Reply To: protein structure prediction using relax — high-powered jobs

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June 7, 2011 at 8:11 pm #5727
Anonymous

    Hi,

    I was just trying out the example from the paper listed above (without including the map just yet) — I keep running into this error:
    protocols.jd2.ThreadingJobInputter: (0) Warning: no template pdb provided for alignment

    My command:

    ~/mr_protocols.linuxgccrelease @flags

    Flags file:
    -database /work/rf/rosetta/rosetta_database
    -MR:mode cm
    -in:file:extended_pose 1
    -in:file:fasta fj6376.fasta
    -in:file:alignment 2h1q.ali
    -in:file:template_pdb 2h1q.pdb

    -loops:frag_sizes 9 3 1
    -loops:frag_files aaFJ63_09_05.200_v1_3.gz aaFJ63_03_05.200_v1_3.gz none
    -loops:random_order
    -loops:random_grow_loops_by 5
    -loops:extended
    -loops:remodel quick_ccd
    -loops:relax relax

    -relax:default_repeats 4
    -relax:jump_move true

    #-edensity:mapreso 1.6
    #-edensity:grid_spacing 1.5
    #-edensity:mapfile target.map
    #-edensity:sliding_window_wt 1.0
    #-edensity:sliding_window 5

    -cm:aln_format grishin
    -MR:max_gaplength_to_model 10
    -nstruct 1

    My directory contents includes 2h1q.pdb

    Also, I tried another case where I just used the words “target” “template” etc… without the specific details and no luck. Am I missing something obvious?

    Thanks.

    ***

    Full output:

