41)
Message boards :
RALPH@home bug list :
Bug reports for Ralph 5.30 and 5.31 and 5.32
(Message 2411)
Posted 17 Oct 2006 by Chu
Post:
I was gonna mention 2rio is a very large protein and uses a lot of meory, but that is clearly not a problem for your computer:-) Some users have reported similiar problem before, and we hope we can reproduce it reliably on our local computers in order to debug.
while crunching the result named FRA_2rio_CASP7_hom001_1_2rio_1_1a06__IGNORE_THE_REST_232_1281_3_0, when i showed the graphics, the rosetta application stopped responding
the version was 5.32 on a windows system
each thread (science and graphics) each took up all the cycles on 2 of my CPUs (i have a multiCPU machine)
stopping/exiting boinc closed the app without a problem, and it was working again when boinc was restarted
it was working fine before i viewed the graphics too, no problems at all since 5.32 was released
|
42)
Message boards :
RALPH@home bug list :
Bug reports for Ralph 5.30 and 5.31 and 5.32
(Message 2410)
Posted 17 Oct 2006 by Chu
Post:
Sometimes the protein being simulated blows up and then the run is stuck. Not sure that is responsible for your error, but that should be stopped by the watchdog after a while if you do not abort it.
My Ralph just stopped the progress @1.002%. CPU-time went up, but nothing else seems to happen.
I've suspended the WU for now, should I abort it or do anything else?
This is the stderr.txt:
Graphics are disabled due to configuration...
# random seed: 2898263
# cpu_run_time_pref: 14400
Graphics are disabled due to configuration...
# cpu_run_time_pref: 14400
And this is the stdout.txt:
[REAL OPT]Default value for [-cpu_frac] 10
[REAL OPT]Default value for [-frame_rate] 10
[INT OPT]New value for [-cpu_run_time] 3600
command executed: rosetta_beta_5.32_i686-pc-linux-gnu aa t339 _ -relax -looprlx -nstruct 5 -farlx -ex1 -ex2 -loop_model -termini -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -idl_no_chain_break -vary_omega -output_silent_gz -output_chi_silent -protein_name_prefix idlrlx_hom001_ -frags_name_prefix idlrlx_boinc_hom001_ -s T0339_t339_1_2.pdb -paths paths_200_idlrlx.txt -do_farlx_checkpointing -checkpointing_interval 10 -cpu_run_time 3600 -watchdog -constant_seed -jran 2898263
[STR OPT]New value for [-paths] paths_200_idlrlx.txt.
[INT OPT]Default value for [-seed_offset] 0
[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]New TRUE value for [-relax]
[T/F OPT]Default FALSE value for [-sim_aneal]
[T/F OPT]Default FALSE value for [-cenrlx]
[T/F OPT]New TRUE value for [-farlx]
[T/F OPT]Default FALSE value for [-record_irms_before_relax]
[T/F OPT]Default FALSE value for [-force_expand]
[T/F OPT]New TRUE value for [-looprlx]
[T/F OPT]Default FALSE value for [-pose_relax]
[T/F OPT]Default FALSE value for [-minimize]
[T/F OPT]Default FALSE value for [-loop_farlx_only]
Rosetta mode: relax
[T/F OPT]Default FALSE value for [-chain]
[T/F OPT]Default FALSE value for [-protein]
[T/F OPT]Default FALSE value for [-series]
series_code = aa :: protein_name is t339:: chain_id is _.
[INT OPT]New value for [-nstruct] 5
[T/F OPT]Default FALSE value for [-read_all_chains]
[T/F OPT]Default FALSE value for [-preserve_header]
[T/F OPT]Default FALSE value for [-use_pdb_numbering]
[T/F OPT]Default FALSE value for [-flip_symmetric_sidechains]
[T/F OPT]Default FALSE value for [-fa_input]
[T/F OPT]Default FALSE value for [-overwrite]
[T/F OPT]Default FALSE value for [-output_pdb_gz]
[T/F OPT]New TRUE value for [-output_silent_gz]
[T/F OPT]Default FALSE value for [-output_scorefile_gz]
[T/F OPT]Default FALSE value for [-sasapack_bvalues]
[T/F OPT]Default FALSE value for [-cenlist_values]
[T/F OPT]New TRUE value for [-termini]
[T/F OPT]Default FALSE value for [-use_trie]
[T/F OPT]Default FALSE value for [-no_trie]
[T/F OPT]Default FALSE value for [-use_conformer]
[T/F OPT]Default FALSE value for [-use_bbind_conformer]
[T/F OPT]Default FALSE value for [-trials_trie]
[T/F OPT]Default FALSE value for [-no_trials_trie]
[T/F OPT]Default FALSE value for [-output_interaction_graph_memory_usage]
[T/F OPT]Default FALSE value for [-read_interaction_graph]
[T/F OPT]Default FALSE value for [-write_interaction_graph]
[STR OPT]Default value for [-ig_file] .
[T/F OPT]Default FALSE value for [-use_sasa_pack_score]
[T/F OPT]Default FALSE value for [-output_dot_kinemage]
[T/F OPT]Default FALSE value for [-pack_low_temp_annealing]
[T/F OPT]Default FALSE value for [-no_his_his_pairE]
[T/F OPT]Default FALSE value for [-silent_input]
[T/F OPT]Default FALSE value for [-timer]
[T/F OPT]Default FALSE value for [-count_attempts]
[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]New TRUE value for [-output_chi_silent]
[T/F OPT]Default FALSE value for [-accept_all]
[T/F OPT]Default FALSE value for [-skip_missing_residues]
[STR OPT]Default value for [-cst] cst.
[STR OPT]Default value for [-dpl] dpl.
[STR OPT]Default value for [-resfile] none.
[STR OPT]Default value for [-equiv_resfile] none.
[T/F OPT]Default FALSE value for [-auto_resfile]
[T/F OPT]Default FALSE value for [-chain_inc]
WARNING::refold_input T, allow_missing T
setting refold_input F
[T/F OPT]Default FALSE value for [-full_filename]
[T/F OPT]Default FALSE value for [-map_sequence]
[INT OPT]Default value for [-max_frags] 200
[T/F OPT]Default FALSE value for [-output_centroids]
[STR OPT]New value for [-protein_name_prefix] idlrlx_hom001_.
[STR OPT]New value for [-frags_name_prefix] idlrlx_boinc_hom001_.
