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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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( 3336 1kko_A)  ( 1096 1ec7_A)     0.5999   0.9991   3.9272 (   0    9   15)   0     0.5999   0.9991   10   6
( 3336 1kko_A)  ( 3009 1jpd_X)     0.7937   0.9813   3.1528 (   1   19   28)   0     0.7937   0.9813   10   8
( 3336 1kko_A)  ( 3011 1jpm_A)     0.5000   0.5000   4.0598 (   0    7   10)   0     0.5000   0.5000   10  10
( 3336 1kko_A)  ( 3336 1kko_A)     1.0000   1.0000   0.0000 (   0   33   45)   0     1.0000   1.0000   10  10
( 3336 1kko_A)  ( 4037 1muc_A)     0.7999   0.9997   2.9808 (   0   18   28)   0     0.7999   0.9997   10   8
( 3336 1kko_A)  ( 4726 1one_A)     0.7999   0.9996   3.2183 (   0   17   28)   0     0.7999   0.9996   10   8
( 3336 1kko_A)  ( 5708 1rvk_A)     0.7996   0.8882   4.2561 (   0   18   28)   0     0.7996   0.8882   10   9
( 3336 1kko_A)  ( 6490 2mnr  )     0.6908   0.7624   6.6439 (   1   15   21)   0     0.6908   0.7624   10   9

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