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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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( 3370 1kny_A)  ( 1399 1f5a_A)     0.4531   0.3954   5.1382 (   1    6   10)   0     0.5384   0.4753   10  12
( 3370 1kny_A)  ( 2782 1jaj_A)     0.4998   0.2941   6.5921 (   0    3   10)   0     0.5998   0.3529   10  17
( 3370 1kny_A)  ( 2980 1jms_A)     0.6997   0.5384   4.5832 (   0   15   21)   0     0.6997   0.5384   10  13
( 3370 1kny_A)  ( 2990 1jn3_A)     0.6000   0.4615   2.1295 (   0    9   15)   0     0.6000   0.4615   10  13
( 3370 1kny_A)  ( 3370 1kny_A)     1.0000   1.0000   0.0000 (   0   34   45)   0     1.0000   1.0000   10  10
( 3370 1kny_A)  ( 3938 1miw_A)     0.6894   0.6894   3.2347 (   1   14   21)   0     0.6894   0.6894   10  10
( 3370 1kny_A)  ( 4332 1no5_A)     0.6893   0.8441   3.8002 (   1   14   21)   0     0.6893   0.8441   10   8
( 3370 1kny_A)  ( 4788 1ou5_A)     0.4201   0.4293   4.4319 (   2    9   15)   0     0.4201   0.4443   10   9
( 3370 1kny_A)  ( 5141 1px5_A)     0.4996   0.4165   7.5054 (   0    3   10)   0     0.4996   0.4165   10  12
( 3370 1kny_A)  ( 5589 1r89_A)     0.5735   0.5735   2.6384 (   1    9   15)   0     0.5999   0.5999   10  10
( 3370 1kny_A)  ( 5740 1rzt_A)     0.6999   0.4667   3.4889 (   0   15   21)   0     0.6999   0.5143   10  15
( 3370 1kny_A)  ( 6281 1vj7_A)     0.5736   0.5736   2.0900 (   1    9   15)   0     0.5736   0.5736   10  10
( 3370 1kny_A)  ( 6336 1wot_A)     0.5000   0.8327   4.4684 (   0    7   10)   0     0.5000   0.8327   10   6

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