[T/F OPT]Default FALSE value for [-protein_name_prefix_homolog]
[REAL OPT]Default value for [-vdw_reweight] 1
[REAL OPT]Default value for [-env_reweight] 1
[REAL OPT]Default value for [-pair_reweight] 1
[REAL OPT]Default value for [-cb_reweight] 1
[REAL OPT]Default value for [-sheet_reweight] 1
[REAL OPT]Default value for [-ss_reweight] 1
[REAL OPT]Default value for [-hs_reweight] 1
[REAL OPT]Default value for [-rsigma_reweight] 1
[REAL OPT]Default value for [-rg_reweight] 1
[REAL OPT]Default value for [-pc_reweight] 1
[REAL OPT]Default value for [-fa_atr_reweight] 1
[REAL OPT]Default value for [-fa_rep_reweight] 1
[REAL OPT]Default value for [-fa_dun_reweight ] 1
[REAL OPT]Default value for [-fa_pair_reweight] 1
[REAL OPT]Default value for [-fa_plane_reweight] 1
[REAL OPT]Default value for [-fa_solv_reweight] 1
[REAL OPT]Default value for [-fa_ref_reweight ] 1
[REAL OPT]Default value for [-fa_pH_reweight] 1
[REAL OPT]Default value for [-fa_h2o_reweight] 1
[REAL OPT]Default value for [-fa_prob1b_reweight] 1
[REAL OPT]Default value for [-fa_gb_elec_reweigh] 1
[REAL OPT]Default value for [-hb_srbb_reweight] 1
[REAL OPT]Default value for [-hb_lrbb_reweight] 1
[REAL OPT]Default value for [-hb_sc_reweight] 1
[REAL OPT]Default value for [-chainbreak_reweight] 1
[T/F OPT]Default FALSE value for [-find_disulf]
[T/F OPT]Default FALSE value for [-fix_disulf]
[T/F OPT]Default FALSE value for [-enable_ligand_aa]
[T/F OPT]Default FALSE value for [-phospho_ser]
[T/F OPT]Default FALSE value for [-surface]
[T/F OPT]Default FALSE value for [-loops]
[T/F OPT]Default FALSE value for [-taboo]
[T/F OPT]New TRUE value for [-vary_omega]
[T/F OPT]Default FALSE value for [-geometric_sol]
[T/F OPT]Default FALSE value for [-multi_chain]
[T/F OPT]New TRUE value for [-ex1]
[T/F OPT]New TRUE 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 [-rot_pert]
[T/F OPT]Default FALSE value for [-rot_pert_input]
[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 [-solvate]
[T/F OPT]Default FALSE value for [-pH]
[T/F OPT]Default FALSE value for [-try_both_his_tautomers]
[T/F OPT]Default FALSE value for [-hydrate_dna]
[T/F OPT]Default FALSE value for [-ex_dna_waters]
[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]
[T/F OPT]Default FALSE value for [-ligand]
[T/F OPT]Default FALSE value for [-enzyme_design]
[T/F OPT]Default FALSE value for [-score_contact_flag]
[T/F OPT]Default FALSE value for [-score_contact_weight]
[T/F OPT]Default FALSE value for [-score_contact_threshold]
[T/F OPT]Default FALSE value for [-scorefxn]
default centroid scorefxn: 6
default fullatom scorefxn: 12
[INT OPT]Default value for [-run_level] 0
[T/F OPT]Default FALSE value for [-silent]
[T/F OPT]New TRUE value for [-output_silent_gz]
run level: -4
[T/F OPT]Default FALSE value for [-benchmark]
[T/F OPT]Default FALSE value for [-debug]
[INT OPT]Default value for [-sym_des_units] 1
[T/F OPT]Default FALSE value for [-mj_min]
[REAL OPT]Default value for [-mod_hhrep_height] 1
[REAL OPT]Default value for [-mod_hhrep_width] 1
[REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
[REAL OPT]Default value for [-mod_hhrep_exponent] 4
[REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
[REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
[STR OPT]New value for [-s] T0339_t339_1_2.pdb.
Starting structure: T0339_t339_1_2
Reading ./Rama_smooth_dyn.dat_ss_6.4.gz
Reading ./phi.theta.36.HS.resmooth.gz
Reading ./phi.theta.36.SS.resmooth.gz
[STR OPT]Default value for [-atom_vdw_set] hybrid.
[T/F OPT]Default FALSE value for [-IUPAC]
Atom_mode set to all
Reading ./paircutoffs.gz
[T/F OPT]Default FALSE value for [-decoystats]
set_decoystats_flag: from,to F F
[T/F OPT]Default FALSE value for [-decoyfeatures]
[T/F OPT]Default FALSE value for [-evolution]
[T/F OPT]Default FALSE value for [-evol_recomb]
[T/F OPT]Default FALSE value for [-profile]
BOINC :: [2006-10-12 12:51:59] :: mode: relax :: nstartnum: 1 :: number_of_output: 5 :: num_decoys: 0 :: pct_complete: 0.01
[T/F OPT]New TRUE value for [-watchdog]
[INT OPT]Default value for [-watchdog_time] 3600
[REAL OPT]Default value for [-cpu_run_timeout_factor] 4
[T/F OPT]Default FALSE value for [-dummy_model]
Searching for dat file: ./idlrlx_hom001_t339.dat
Searching for dat file: ./idlrlx_hom001_t339.dat
WARNING!! .dat file not found!
Looking for fasta file: ./idlrlx_hom001_t339_.fasta
Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
Looking for psipred file: ./idlrlx_hom001_t339_.jones
Looking for psipred file: ./idlrlx_hom001_t339_.psipred
Looking for psipred file: ./idlrlx_hom001_t339_.jones
Looking for psipred file: ./idlrlx_hom001_t339_.psipred
WARNING :: Unable to find psipred file!
[T/F OPT]Default FALSE value for [-tight_hb]
File: ./idlrlx_hom001_t339_.cst not found
Running without distance constraints
File: ./idlrlx_hom001_t339_.dpl not found
Dipolar constraints will not be used
fragment file: ./idlrlx_boinc_hom001_aat339_03_05.200_v1_3.gz
Total Residue 416
frag size: 3 frags/residue: 200
fragment file: ./idlrlx_boinc_hom001_aat339_09_05.200_v1_3.gz
Total Residue 416
frag size: 9 frags/residue: 25
generating 1mer library from 3mer library
[T/F OPT]Default FALSE value for [-ssblocks]
[T/F OPT]Default FALSE value for [-check_homs]
calculating fragment_diversity...
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
[T/F OPT]Default FALSE value for [-barcode_mode]
disabling all filters
[REAL OPT]Default value for [-co] -1
[REAL OPT]Default value for [-rms] -1
Searching for pdb...: ./idlrlx_hom001_t339.pdb
Searching for pdb...: ./idlrlx_hom001_t339.pdb
no pdb file for idlrlx_hom001_t339
[T/F OPT]Default FALSE value for [-repeatin]
[T/F OPT]Default FALSE value for [-repeatout]
[T/F OPT]Default FALSE value for [-clnt]
reading starting structure: ./T0339_t339_1_2.pdb.gz
[T/F OPT]Default FALSE value for [-use_native_centroid]
[T/F OPT]New TRUE value for [-constant_seed]
[INT OPT]New value for [-jran] 2898263
# =====================================
# random seed: 2898263
# =====================================
WARNING: 52 missing backbone atoms at 13 residues in pdb file
allow_missing= 1
skip_missing= 0
WARNING: 13 centroids were placed at 0,0,0
WARNING:: end of pdb file reached: angle, secstruct, & res info not found
Looking for dssp file: ./T0339_t339_1_2.dssp
dssp file not found
Looking for secondary structure assignment file: ./T0339_t339_1_2.ssa
ssa file not found
calculating secondary structure from torsion angles
[T/F OPT]Default FALSE value for [-use_input_bond]
[T/F OPT]Default FALSE value for [-regions]
[T/F OPT]Default FALSE value for [-apply_filters]
[T/F OPT]Default FALSE value for [-knot_filter]
[T/F OPT]Default FALSE value for [-poke_filter]
[T/F OPT]Default FALSE value for [-score_contact_fullatom]
[T/F OPT]New TRUE value for [-long_range_hb_weight]
[T/F OPT]New TRUE value for [-long_range_hb_weight]
[REAL OPT]New value for [-long_range_hb_weight] 1
[T/F OPT]New TRUE value for [-short_range_hb_weight]
[T/F OPT]New TRUE value for [-short_range_hb_weight]
[REAL OPT]New value for [-short_range_hb_weight] 0.5
[REAL OPT]Default value for [-fa_plane_weight] 0
[REAL OPT]Default value for [-omega_weight] 0.5
[T/F OPT]Default FALSE value for [-rand_envpair_res_wt]
[REAL OPT]Default value for [-parallel_weight] 1
[REAL OPT]Default value for [-antiparallel_weight] 1
[T/F OPT]Default FALSE value for [-rand_SS_wt]
[T/F OPT]Default FALSE value for [-random_parallel_antiparallel]
[T/F OPT]Default FALSE value for [-rand_cst_res_wt]
[T/F OPT]Default FALSE value for [-use_barcode_to_score]
initializing full atom functions
[T/F OPT]Default FALSE value for [-soft_rep]
[T/F OPT]Default FALSE value for [-soft_rep_design]
[T/F OPT]Default FALSE value for [-smooth_etable]
[T/F OPT]Default FALSE value for [-reduce_templates]
[T/F OPT]Default FALSE value for [-gen_born]
[T/F OPT]Default FALSE value for [-small_radii]
[T/F OPT]Default FALSE value for [-use_bw]
[T/F OPT]Default FALSE value for [-use_aw]
[T/F OPT]Default FALSE value for [-dna_weights]
[STR OPT]Default value for [-fa_lj_rep_slope] highres.
