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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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( 5003 1pgj_A)  (  378 1bg6  )     0.3076   0.3634   9.5026 (   0    5    6)   0     0.4573   0.4919   13  11
( 5003 1pgj_A)  ( 2726 1j3v_A)     0.3846   0.8332   2.8713 (   0    5   10)   0     0.3846   0.8332   13   6
( 5003 1pgj_A)  ( 3415 1ks9_A)     0.3077   0.5712   5.8422 (   0    4    6)   0     0.4637   0.7910   13   7
( 5003 1pgj_A)  ( 3638 1lj8_A)     0.3456   0.3456   7.1202 (   2    9   10)   0     0.5376   0.5376   13  13
( 5003 1pgj_A)  ( 3855 1m66_A)     0.3075   0.5680  11.0950 (   0    4    6)   0     0.3489   0.5680   13   7
( 5003 1pgj_A)  ( 4342 1np3_A)     0.3076   0.3996  10.3248 (   0    3    6)   0     0.3076   0.3996   13  10
( 5003 1pgj_A)  ( 5003 1pgj_A)     1.0000   1.0000   0.0000 (   0   62   78)   0     1.0000   1.0000   13  13
( 5003 1pgj_A)  ( 5388 1qmg_A)     0.3076   0.2105  10.6993 (   0    5    6)   0     0.3564   0.3087   13  19
( 5003 1pgj_A)  ( 6506 2pgd  )     0.9230   0.9230   2.3295 (   0   49   66)   0     0.9230   0.9230   13  13

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