J-factor versus linker number. As the linker number is increased, the two 20 degree bends change their phasing with respect to the ATract bend.

$nchains=200000; $icalcs=100; (# whole chains = 4x10^8)

corona (lapham): [~/cyclize/samples/kink]> get_j.pl phasing_example_*/an*header
directory name                  J factor     Error
phasing_example_1                 182.29    (4.58)
phasing_example_10                  8.02    (0.47)
phasing_example_2                 684.60   (13.84)
phasing_example_3                1564.36   (28.15)
phasing_example_4                1371.83   (25.03)
phasing_example_5                 702.08   (14.08)
phasing_example_6                 187.05    (4.96)
phasing_example_7                  13.44    (0.66)
phasing_example_8                   0.83    (0.14)
phasing_example_9                   2.42    (0.25)

Repeating this experiment with a larger number of chains:

$nchains=1000000; $icalcs=100; (# whole chains = 1x10^10)

corona (lapham): [~/cyclize/samples/kink2]> get_j.pl phasing_example_*/an*header
directory name                  J factor     Error
phasing_example_1                 222.84    (6.94)
phasing_example_10                 10.79    (0.43)
phasing_example_2                 810.96   (22.96)
phasing_example_3                1623.64   (44.37)
phasing_example_4                1488.41   (41.06)
phasing_example_5                 687.04   (19.86)
phasing_example_6                 169.31    (5.22)
phasing_example_7                  17.78    (0.64)
phasing_example_8                   2.13    (0.12)
phasing_example_9                   1.58    (0.09)

Graphically... Shown in red is the 1x10^10 whole chain calculation and in black is the 4x10^8 calculation.