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I have a MKV file with the following encoding settings. I know the file was encoded in Handbrake because it says so in the meta data.

cabac=1
ref=5
deblock=1:0:0
analyse=0x3:0x133
me=umh
subme=9
psy=1
psy_rd=1.00:0.15
mixed_ref=1
me_range=24
chroma_me=1
trellis=2
8x8dct=1
cqm=0
deadzone=21,11
fast_pskip=1
chroma_qp_offset=-4
threads=12
lookahead_threads=1
sliced_threads=0
nr=0
decimate=1
interlaced=0
bluray_compat=0
constrained_intra=0
bframes=5
b_pyramid=2
b_adapt=2
b_bias=0
direct=3
weightb=1
open_gop=0
weightp=2
keyint=240
keyint_min=23
scenecut=40
intra_refresh=0
rc_lookahead=60
rc=crf
mbtree=1
crf=27.0
qcomp=0.60
qpmin=0
qpmax=69
qpstep=4
vbv_maxrate=10000
vbv_bufsize=10000
crf_max=51.0
nal_hrd=none
filler=0
ip_ratio=1.40
aq=1:1.00

I have used FFMPEG for a while, but I am not sure what these settings are, what they do or how I can make FFMPEG encode with the same settings.

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All of these parameters are specific to the x264 encoder which is used to produce H.264 streams.

x264 has long since introduced a preset system whereby different permutations of values of these parameters can be set at once using -preset value in FFmpeg, e.g. ffmpeg -i in.mp4 -c:v ibx264 -preset slow out.mp4

AFAICT, the permutation of parameters shown in your file don't match any preset. However, you can set preset to slow, and then override the individual parameters, e.g.

ffmpeg -i in.mp4 -c:v ibx264 -preset slow -x264opts "me=umh:subme=9:psy_rd=1.00:0.15" out.mp4

For a guide to individual parameters, see https://en.wikibooks.org/wiki/MeGUI/x264_Settings.

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