WU stuck at 00:03:06 for about 45min

Author	Message
Saenger Send message Joined: 19 Sep 05 Posts: 271 Credit: 824,883 RAC: 0	Message 29655 - Posted: 19 Oct 2006, 20:16:58 UTC Last modified: 19 Oct 2006, 20:19:35 UTC I had something similar (at least imho) with Ralph, is it my puter? Is it an error with the WUs? Does anybody read anything in this data? I've suspended the WU for a short time, so that Docking was crunching, but I managed to let it crunch again and it didn't have any progress again. So I did a restart of BOINC, and it crunched from scratch (00:00:00) again, it has now reached 00:04:00, so I hope everything is OK, but I want to let you know (and get some help if needed). I havn't seen much differences in the stderr.txt and stdout.txt on first sight, and dont want to post more of this huge quotes. Here's the messages from BOINC: [color=#CC33CC]Don 19 Okt 2006 21:01:49 CEST\|rosetta@home\|Starting task BENCH_ABRELAX_SAVE_ALL_OUT_1ubi__BARCODE_CONTROL_filters_1284_1386_0 using rosetta version 532 Don 19 Okt 2006 21:48:13 CEST\|rosetta@home\|Pausing task BENCH_ABRELAX_SAVE_ALL_OUT_1ubi__BARCODE_CONTROL_filters_1284_1386_0 (left in memory)[/color] The stderr.txt from slot3: [color=#6666CC]Graphics are disabled due to configuration... # random seed: 2493515 terminate called after throwing an instance of 'std::length_error' what(): basic_string::_S_create SIGABRT: abort called Stack trace (20 frames): [0x895338b] [0x896decc] [0xffffe420] [0x89d4474] [0x89c21eb] [0x89bf7ed] [0x89bf822] [0x89bf453] [0x8973e57] [0x89a4809] [0x89a483d] [0x89a4bcd] [0x8369535] [0x88e507f] [0x833d22b] [0x806015d] [0x84137bb] [0x8514229] [0x89cd3b4] [0x8048111] Exiting... * glibc detected * double free or corruption (out): 0x09440488 * SIGABRT: abort called Stack trace (32 frames): [0x895338b] [0x896decc] [0xffffe420] [0x89d4474] [0x89e931f] [0x89ee385] [0x89ee663] [0x89bf7d1] [0x89a4b1a] [0x89a4d51] [0x836e860] [0x89d49bf] [0x89533d6] [0x896decc] [0xffffe420] [0x89d4474] [0x89c21eb] [0x89bf7ed] [0x89bf822] [0x89bf453] [0x8973e57] [0x89a4809] [0x89a483d] [0x89a4bcd] [0x8369535] [0x88e507f] [0x833d22b] [0x806015d] [0x84137bb] [0x8514229] [0x89cd3b4] [0x8048111] Exiting...[/color] And the stdout.txt: [color=#FF6600][REAL OPT]Default value for [-cpu_frac] 10 [REAL OPT]Default value for [-frame_rate] 10 [INT OPT]New value for [-cpu_run_time] 10800 command executed: rosetta_5.32_i686-pc-linux-gnu cc 1ubi _ -output_silent_gz -silent -increase_cycles 10 -new_centroid_packing -abrelax -output_chi_silent -stringent_relax -vary_omega -omega_weight 0.5 -farlx -ex1 -ex2 -termini -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -no_filters -rg_reweight 0.5 -rsd_wt_helix 0.5 -rsd_wt_loop 0.5 -output_all -accept_all -do_farlx_checkpointing -nstruct 30 -relax_score_filter -paths ccfrags200.txt -barcode_mode 3 -output_flavor -ssblocks -relax_score_filter -filter1 -108 -filter2 -125 -cpu_run_time 10800 -watchdog -constant_seed -jran 2493515 [STR OPT]New value for [-paths] ccfrags200.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]Default FALSE value for [-relax] [T/F OPT]New TRUE value for [-abrelax] [T/F OPT]Default FALSE value for [-sim_aneal] [T/F OPT]Default FALSE value for [-cenrlx] [T/F OPT]Default FALSE value for [-record_irms_before_relax] [T/F OPT]Default FALSE value for [-force_expand] [T/F OPT]Default FALSE value for [-minimize] Rosetta mode: abrelax [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 = cc :: protein_name is 1ubi:: chain_id is _. [INT OPT]New value for [-nstruct] 30 [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]New TRUE value for [-no_filters] [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]New TRUE value for [-output_all] [T/F OPT]New TRUE value for [-output_chi_silent] [T/F OPT]New TRUE 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:: output_all option is not applicable because filters are not in use WARNING:: no_filters option is not applicable because all structures are being accepted anyway (-accept_all) [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]Default value for [-protein_name_prefix] . [STR OPT]Default value for [-frags_name_prefix] . [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]New value for [-rg_reweight] 0.5 [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: 4 default fullatom scorefxn: 12 [INT OPT]Default value for [-run_level] 0 [T/F OPT]New TRUE value for [-silent] 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]Default value for [-s] none. [STR OPT]Default value for [-l] none. 