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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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[4587, 432]:
    Comparing 1obd_A and 1bo1_A, based on their crossing files.
    There are 26 (9 H + 17 S) secondary structure elements in 1obd_A, of which 16 satisfy the size requirements.
    There are 23 (11 H + 12 S) secondary structure elements in 1bo1_A, of which 20 satisfy the size requirements.
  4.00004 [ 5.00002]   ((2 . 3) (3 . 4) (6 . 6) (17 . 14))       5.210     {0/5:6}  B:0
  4.00021 [ 5.00011]   ((10 . 6) (11 . 9) (21 . 17) (24 . 19))       7.676     {0/4:6}  B:0
  4.00049 [ 5.00025]   ((1 . 8) (2 . 9) (14 . 18) (22 . 22))       9.537     {0/1:6}  B:0
  4.00077 [ 5.00039]   ((1 . 12) (2 . 13) (6 . 17) (14 . 20))      10.647     {0/5:6}  B:0
  4.00161 [ 5.00082]   ((6 . 1) (14 . 6) (17 . 8) (22 . 13))      12.814     {0/4:6}  B:0
SIMILARITY (1/min{score1}):   0.3070      [and  1/min{score2}:   0.2481]

[4587, 3441]:
    Comparing 1obd_A and 1kut_A, based on their crossing files.
    There are 26 (9 H + 17 S) secondary structure elements in 1obd_A, of which 16 satisfy the size requirements.
    There are 19 (7 H + 12 S) secondary structure elements in 1kut_A, of which 17 satisfy the size requirements.
  2.66683 [ 2.83347]   ((11 . 5) (13 . 7) (14 . 8) (20 . 12) (21 . 13) (22 . 15))       5.350     {0/11:15}  B:0
  2.67128 [ 2.83718]   ((6 . 3) (11 . 5) (13 . 7) (14 . 8) (20 . 12) (21 . 13))       2.757     {1/13:15}  B:0
  3.20132 [ 3.40110]   ((1 . 4) (2 . 5) (21 . 13) (22 . 14) (23 . 17))      10.324     {0/4:10}  B:0
  3.31569 [ 3.49753]   ((14 . 8) (20 . 12) (21 . 13) (23 . 15) (26 . 19))       4.407     {2/10:10}  B:0
  4.00012 [ 4.25010]   ((17 . 2) (21 . 3) (25 . 12) (26 . 13))       6.658     {0/5:6}  B:0
SIMILARITY (1/min{score1}):   0.4533      [and  1/min{score2}:   0.4411]

[4587, 4587]:
    Comparing 1obd_A and 1obd_A, based on their crossing files.
    There are 26 (9 H + 17 S) secondary structure elements in 1obd_A, of which 16 satisfy the size requirements.
    There are 26 (9 H + 17 S) secondary structure elements in 1obd_A, of which 16 satisfy the size requirements.
  1.00000 [ 1.00000]   ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (17 . 17) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26))       0.000     {0/97:120}  B:0
  3.23257 [ 3.23257]   ((3 . 1) (6 . 6) (20 . 20) (21 . 21) (24 . 23))      10.261     {1/7:10}  B:0
  3.23257 [ 3.23257]   ((1 . 3) (6 . 6) (20 . 20) (21 . 21) (23 . 24))      10.261     {1/7:10}  B:0
  4.00106 [ 4.00106]   ((17 . 13) (21 . 20) (24 . 22) (26 . 25))      11.540     {0/3:6}  B:0
  4.00106 [ 4.00106]   ((13 . 17) (20 . 21) (22 . 24) (25 . 26))      11.540     {0/3:6}  B:0
SIMILARITY (1/min{score1}):   1.0000      [and  1/min{score2}:   1.0000]

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