Reading ./bbdep02.May.sortlib.gz
Reading ./plane_data_table_1015.dat.gz
Reading ./pdbpairstats_fine.gz
Reading ./Paa.gz
Reading ./Paa_n.gz
Reading ./Paa_pp.gz
generating Etable...
Starting energy table calculation
Energy table parameter set: polh_aroh Revision: 10024 Date: 2006-08-28 13:54:52 -0700 (Mon, 28 Aug 2006)
[T/F OPT]Default FALSE value for [-mod_hhrep]
[T/F OPT]Default FALSE value for [-output_etables]
[T/F OPT]Default FALSE value for [-mod_etable]
Finished calculating energy tables.
Reading ./avgE_from_pdb.gz
WARNING: Pose::set_coords: backbone missing for residue 92
WARNING: Pose::set_coords: backbone missing for residue 93
WARNING: Pose::set_coords: backbone missing for residue 94
WARNING: Pose::set_coords: backbone missing for residue 95
WARNING: Pose::set_coords: backbone missing for residue 96
WARNING: Pose::set_coords: backbone missing for residue 97
WARNING: Pose::set_coords: backbone missing for residue 98
WARNING: Pose::set_coords: backbone missing for residue 99
WARNING: Pose::set_coords: backbone missing for residue 100
WARNING: Pose::set_coords: backbone missing for residue 101
WARNING: Pose::set_coords: backbone missing for residue 102
WARNING: Pose::set_coords: backbone missing for residue 103
WARNING: Pose::set_coords: backbone missing for residue 104
[REAL OPT]Default value for [-rsd_wt_helix] 1
[REAL OPT]Default value for [-rsd_wt_strand] 1
[REAL OPT]Default value for [-rsd_wt_loop] 1
[T/F OPT]Default FALSE value for [-burial_code]
[T/F OPT]Default FALSE value for [-new_centroid_packing]
[REAL OPT]Default value for [-cb_weight] 1
[REAL OPT]Default value for [-strand_dist_cutoff] 6.5
[T/F OPT]Default FALSE value for [-stretch_strand_dist_cutoff]
[REAL OPT]Default value for [-localstrandpair_penalty] 0
[T/F OPT]Default FALSE value for [-handedness_score]
[T/F OPT]Default FALSE value for [-separate_centroid_pack_score]
Reading ./SASA-masks.dat.gz
Reading ./SASA-angles.dat.gz
========================================
Reading ./sasa_offsets.txt.gz
Reading ./sasa_prob_cdf.txt.gz
NEXT STRUCTURE: ./aaT0339_t339_1_2_0001.pdb
[T/F OPT]Default FALSE value for [-fullatom_loop]
setting pose_flag from: 0 to: 1
WARNING: Pose::set_coords: backbone missing for residue 92
WARNING: Pose::set_coords: backbone missing for residue 93
WARNING: Pose::set_coords: backbone missing for residue 94
WARNING: Pose::set_coords: backbone missing for residue 95
WARNING: Pose::set_coords: backbone missing for residue 96
WARNING: Pose::set_coords: backbone missing for residue 97
WARNING: Pose::set_coords: backbone missing for residue 98
WARNING: Pose::set_coords: backbone missing for residue 99
WARNING: Pose::set_coords: backbone missing for residue 100
WARNING: Pose::set_coords: backbone missing for residue 101
WARNING: Pose::set_coords: backbone missing for residue 102
WARNING: Pose::set_coords: backbone missing for residue 103
WARNING: Pose::set_coords: backbone missing for residue 104
setting pose_flag from: 1 to: 0
[T/F OPT]Default FALSE value for [-obligate_loops]
[INT OPT]New value for [-checkpointing_interval] 10
[T/F OPT]Default FALSE value for [-loop_farlx_only]
[T/F OPT]New TRUE value for [-loop_model]
[STR OPT]Default value for [-loop_file] .
No loop_file specified! Try to find loopfile in start_path!
loop: 91 105
[T/F OPT]Default FALSE value for [-coordcst]
[REAL OPT]Default value for [-score_filter_cutoff] 1
setting pose_flag from: 0 to: 1
[T/F OPT]Default FALSE value for [-ccd_closure]
[T/F OPT]Default FALSE value for [-random_frag]
[T/F OPT]Default FALSE value for [-loops_subset]
[REAL OPT]Default value for [-loop_combine_rate] 0
[T/F OPT]Default FALSE value for [-random_loop]
loop_begin: 91 loop_end: 105 loop_sequence: TSKGHTGGHHSPVKG
[T/F OPT]Default FALSE value for [-alter_seqs]
cutpoint: 93
[REAL OPT]Default value for [-looprlx_cycle_ratio] 1
starting loop pose
pre-computing chuck/gunn move set for frag length 3
pre-computing chuck/gunn move set for frag length 1
accepts: frag,ccd 1 300 1 39.6667 0
accepts: frag,ccd 2 300 1 18.3333 0
accepts: frag,ccd 3 300 1 13.6667 0
accepts: frag,ccd 4 300 1 9 0
accepts: frag,ccd 5 300 1 11.3333 0
accepts: frag,ccd 6 114 93 11.4035 68.8172
accepts: frag,ccd 7 96 102 7.29167 93.1373
accepts: frag,ccd 8 54 123 5.55556 100
accepts: frag,ccd 9 36 132 13.8889 100
accepts: frag,ccd 10 1 150 0 100
[REAL OPT]Default value for [-chain_break_tol] 0.200000003
folded loops: 0
setting pose_flag from: 1 to: 0
score_filter: tag= looprlx score= -29.9825 rank= 1 max_rank= 1 nscores= 1 filter_score= -29.9825
[T/F OPT]Default FALSE value for [-output_loops_built]
[T/F OPT]New TRUE value for [-do_farlx_checkpointing]
BOINC :: [2006-10-12 12:54:48] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 2
setting pose_flag from: 0 to: 1
Pose::dump_pdb: farlxcheck
setting pose_flag from: 1 to: 0
[T/F OPT]Default FALSE value for [-loop_farlx]
setting pose_flag from: 0 to: 1
setting pose_flag from: 1 to: 0
[T/F OPT]Default FALSE value for [-pose_idlz]
setting pose_flag from: 0 to: 1
setting pose_flag from: 1 to: 0
[T/F OPT]Default FALSE value for [-local]
[T/F OPT]New TRUE value for [-idl_no_chain_break]
idealizing residues 1 to 416
minimization
window weight vomega iter fret rms rama bump tether omega phipsi
------ ------ ------ ---- --------- -------- -------- -------- -------- -------- --------
416 1.000 T 0 55202.14 11.096 -23.078 4884.500 49098.828 0.000 0.000
166 0.100 F 8 3034.97 7.120 -22.254 1763.530 2816.730 0.000 0.135
416 0.001 T 93 4.10 0.232 -98.510 7.183 8.220 4.300 7.103
416 1.000 T 23 9.43 0.268 -98.736 2.432 10.462 4.373 7.135
rms to starting angles 2.4926393
root mean dme to starting coordinates 0.166341007
global ca_rms to starting coordinates 0.268366277
[T/F OPT]Default FALSE value for [-looprlx_idealization]
BOINC :: [2006-10-12 12:59:22] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 9
dump_pdb: farlxcheck
