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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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(  612 1cjx_A)  (  611 1cjx_A)     0.7080   0.8200   6.7312 (   2   35   45)   0     0.7093   0.8227   14  12
(  612 1cjx_A)  (  612 1cjx_A)     1.0000   1.0000   0.0000 (   0   69   91)   0     1.0000   1.0000   14  14
(  612 1cjx_A)  ( 1105 1ecs_A)     0.3571   0.5000   4.1858 (   0    2   10)   0     0.5311   0.6493   14  10
(  612 1cjx_A)  ( 1365 1f1u_A)     0.7118   0.9869   7.3925 (   1   33   45)   0     0.7118   0.9869   14  10
(  612 1cjx_A)  ( 1366 1f1u_A)     0.7125   0.8295   6.4497 (   1   30   45)   0     0.7125   0.8295   14  12
(  612 1cjx_A)  ( 1451 1f9z_A)     0.2857   0.4000   1.7398 (   0    1    6)   0     0.4529   0.5381   14  10
(  612 1cjx_A)  ( 2819 1jc4_A)     0.7090   0.8921   4.8060 (   2   35   45)   0     0.7090   0.8921   14  11
(  612 1cjx_A)  ( 2890 1jif_A)     0.3570   0.4541   8.9265 (   0    0   10)   0     0.5311   0.6201   14  11
(  612 1cjx_A)  ( 3175 1k4n_A)     0.7052   0.7052   7.5163 (   2   32   45)   0     0.7052   0.7052   14  14
(  612 1cjx_A)  ( 3347 1kll_A)     0.3570   0.4542   8.2849 (   0    2   10)   0     0.3847   0.4542   14  11
(  612 1cjx_A)  ( 3456 1kw3_B)     0.6416   0.8936   5.9111 (   1   25   36)   0     0.7108   0.9817   14  10
(  612 1cjx_A)  ( 3457 1kw3_B)     0.7132   0.9053   5.5832 (   1   32   45)   0     0.7132   0.9055   14  11
(  612 1cjx_A)  ( 4006 1mpy_A)     0.7117   0.9866   7.3579 (   1   31   45)   0     0.7117   0.9866   14  10
(  612 1cjx_A)  ( 4007 1mpy_A)     0.7768   0.8334   6.4608 (   2   36   55)   0     0.7768   0.8334   14  13
(  612 1cjx_A)  ( 4284 1nki_A)     0.3571   0.4545   5.4425 (   0    1   10)   0     0.4202   0.4609   14  11
(  612 1cjx_A)  ( 5349 1qip_A)     0.3571   0.3333   4.2996 (   0    5   10)   0     0.4145   0.3899   14  15
(  612 1cjx_A)  ( 5597 1r9c_A)     0.2857   0.4000   5.0316 (   0    0    6)   0     0.4280   0.5967   14  10

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