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] default. [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 :: [2006-10-19 21:01:50] :: mode: abrelax :: nstartnum: 1 :: number_of_output: 30 :: 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: ./1ubi.dat Searching for dat file: ./1ubi.dat WARNING!! .dat file not found! Looking for fasta file: ./1ubi_.fasta Looking for psipred file: ./1ubi_.psipred_ss2 Protein type: alpha/beta Fraction beta: 0.524999976 [T/F OPT]Default FALSE value for [-tight_hb] File: ./1ubi_.cst not found Running without distance constraints File: ./1ubi_.dpl not found Dipolar constraints will not be used fragment file: ./cc1ubi_03_05.200_v1_3.gz Total Residue 71 frag size: 3 frags/residue: 200 fragment file: ./cc1ubi_09_05.200_v1_3.gz Total Residue 71 frag size: 9 frags/residue: 200 generating 1mer library from 3mer library [T/F OPT]New TRUE value for [-ssblocks] 1 0 0.419999987 -4.53112622E+2800 2 0.00499999989 0.935000002 NAN21 3 0 0.99000001 7.43514767E+3121 4 0.0149999997 0.975000024 -7.07653086E+2121 5 0.00499999989 0.980000019 0.014999999721 6 0.0199999996 0.879999995 -5.02287288E+3421 7 0.00499999989 0.230000004 -1.07632263E+3400 8 0.0299999993 0.0949999988 1008462700 9 0 0.0350000001 1.1051899200 10 0 0.0199999996 -4.86515375E+1700 11 0 0.38499999 -5.40238264E+2400 12 0 0.944999993 -5.71449153E+3321 13 0 0.959999979 0.039999999121 14 0 0.970000029 -5.37093814E+2621 15 0.0299999993 0.879999995 0.082622528121 16 0.075000003 0.704999983 -6.26340794E+2521 17 0.0399999991 0.449999988 0.50931882900 18 0.0250000004 0.0450000018 8.2224435800 19 0.0450000018 0.0199999996 0.93500000200 20 0.449999988 0 0.55000001200 21 0.639999986 0 -6.43012749E+3100 22 0.689999998 0.0149999997 0.29929709400 23 1 0 -1.280193E+1811 24 1 0 -5.22672242E-2611 25 1 0 1.66652664E+2611 26 0.995000005 0 -1.16750476E+2611 27 1 0 1.92501696E+3511 28 0.99000001 0.00999999978 -4.1473075E+3511 29 0.995000005 0 -7.68422644E+2411 30 0.985000014 0 0.014999999711 31 0.939999998 0 7.48192623E+3211 32 0.894999981 0 0.10499999711 33 0.680000007 0.00999999978 0.31484383300 34 0.204999998 0.0250000004 -2.06377861E+1100 35 0.0149999997 0.00499999989 0.98000001900 36 0.0700000003 0.0500000007 0.87999999500 37 0.234999999 0.00999999978 6.77330551E+1100 38 0.495000005 0.00499999989 6.86923619E+2600 39 0.349999994 0.144999996 0.50588458800 40 0.234999999 0.435000002 1202740.3800 41 0.119999997 0.675000012 0.20499765900 42 0.115000002 0.829999983 0.054999999721 43 0.0299999993 0.930000007 1.08132585E+2721 44 0.0450000018 0.824999988 -5.11042891E+3421 45 0.0900000036 0.584999979 -5.45260023E+3100 46 0.0450000018 0.100000001 -1.56735525E+3000 47 0.0399999991 0.144999996 3.48173384E+3400 48 0.159999996 0.61500001 -35230.175800 49 0.140000001 0.61500001 0.24500000500 50 0.104999997 0.194999993 -5.40775526E+2400 51 0.0399999991 0.0299999993 -8.3853487E+2300 52 0.0500000007 0 1.27996769E+2400 53 0.275000006 0.00499999989 0.72000002900 54 0.474999994 0.075000003 0.44999998800 55 0.50999999 0.219999999 0.27000001100 56 0.670000017 0.0700000003 -8.82319575E+2600 57 0.644999981 0.0649999976 2.09838807E+2100 58 0.569999993 0.0549999997 0.37500 59 0.245000005 0.155000001 1.20223014E+0900 60 0.0500000007 0.104999997 2.02538406E+2600 61 0.0299999993 0.155000001 0.81499999800 62 0.0250000004 0.0649999976 0.91000002600 63 0.0199999996 0.0299999993 -1.68869422E+2300 64 0 0.0450000018 0.95499998300 65 0 0.294999987 -1.52745832E+2900 66 0.00499999989 0.850000024 1.64558064E+1721 67 0.00999999978 0.88499999 0.10499999721 68 0.00999999978 0.985000014 -3.09171439E+2121 69 0.00499999989 0.99000001 0.0049999998921 70 0.00499999989 0.980000019 3.2483898E+1421 71 0 0.579999983 0.41941481800 1 2 6 0.952000022 2 12 16 0.89200002 3 24 31 0.988124967 4 42 44 0.861666679 5 66 70 0.938000023 [T/F OPT]Default FALSE value for [-check_homs] calculating fragment_diversity... [T/F OPT]New TRUE value for [-barcode_mode] [INT