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Top-ranked similarities (based on backbone shifts), 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:
( ix1 chain1 )  ( ix2 chain2 )   rho___12 rho___21 L2_ERROR (Xbad Xsig Xtot) BRK   maxrho12 maxrho21  SS1 SS2

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( 5546 1r46_A)  (  335 1bag  )     0.7775   0.9992   3.8637 (   0   10   21)   0     0.7775   0.9992    9   7
( 5546 1r46_A)  (  367 1bf2  )     0.8885   0.7998   3.5619 (   0   17   28)   0     0.8885   0.7998    9  10
( 5546 1r46_A)  ( 1028 1e43_A)     0.7776   0.7776   3.5479 (   0   12   21)   0     0.7776   0.7776    9   9
( 5546 1r46_A)  ( 1729 1g5a_A)     0.7777   0.9997   2.9266 (   0   13   21)   0     0.7777   0.9997    9   7
( 5546 1r46_A)  ( 1839 1gjw_A)     0.5554   0.7138   5.0710 (   0    4   10)   0     0.6661   0.8551    9   7
( 5546 1r46_A)  ( 2063 1h3g_A)     0.8799   0.8799   4.0551 (   1   20   28)   0     0.8799   0.8799    9   9
( 5546 1r46_A)  ( 2232 1hl9_A)     0.8880   0.8880   4.5354 (   0   21   28)   0     0.8880   0.8880    9   9
( 5546 1r46_A)  ( 2311 1hx0_A)     0.8558   0.9435   3.3302 (   1   14   28)   0     0.8877   0.9979    9   8
( 5546 1r46_A)  ( 2622 1iv8_A)     0.8886   0.9996   3.2773 (   0   20   28)   0     0.8886   0.9996    9   8
( 5546 1r46_A)  ( 2687 1j0h_A)     0.7776   0.8747   3.4351 (   0   15   21)   0     0.7776   0.8747    9   8
( 5546 1r46_A)  ( 2879 1ji1_A)     0.8784   0.8784   2.9872 (   1   19   28)   0     0.8784   0.8784    9   9
( 5546 1r46_A)  ( 2882 1ji2_A)     0.8782   0.9811   3.5557 (   1   19   28)   0     0.8782   0.9811    9   8
( 5546 1r46_A)  ( 3426 1ktb_A)     0.7777   0.8749   2.3008 (   0   14   21)   0     0.7777   0.8749    9   8
( 5546 1r46_A)  ( 3839 1m53_A)     0.7777   0.9998   2.7908 (   0   13   21)   0     0.7777   0.9998    9   7
( 5546 1r46_A)  ( 3878 1m7x_A)     0.7775   0.9992   3.8416 (   0   12   21)   0     0.7775   0.9992    9   7
( 5546 1r46_A)  ( 4072 1mxg_A)     0.6666   0.8569   3.2555 (   0    7   15)   0     0.6666   0.8569    9   7
( 5546 1r46_A)  ( 4335 1nof_A)     0.8872   0.7990   5.3181 (   0   16   28)   0     0.8872   0.7990    9  10
( 5546 1r46_A)  ( 4646 1ogs_A)     0.4444   0.3333   5.9117 (   0    2    6)   0     0.7776   0.5833    9  12
( 5546 1r46_A)  ( 5341 1qho_A)     0.8887   0.9996   3.1356 (   0   16   28)   0     0.8887   0.9996    9   8
( 5546 1r46_A)  ( 5472 1qw9_A)     0.5551   0.4544   6.9515 (   0    3   10)   0     0.8852   0.7259    9  11
( 5546 1r46_A)  ( 5546 1r46_A)     1.0000   1.0000   0.0000 (   0   28   36)   0     1.0000   1.0000    9   9
( 5546 1r46_A)  ( 5953 1uas_A)     0.8784   0.9814   3.1331 (   1   19   28)   0     0.8784   0.9814    9   8
( 5546 1r46_A)  ( 6023 1uhv_A)     0.8867   0.7265   5.6964 (   0   10   28)   0     0.8867   0.7265    9  11
( 5546 1r46_A)  ( 6067 1uok  )     0.7777   0.9998   2.6957 (   0   11   21)   0     0.7777   0.9998    9   7
( 5546 1r46_A)  ( 6644 7taa  )     0.8800   0.8800   3.6961 (   1   20   28)   0     0.8800   0.8800    9   9

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