[INT OPT]Default value for [-lj_ramp_cycles] 8
[REAL OPT]Default value for [-stage2_lj_rep_weight] 1
[T/F OPT]Default FALSE value for [-minimize_exclude_helix]
[T/F OPT]Default FALSE value for [-minimize_exclude_strand]
[INT OPT]Default value for [-local_min_window] 5
[T/F OPT]Default FALSE value for [-no_minimize_set_local_min]
[T/F OPT]Default FALSE value for [-no_farlx_rot_trials]
[T/F OPT]Default FALSE value for [-stringent_relax]
[REAL OPT]New value for [-farlx_cycle_ratio] 1
CYCLES::number is 1 x total_residue: 416
[T/F OPT]Default FALSE value for [-more_relax_cycles]
initializing full atom coordinates
BOINC :: [2006-10-12 13:00:51] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 10
dump_fullatom_pdb: farlxcheck
[T/F OPT]Default FALSE value for [-vary_chi_before_stage1]
starting score -367.7052 rms 0
starting full atom minimization
[REAL OPT]Default value for [-ediff_cutoff] 15
BOINC :: [2006-10-12 13:20:45] :: checkpoint_decoys() :: saved decoy info :: attempted_decoys: 0 :: num_decoys: 0 :: farlx_stage: 11
dump_fullatom_pdb: farlxcheck
---------------------------------------------------
repack trials: 11 accepts: 4 %: 36.36 e/trial: -1.36356
smallmin trials: 90 accepts: 0 %: 0.00 e/trial: 0.00000
stage1 score: -777.302795
---------------------------------------------------
[T/F OPT]Default FALSE value for [-relax_score_filter]
[T/F OPT]Default FALSE value for [-stringentrelax_before_stage2]
[T/F OPT]Default FALSE value for [-vary_chi_before_stage2]
[INT OPT]Default value for [-stage2_cycles] 416
[INT OPT]Default value for [-nwobble1_crank] 3
[INT OPT]Default value for [-nwobble2_crank] 2
[INT OPT]Default value for [-nwobble_wobble] 1
[INT OPT]Default value for [-crank_size] 3
[INT OPT]Default value for [-wobble_size] 3
[INT OPT]Default value for [-stage2_repack_period] 25
[T/F OPT]Default FALSE value for [-wobble_CCD]
[T/F OPT]Default FALSE value for [-skip_fragment_moves]
[T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_crank]
[T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_wobble]
[REAL OPT]Default value for [-cpu_frac] 10
[REAL OPT]Default value for [-frame_rate] 10
[INT OPT]New value for [-cpu_run_time] 3600
command executed: rosetta_beta_5.32_i686-pc-linux-gnu aa t339 _ -relax -looprlx -nstruct 5 -farlx -ex1 -ex2 -loop_model -termini -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -idl_no_chain_break -vary_omega -output_silent_gz -output_chi_silent -protein_name_prefix idlrlx_hom001_ -frags_name_prefix idlrlx_boinc_hom001_ -s T0339_t339_1_2.pdb -paths paths_200_idlrlx.txt -do_farlx_checkpointing -checkpointing_interval 10 -cpu_run_time 3600 -watchdog -constant_seed -jran 2898263
[STR OPT]New value for [-paths] paths_200_idlrlx.txt.
[INT OPT]Default value for [-seed_offset] 0
[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]New TRUE value for [-relax]
[T/F OPT]Default FALSE value for [-sim_aneal]
[T/F OPT]Default FALSE value for [-cenrlx]
[T/F OPT]New TRUE value for [-farlx]
[T/F OPT]Default FALSE value for [-record_irms_before_relax]
[T/F OPT]Default FALSE value for [-force_expand]
[T/F OPT]New TRUE value for [-looprlx]
[T/F OPT]Default FALSE value for [-pose_relax]
[T/F OPT]Default FALSE value for [-minimize]
[T/F OPT]Default FALSE value for [-loop_farlx_only]
Rosetta mode: relax
[T/F OPT]Default FALSE value for [-chain]
[T/F OPT]Default FALSE value for [-protein]
[T/F OPT]Default FALSE value for [-series]
series_code = aa :: protein_name is t339:: chain_id is _.
[INT OPT]New value for [-nstruct] 5
[T/F OPT]Default FALSE value for [-read_all_chains]
[T/F OPT]Default FALSE value for [-preserve_header]
[T/F OPT]Default FALSE value for [-use_pdb_numbering]
[T/F OPT]Default FALSE value for [-flip_symmetric_sidechains]
[T/F OPT]Default FALSE value for [-fa_input]
[T/F OPT]Default FALSE value for [-overwrite]
[T/F OPT]Default FALSE value for [-output_pdb_gz]
[T/F OPT]New TRUE value for [-output_silent_gz]
[T/F OPT]Default FALSE value for [-output_scorefile_gz]
[T/F OPT]Default FALSE value for [-sasapack_bvalues]
[T/F OPT]Default FALSE value for [-cenlist_values]
[T/F OPT]New TRUE value for [-termini]
[T/F OPT]Default FALSE value for [-use_trie]
[T/F OPT]Default FALSE value for [-no_trie]
[T/F OPT]Default FALSE value for [-use_conformer]
[T/F OPT]Default FALSE value for [-use_bbind_conformer]
[T/F OPT]Default FALSE value for [-trials_trie]
[T/F OPT]Default FALSE value for [-no_trials_trie]
[T/F OPT]Default FALSE value for [-output_interaction_graph_memory_usage]
[T/F OPT]Default FALSE value for [-read_interaction_graph]
[T/F OPT]Default FALSE value for [-write_interaction_graph]
[STR OPT]Default value for [-ig_file] .
[T/F OPT]Default FALSE value for [-use_sasa_pack_score]
[T/F OPT]Default FALSE value for [-output_dot_kinemage]
[T/F OPT]Default FALSE value for [-pack_low_temp_annealing]
[T/F OPT]Default FALSE value for [-no_his_his_pairE]
[T/F OPT]Default FALSE value for [-silent_input]
[T/F OPT]Default FALSE value for [-timer]
[T/F OPT]Default FALSE value for [-count_attempts]
[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]New TRUE value for [-output_chi_silent]
[T/F OPT]Default FALSE value for [-accept_all]
[T/F OPT]Default FALSE value for [-skip_missing_residues]
[STR OPT]Default value for [-cst] cst.
[STR OPT]Default value for [-dpl] dpl.
[STR OPT]Default value for [-resfile] none.
[STR OPT]Default value for [-equiv_resfile] none.
[T/F OPT]Default FALSE value for [-auto_resfile]
[T/F OPT]Default FALSE value for [-chain_inc]
WARNING::refold_input T, allow_missing T
setting refold_input F
[T/F OPT]Default FALSE value for [-full_filename]
[T/F OPT]Default FALSE value for [-map_sequence]
[INT OPT]Default value for [-max_frags] 200
[T/F OPT]Default FALSE value for [-output_centroids]
[STR OPT]New value for [-protein_name_prefix] idlrlx_hom001_.
[STR OPT]New value for [-frags_name_prefix] idlrlx_boinc_hom001_.
