command executed: rosetta.gcc -s 1ubq.pdb -design -fixbb -resfile resfile -ex1 -pdbout test -ndruns 3
[STR  OPT]Default value for [-paths] paths.txt.
[T/F  OPT]Default FALSE value for [-version]
[T/F  OPT]Default FALSE value for [-score]
[T/F  OPT]Default FALSE value for [-abinitio]
[T/F  OPT]Default FALSE value for [-refine]
[T/F  OPT]Default FALSE value for [-assemble]
[T/F  OPT]Default FALSE value for [-idealize]
[T/F  OPT]Default FALSE value for [-relax]
[T/F  OPT]New TRUE value for [-design]
[T/F  OPT]Default FALSE value for [-onlypack]
[T/F  OPT]New TRUE value for [-fixbb]
[T/F  OPT]Default FALSE value for [-mcmin_trials]
[T/F  OPT]Default FALSE value for [-design_loops_dock]
[T/F  OPT]Default FALSE value for [-mut_list]
[T/F  OPT]Default FALSE value for [-rotamerize]
[T/F  OPT]Default FALSE value for [-rot_opt]
[T/F  OPT]Default FALSE value for [-design_trials]
[T/F  OPT]Default FALSE value for [-mvbb]
[T/F  OPT]Default FALSE value for [-fixseq]
[T/F  OPT]Default FALSE value for [-tail]
[T/F  OPT]Default FALSE value for [-design_inter]
[T/F  OPT]Default FALSE value for [-alter_spec]
[T/F  OPT]Default FALSE value for [-design_in_pieces]
[T/F  OPT]Default FALSE value for [-dna_interface]
[T/F  OPT]Default FALSE value for [-analyze_dna_interface]
[T/F  OPT]Default FALSE value for [-force_basepair_muts]
[T/F  OPT]Default FALSE value for [-natrot]
[T/F  OPT]Default FALSE value for [-optE]
[T/F  OPT]Default FALSE value for [-optE_ctsa]
[T/F  OPT]Default FALSE value for [-optE_inter]
[T/F  OPT]Default FALSE value for [-optE_ctsa]
[T/F  OPT]Default FALSE value for [-optE_inter]
[STR  OPT]Default value for [-Eout] default.
[STR  OPT]Default value for [-sqc] none.
[STR  OPT]New value for [-pdbout] test.
[INT  OPT]New value for [-ndruns]  3
[INT  OPT]Default value for [-begin]  0
[INT  OPT]Default value for [-end]  0
[STR  OPT]Default value for [-alter_spec_mutlist] mutlist.
[STR  OPT]Default value for [-point_mut_energies] none.
[STR  OPT]Default value for [-mut_mut_energies] none.
[STR  OPT]Default value for [-design_mutlist] none.
[T/F  OPT]Default FALSE value for [-safety]
[T/F  OPT]Default FALSE value for [-design_dock]
[T/F  OPT]Default FALSE value for [-favor_native_residue]
Rosetta mode: design    
[T/F  OPT]Default FALSE value for [-chain]
[T/F  OPT]Default FALSE value for [-protein]
[T/F  OPT]Default FALSE value for [-series]
[INT  OPT]Default value for [-nstruct]  1
[T/F  OPT]Default FALSE value for [-read_all_chains]
[T/F  OPT]Default FALSE value for [-repack]
[T/F  OPT]Default FALSE value for [-overwrite]
[T/F  OPT]Default FALSE value for [-silent_input]
[T/F  OPT]Default FALSE value for [-timer]
[T/F  OPT]Default FALSE value for [-status]
[T/F  OPT]Default FALSE value for [-ise_movie]
[T/F  OPT]Default FALSE value for [-output_all]
[T/F  OPT]Default FALSE value for [-skip_missing_residues]
[T/F  OPT]Default FALSE value for [-use_input_sc]
[STR  OPT]Default value for [-cst] cst.
[STR  OPT]Default value for [-dpl] dpl.
[STR  OPT]New value for [-resfile] resfile.