OPT]New value for [-barcode_mode] 3 [T/F OPT]Default FALSE value for [-increment_barcode] [T/F OPT]Default FALSE value for [-barcode_file] [T/F OPT]Default FALSE value for [-barcode_from_fragments] [T/F OPT]Default FALSE value for [-barcode_force_rotamer] RG cutoff: 14.4224548 [REAL OPT]Default value for [-co] -1 Contact order cutoff: 12.9769993 [REAL OPT]Default value for [-rms] -1 Searching for pdb...: ./1ubi.pdb [T/F OPT]Default FALSE value for [-use_native_centroid] Looking for dssp file: ./1ubi.dssp dssp file not found Looking for secondary structure assignment file: ./1ubi_.ssa ssa file not found calculating secondary structure from torsion angles [REAL OPT]Default value for [-parallel_weight] 1 [REAL OPT]Default value for [-antiparallel_weight] 1 [T/F OPT]Default FALSE value for [-use_barcode_to_score] [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]New value for [-omega_weight] 0.5 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 [T/F OPT]New TRUE value for [-constant_seed] [INT OPT]New value for [-jran] 2493515 # ===================================== # random seed: 2493515 # ===================================== [REAL OPT]New value for [-rsd_wt_helix] 0.5 [REAL OPT]Default value for [-rsd_wt_strand] 1 [REAL OPT]New value for [-rsd_wt_loop] 0.5 [T/F OPT]Default FALSE value for [-burial_code] [T/F OPT]New TRUE value for [-new_centroid_packing] [REAL OPT]Default value for [-cb_weight] 1 [REAL OPT]Default value for [-centroid_pack_weight] 2 [T/F OPT]Default FALSE value for [-separate_centroid_pack_score] [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] Reading ./SASA-masks.dat.gz Reading ./SASA-angles.dat.gz ======================================== Reading ./sasa_offsets.txt.gz Reading ./sasa_prob_cdf.txt.gz [T/F OPT]Default FALSE value for [-repeatin] [T/F OPT]Default FALSE value for [-repeatout] [T/F OPT]Default FALSE value for [-clnt] Current barcode settings: NEXT STRUCTURE: ./cc1ubi0001.pdb [INT OPT]Default value for [-number_3mer_frags] 200 [INT OPT]Default value for [-number_9mer_frags] 25 [T/F OPT]Default FALSE value for [-use_random_top_frags] [REAL OPT]New value for [-increase_cycles] 10 [T/F OPT]Default FALSE value for [-just_smooth_cycles] [T/F OPT]Default FALSE value for [-optimize_rmsd] [T/F OPT]Default FALSE value for [-rand_envpair_res_wt] [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] [REAL OPT]Default value for [-abinitio_temperature] 2 [T/F OPT]Default FALSE value for [-random_frag] starting fragment insertions... Size: 9 NUMBER OF FRAGS FOR POS: 1 25 Size: 9 NUMBER OF FRAGS FOR POS: 2 25 Size: 9 NUMBER OF FRAGS FOR POS: 3 25 Size: 9 NUMBER OF FRAGS FOR POS: 4 25 Size: 9 NUMBER OF FRAGS FOR POS: 5 25 Size: 9 NUMBER OF FRAGS FOR POS: 6 25 Size: 9 NUMBER OF FRAGS FOR POS: 7 25 Size: 9 NUMBER OF FRAGS FOR POS: 8 25 Size: 9 NUMBER OF FRAGS FOR POS: 9 25 Size: 9 NUMBER OF FRAGS FOR POS: 10 25 Size: 9 NUMBER OF FRAGS FOR POS: 11 25 Size: 9 NUMBER OF FRAGS FOR POS: 12 25 Size: 9 NUMBER OF FRAGS FOR POS: 13 25 Size: 9 NUMBER OF FRAGS FOR POS: 14 25 Size: 9 NUMBER OF FRAGS FOR POS: 15 25 Size: 9 NUMBER OF FRAGS FOR POS: 16 25 Size: 9 NUMBER OF FRAGS FOR POS: 17 25 Size: 9 NUMBER OF FRAGS FOR POS: 18 25 Size: 9 NUMBER OF FRAGS FOR POS: 19 25 Size: 9 NUMBER OF FRAGS FOR POS: 20 25 Size: 9 NUMBER OF FRAGS FOR POS: 21 25 Size: 9 NUMBER OF FRAGS FOR POS: 22 25 Size: 9 NUMBER OF FRAGS FOR POS: 23 25 Size: 9 NUMBER OF FRAGS FOR POS: 24 25 Size: 9 NUMBER OF FRAGS FOR POS: 25 25 Size: 9 NUMBER OF FRAGS FOR POS: 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Size: 3 NUMBER OF FRAGS FOR POS: 65 200 Size: 3 NUMBER OF FRAGS FOR POS: 66 200 Size: 3 NUMBER OF FRAGS FOR POS: 67 200 Size: 3 NUMBER OF FRAGS FOR POS: 68 200 Size: 3 NUMBER OF FRAGS FOR POS: 69 200 [T/F OPT]Default FALSE value for [-jitter_frag] score0 done: (best, low) rms 0 0 16.5505676 --------------------------------------------------------- score1 done: (best, low) rms (best,low) 8.2251358 -21.1778584 13.3440809 7.90915155 standard trials: 20000 accepts: 3226 %: 16.13 e/trial: -0.00096 ----------------------------------------------------- Alternate score2/score5... kk score2 score5 low_score n_low_accept rms rms_min low_rms 0 -28.241 -17.728 -28.241 40 