . 6) (25 . 8) (28 . 11) (29 . 12))       8.374     {0/6:10}  B:0
  4.50005 [ 3.50011]   ((15 . 2) (25 . 11) (28 . 12) (29 . 15))       5.873     {0/4:6}  B:0
SIMILARITY (1/min{score1}):   0.4443      [and  1/min{score2}:   0.5708]

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