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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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(   41 1a4i_A)  (   41 1a4i_A)     1.0000   1.0000   0.0000 (   0    8   21)   0     1.0000   1.0000    7   7
(   41 1a4i_A)  (  258 1b0a_A)     0.9998   0.9998   2.6790 (   0    6   21)   0     0.9998   0.9998    7   7
(   41 1a4i_A)  (  505 1c1d_A)     0.8562   0.6664   4.7729 (   0    2   15)   0     0.8562   0.6664    7   9
(   41 1a4i_A)  ( 1116 1edz_A)     0.9999   0.8750   1.6455 (   0    8   21)   0     0.9999   0.8750    7   8
(   41 1a4i_A)  ( 1947 1gtm_A)     0.7131   0.5552   6.4653 (   0    1   10)   0     0.8499   0.6646    7   9
(   41 1a4i_A)  ( 2015 1gz3_A)     0.9945   0.4117   6.1718 (   0    6   21)   0     0.9945   0.4117    7  17
(   41 1a4i_A)  ( 2269 1hrd_A)     0.8560   0.4615   5.0192 (   0    2   15)   0     0.8560   0.4615    7  13
(   41 1a4i_A)  ( 2308 1hwx_A)     0.8564   0.4999   4.5813 (   0    2   15)   0     0.8564   0.4999    7  12
(   41 1a4i_A)  ( 3609 1leh_A)     0.5711   0.4998   5.9901 (   0    0    6)   0     0.7138   0.6247    7   8
(   41 1a4i_A)  ( 3733 1lu9_A)     0.8570   0.6666   2.7886 (   0    2   15)   0     0.8570   0.6666    7   9
(   41 1a4i_A)  ( 4350 1npy_A)     0.8570   0.6000   3.0496 (   0    2   15)   0     0.8570   0.6000    7  10
(   41 1a4i_A)  ( 4446 1nyt_A)     0.8568   0.6666   3.6406 (   0    2   15)   0     0.8568   0.6666    7   9
(   41 1a4i_A)  ( 6256 1vi2_A)     0.8571   0.6000   2.6088 (   0    2   15)   0     0.8571   0.6000    7  10

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