7.909 5.307 7.909 converged 2.4837029 108201 1 -17.052 -9.222 -22.800 43 6.118 4.767 5.403 2 -26.146 -14.381 -38.438 45 7.140 4.632 8.425 3 -32.209 -17.105 -21.354 45 7.757 4.632 8.425 4 -40.248 -13.968 -45.880 50 6.647 4.632 5.594 5 -2.007 9.041 -24.702 53 14.879 4.632 6.150 6 -33.292 -11.389 -50.060 53 6.156 4.632 6.150 7 -28.736 -21.235 -24.991 54 3.925 3.377 3.806 8 -39.397 -24.266 -54.816 62 5.231 2.826 4.610 converged 2.40157747 244351 9 -53.607 -35.614 -54.906 63 4.120 2.826 4.333 converged 2.76985812 232100 10 -28.509 -10.986 -54.905 63 6.041 2.826 4.333 standard trials: 177450 accepts: 8574 %: 4.83 e/trial: 0.00051 ----------------------------------------------------- Starting score3 moves... kk,score3,low_score,rms_err,low_rms,rms_min,naccept 0 -17.927 -17.927 4.333 4.333 2.826 11800[/color] Grüße vom Sänger** ID: 29655 · Rating: 0 · rate: / Reply Quote

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I had something similar (at least imho) with Ralph, is it my puter? Is it an error with the WUs? Does anybody read anything in this data?

I've suspended the WU for a short time, so that Docking was crunching, but I managed to let it crunch again and it didn't have any progress again. So I did a restart of BOINC, and it crunched from scratch (00:00:00) again, it has now reached 00:04:00, so I hope everything is OK, but I want to let you know (and get some help if needed).

I havn't seen much differences in the stderr.txt and stdout.txt on first sight, and dont want to post more of this huge quotes.

Here's the messages from BOINC:

[color=#CC33CC]Don 19 Okt 2006 21:01:49 CEST|rosetta@home|Starting task BENCH_ABRELAX_SAVE_ALL_OUT_1ubi__BARCODE_CONTROL_filters_1284_1386_0 using rosetta version 532
Don 19 Okt 2006 21:48:13 CEST|rosetta@home|Pausing task BENCH_ABRELAX_SAVE_ALL_OUT_1ubi__BARCODE_CONTROL_filters_1284_1386_0 (left in memory)[/color]

The stderr.txt from slot3:

[color=#6666CC]Graphics are disabled due to configuration...
# random seed: 2493515
terminate called after throwing an instance of 'std::length_error'
  what():  basic_string::_S_create
SIGABRT: abort called
Stack trace (20 frames):
[0x895338b]
[0x896decc]
[0xffffe420]
[0x89d4474]
[0x89c21eb]
[0x89bf7ed]
[0x89bf822]
[0x89bf453]
[0x8973e57]
[0x89a4809]
[0x89a483d]
[0x89a4bcd]
[0x8369535]
[0x88e507f]
[0x833d22b]
[0x806015d]
[0x84137bb]
[0x8514229]
[0x89cd3b4]
[0x8048111]

Exiting...
*** glibc detected *** double free or corruption (out): 0x09440488 ***
SIGABRT: abort called
Stack trace (32 frames):
[0x895338b]
[0x896decc]
[0xffffe420]
[0x89d4474]
[0x89e931f]
[0x89ee385]
[0x89ee663]
[0x89bf7d1]
[0x89a4b1a]
[0x89a4d51]
[0x836e860]
[0x89d49bf]
[0x89533d6]
[0x896decc]
[0xffffe420]
[0x89d4474]
[0x89c21eb]
[0x89bf7ed]
[0x89bf822]
[0x89bf453]
[0x8973e57]
[0x89a4809]
[0x89a483d]
[0x89a4bcd]
[0x8369535]
[0x88e507f]
[0x833d22b]
[0x806015d]
[0x84137bb]
[0x8514229]
[0x89cd3b4]
[0x8048111]

Exiting...[/color]

And the stdout.txt:

[color=#FF6600][REAL OPT]Default value for [-cpu_frac]   10
[REAL OPT]Default value for [-frame_rate]   10
[INT  OPT]New value for [-cpu_run_time]  10800
command executed: rosetta_5.32_i686-pc-linux-gnu cc 1ubi _ -output_silent_gz -silent -increase_cycles 10 -new_centroid_packing -abrelax -output_chi_silent -stringent_relax -vary_omega -omega_weight 0.5 -farlx -ex1 -ex2 -termini -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -no_filters -rg_reweight 0.5 -rsd_wt_helix 0.5 -rsd_wt_loop 0.5 -output_all -accept_all -do_farlx_checkpointing -nstruct 30 -relax_score_filter -paths ccfrags200.txt -barcode_mode 3 -output_flavor -ssblocks -relax_score_filter -filter1 -108 -filter2 -125 -cpu_run_time 10800 -watchdog -constant_seed -jran 2493515
[STR  OPT]New value for [-paths] ccfrags200.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]Default FALSE value for [-relax]
[T/F  OPT]New TRUE value for [-abrelax]
[T/F  OPT]Default FALSE value for [-sim_aneal]
[T/F  OPT]Default FALSE value for [-cenrlx]
[T/F  OPT]Default FALSE value for [-record_irms_before_relax]
[T/F  OPT]Default FALSE value for [-force_expand]
[T/F  OPT]Default FALSE value for [-minimize]
Rosetta mode: abrelax
[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 = cc :: protein_name is 1ubi:: chain_id is _.
