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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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( 3961 1mkm_A)  (  100 1acf  )     0.8119   0.7459   4.7222 (   1   20   36)   0     0.8119   0.7459   11  12
( 3961 1mkm_A)  (  496 1byw_A)     0.5284   0.6796   3.8490 (   1    9   15)   0     0.5284   0.6796   11   8
( 3961 1mkm_A)  ( 1279 1ew0_A)     0.6311   0.6916   4.7852 (   1   15   21)   0     0.6311   0.6916   11  10
( 3961 1mkm_A)  ( 1402 1f5m_A)     0.8181   0.8181   2.8085 (   0   25   36)   0     0.8181   0.8181   11  11
( 3961 1mkm_A)  ( 1985 1gw5_M)     0.4544   0.5552   6.3520 (   0    6   10)   0     0.7269   0.8878   11   9
( 3961 1mkm_A)  ( 1986 1gw5_S)     0.5454   0.6000   3.4463 (   0    8   15)   0     0.6363   0.6999   11  10
( 3961 1mkm_A)  ( 2072 1h3q_A)     0.4542   0.5546   8.2197 (   0    5   10)   0     0.7268   0.8876   11   9
( 3961 1mkm_A)  ( 2139 1h8m_A)     0.3634   0.4986  10.3344 (   0    5    6)   0     0.3634   0.4986   11   8
( 3961 1mkm_A)  ( 2472 1ifq_A)     0.3635   0.4994   8.5099 (   0    3    6)   0     0.4089   0.4994   11   8
( 3961 1mkm_A)  ( 2727 1j3w_A)     0.7269   0.9983   4.5788 (   0   18   28)   0     0.7269   0.9983   11   8
( 3961 1mkm_A)  ( 3527 1l3l_A)     0.7269   0.6664   4.6968 (   0   19   28)   0     0.7269   0.6664   11  12
( 3961 1mkm_A)  ( 3652 1ll8_A)   nil
( 3961 1mkm_A)  ( 3903 1mc0_A)     0.7271   0.6666   3.6511 (   0   21   28)   0     0.7271   0.6666   11  12
( 3961 1mkm_A)  ( 3904 1mc0_A)     0.7271   0.8883   4.1023 (   0   19   28)   0     0.7271   0.8883   11   9
( 3961 1mkm_A)  ( 3961 1mkm_A)     1.0000   1.0000   0.0000 (   0   47   55)   0     1.0000   1.0000   11  11
( 3961 1mkm_A)  ( 4177 1n9l_A)     0.5284   0.6796   4.0128 (   1    9   15)   0     0.5284   0.6796   11   8
( 3961 1mkm_A)  ( 4366 1nrj_A)     0.4544   0.4998   6.6015 (   0    3   10)   0     0.6360   0.6995   11  10
( 3961 1mkm_A)  ( 4420 1nwz_A)     0.4545   0.4545   5.8600 (   0    8   10)   0     0.7269   0.7269   11  11
( 3961 1mkm_A)  ( 4674 1oj5_A)     0.5453   0.6664   4.9705 (   0    8   15)   0     0.5453   0.6664   11   9
( 3961 1mkm_A)  ( 4676 1ojg_A)     0.3635   0.4439   9.3455 (   0    3    6)   0     0.6243   0.7466   11   9
( 3961 1mkm_A)  ( 4856 1p0z_A)     0.3636   0.3999   6.2557 (   0    4    6)   0     0.7223   0.7921   11  10
( 3961 1mkm_A)  ( 4938 1p97_A)     0.3636   0.5712   5.6765 (   0    4    6)   0     0.3636   0.5712   11   7
( 3961 1mkm_A)  ( 5065 1pne  )     0.6363   0.6363   3.1460 (   0   12   21)   0     0.8159   0.8159   11  11
( 3961 1mkm_A)  ( 6238 1vhm_A)     0.8181   0.8999   2.3205 (   0   25   36)   0     0.8181   0.8999   11  10
( 3961 1mkm_A)  ( 6584 3nul  )     0.7270   0.7996   4.1923 (   0   15   28)   0     0.7270   0.7996   11  10

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