Getting PDB file(s) from the PDB server...

Running command: imembrane --verbose --joy --transmembrane --maxhits 10 --inputid template --struc template.atm --outdir imem  --cutoff-e 1.0 --cutoff-e2 0.002 --iterations 3 --cutoff-pid 0.00 --cutoff-pannot 0.5 --cutoff-pcov 0.5 --cutoff-rmsd 10.0 --cutoff-tm 0.5

Search options:
fast	0
exhaustive	0
e	1.000000
e2	0.002000
tm	0.500000
rmsd	10.000000
pid	0.000000
pcov	0.500000
pannot	0.500000

BLAST search: successful
Allowing only one db entry per PDB chain

Saving    hit      1 /     12 : 2VT4.0.A.0.1
Saving    hit      2 /     12 : 1U19.0.A.0.1
Saving    hit      3 /     12 : 1L9H.0.A.0.1
Saving    hit      4 /     12 : 2J4Y.0.A.0.1
Saving    hit      5 /     12 : 2I35.0.A.0.1
Saving    hit      6 /     12 : 1F88.1.A.0.1
Saving    hit      7 /     12 : 1GZM.0.A.0.1
Saving    hit      8 /     12 : 3CAP.0.A.0.1
Saving    hit      9 /     12 : 3DQB.0.A.0.1
Saving    hit     10 /     12 : 2ZIY.0.A.0.1
Saving    hit     11 /     12 : 2Z73.0.A.0.1
Saving    hit     12 /     12 : 3EML.0.A.0.1

Running command: temcat input_alignment.ali imem/tophit/query_annotation.tem > modelling.tem


Running command: medeller  -6 --verbose --atm --substtables /Users/seb/medeller/substtables -a ../modelling.tem -i target --pairs template ../imem/tophit/layer.atm

hiacc_loop_strategy = mem
Parsing input files
Initialising CoreBuilder
Loading substitution tables
Building model core
Modelling loops (high-accuracy)
Modelling loops (high-coverage)

Running command: imem_project --dbdir ../imem --insubdir tophit --dbid template --inputid target --struc target_template.core.atm --outsubdir core


Running command: imem_project --dbdir ../imem --insubdir tophit --dbid template --inputid target --struc target_template.hiacc.atm --outsubdir hiacc


Running command: imem_project --dbdir ../imem --insubdir tophit --dbid template --inputid target --struc target_template.hicov.atm --outsubdir hicov