[INT  OPT]New value for [-nstruct]  30
[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]New TRUE value for [-no_filters]
[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]New TRUE value for [-output_all]
[T/F  OPT]New TRUE value for [-output_chi_silent]
[T/F  OPT]New TRUE 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::
output_all option is not applicable because filters are not in use
WARNING::
no_filters option is not applicable because all structures are being accepted anyway (-accept_all)
[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]Default value for [-protein_name_prefix] .
[STR  OPT]Default value for [-frags_name_prefix] .
[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]New value for [-rg_reweight]   0.5
[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:  4
default fullatom scorefxn:  12
[INT  OPT]Default value for [-run_level]  0
[T/F  OPT]New TRUE value for [-silent]
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]Default value for [-s] none.
[STR  OPT]Default value for [-l] none.
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] default.
[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 :: [2006-10-19 21:01:50] :: mode: abrelax :: nstartnum: 1 :: number_of_output: 30 :: 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: ./1ubi.dat
Searching for dat file: ./1ubi.dat
WARNING!! .dat file not found!
Looking for fasta file: ./1ubi_.fasta
Looking for psipred file: ./1ubi_.psipred_ss2
Protein type: alpha/beta  Fraction beta:   0.524999976
[T/F  OPT]Default FALSE value for [-tight_hb]
File: ./1ubi_.cst not found
Running without distance constraints
File: ./1ubi_.dpl not found
Dipolar constraints will not be used
fragment file: ./cc1ubi_03_05.200_v1_3.gz
Total Residue 71
frag size: 3    frags/residue: 200
fragment file: ./cc1ubi_09_05.200_v1_3.gz
Total Residue 71
frag size: 9    frags/residue: 200
generating 1mer library from 3mer library
[T/F  OPT]New TRUE value for [-ssblocks]
 1  0  0.419999987 -4.53112622E+2800
 2  0.00499999989  0.935000002 NAN21
 3  0  0.99000001  7.43514767E+3121
 4  0.0149999997  0.975000024 -7.07653086E+2121
 5  0.00499999989  0.980000019  0.014999999721
 6  0.0199999996  0.879999995 -5.02287288E+3421
 7  0.00499999989  0.230000004 -1.07632263E+3400
 8  0.0299999993  0.0949999988  1008462700
 9  0  0.0350000001  1.1051899200
 10  0  0.0199999996 -4.86515375E+1700
 11  0  0.38499999 -5.40238264E+2400
 12  0  0.944999993 -5.71449153E+3321
 13  0  0.959999979  0.039999999121
 14  0  0.970000029 -5.37093814E+2621
 15  0.0299999993  0.879999995  0.082622528121
 16  0.075000003  0.704999983 -6.26340794E+2521
 17  0.0399999991  0.449999988  0.50931882900
 18  0.0250000004  0.0450000018  8.2224435800
 19  0.0450000018  0.0199999996  0.93500000200
 20  0.449999988  0  0.55000001200
 21  0.639999986  0 -6.43012749E+3100
 22  0.689999998  0.0149999997  0.29929709400
 23  1  0 -1.280193E+1811
 24  1  0 -5.22672242E-2611
 25  1  0  1.66652664E+2611
 26  0.995000005  0 -1.16750476E+2611
 27  1  0  1.92501696E+3511
 28  0.99000001  0.00999999978 -4.1473075E+3511
 29  0.995000005  0 -7.68422644E+2411
 30  0.985000014  0  0.014999999711
 31  0.939999998  0  7.48192623E+3211
 32  0.894999981  0  0.10499999711
 33  0.680000007  0.00999999978  0.31484383300
 34  0.204999998  0.0250000004 -2.06377861E+1100
 35  0.0149999997  0.00499999989  0.98000001900
 36  0.0700000003  0.0500000007  0.87999999500
 37  0.234999999  0.00999999978  6.77330551E+1100
 38  0.495000005  0.00499999989  6.86923619E+2600
 39  0.349999994  0.144999996  0.50588458800
 40  0.234999999  0.435000002  1202740.3800
 41  0.119999997  0.675000012  0.20499765900
 42  0.115000002  0.829999983  0.054999999721
 43  0.0299999993  0.930000007  1.08132585E+2721
 44  0.0450000018  0.824999988 -5.11042891E+3421
 45  0.0900000036  0.584999979 -5.45260023E+3100
 46  0.0450000018  0.100000001 -1.56735525E+3000
 47  0.0399999991  0.144999996  3.48173384E+3400
 48  0.159999996  0.61500001 -35230.175800
 49  0.140000001  0.61500001  0.24500000500
 50  0.104999997  0.194999993 -5.40775526E+2400
 51  0.0399999991  0.0299999993 -8.3853487E+2300
 52  0.0500000007  0  1.27996769E+2400
 53  0.275000006  0.00499999989  0.72000002900
 54  0.474999994  0.075000003  0.44999998800
 55  0.50999999  0.219999999  0.27000001100
 56  0.670000017  0.0700000003 -8.82319575E+2600
 57  0.644999981  0.0649999976  2.09838807E+2100
 58  0.569999993  0.0549999997  0.37500
 59  0.245000005  0.155000001  1.20223014E+0900
 60  0.0500000007  0.104999997  2.02538406E+2600
 61  0.0299999993  0.155000001  0.81499999800
 62  0.0250000004  0.0649999976  0.91000002600
 63  0.0199999996  0.0299999993 -1.68869422E+2300
 64  0  0.0450000018  0.95499998300
 65  0  0.294999987 -1.52745832E+2900
 66  0.00499999989  0.850000024  1.64558064E+1721
 67  0.00999999978  0.88499999  0.10499999721
 68  0.00999999978  0.985000014 -3.09171439E+2121
 69  0.00499999989  0.99000001  0.0049999998921
 70  0.00499999989  0.980000019  3.2483898E+1421
 71  0  0.579999983  0.41941481800
 1 2 6  0.952000022
 2 12 16  0.89200002
 3 24 31  0.988124967
 4 42 44  0.861666679
 5 66 70  0.938000023
[T/F  OPT]Default FALSE value for [-check_homs]
calculating fragment_diversity...