[T/F  OPT]Default FALSE value for [-auto_resfile]
[T/F  OPT]Default FALSE value for [-chain_inc]
WARNING::
constraints will not be used: query not defined
by series_code,protein_name,and chain_id
WARNING:: nstruct > 0 but output_coord F
no pdb files will be output
[T/F  OPT]Default FALSE value for [-full_filename]
[T/F  OPT]Default FALSE value for [-loops]
[T/F  OPT]Default FALSE value for [-taboo]
[T/F  OPT]New TRUE value for [-ex1]
[T/F  OPT]Default FALSE value for [-ex2]
[T/F  OPT]Default FALSE value for [-ex3]
[T/F  OPT]Default FALSE value for [-ex4]
[T/F  OPT]Default FALSE value for [-ex1aro]
[T/F  OPT]Default FALSE value for [-ex1aro_half]
[T/F  OPT]Default FALSE value for [-ex2aro_only]
[INT  OPT]Default value for [-extrachi_cutoff]  18
[T/F  OPT]Default FALSE value for [-exdb]
[T/F  OPT]Default FALSE value for [-use_electrostatic_repulsion]
[T/F  OPT]Default FALSE value for [-explicit_h2o]
[T/F  OPT]Default FALSE value for [-try_both_his_tautomers]
[T/F  OPT]Default FALSE value for [-minimize_rot]
[T/F  OPT]Default FALSE value for [-read_hetero_h2o]
[T/F  OPT]Default FALSE value for [-Wint_score_only]
[T/F  OPT]Default FALSE value for [-Wint_repack_only]
Weights for packing and scoring: using interface weight for scoring is set to be  F
 and using old packer weight for repacking is set to be  F
[T/F  OPT]Default FALSE value for [-scorefxn]
default centroid scorefxn:  4
default fullatom scorefxn:  12
[INT  OPT]Default value for [-run_level]  0
[T/F  OPT]Default FALSE value for [-silent]
[T/F  OPT]Default FALSE value for [-verbose]
[T/F  OPT]Default FALSE value for [-gush]
[T/F  OPT]Default FALSE value for [-yap]
[T/F  OPT]Default FALSE value for [-chat]
[T/F  OPT]Default FALSE value for [-inform]
[T/F  OPT]Default FALSE value for [-quiet]
run level:  0
[T/F  OPT]Default FALSE value for [-benchmark]
[T/F  OPT]Default FALSE value for [-debug]
[STR  OPT]New value for [-s] 1ubq.pdb.
Starting structure: 1ubq
Reading ../../rosetta_database/Rama_smooth_dyn.dat_ss_6.4
Reading ../../rosetta_database/phi.theta.36.HS.resmooth
Reading ../../rosetta_database/phi.theta.36.SS.resmooth
[STR  OPT]Default value for [-atom_vdw_set] default.
[T/F  OPT]Default FALSE value for [-IUPAC]
Atom_mode set to all       
Reading ../../rosetta_database/paircutoffs
[T/F  OPT]Default FALSE value for [-decoystats]
set_decoystats_flag: from,to F F
[T/F  OPT]Default FALSE value for [-jumping]
[T/F  OPT]Default FALSE value for [-barcode_mode]
disabling all filters
WARNING:: total_residue is not yet defined
default cutoffs for rg and co filters cannot be determined
[REAL OPT]Default value for [-co]  -1
[REAL OPT]Default value for [-rms]  -1
[T/F  OPT]Default FALSE value for [-repeatin]
[T/F  OPT]Default FALSE value for [-repeatout]
reading starting structure: ./1ubq.pdb
[T/F  OPT]Default FALSE value for [-find_disulf]
[T/F  OPT]Default FALSE value for [-fix_disulf]
initializing full atom functions
[T/F  OPT]Default FALSE value for [-soft_rep]
[T/F  OPT]Default FALSE value for [-gen_born]
[STR  OPT]Default value for [-fa_lj_rep_slope] highres.
Reading ../../rosetta_database/bbdep02.May.sortlib
Reading ../../rosetta_database/plane_data_table_1015.dat
Reading ../../rosetta_database/pdbpairstats_fine
Reading ../../rosetta_database/Paa
Reading ../../rosetta_database/Paa_n
Reading ../../rosetta_database/Paa_pp
generating Etable...
Starting energy table calculation
Energy table parameter set: polh_aroh  Revision: 1.5 Date: 2004/10/06 17:24:51
Finished calculating energy tables.
Reading ../../rosetta_database/avgE_from_pdb
Filling missing atoms
optimizing missing atoms
optimizing hydrogen positions
[T/F  OPT]Default FALSE value for [-constant_seed]
[INT  OPT]Default value for [-seed_offset]  0
# =====================================
# random seed: 1106721
# =====================================
WARNING:: end of pdb file reached: angle, secstruct, & res info not found
Looking for dssp file: ./1ubq.dssp
dssp file not found
Looking for secondary structure assignment file: ./1ubq.ssa
ssa file not found
calculating secondary structure from torsion angles
[T/F  OPT]Default FALSE value for [-regions]
[T/F  OPT]Default FALSE value for [-use_input_bond]
[T/F  OPT]Default FALSE value for [-knot_filter]
Reading ../../rosetta_database/SASA-masks.dat
Reading ../../rosetta_database/SASA-angles.dat
========================================
Reading ../../rosetta_database/sasa_offsets.txt
Constraints Scores
viol stage res1  atom1 res2  atom2    dist    upper    delta    aa1   aa2   score
 Constraints: 0 Scores Total   0
[T/F  OPT]Default FALSE value for [-movie]
[T/F  OPT]Default FALSE value for [-trajectory]

Start of design structure

designing with this many rotamers  264
[T/F  OPT]Default FALSE value for [-profile]
======================================================
DONE ::     1 starting structures built         1 (nstruct) times
This process generated      1 decoys from       1 attempts
                            0 starting pdbs were skipped
======================================================