[T/F OPT]Default FALSE value for [-protein_name_prefix_homolog]
[REAL OPT]Default value for [-vdw_reweight] 1
[REAL OPT]Default value for [-env_reweight] 1
[REAL OPT]Default value for [-pair_reweight] 1
[REAL OPT]Default value for [-cb_reweight] 1
[REAL OPT]Default value for [-sheet_reweight] 1
[REAL OPT]Default value for [-ss_reweight] 1
[REAL OPT]Default value for [-hs_reweight] 1
[REAL OPT]Default value for [-rsigma_reweight] 1
[REAL OPT]Default value for [-rg_reweight] 1
[REAL OPT]Default value for [-pc_reweight] 1
[REAL OPT]Default value for [-fa_atr_reweight] 1
[REAL OPT]Default value for [-fa_rep_reweight] 1
[REAL OPT]Default value for [-fa_dun_reweight ] 1
[REAL OPT]Default value for [-fa_pair_reweight] 1
[REAL OPT]Default value for [-fa_plane_reweight] 1
[REAL OPT]Default value for [-fa_solv_reweight] 1
[REAL OPT]Default value for [-fa_ref_reweight ] 1
[REAL OPT]Default value for [-fa_pH_reweight] 1
[REAL OPT]Default value for [-fa_h2o_reweight] 1
[REAL OPT]Default value for [-fa_prob1b_reweight] 1
[REAL OPT]Default value for [-fa_gb_elec_reweigh] 1
[REAL OPT]Default value for [-hb_srbb_reweight] 1
[REAL OPT]Default value for [-hb_lrbb_reweight] 1
[REAL OPT]Default value for [-hb_sc_reweight] 1
[REAL OPT]Default value for [-chainbreak_reweight] 1
[T/F OPT]Default FALSE value for [-find_disulf]
[T/F OPT]Default FALSE value for [-fix_disulf]
[T/F OPT]Default FALSE value for [-enable_ligand_aa]
[T/F OPT]Default FALSE value for [-phospho_ser]
[T/F OPT]Default FALSE value for [-surface]
[T/F OPT]Default FALSE value for [-loops]
[T/F OPT]Default FALSE value for [-taboo]
[T/F OPT]New TRUE value for [-vary_omega]
[T/F OPT]Default FALSE value for [-geometric_sol]
[T/F OPT]Default FALSE value for [-multi_chain]
[T/F OPT]New TRUE value for [-ex1]
[T/F OPT]New TRUE 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 [-rot_pert]
[T/F OPT]Default FALSE value for [-rot_pert_input]
[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 [-solvate]
[T/F OPT]Default FALSE value for [-pH]
[T/F OPT]Default FALSE value for [-try_both_his_tautomers]
[T/F OPT]Default FALSE value for [-hydrate_dna]
[T/F OPT]Default FALSE value for [-ex_dna_waters]
[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]
[T/F OPT]Default FALSE value for [-ligand]
[T/F OPT]Default FALSE value for [-enzyme_design]
[T/F OPT]Default FALSE value for [-score_contact_flag]
[T/F OPT]Default FALSE value for [-score_contact_weight]
[T/F OPT]Default FALSE value for [-score_contact_threshold]
[T/F OPT]Default FALSE value for [-scorefxn]
default centroid scorefxn: 6
default fullatom scorefxn: 12
[INT OPT]Default value for [-run_level] 0
[T/F OPT]Default FALSE value for [-silent]
[T/F OPT]New TRUE value for [-output_silent_gz]
run level: -4
[T/F OPT]Default FALSE value for [-benchmark]
[T/F OPT]Default FALSE value for [-debug]
[INT OPT]Default value for [-sym_des_units] 1
[T/F OPT]Default FALSE value for [-mj_min]
[REAL OPT]Default value for [-mod_hhrep_height] 1
[REAL OPT]Default value for [-mod_hhrep_width] 1
[REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
[REAL OPT]Default value for [-mod_hhrep_exponent] 4
[REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
[REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
[STR OPT]New value for [-s] T0339_t339_1_2.pdb.
Starting structure: T0339_t339_1_2
Reading ./Rama_smooth_dyn.dat_ss_6.4.gz
Reading ./phi.theta.36.HS.resmooth.gz
Reading ./phi.theta.36.SS.resmooth.gz
[STR OPT]Default value for [-atom_vdw_set] hybrid.
[T/F OPT]Default FALSE value for [-IUPAC]
Atom_mode set to all
Reading ./paircutoffs.gz
[T/F OPT]Default FALSE value for [-decoystats]
set_decoystats_flag: from,to F F
[T/F OPT]Default FALSE value for [-decoyfeatures]
[T/F OPT]Default FALSE value for [-evolution]
[T/F OPT]Default FALSE value for [-evol_recomb]
[T/F OPT]Default FALSE value for [-profile]
BOINC :: [2006-10-12 19:33:06] :: mode: relax :: nstartnum: 1 :: number_of_output: 5 :: num_decoys: 0 :: pct_complete: 0.01
[T/F OPT]New TRUE value for [-watchdog]
[INT OPT]Default value for [-watchdog_time] 3600
[REAL OPT]Default value for [-cpu_run_timeout_factor] 4
[T/F OPT]Default FALSE value for [-dummy_model]
Searching for dat file: ./idlrlx_hom001_t339.dat
Searching for dat file: ./idlrlx_hom001_t339.dat
WARNING!! .dat file not found!
Looking for fasta file: ./idlrlx_hom001_t339_.fasta
Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
Looking for psipred file: ./idlrlx_hom001_t339_.psipred_ss2
Looking for psipred file: ./idlrlx_hom001_t339_.jones
Looking for psipred file: ./idlrlx_hom001_t339_.psipred
Looking for psipred file: ./idlrlx_hom001_t339_.jones
Looking for psipred file: ./idlrlx_hom001_t339_.psipred
WARNING :: Unable to find psipred file!
[T/F OPT]Default FALSE value for [-tight_hb]
File: ./idlrlx_hom001_t339_.cst not found
Running without distance constraints
File: ./idlrlx_hom001_t339_.dpl not found
Dipolar constraints will not be used
fragment file: ./idlrlx_boinc_hom001_aat339_03_05.200_v1_3.gz
Total Residue 416
frag size: 3 frags/residue: 200
fragment file: ./idlrlx_boinc_hom001_aat339_09_05.200_v1_3.gz
Total Residue 416
frag size: 9 frags/residue: 25
generating 1mer library from 3mer library
[T/F OPT]Default FALSE value for [-ssblocks]
[T/F OPT]Default FALSE value for [-check_homs]
calculating fragment_diversity...
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
dihedral_bin: unusual angle
[T/F OPT]Default FALSE value for [-barcode_mode]
disabling all filters
[REAL OPT]Default value for [-co] -1
[REAL OPT]Default value for [-rms] -1
Searching for pdb...: ./idlrlx_hom001_t339.pdb
Searching for pdb...: ./idlrlx_hom001_t339.pdb
no pdb file for idlrlx_hom001_t339
[T/F OPT]Default FALSE value for [-repeatin]
[T/F OPT]Default FALSE value for [-repeatout]
[T/F OPT]Default FALSE value for [-clnt]
WARNING: check_decoy_exists: unexpected decoy number: start#,decoy#,lastdecoy# 1 1 5 0
reading starting structure: ./T0339_t339_1_2.pdb.gz
[T/F OPT]Default FALSE value for [-use_native_centroid]
[T/F OPT]New TRUE value for [-constant_seed]
WARNING: 52 missing backbone atoms at 13 residues in pdb file
allow_missing= 1
skip_missing= 0
WARNING: 13 centroids were placed at 0,0,0
WARNING:: end of pdb file reached: angle, secstruct, & res info not found
Looking for dssp file: ./T0339_t339_1_2.dssp
dssp file not found
Looking for secondary structure assignment file: ./T0339_t339_1_2.ssa
ssa file not found
calculating secondary structure from torsion angles
[T/F OPT]Default FALSE value for [-use_input_bond]
[T/F OPT]Default FALSE value for [-regions]
[T/F OPT]Default FALSE value for [-apply_filters]
[T/F OPT]Default FALSE value for [-knot_filter]
[T/F OPT]Default FALSE value for [-poke_filter]
[T/F OPT]Default FALSE value for [-score_contact_fullatom]
[T/F OPT]New TRUE value for [-long_range_hb_weight]
[T/F OPT]New TRUE value for [-long_range_hb_weight]
[REAL OPT]New value for [-long_range_hb_weight] 1
[T/F OPT]New TRUE value for [-short_range_hb_weight]
[T/F OPT]New TRUE value for [-short_range_hb_weight]
[REAL OPT]New value for [-short_range_hb_weight] 0.5
[REAL OPT]Default value for [-fa_plane_weight] 0
[REAL OPT]Default value for [-omega_weight] 0.5
[T/F OPT]Default FALSE value for [-rand_envpair_res_wt]
[REAL OPT]Default value for [-parallel_weight] 1
[REAL OPT]Default value for [-antiparallel_weight] 1
[T/F OPT]Default FALSE value for [-rand_SS_wt]
[T/F OPT]Default FALSE value for [-random_parallel_antiparallel]
[T/F OPT]Default FALSE value for [-rand_cst_res_wt]
[T/F OPT]Default FALSE value for [-use_barcode_to_score]
initializing full atom functions
[T/F OPT]Default FALSE value for [-soft_rep]
[T/F OPT]Default FALSE value for [-soft_rep_design]
[T/F OPT]Default FALSE value for [-smooth_etable]
[T/F OPT]Default FALSE value for [-reduce_templates]
[T/F OPT]Default FALSE value for [-gen_born]
[T/F OPT]Default FALSE value for [-small_radii]
[T/F OPT]Default FALSE value for [-use_bw]
[T/F OPT]Default FALSE value for [-use_aw]
[T/F OPT]Default FALSE value for [-dna_weights]
[STR OPT]Default value for [-fa_lj_rep_slope] highres.
