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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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( 4169 1n8y_C)  (   44 1a4y_A)     0.7494   0.2727   4.9763 (   0    0   36)   0     0.7495   0.2727   12  33
( 4169 1n8y_C)  (   83 1a9n_A)     0.5000   0.5454   3.1049 (   0    0   15)   0     0.5833   0.6363   12  11
( 4169 1n8y_C)  (  791 1dce_A)     0.6664   0.7268   4.8884 (   0    7   28)   0     0.6664   0.7268   12  11
( 4169 1n8y_C)  ( 1616 1fs2_A)     0.6666   0.4706   3.2741 (   0    0   28)   0     0.6666   0.4706   12  17
( 4169 1n8y_C)  ( 2109 1h6t_A)     0.6666   0.4706   2.8722 (   0    0   28)   0     0.6666   0.4706   12  17
( 4169 1n8y_C)  ( 2111 1h6u_A)     0.6666   0.4211   2.5877 (   0    0   28)   0     0.6666   0.4211   12  19
( 4169 1n8y_C)  ( 2488 1igr_A)     0.5000   0.8570   3.0160 (   0    2   15)   0     0.5000   0.8570   12   7
( 4169 1n8y_C)  ( 2490 1igr_A)     0.5833   0.8748   3.2397 (   0    6   21)   0     0.6657   0.9929   12   8
( 4169 1n8y_C)  ( 2547 1io0_A)     0.6666   0.7272   3.4093 (   0    5   28)   0     0.6666   0.7272   12  11
( 4169 1n8y_C)  ( 2955 1jl5_A)     0.5000   0.3333   3.3819 (   0    0   15)   0     0.5832   0.3889   12  18
( 4169 1n8y_C)  ( 3856 1m6b_A)     0.5000   0.7500   1.6780 (   0    0   15)   0     0.5000   0.7500   12   8
( 4169 1n8y_C)  ( 3857 1m6b_A)     0.9167   0.9167   0.7462 (   0   33   55)   0     0.9167   0.9167   12  12
( 4169 1n8y_C)  ( 3890 1m9l_A)     0.8045   0.5232   5.3836 (   2   27   45)   0     0.8045   0.5232   12  19
( 4169 1n8y_C)  ( 4167 1n8y_C)     0.6667   0.8000   2.3258 (   0   12   28)   0     0.6667   0.8000   12  10
( 4169 1n8y_C)  ( 4169 1n8y_C)     1.0000   1.0000   0.0000 (   0   44   66)   0     1.0000   1.0000   12  12
( 4169 1n8y_C)  ( 4516 1o6v_A)     0.6666   0.2353   2.8798 (   0    0   28)   0     0.6666   0.2353   12  34
( 4169 1n8y_C)  ( 4645 1ogq_A)     0.6666   0.2963   3.7793 (   0    0   28)   0     0.7492   0.3333   12  27
( 4169 1n8y_C)  ( 4850 1ozn_A)     0.4167   0.3571   1.5179 (   0    0   10)   0     0.4999   0.4285   12  14
( 4169 1n8y_C)  ( 4940 1p9a_G)     0.5000   0.4286   2.5179 (   0    0   15)   0     0.5000   0.4286   12  14
( 4169 1n8y_C)  ( 5011 1pgv_A)     0.6666   0.7272   2.8320 (   0    6   28)   0     0.6666   0.7272   12  11
( 4169 1n8y_C)  ( 6362 1yrg_A)     0.8317   0.4347   5.7015 (   0    0   45)   0     0.8317   0.4347   12  23

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