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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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( 4446 1nyt_A)  (   41 1a4i_A)     0.6666   0.8568   3.6406 (   0    2   15)   0     0.6666   0.8568    9   7
( 4446 1nyt_A)  (  258 1b0a_A)     0.6666   0.8568   3.7693 (   0    0   15)   0     0.6666   0.8568    9   7
( 4446 1nyt_A)  (  505 1c1d_A)     0.6040   0.6040   5.2279 (   1    8   15)   0     0.6040   0.6040    9   9
( 4446 1nyt_A)  ( 1116 1edz_A)     0.6665   0.7497   4.1214 (   0    3   15)   0     0.6665   0.7497    9   8
( 4446 1nyt_A)  ( 1947 1gtm_A)     0.4444   0.4444   4.4760 (   0    1    6)   0     0.4444   0.4444    9   9
( 4446 1nyt_A)  ( 2015 1gz3_A)     0.5554   0.2941   5.5368 (   0    1   10)   0     0.5554   0.3049    9  17
( 4446 1nyt_A)  ( 2269 1hrd_A)     0.6040   0.4495   5.2370 (   1    8   15)   0     0.6040   0.4495    9  13
( 4446 1nyt_A)  ( 2308 1hwx_A)     0.6040   0.4825   4.8416 (   1    8   15)   0     0.6040   0.4825    9  12
( 4446 1nyt_A)  ( 3609 1leh_A)     0.5553   0.6246   5.6568 (   0    4   10)   0     0.6660   0.7488    9   8
( 4446 1nyt_A)  ( 3733 1lu9_A)     0.6666   0.6666   3.4778 (   0    6   15)   0     0.6666   0.6666    9   9
( 4446 1nyt_A)  ( 4350 1npy_A)     0.9998   0.8999   2.6079 (   0   19   36)   0     0.9998   0.8999    9  10
( 4446 1nyt_A)  ( 4446 1nyt_A)     1.0000   1.0000   0.0000 (   0   23   36)   0     1.0000   1.0000    9   9
( 4446 1nyt_A)  ( 6256 1vi2_A)     0.9999   0.9000   1.9418 (   0   21   36)   0     0.9999   0.9000    9  10

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