[T/F  OPT]New TRUE value for [-barcode_mode]
[INT  OPT]New value for [-barcode_mode]  3
[T/F  OPT]Default FALSE value for [-increment_barcode]
[T/F  OPT]Default FALSE value for [-barcode_file]
[T/F  OPT]Default FALSE value for [-barcode_from_fragments]
[T/F  OPT]Default FALSE value for [-barcode_force_rotamer]
RG cutoff:   14.4224548
[REAL OPT]Default value for [-co]  -1
Contact order cutoff:   12.9769993
[REAL OPT]Default value for [-rms]  -1
Searching for pdb...: ./1ubi.pdb
[T/F  OPT]Default FALSE value for [-use_native_centroid]
Looking for dssp file: ./1ubi.dssp
dssp file not found
Looking for secondary structure assignment file: ./1ubi_.ssa
ssa file not found
calculating secondary structure from torsion angles
[REAL OPT]Default value for [-parallel_weight]   1
[REAL OPT]Default value for [-antiparallel_weight]   1
[T/F  OPT]Default FALSE value for [-use_barcode_to_score]
[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]New value for [-omega_weight]   0.5
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
[T/F  OPT]New TRUE value for [-constant_seed]
[INT  OPT]New value for [-jran]  2493515
# =====================================
# random seed: 2493515
# =====================================
[REAL OPT]New value for [-rsd_wt_helix]   0.5
[REAL OPT]Default value for [-rsd_wt_strand]   1
[REAL OPT]New value for [-rsd_wt_loop]   0.5
[T/F  OPT]Default FALSE value for [-burial_code]
[T/F  OPT]New TRUE value for [-new_centroid_packing]
[REAL OPT]Default value for [-cb_weight]   1
[REAL OPT]Default value for [-centroid_pack_weight]   2
[T/F  OPT]Default FALSE value for [-separate_centroid_pack_score]
[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]
Reading ./SASA-masks.dat.gz
Reading ./SASA-angles.dat.gz
========================================
Reading ./sasa_offsets.txt.gz
Reading ./sasa_prob_cdf.txt.gz
[T/F  OPT]Default FALSE value for [-repeatin]
[T/F  OPT]Default FALSE value for [-repeatout]
[T/F  OPT]Default FALSE value for [-clnt]
Current barcode settings: 
NEXT STRUCTURE: ./cc1ubi0001.pdb
[INT  OPT]Default value for [-number_3mer_frags]  200
[INT  OPT]Default value for [-number_9mer_frags]  25
[T/F  OPT]Default FALSE value for [-use_random_top_frags]
[REAL OPT]New value for [-increase_cycles]   10
[T/F  OPT]Default FALSE value for [-just_smooth_cycles]
[T/F  OPT]Default FALSE value for [-optimize_rmsd]
[T/F  OPT]Default FALSE value for [-rand_envpair_res_wt]
[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]
[REAL OPT]Default value for [-abinitio_temperature]   2
[T/F  OPT]Default FALSE value for [-random_frag]
starting fragment insertions...