Reading ./bbdep02.May.sortlib.gz
Reading ./plane_data_table_1015.dat.gz
Reading ./pdbpairstats_fine.gz
Reading ./Paa.gz
Reading ./Paa_n.gz
Reading ./Paa_pp.gz
generating Etable...
Starting energy table calculation
Energy table parameter set: polh_aroh Revision: 10024 Date: 2006-08-28 13:54:52 -0700 (Mon, 28 Aug 2006)
[T/F OPT]Default FALSE value for [-mod_hhrep]
[T/F OPT]Default FALSE value for [-output_etables]
[T/F OPT]Default FALSE value for [-mod_etable]
Finished calculating energy tables.
Reading ./avgE_from_pdb.gz
WARNING: Pose::set_coords: backbone missing for residue 92
WARNING: Pose::set_coords: backbone missing for residue 93
WARNING: Pose::set_coords: backbone missing for residue 94
WARNING: Pose::set_coords: backbone missing for residue 95
WARNING: Pose::set_coords: backbone missing for residue 96
WARNING: Pose::set_coords: backbone missing for residue 97
WARNING: Pose::set_coords: backbone missing for residue 98
WARNING: Pose::set_coords: backbone missing for residue 99
WARNING: Pose::set_coords: backbone missing for residue 100
WARNING: Pose::set_coords: backbone missing for residue 101
WARNING: Pose::set_coords: backbone missing for residue 102
WARNING: Pose::set_coords: backbone missing for residue 103
WARNING: Pose::set_coords: backbone missing for residue 104
[REAL OPT]Default value for [-rsd_wt_helix] 1
[REAL OPT]Default value for [-rsd_wt_strand] 1
[REAL OPT]Default value for [-rsd_wt_loop] 1
[T/F OPT]Default FALSE value for [-burial_code]
[T/F OPT]Default FALSE value for [-new_centroid_packing]
[REAL OPT]Default value for [-cb_weight] 1
[REAL OPT]Default value for [-strand_dist_cutoff] 6.5
[T/F OPT]Default FALSE value for [-stretch_strand_dist_cutoff]
[REAL OPT]Default value for [-localstrandpair_penalty] 0
[T/F OPT]Default FALSE value for [-handedness_score]
[T/F OPT]Default FALSE value for [-separate_centroid_pack_score]
Reading ./SASA-masks.dat.gz
Reading ./SASA-angles.dat.gz
========================================
Reading ./sasa_offsets.txt.gz
Reading ./sasa_prob_cdf.txt.gz
NEXT STRUCTURE: ./aaT0339_t339_1_2_0001.pdb
[T/F OPT]Default FALSE value for [-fullatom_loop]
[INT OPT]Default value for [-lj_ramp_cycles] 8
[REAL OPT]Default value for [-stage2_lj_rep_weight] 1
[T/F OPT]Default FALSE value for [-minimize_exclude_helix]
[T/F OPT]Default FALSE value for [-minimize_exclude_strand]
[INT OPT]Default value for [-local_min_window] 5
[T/F OPT]Default FALSE value for [-no_minimize_set_local_min]
[T/F OPT]Default FALSE value for [-no_farlx_rot_trials]
[T/F OPT]Default FALSE value for [-stringent_relax]
[REAL OPT]New value for [-farlx_cycle_ratio] 1
CYCLES::number is 1 x total_residue: 416
[T/F OPT]Default FALSE value for [-more_relax_cycles]
initializing full atom coordinates
WARNING: Pose::set_coords: backbone missing for residue 92
WARNING: Pose::set_coords: backbone missing for residue 93
WARNING: Pose::set_coords: backbone missing for residue 94
WARNING: Pose::set_coords: backbone missing for residue 95
WARNING: Pose::set_coords: backbone missing for residue 96
WARNING: Pose::set_coords: backbone missing for residue 97
WARNING: Pose::set_coords: backbone missing for residue 98
WARNING: Pose::set_coords: backbone missing for residue 99
WARNING: Pose::set_coords: backbone missing for residue 100
WARNING: Pose::set_coords: backbone missing for residue 101
WARNING: Pose::set_coords: backbone missing for residue 102
WARNING: Pose::set_coords: backbone missing for residue 103
WARNING: Pose::set_coords: backbone missing for residue 104
[T/F OPT]New TRUE value for [-do_farlx_checkpointing]
reading starting structure: farlxcheck
Filling missing atoms
optimizing missing atoms
optimizing hydrogen positions
[T/F OPT]New TRUE value for [-constant_seed]
---------------------------------------------------
repack trials: 1 accepts: 1 %: 100.00 e/trial: -1.15601
stage1 score: -779.712646
---------------------------------------------------
[T/F OPT]Default FALSE value for [-relax_score_filter]
[T/F OPT]Default FALSE value for [-stringentrelax_before_stage2]
[T/F OPT]Default FALSE value for [-vary_chi_before_stage2]
[INT OPT]Default value for [-stage2_cycles] 416
[INT OPT]Default value for [-nwobble1_crank] 3
[INT OPT]Default value for [-nwobble2_crank] 2
[INT OPT]Default value for [-nwobble_wobble] 1
[INT OPT]Default value for [-crank_size] 3
[INT OPT]Default value for [-wobble_size] 3
[INT OPT]Default value for [-stage2_repack_period] 25
[T/F OPT]Default FALSE value for [-wobble_CCD]
[REAL OPT]Default value for [-ediff_cutoff] 15
[T/F OPT]Default FALSE value for [-skip_fragment_moves]
pre-computing chuck/gunn move set for frag length 3
[T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_crank]
[T/F OPT]Default FALSE value for [-no_minimize_exclude_frag_in_wobble]
|
43)
Message boards :
RALPH@home bug list :
Bug reports for Ralph 5.30 and 5.31 and 5.32
(Message 2403)
Posted 13 Oct 2006 by Chu
Post:
It looks that the run was stuck and the score was not changed for a long time. So it was forced to stop ... Why that happened will be investigated. Thanks for the report.
this was a new one...
