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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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(  505 1c1d_A)  (   41 1a4i_A)     0.6664   0.8562   4.7729 (   0    2   15)   0     0.6664   0.8562    9   7
(  505 1c1d_A)  (  258 1b0a_A)     0.6661   0.8550   5.9102 (   0    0   15)   0     0.6661   0.8550    9   7
(  505 1c1d_A)  (  505 1c1d_A)     1.0000   1.0000   0.0000 (   0   27   36)   0     1.0000   1.0000    9   9
(  505 1c1d_A)  ( 1116 1edz_A)     0.6662   0.7492   5.3765 (   0    3   15)   0     0.6662   0.7492    9   8
(  505 1c1d_A)  ( 1947 1gtm_A)     0.8833   0.8833   7.1885 (   0   17   28)   0     0.8833   0.8833    9   9
(  505 1c1d_A)  ( 2015 1gz3_A)     0.6665   0.3529   4.2938 (   0    9   15)   0     0.6665   0.4071    9  17
(  505 1c1d_A)  ( 2269 1hrd_A)     0.9966   0.6918   5.4698 (   0   25   36)   0     0.9966   0.6918    9  13
(  505 1c1d_A)  ( 2308 1hwx_A)     0.8886   0.6666   3.4847 (   0   20   28)   0     0.9808   0.7453    9  12
(  505 1c1d_A)  ( 3609 1leh_A)     0.8885   0.9993   3.7221 (   0   17   28)   0     0.8885   0.9993    9   8
(  505 1c1d_A)  ( 3733 1lu9_A)     0.6664   0.6664   4.7953 (   0    6   15)   0     0.6664   0.6664    9   9
(  505 1c1d_A)  ( 4350 1npy_A)     0.5736   0.5385   5.1637 (   1    7   15)   0     0.5736   0.5385    9  10
(  505 1c1d_A)  ( 4446 1nyt_A)     0.6040   0.6040   5.2279 (   1    8   15)   0     0.6040   0.6040    9   9
(  505 1c1d_A)  ( 6256 1vi2_A)     0.5736   0.5385   4.9027 (   1    7   15)   0     0.5736   0.5385    9  10

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