    [rf@tig241 test]$ /work/rf/rosetta/rosetta_source/bin/mr_protocols.linuxgccrelease @flags -overwrite true
    core.init: (0) Mini-Rosetta version exported from unknown
    core.init: (0) command: /work/rf/rosetta/rosetta_source/bin/mr_protocols.linuxgccrelease @flags -overwrite true
    core.init: (0) ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=227767109 seed_offset=0 real_seed=227767109
    core.init.random: (0) RandomGenerator:init: Normal mode, seed=227767109 RG_type=mt19937
    core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: standard
    core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
    core.scoring.etable: (0) Starting energy table calculation
    core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
    core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
    core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
    core.scoring.etable: (0) Finished calculating energy tables.
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/pdb_pair_stats_fine
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA_n
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA_pp
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/Rama_smooth_dyn.dat_ss_6.4
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/env_log.txt
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/cbeta_den.txt
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/pair_log.txt
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/cenpack_log.txt
    core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: standard
    core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
    protocols.loops.loops_main: (0) Frag libraries debug aaFJ63_09_05.200_v1_3.gz 9
    core.io.fragments: (0) reading fragments from file: aaFJ63_09_05.200_v1_3.gz …
    core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader…
    core.fragments.ConstantLengthFragSet: (0) finished reading top 200 9mer fragments from file aaFJ63_09_05.200_v1_3.gz
    protocols.loops.loops_main: (0) Frag libraries debug aaFJ63_03_05.200_v1_3.gz 3
    core.io.fragments: (0) reading fragments from file: aaFJ63_03_05.200_v1_3.gz …
    core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader…
    core.fragments.ConstantLengthFragSet: (0) finished reading top 200 3mer fragments from file aaFJ63_03_05.200_v1_3.gz
    protocols.loops.loops_main: (0) Frag libraries debug none 1
    protocols.loops.loops_main: (0) Set up 1-mer library from 3-mer library
    protocols.loops.loops_main: (0) Fragment libraries: 1 147600
    protocols.loops.loops_main: (0) Fragment libraries: 3 49200
    protocols.loops.loops_main: (0) Fragment libraries: 9 48000
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE1 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE1 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 48
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 48
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 48
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 48
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG1 on residue THR 49
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG2 on residue THR 49
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH1 on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH2 on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 56
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 56
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 56
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 56
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 93
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 93
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 93
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 93
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue ASP 104
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OD1 on residue ASP 104
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OD2 on residue ASP 104
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 131
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 131
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 131
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue LEU 133
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue LEU 133
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue LEU 133
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue ARG 190
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH1 on residue ARG 190
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH2 on residue ARG 190
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 219
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 219
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue LYS 233
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue LYS 233
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 233
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 233
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue LYS 235
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 235
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 235
    core.pack.task: (0) Packer task: initialize from command line()
    core.pack.pack_missing_sidechains: (0) packing residue number 1 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 47 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 48 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 49 because of missing atom number 6 atom name OG1
    core.pack.pack_missing_sidechains: (0) packing residue number 50 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 56 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 93 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 104 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 131 because of missing atom number 7 atom name CD
    core.pack.pack_missing_sidechains: (0) packing residue number 133 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 190 because of missing atom number 9 atom name CZ
    core.pack.pack_missing_sidechains: (0) packing residue number 219 because of missing atom number 8 atom name CE
    core.pack.pack_missing_sidechains: (0) packing residue number 233 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 235 because of missing atom number 7 atom name CD
    core.scoring.dunbrack: (0) Dunbrack library took 0.07 seconds to load from binary
    core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
    core.pack.pack_rotamers: (0) built 145 rotamers at 14 positions.
    core.pack.pack_rotamers: (0) IG: 12300 bytes
    protocols.jd2.ThreadingJobInputter: (0) Warning: no template pdb provided for alignment 2H1Q.PDB
    protocols.jd2.JobDistributor: (0) no more batches to process…
    protocols.jd2.JobDistributor: (0) 0 jobs considered, 0 jobs attempted in 0 seconds
    protocols.jd2.JobDistributor: (0) no jobs were attempted, did you forget to pass -overwrite?
    [rf@tig241 test]$ /work/rf/rosetta/rosetta_source/bin/mr_protocols.mpi.linuxgccrelease @flags -overwrite true
    core.init: (0) Mini-Rosetta version exported from unknown
    core.init: (0) command: /work/rf/rosetta/rosetta_source/bin/mr_protocols.mpi.linuxgccrelease @flags -overwrite true
    core.init: (0) ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1806468607 seed_offset=0 real_seed=1806468607
    core.init.random: (0) RandomGenerator:init: Normal mode, seed=1806468607 RG_type=mt19937
    core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: standard
    core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
    core.scoring.etable: (0) Starting energy table calculation
    core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
    core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
    core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
    core.scoring.etable: (0) Finished calculating energy tables.
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/pdb_pair_stats_fine
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA_n
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA_pp
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/Rama_smooth_dyn.dat_ss_6.4
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/env_log.txt
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/cbeta_den.txt
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/pair_log.txt
    core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/cenpack_log.txt
    core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: standard
    core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
    protocols.loops.loops_main: (0) Frag libraries debug aaFJ63_09_05.200_v1_3.gz 9
    core.io.fragments: (0) reading fragments from file: aaFJ63_09_05.200_v1_3.gz …
    core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader…
    core.fragments.ConstantLengthFragSet: (0) finished reading top 200 9mer fragments from file aaFJ63_09_05.200_v1_3.gz
    protocols.loops.loops_main: (0) Frag libraries debug aaFJ63_03_05.200_v1_3.gz 3
    core.io.fragments: (0) reading fragments from file: aaFJ63_03_05.200_v1_3.gz …
    core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader…
    core.fragments.ConstantLengthFragSet: (0) finished reading top 200 3mer fragments from file aaFJ63_03_05.200_v1_3.gz
    protocols.loops.loops_main: (0) Frag libraries debug none 1
    protocols.loops.loops_main: (0) Set up 1-mer library from 3-mer library
    protocols.loops.loops_main: (0) Fragment libraries: 1 147600
    protocols.loops.loops_main: (0) Fragment libraries: 3 49200
    protocols.loops.loops_main: (0) Fragment libraries: 9 48000
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE1 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE1 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 48
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 48
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 48
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 48
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG1 on residue THR 49
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG2 on residue THR 49
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH1 on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH2 on residue ARG 50
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 56
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 56
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 56
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 56
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 93
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 93
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 93
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 93
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue ASP 104
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OD1 on residue ASP 104
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OD2 on residue ASP 104
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 131
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 131
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 131
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue LEU 133
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue LEU 133
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue LEU 133
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue ARG 190
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH1 on residue ARG 190
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH2 on residue ARG 190
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 219
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 219
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue LYS 233
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue LYS 233
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 233
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 233
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue LYS 235
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 235
    core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 235
    core.pack.task: (0) Packer task: initialize from command line()
    core.pack.pack_missing_sidechains: (0) packing residue number 1 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 47 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 48 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 49 because of missing atom number 6 atom name OG1
    core.pack.pack_missing_sidechains: (0) packing residue number 50 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 56 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 93 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 104 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 131 because of missing atom number 7 atom name CD
    core.pack.pack_missing_sidechains: (0) packing residue number 133 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 190 because of missing atom number 9 atom name CZ
    core.pack.pack_missing_sidechains: (0) packing residue number 219 because of missing atom number 8 atom name CE
    core.pack.pack_missing_sidechains: (0) packing residue number 233 because of missing atom number 6 atom name CG
    core.pack.pack_missing_sidechains: (0) packing residue number 235 because of missing atom number 7 atom name CD
    core.scoring.dunbrack: (0) Dunbrack library took 0.08 seconds to load from binary
    core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
    core.pack.pack_rotamers: (0) built 145 rotamers at 14 positions.
    core.pack.pack_rotamers: (0) IG: 12300 bytes
    protocols.jd2.ThreadingJobInputter: (0) Warning: no template pdb provided for alignment 2H1Q.PDB
    protocols.jd2.JobDistributor: (0) no more batches to process…
    protocols.jd2.JobDistributor: (0) 0 jobs considered, 0 jobs attempted in 0 seconds
    protocols.jd2.JobDistributor: (0) no jobs were attempted, did you forget to pass -overwrite?