13/10/2006 01:07:22|ralph@home|Computation for task IDL_RLX_NT_t293_CASP7_hom001_1_1342_5_0 finished
13/10/2006 01:07:22|ralph@home|Starting task IDL_RLX_NT_t294_CASP7_hom001_1_1342_5_0 using rosetta_beta version 532
13/10/2006 01:07:24|ralph@home|Started upload of file IDL_RLX_NT_t293_CASP7_hom001_1_1342_5_0_0
13/10/2006 01:07:29|ralph@home|Finished upload of file IDL_RLX_NT_t293_CASP7_hom001_1_1342_5_0_0
13/10/2006 01:07:29|ralph@home|Throughput 12437 bytes/sec
13/10/2006 03:37:37|ralph@home|Unrecoverable error for result IDL_RLX_NT_t294_CASP7_hom001_1_1342_5_0 (One or more arguments are invalid (0x80000003) - exit code -2147483645 (0x80000003))
13/10/2006 03:37:37|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
13/10/2006 03:37:37||Rescheduling CPU: application exited
13/10/2006 03:37:37|ralph@home|Computation for task IDL_RLX_NT_t294_CASP7_hom001_1_1342_5_0 finished
|
44)
Message boards :
RALPH@home bug list :
Bug reports for Ralph 5.30 and 5.31 and 5.32
(Message 2395)
Posted 12 Oct 2006 by Chu
Post:
We have seen errors (stop in options.cc ) for jobs batch 1349 and will fix that soon. Sorry about this.
|
45)
Message boards :
RALPH@home bug list :
Bug reports for Ralph 5.30 and 5.31 and 5.32
(Message 2391)
Posted 11 Oct 2006 by Chu
Post:
Hi, it looks like that you may have a corrupted rosetta_database which could be caused by various reasons...
and next one:
2006-10-11 14:02:26|ralph@home|Unrecoverable error for result DOC_2VIR_u_pert_mcm_bbmin_1340_17_2 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))
Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 2895576
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: LYS 9 3 0 2 0
chi no 2 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458
2006-10-11 14:19:44|ralph@home|Unrecoverable error for result IDL_RLX_NT_t291_CASP7_hom001_1_1342_4_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))
Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 2895459
# cpu_run_time_pref: 3600
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: ARG 15 3 2 1 0
chi no 4 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458
2006-10-11 14:29:43|ralph@home|Unrecoverable error for result 5croA_BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_17_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))
Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 2898706
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: LYS 9 3 2 0 0
chi no 3 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458
|
46)
Message boards :
RALPH@home bug list :
Bug reports for Ralph 5.30 and 5.31 and 5.32
(Message 2381)
Posted 10 Oct 2006 by Chu
Post:
Your runs are ok, and we have known for a while on Windows platform those output files are gzipped but the original files can not be deleted right away. They will evnentually be after the WU is finished.
not an error as the w/u finished ok but did get this
stderr out <core_client_version>5.4.11</core_client_version>
<stderr_txt>
# random seed: 2896098
# cpu_run_time_pref: 3600
WARNING! error deleting file .aa1IGC.out
WARNING! error deleting file .aa1IGC.out.bonds
WARNING! error deleting file .aa1IGC.out.rot_templates
======================================================
DONE :: 1 starting structures built 1 (nstruct) times
This process generated 1 decoys from 1 attempts
0 starting pdbs were skipped
======================================================
I had the same issue.
Result ID 288375
Name DOC_4HTC_u_pert_mcm_bbmin_1340_20_0
Workunit 254288
Created 10 Oct 2006 11:51:18 UTC
Sent 10 Oct 2006 12:13:39 UTC
Received 10 Oct 2006 16:10:29 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x0)
Computer ID 250
Report deadline 14 Oct 2006 12:13:39 UTC
CPU time 13897.25
stderr out
<core_client_version>5.6.5</core_client_version>
[CDATA[
<stderr_txt>
# random seed: 2895533
# cpu_run_time_pref: 14400
WARNING! error deleting file .aa4HTC.out
WARNING! error deleting file .aa4HTC.out.bonds
WARNING! error deleting file .aa4HTC.out.rot_templates
======================================================
DONE :: 1 starting structures built 23 (nstruct) times
This process generated 23 decoys from 23 attempts
0 starting pdbs were skipped
======================================================
BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...
</stderr_txt>
]]
Validate state Valid
Claimed credit 47.6463856052397
Granted credit 50.3978804981935
application version 5.32
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47)
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RALPH@home bug list :
Bug reports for Ralph 5.30 and 5.31 and 5.32
(Message 2380)
Posted 10 Oct 2006 by Chu
Post:
Hi, this is a known issue, not just for V5.31. it might be due to the sensitivity of the mouse control setup in the graphics and will be fixed in the futural release.
To answer the second question, for docking WUs, there will be two proteins drawn. One in blue and the other in red. The calculation is, given the structures of two proteins, to search the optimal relatvie orientation between these two "objects" which gives the best anergy according to Rosetta scoring function. The docking protocol mainly comprises two parts. The first step is with low-resolution (only backbone is shown in the graphic) and is meant to find quickly a roughly fit shape complementarity between the two proteins. In the second step, the two proteins are represented by full atoms and the search space is mainly confined locally aiming at refining detailed protein-protein interactions across the interface. This step is relatively time-consuming and a lot of computation is used for optimizing sidechain interactions. Appearing on the graphics, the proteins sometimes do not move at all and that is because we currently have a hard time showing every step of sidechain movement ( we tried that in 5.28, but it resulted in a lot of errors probably due to some graphic issue) But generally users should be able to see in the fullatom docking stage that sidechains wiggle and the relative orientation of the two proteins changes from time to time in a small scale. Compared to ab initio and relax WUs, there are less steps and the run time is about on the same scale. And currently some dianostics on the screen saver such as score and rmsd do not always update timely due to some limitations in Rosetta code and since rmsd is calculated differently in docking, the value might be too large to be shown in the plot area. I will try to put more information explaing scientific aspect of docking soon.
Thanks for everybody's help here.
V5.31 docking. The graphic doesn't react properly to mouse control when not fully maximized. If I attempt to rotate the Low Energy image, the Native image does the rotating...if any reaction at all. Although I was able to right click and enlarge the low energy image. I could not enlarge the Native structure.
Is there any details on what to expect of a docking WU?? i.e. long running models, and low numbers of steps?
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48)
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Bug reports for Ralph 5.30 and 5.31 and 5.32
(Message 2374)
Posted 10 Oct 2006 by Chu
Post:
We have noticed this kind of errors under 5.31 and just updated the app to 5.32. Hopefully it will be fixed.
>>> Getting a few errors:-
http://ralph.bakerlab.org/workunit.php?wuid=252767
http://ralph.bakerlab.org/workunit.php?wuid=252768
Windows machine, getting error message
"Incorrect function. (0x1)-exit code 1 (0x1)
ERROR:: Exit at: dock_structure.cc line:431"
Also error on Linux machine:-
http://ralph.bakerlab.org/workunit.php?wuid=252033
"process exited with code 1 (0x1)
ERROR:: Exit at: dock_structure.cc line:431"
Note:-- Thanks Chu for responding to my troubles with 5.28, hopefully I will have no more trouble like that, although I now have my 4800+ AMD machine duplicated across Ralph, Rosetta and Einstein projects, I will have to live with it.
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49)
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Bug Report for Ralph 5.28
(Message 2368)
Posted 9 Oct 2006 by Chu
Post:
Hi Conan, I do not know what is causing that problem. We did not change any boinc program and only updated Rosetta application. Sorry for the inconvenience.
>>> After a day of trying to get rid of the Runtime errors caused by Ralph screensaver and not being able to get Boinc running at all. I ended up re-downloading Boinc and installing a different version as my version no matter how many times I installed it would not run with due to visual C++ runtime errors.
