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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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( 2247 1hnj_A)  (  120 1afw_A)     0.6066   0.5734   4.8921 (   3   27   36)   0     0.6332   0.5931   14  15
( 2247 1hnj_A)  (  394 1bi5_A)     0.8558   0.8127   3.9130 (   5   59   78)   0     0.8558   0.8127   14  15
( 2247 1hnj_A)  (  395 1bi5_A)     0.5000   0.8747   3.4675 (   0   15   21)   0     0.5000   0.8747   14   8
( 2247 1hnj_A)  ( 1187 1ek4_A)     0.7081   0.5859   2.7029 (   2   33   45)   0     0.7081   0.5859   14  17
( 2247 1hnj_A)  ( 1188 1ek4_A)     0.5714   0.7997   3.8166 (   0   17   28)   0     0.5714   0.7997   14  10
( 2247 1hnj_A)  ( 2247 1hnj_A)     1.0000   1.0000   0.0000 (   0   74   91)   0     1.0000   1.0000   14  14
( 2247 1hnj_A)  ( 2248 1hnj_A)     0.5000   0.8745   3.9026 (   0   13   21)   0     0.5000   0.8745   14   8
( 2247 1hnj_A)  ( 2349 1hzp_A)     0.8570   0.9997   1.3362 (   1   54   66)   0     0.8570   0.9997   14  12
( 2247 1hnj_A)  ( 2350 1hzp_A)     0.3795   0.3831   5.9843 (   8   31   45)   0     0.3795   0.3831   14  12
( 2247 1hnj_A)  ( 3817 1m3k_A)     0.5714   0.4706   1.9781 (   0   21   28)   0     0.5714   0.4706   14  17
( 2247 1hnj_A)  ( 3818 1m3k_A)     0.5000   0.9998   2.7144 (   0   12   21)   0     0.5000   0.9998   14   7
( 2247 1hnj_A)  ( 4811 1ox0_A)     0.5714   0.5333   3.0974 (   0   18   28)   0     0.5714   0.5333   14  15
( 2247 1hnj_A)  ( 4812 1ox0_A)     0.5000   0.8747   3.5527 (   0   16   21)   0     0.5000   0.8747   14   8
( 2247 1hnj_A)  ( 5958 1ub7_A)     0.5000   0.8747   3.5623 (   0   12   21)   0     0.5000   0.8747   14   8

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