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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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( 4211 1ne9_A)  (  433 1bo4_A)     0.6666   0.7999   3.0073 (   0   21   28)   0     0.6666   0.7999   12  10
( 4211 1ne9_A)  (  435 1bob  )     0.6649   0.3808   3.4484 (   1   21   28)   0     0.6649   0.3808   12  21
( 4211 1ne9_A)  (  610 1cjw_A)     0.7484   0.6913   2.7312 (   1   25   36)   0     0.7484   0.6913   12  13
( 4211 1ne9_A)  ( 1657 1fy7_A)     0.5831   0.3684   5.6581 (   0   15   21)   0     0.6480   0.4191   12  19
( 4211 1ne9_A)  ( 1831 1ghe_A)     0.7499   0.6922   3.2805 (   0   26   36)   0     0.7499   0.6922   12  13
( 4211 1ne9_A)  ( 2356 1i12_A)     0.7499   0.8997   3.4763 (   0   27   36)   0     0.7499   0.8997   12  10
( 4211 1ne9_A)  ( 2668 1iyk_A)     0.6664   0.7269   4.8141 (   0   19   28)   0     0.6664   0.7269   12  11
( 4211 1ne9_A)  ( 2669 1iyk_A)     0.7499   0.5625   3.3099 (   0   27   36)   0     0.7499   0.5625   12  16
( 4211 1ne9_A)  ( 3485 1kzf_A)     0.6648   0.4995   4.5987 (   1   21   28)   0     0.6648   0.4995   12  16
( 4211 1ne9_A)  ( 3712 1lrz_A)     0.7475   0.7475   4.6867 (   1   23   36)   0     0.7475   0.7475   12  12
( 4211 1ne9_A)  ( 3713 1lrz_A)     0.9224   0.7715   3.6570 (   4   51   66)   0     0.9224   0.7715   12  15
( 4211 1ne9_A)  ( 3828 1m44_A)     0.7497   0.6427   4.2163 (   0   25   36)   0     0.7497   0.6427   12  14
( 4211 1ne9_A)  ( 3954 1mk4_A)     0.7499   0.7499   3.0132 (   0   27   36)   0     0.7499   0.7499   12  12
( 4211 1ne9_A)  ( 4148 1n71_A)     0.7484   0.7484   2.9165 (   1   25   36)   0     0.7484   0.7484   12  12
( 4211 1ne9_A)  ( 4210 1ne9_A)     0.6625   0.7898   4.9494 (   1   17   28)   0     0.6625   0.7898   12  10
( 4211 1ne9_A)  ( 4211 1ne9_A)     1.0000   1.0000   0.0000 (   0   54   66)   0     1.0000   1.0000   12  12
( 4211 1ne9_A)  ( 4377 1nsl_A)     0.7499   0.6922   3.5600 (   0   27   36)   0     0.7499   0.6922   12  13
( 4211 1ne9_A)  ( 4852 1p0h_A)     0.7500   0.4737   2.6835 (   0   26   36)   0     0.8321   0.5262   12  19
( 4211 1ne9_A)  ( 5189 1q2y_A)     0.7484   0.8961   2.8514 (   1   25   36)   0     0.7484   0.8961   12  10
( 4211 1ne9_A)  ( 5445 1qso_A)     0.8235   0.8941   4.3808 (   2   36   45)   0     0.8235   0.8941   12  11
( 4211 1ne9_A)  ( 5446 1qst_A)     0.7499   0.8181   2.8254 (   0   27   36)   0     0.7499   0.8181   12  11
( 4211 1ne9_A)  ( 5557 1r57_A)     0.5833   0.8747   3.5253 (   0   13   21)   0     0.5833   0.8747   12   8
( 4211 1ne9_A)  ( 5841 1sqh_A)     0.8307   0.4544   5.7840 (   1   32   45)   0     0.8307   0.4544   12  22
( 4211 1ne9_A)  ( 6003 1ufh_A)     0.7485   0.9936   4.6286 (   1   27   36)   0     0.7485   0.9936   12   9
( 4211 1ne9_A)  ( 6244 1vhs_A)     0.7487   0.6914   2.5046 (   1   26   36)   0     0.7487   0.6914   12  13

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