  Size:  9  NUMBER OF FRAGS FOR POS:  1 25
  Size:  9  NUMBER OF FRAGS FOR POS:  2 25
  Size:  9  NUMBER OF FRAGS FOR POS:  3 25
  Size:  9  NUMBER OF FRAGS FOR POS:  4 25
  Size:  9  NUMBER OF FRAGS FOR POS:  5 25
  Size:  9  NUMBER OF FRAGS FOR POS:  6 25
  Size:  9  NUMBER OF FRAGS FOR POS:  7 25
  Size:  9  NUMBER OF FRAGS FOR POS:  8 25
  Size:  9  NUMBER OF FRAGS FOR POS:  9 25
  Size:  9  NUMBER OF FRAGS FOR POS:  10 25
  Size:  9  NUMBER OF FRAGS FOR POS:  11 25
  Size:  9  NUMBER OF FRAGS FOR POS:  12 25
  Size:  9  NUMBER OF FRAGS FOR POS:  13 25
  Size:  9  NUMBER OF FRAGS FOR POS:  14 25
  Size:  9  NUMBER OF FRAGS FOR POS:  15 25
  Size:  9  NUMBER OF FRAGS FOR POS:  16 25
  Size:  9  NUMBER OF FRAGS FOR POS:  17 25
  Size:  9  NUMBER OF FRAGS FOR POS:  18 25
  Size:  9  NUMBER OF FRAGS FOR POS:  19 25
  Size:  9  NUMBER OF FRAGS FOR POS:  20 25
  Size:  9  NUMBER OF FRAGS FOR POS:  21 25
  Size:  9  NUMBER OF FRAGS FOR POS:  22 25
  Size:  9  NUMBER OF FRAGS FOR POS:  23 25
  Size:  9  NUMBER OF FRAGS FOR POS:  24 25
  Size:  9  NUMBER OF FRAGS FOR POS:  25 25
  Size:  9  NUMBER OF FRAGS FOR POS:  26 25
  Size:  9  NUMBER OF FRAGS FOR POS:  27 25
  Size:  9  NUMBER OF FRAGS FOR POS:  28 25
  Size:  9  NUMBER OF FRAGS FOR POS:  29 25
  Size:  9  NUMBER OF FRAGS FOR POS:  30 25
  Size:  9  NUMBER OF FRAGS FOR POS:  31 25
  Size:  9  NUMBER OF FRAGS FOR POS:  32 25
  Size:  9  NUMBER OF FRAGS FOR POS:  33 25
  Size:  9  NUMBER OF FRAGS FOR POS:  34 25
  Size:  9  NUMBER OF FRAGS FOR POS:  35 25
  Size:  9  NUMBER OF FRAGS FOR POS:  36 25
  Size:  9  NUMBER OF FRAGS FOR POS:  37 25
  Size:  9  NUMBER OF FRAGS FOR POS:  38 25
  Size:  9  NUMBER OF FRAGS FOR POS:  39 25
  Size:  9  NUMBER OF FRAGS FOR POS:  40 25
  Size:  9  NUMBER OF FRAGS FOR POS:  41 25
  Size:  9  NUMBER OF FRAGS FOR POS:  42 25
  Size:  9  NUMBER OF FRAGS FOR POS:  43 25
  Size:  9  NUMBER OF FRAGS FOR POS:  44 25
  Size:  9  NUMBER OF FRAGS FOR POS:  45 25
  Size:  9  NUMBER OF FRAGS FOR POS:  46 25
  Size:  9  NUMBER OF FRAGS FOR POS:  47 25
  Size:  9  NUMBER OF FRAGS FOR POS:  48 25
  Size:  9  NUMBER OF FRAGS FOR POS:  49 25
  Size:  9  NUMBER OF FRAGS FOR POS:  50 25
  Size:  9  NUMBER OF FRAGS FOR POS:  51 25
  Size:  9  NUMBER OF FRAGS FOR POS:  52 25
  Size:  9  NUMBER OF FRAGS FOR POS:  53 25
  Size:  9  NUMBER OF FRAGS FOR POS:  54 25
  Size:  9  NUMBER OF FRAGS FOR POS:  55 25
  Size:  9  NUMBER OF FRAGS FOR POS:  56 25
  Size:  9  NUMBER OF FRAGS FOR POS:  57 25
  Size:  9  NUMBER OF FRAGS FOR POS:  58 25
  Size:  9  NUMBER OF FRAGS FOR POS:  59 25
  Size:  9  NUMBER OF FRAGS FOR POS:  60 25
  Size:  9  NUMBER OF FRAGS FOR POS:  61 25
  Size:  9  NUMBER OF FRAGS FOR POS:  62 25
  Size:  9  NUMBER OF FRAGS FOR POS:  63 25
  Size:  3  NUMBER OF FRAGS FOR POS:  1 200
  Size:  3  NUMBER OF FRAGS FOR POS:  2 200
  Size:  3  NUMBER OF FRAGS FOR POS:  3 200
  Size:  3  NUMBER OF FRAGS FOR POS:  4 200
  Size:  3  NUMBER OF FRAGS FOR POS:  5 200
  Size:  3  NUMBER OF FRAGS FOR POS:  6 200
  Size:  3  NUMBER OF FRAGS FOR POS:  7 200
  Size:  3  NUMBER OF FRAGS FOR POS:  8 200
  Size:  3  NUMBER OF FRAGS FOR POS:  9 200
  Size:  3  NUMBER OF FRAGS FOR POS:  10 200
  Size:  3  NUMBER OF FRAGS FOR POS:  11 200
  Size:  3  NUMBER OF FRAGS FOR POS:  12 200
  Size:  3  NUMBER OF FRAGS FOR POS:  13 200
  Size:  3  NUMBER OF FRAGS FOR POS:  14 200
  Size:  3  NUMBER OF FRAGS FOR POS:  15 200