It ran and dumped all my work units, downloading a heap of new ones, which then got dumped again when I tried to add my back up files back in and now Einstein and Ralph won't talk to the servers saying they are backing off for 18 hours or so.
I think this is due to all the WU's that got dumped.
Anyway I sorted things out sort off and I am crunching again.
Not happy with what Ralph did to the Boinc programme and my computer, causing me to lose a days work a couple of times.
I have also found the fresh download has registered my computer twice now.
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50)
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Bug Report for Ralph 5.28
(Message 2367)
Posted 9 Oct 2006 by Chu
Post:
Hi Brian, please let us know if you see this problem again with newer updates other than 5.28 and then we will look into it to see if it is a general problem. One thing which might be helpful is to update your bonic software... Thanks for you help and feedback
Hi again. Thought I should update you on my previous post. I checked the computer this morning and it was running slow again, so I checked BONIC to see what was up. Another project was running (different from last time) not 5.28. I checked Task Manager to see what was going on and sure enough, the cpu was at 100% even though BONIC was in suspend mode, and 5.28 was the top in cpu time (over 7hours on a 3 hour wu). I decided to try something different and exited BOINC instead of ending 5.28's process, and right after it closed cpu percentage dropped. Started BONIC back up and the wu/result was now back at '---'for 'CPU time' and '3:40:21' for 'To completion' (was at 0:21:35?? and 7:??:??, don't remember exact numbers). I decided to abort the wu since this was the second time I found it had locked up BONIC and the computer.
Take care...
Brian
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51)
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Bug Report for Ralph 5.29
(Message 2349)
Posted 7 Oct 2006 by Chu
Post:
ERRORS from IDL_RLX WUs are probably due to some missing files or logic errors in Rosetta code (bqian will look into that). So far the rate of "Unhandle File Exception" errors is much lower than that for App.5.28. We will watch closely other erros reported here. Thank everyone for help!
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52)
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Bug Report for Ralph 5.29
(Message 2331)
Posted 7 Oct 2006 by Chu
Post:
Ralph has been updated to 5.29. In this version, we mainly address two problems seen in 5.28 update.
1. fix a problem of job errors when application is supended, removed fromm memory and restarted again.
2. fix (hopefully) the widely observed "File Handle Exception" eorros when full_atom graphic is turned on and off.
Users are expected to see in the "Searching" box that when "Searching_Backbone" is on, only backbone is drawn and when "Searching_all_atom" is on, backbone plus sidechains are drawn. Sidechain flickering is turnned off in this update as it might also be responsible for the "File Handle Exception" error.
Please report bugs in this post.
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53)
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Bug Report for Ralph 5.28
(Message 2327)
Posted 6 Oct 2006 by Chu
Post:
Thanks for the suggestion, feet1st. I will give it a try here.
What are side chains?
For general knowledge about protein and amino acid, please visit here. I notice that some key terms like "sidechains" are missing and we will update that soon. Here is something I wrote quickly and it definitely needs to be improved.
20 natural amino acids have part of their structures in common and they are connected via peptide-bond linkages to form the topology of a protein structure. The common part is called "backbone". Amino acids differ from each other by its unique chemical group which connects to the C-alpha atom of the backbone and that group is called "side chain".
Why do they blink on and off?
Sidechains are part of protein structures but we only choose to show them on screen during some certain stages when they are being changed by the program.
Why can't I see side chains in the other boxes? Mine must be broken.
So far we only enable the sidechain drawing for the "searching" box.
Are we doing calculations differently now on the side chains? Or simply illustraiting the calculations we've been doing all along?
Sidechain calculation has been part of Rosetta program for a long time, but we only start to have them illustrated on the screen recently.
I understand the above is still far from an adequate description. But I will try my best to provide more information on future updates and this will give people like you guys who volunteer to help testing a better chance to send us feedbacks. Many thanks again.
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54)
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Bug Report for Ralph 5.28
(Message 2318)
Posted 5 Oct 2006 by Chu
Post:
The current setup in the screensaver graphic is to flash protein sidechains only in "Try Rotamer" and "Packing" stage. "Try Rotamers" is supposed to be very fast each time, and we called them a lot in the code. So people are expected to see protein sidechains flashed on and off most of the time. I think the trajectory is still moving forward as reflected by the moving protein in the accepted box. So it looks like a graphic issue. I am wondering if the more demanding task (showing sidechains on and off quickly) for the graphic is the reason for more frequent "Unhandle Exception" errors we have seen in this updated application. I tried to google what the error code(0x0000005 means when it happens, some people suggest a hardware issue, but no firm answers. Anybody has an idea?
While displaying graphics for this WU, the first box seems stuck with status message "Try Rotamers", and the graphic in that first box is not refreshing. The Accepted box is jumping around, but no movement in first box.
...while I was typing the above, it went to "Packing" status (step 340,000) and now it seems to be progressing normally and refreshing the graphic.
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55)
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Bug Report for Ralph 5.28
(Message 2317)
Posted 5 Oct 2006 by Chu
Post:
Thanks. This will be very useful for us to track down those hidden bugs in the code.
Next two WU's with the same:
2006-10-05 10:58:45|ralph@home|Unrecoverable error for result DOCK_1FQ1_unbound_perturb_benchmark_1330_19_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))
2006-10-05 11:04:21|ralph@home|Unrecoverable error for result DOCK_1MEL_unbound_perturb_benchmark_1330_20_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))
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56)
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Bug Report for Ralph 5.28
(Message 2305)
Posted 3 Oct 2006 by Chu
Post:
Ralph has been updated to 5.28. In this version, we added all-atom sidechain display to the screensaver during Rosetta sidechain refinement stage. Also users now can rotate any of the four displayed model on the screen using a mouse. Several new flags have been added to Rosetta too.
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57)
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Bug Report for Ralph 5.27
(Message 2304)
Posted 3 Oct 2006 by Chu
Post:
Hi, this particular protein test case returns a lot of failed WUs and it could be due to its large protein size. We are looking into the reason now. Thanks for the feedback.
I'm not sure if this is a client or WU problem. But WUID 241813 has now been running for over 24 hours. It has shown as 100% complete for at least the last 14 hours. I'm aborting it.
<Edit>
I had to close Boinc to get the Ralph client to end. Boinc showed it had switched to a Seti@home task but task manager showed Ralph 5.27 was still running at 90+% cpu.
When I restarted Boinc, it logged the following error...
9/30/2006 11:22:59 AM||Data directory: C:Program FilesBOINC
9/30/2006 11:22:59 AM|ralph@home|State file error: result DOCK_1EFU_unbound_perturb_benchmark_1315_10_1 is in wrong state
9/30/2006 11:22:59 AM||Processor: 1 AuthenticAMD AMD Athlon(tm) XP 2000+
</edit>
This PC is running Boinc 5.6.4 on Win2K.
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58)
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Bug Report for Ralph 5.27
(Message 2295)
Posted 27 Sep 2006 by Chu
Post:
Ralph has been updated to 5.27. In this version, we fixed a problem in the 5.26 of reporting percentage of progess correctly for the docking application. Also, several new flags are added for full atom relax application.
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59)
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Bug Report for Ralph 5.26
(Message 2292)
Posted 26 Sep 2006 by Chu
Post:
The validator has been updated to handle the docking output file with a slightly diifferent format and a couple of returning results have been validated with the new validator.
Docking application is being checkpointed, but the percentage of completion shown on the graphic was updated incorrectly in docking. This will be fixed in the next updated version.
Thanks for everyone's effort again.
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Bug Report for Ralph 5.26
(Message 2290)
Posted 26 Sep 2006 by Chu
Post:
Thanks for all the feedbacks and reports. I started working on adding docking into Rosetta@home only from recently and am still learning how Rosetta@home and boinc work. I will consult with other experienced project developers in Baker Lab to invesgigate these errors and come back soon with answers.
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