Extracted targetid from FASTA file: '1U19A'
Extracted chain 'A' from input file: templateA
Estimated target-template percent identity: 20.22
Sequence lengths: target=348, template=274

Search options:
fast	0
exhaustive	0
e	10.000000
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 /     18 : 2VT4.0.A.0.1
Saving    hit      2 /     18 : 1U19.0.A.0.1
Saving    hit      3 /     18 : 1L9H.0.A.0.1
Saving    hit      4 /     18 : 2J4Y.0.A.0.1
Saving    hit      5 /     18 : 2I35.0.A.0.1
Saving    hit      6 /     18 : 1GZM.0.A.0.1
Saving    hit      7 /     18 : 1F88.1.A.0.1
Saving    hit      8 /     18 : 3DQB.0.A.0.1
Saving    hit      9 /     18 : 3CAP.0.A.0.1
Saving    hit     10 /     18 : 2ZIY.0.A.0.1
Saving    hit     11 /     18 : 2Z73.0.A.0.1
Saving    hit     12 /     18 : 3EML.0.A.0.1
Rejecting hit     13 /     18 : 2J8C.0.M.0.1
Rejecting hit     14 /     18 : 1AIJ.0.M.1.1
Rejecting hit     15 /     18 : 1AIG.0.M.1.1
Rejecting hit     16 /     18 : 1OGV.5.M.0.1
Rejecting hit     17 /     18 : 1VF5.0.O.0.1
Rejecting hit     18 /     18 : 1VF5.0.B.0.1
Making fasta-formatted sequence from iMembrane .tem file
Running Psi-blast search for: sequence
Extracting sequences from Psi-blast results with >15% id to: sequence
Shortening sequence names to a sensible length for: sequence
Randomising homolog order for: sequence
I see 1164 sequences
Removing homologs of >3/2 or <2/3 the length of the structural template for: sequence
There are 1151/1164 seqs remaining
Adding query to filtered homologs for: sequence
Filtering homologs to 80% sequence identity for: sequence
Running Psi-blast search for: structure
Extracting sequences from Psi-blast results with >15% id to: structure
Shortening sequence names to a sensible length for: structure
Randomising homolog order for: structure
I see 1246 sequences
Removing homologs of >3/2 or <2/3 the length of the structural template for: structure
There are 822/1246 seqs remaining
Adding query to filtered homologs for: structure
Filtering homologs to 80% sequence identity for: structure
Combining equal numbers of homologs from the filtered structure and sequence blast searches into one file
There are 146 seqs after combining homologs
Checking that no homologs are too short/long compared with the structural template
There are 146/146 seqs remaining
Filtering combined set of homologs to 80% sequence identity
I see 146 sequences
Taking at most 125 sequences for alignment
Converting all sequences to upper case
Homolog selection successful


Beginning alignment
Building sequence library
Combining 70 and 96
Combining 29 and 66
Combining 8 and 104
Combining 39 and 90
Combining 4 and 24
Combining 30 and 63
Combining 67 and 76
Combining 18 and 116
Combining 36 and 115
Combining 2 and 15
Combining 14 and 29
Combining 38 and 111
Combining 3 and 85
Combining 84 and 118
Combining 6 and 119
Combining 81 and 82
Combining 26 and 70
Combining 67 and 79
Combining 34 and 94
Combining 2 and 7
Combining 27 and 101
Combining 30 and 44
Combining 18 and 40
Combining 62 and 100
Combining 30 and 103
Combining 4 and 95
Combining 1 and 61
Combining 2 and 5
Combining 18 and 102
Combining 34 and 73
Combining 3 and 41
Combining 43 and 88
Combining 48 and 124
Combining 19 and 52
Combining 87 and 113
Combining 2 and 121
Combining 8 and 81
Combining 21 and 32
Combining 39 and 55
Combining 105 and 122
Combining 19 and 105
Combining 48 and 67
Combining 18 and 31
Combining 13 and 117
Combining 3 and 34
Combining 53 and 84
Combining 3 and 120
Combining 45 and 99
Combining 27 and 45
Combining 6 and 10
Combining 72 and 108
Combining 6 and 49
Combining 69 and 123
Combining 2 and 125
Combining 46 and 62
Combining 21 and 65
Combining 30 and 107
Combining 48 and 53
Combining 98 and 114
Combining 4 and 19
Combining 13 and 42
Combining 26 and 46
Combining 20 and 51
Combining 30 and 60
Combining 13 and 36
Combining 57 and 93
Combining 3 and 72
Combining 16 and 87
Combining 50 and 71
Combining 20 and 68
Combining 26 and 30
Combining 1 and 112
Combining 69 and 98
Combining 27 and 48
Combining 64 and 83
Combining 43 and 57
Combining 2 and 3
Combining 6 and 18
Combining 20 and 58
Combining 20 and 56
Combining 1 and 23
Combining 16 and 35
Combining 11 and 39
Combining 37 and 75
Combining 1 and 106
Combining 12 and 77
Combining 8 and 21
Combining 1 and 109
Combining 12 and 28
Combining 91 and 97
Combining 26 and 74
Combining 37 and 50
Combining 33 and 86
Combining 1 and 16
Combining 2 and 27
Combining 1 and 14
Combining 12 and 91
Combining 11 and 43
Combining 8 and 11
Combining 2 and 6
Combining 1 and 92
Combining 22 and 38
Combining 25 and 80
Combining 4 and 13
Combining 8 and 17
Combining 26 and 59
Combining 9 and 25
Combining 8 and 33
Combining 2 and 4
Combining 9 and 37
Combining 8 and 26
Combining 20 and 89
Combining 12 and 22
Combining 9 and 110
Combining 2 and 69
Combining 12 and 64
Combining 12 and 20
Combining 9 and 12
Combining 9 and 78
Combining 1 and 9
Combining 8 and 54
Combining 1 and 47
Combining 1 and 8
Combining 1 and 2
Alignment successful...
Parsing input files
Initialising CoreBuilder
Loading substitution tables
Building model core
Modelling loops (high-accuracy)
Modelling loops (high-coverage)
Completing model

Models can be found in /data/pegasus/kelm/medeller/example/output/medeller:
model.complete.pdb
model.core.pdb
model.hiacc.pdb
model.hicov.pdb
