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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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( 5525 1r1k_D)  (   25 1a28_A)     0.8323   0.7138   4.3973 (   1   38   45)   0     0.8323   0.7138   12  14
( 5525 1r1k_D)  ( 1472 1fcy_A)     0.8916   0.9623   1.6990 (   3   47   55)   0     0.8916   0.9623   12  11
( 5525 1r1k_D)  ( 1701 1g2n_A)     0.7982   0.7982   2.7757 (   3   38   45)   0     0.7982   0.7982   12  12
( 5525 1r1k_D)  ( 2467 1ie9_A)     0.9092   0.7822   4.0951 (   2   44   55)   0     0.9092   0.7822   12  14
( 5525 1r1k_D)  ( 3446 1kv6_A)     0.9077   0.8401   5.4948 (   2   44   55)   0     0.9077   0.8401   12  13
( 5525 1r1k_D)  ( 3743 1lv2_A)     0.7476   0.6698   6.0734 (   4   39   45)   0     0.7476   0.6698   12  14
( 5525 1r1k_D)  ( 4121 1n46_A)     0.7878   0.7878   3.3503 (   5   48   55)   0     0.7878   0.7878   12  12
( 5525 1r1k_D)  ( 4352 1nq7_A)     0.9109   0.6861   3.7944 (   2   47   55)   0     0.9109   0.6861   12  16
( 5525 1r1k_D)  ( 4370 1nrl_A)     0.8321   0.6247   4.8284 (   1   39   45)   0     0.8321   0.6415   12  16
( 5525 1r1k_D)  ( 4773 1osh_A)     0.7398   0.8755   4.1614 (   2   31   36)   0     0.7398   0.8755   12  10
( 5525 1r1k_D)  ( 4988 1pdu_A)     0.8362   0.7446   4.1222 (   4   45   55)   0     0.8362   0.7446   12  14
( 5525 1r1k_D)  ( 5034 1pk5_A)     0.7143   0.6794   5.7481 (   7   54   66)   0     0.7143   0.6794   12  14
( 5525 1r1k_D)  ( 5079 1pq9_A)     0.9163   0.9994   2.1414 (   1   48   55)   0     0.9163   0.9994   12  11
( 5525 1r1k_D)  ( 5365 1qkm_A)     0.8224   0.8224   4.4656 (   2   35   45)   0     0.8224   0.8224   12  12
( 5525 1r1k_D)  ( 5525 1r1k_D)     1.0000   1.0000   0.0000 (   0   60   66)   0     1.0000   1.0000   12  12
( 5525 1r1k_D)  ( 6515 2prg_A)     0.9162   0.7332   2.6049 (   1   48   55)   0     0.9162   0.7332   12  15

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