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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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(  120 1afw_A)  (  120 1afw_A)     1.0000   1.0000   0.0000 (   0   92  105)   0     1.0000   1.0000   15  15
(  120 1afw_A)  (  394 1bi5_A)     0.5992   0.5992   5.1510 (   1   24   36)   0     0.6428   0.6428   15  15
(  120 1afw_A)  (  395 1bi5_A)     0.4667   0.8746   3.7425 (   0   14   21)   0     0.4667   0.8746   15   8
(  120 1afw_A)  ( 1187 1ek4_A)     0.6621   0.5858   4.5043 (   2   33   45)   0     0.6621   0.5999   15  17
(  120 1afw_A)  ( 1188 1ek4_A)     0.5333   0.7996   4.1001 (   0   17   28)   0     0.5333   0.7996   15  10
(  120 1afw_A)  ( 2247 1hnj_A)     0.5734   0.6066   4.8921 (   3   27   36)   0     0.5931   0.6332   15  14
(  120 1afw_A)  ( 2248 1hnj_A)     0.4666   0.8743   4.2907 (   0   13   21)   0     0.5332   0.9970   15   8
(  120 1afw_A)  ( 2349 1hzp_A)     0.5333   0.6667   2.1392 (   0   20   28)   0     0.5696   0.6706   15  12
(  120 1afw_A)  ( 2350 1hzp_A)     0.4000   0.5000   3.7270 (   0    9   15)   0     0.4000   0.5000   15  12
(  120 1afw_A)  ( 3817 1m3k_A)     0.8000   0.7059   2.0582 (   0   53   66)   0     0.8000   0.7059   15  17
(  120 1afw_A)  ( 3818 1m3k_A)     0.4667   0.9995   3.4405 (   0   12   21)   0     0.4667   0.9995   15   7
(  120 1afw_A)  ( 4811 1ox0_A)     0.3333   0.3333   5.9592 (   0    6   10)   0     0.6628   0.6628   15  15
(  120 1afw_A)  ( 4812 1ox0_A)     0.4666   0.8745   3.9917 (   0   15   21)   0     0.4666   0.8745   15   8
(  120 1afw_A)  ( 5958 1ub7_A)     0.4666   0.8745   4.0025 (   0   12   21)   0     0.4666   0.8745   15   8

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