  Size:  3  NUMBER OF FRAGS FOR POS:  16 200
  Size:  3  NUMBER OF FRAGS FOR POS:  17 200
  Size:  3  NUMBER OF FRAGS FOR POS:  18 200
  Size:  3  NUMBER OF FRAGS FOR POS:  19 200
  Size:  3  NUMBER OF FRAGS FOR POS:  20 200
  Size:  3  NUMBER OF FRAGS FOR POS:  21 200
  Size:  3  NUMBER OF FRAGS FOR POS:  22 200
  Size:  3  NUMBER OF FRAGS FOR POS:  23 200
  Size:  3  NUMBER OF FRAGS FOR POS:  24 200
  Size:  3  NUMBER OF FRAGS FOR POS:  25 200
  Size:  3  NUMBER OF FRAGS FOR POS:  26 200
  Size:  3  NUMBER OF FRAGS FOR POS:  27 200
  Size:  3  NUMBER OF FRAGS FOR POS:  28 200
  Size:  3  NUMBER OF FRAGS FOR POS:  29 200
  Size:  3  NUMBER OF FRAGS FOR POS:  30 200
  Size:  3  NUMBER OF FRAGS FOR POS:  31 200
  Size:  3  NUMBER OF FRAGS FOR POS:  32 200
  Size:  3  NUMBER OF FRAGS FOR POS:  33 200
  Size:  3  NUMBER OF FRAGS FOR POS:  34 200
  Size:  3  NUMBER OF FRAGS FOR POS:  35 200
  Size:  3  NUMBER OF FRAGS FOR POS:  36 200
  Size:  3  NUMBER OF FRAGS FOR POS:  37 200
  Size:  3  NUMBER OF FRAGS FOR POS:  38 200
  Size:  3  NUMBER OF FRAGS FOR POS:  39 200
  Size:  3  NUMBER OF FRAGS FOR POS:  40 200
  Size:  3  NUMBER OF FRAGS FOR POS:  41 200
  Size:  3  NUMBER OF FRAGS FOR POS:  42 200
  Size:  3  NUMBER OF FRAGS FOR POS:  43 200
  Size:  3  NUMBER OF FRAGS FOR POS:  44 200
  Size:  3  NUMBER OF FRAGS FOR POS:  45 200
  Size:  3  NUMBER OF FRAGS FOR POS:  46 200
  Size:  3  NUMBER OF FRAGS FOR POS:  47 200
  Size:  3  NUMBER OF FRAGS FOR POS:  48 200
  Size:  3  NUMBER OF FRAGS FOR POS:  49 200
  Size:  3  NUMBER OF FRAGS FOR POS:  50 200
  Size:  3  NUMBER OF FRAGS FOR POS:  51 200
  Size:  3  NUMBER OF FRAGS FOR POS:  52 200
  Size:  3  NUMBER OF FRAGS FOR POS:  53 200
  Size:  3  NUMBER OF FRAGS FOR POS:  54 200
  Size:  3  NUMBER OF FRAGS FOR POS:  55 200
  Size:  3  NUMBER OF FRAGS FOR POS:  56 200
  Size:  3  NUMBER OF FRAGS FOR POS:  57 200
  Size:  3  NUMBER OF FRAGS FOR POS:  58 200
  Size:  3  NUMBER OF FRAGS FOR POS:  59 200
  Size:  3  NUMBER OF FRAGS FOR POS:  60 200
  Size:  3  NUMBER OF FRAGS FOR POS:  61 200
  Size:  3  NUMBER OF FRAGS FOR POS:  62 200
  Size:  3  NUMBER OF FRAGS FOR POS:  63 200
  Size:  3  NUMBER OF FRAGS FOR POS:  64 200
  Size:  3  NUMBER OF FRAGS FOR POS:  65 200
  Size:  3  NUMBER OF FRAGS FOR POS:  66 200
  Size:  3  NUMBER OF FRAGS FOR POS:  67 200
  Size:  3  NUMBER OF FRAGS FOR POS:  68 200
  Size:  3  NUMBER OF FRAGS FOR POS:  69 200
[T/F  OPT]Default FALSE value for [-jitter_frag]
score0 done: (best, low) rms
  0  0  16.5505676
---------------------------------------------------------
score1 done: (best, low) rms (best,low)
  8.2251358 -21.1778584  13.3440809  7.90915155
standard     trials:  20000 accepts:   3226 %:  16.13 e/trial:  -0.00096
-----------------------------------------------------
Alternate score2/score5...
kk score2 score5 low_score n_low_accept rms rms_min low_rms
  0  -28.241  -17.728  -28.241   40    7.909    5.307    7.909
converged  2.4837029 108201
  1  -17.052   -9.222  -22.800   43    6.118    4.767    5.403
  2  -26.146  -14.381  -38.438   45    7.140    4.632    8.425
  3  -32.209  -17.105  -21.354   45    7.757    4.632    8.425
  4  -40.248  -13.968  -45.880   50    6.647    4.632    5.594
  5   -2.007    9.041  -24.702   53   14.879    4.632    6.150
  6  -33.292  -11.389  -50.060   53    6.156    4.632    6.150
  7  -28.736  -21.235  -24.991   54    3.925    3.377    3.806
  8  -39.397  -24.266  -54.816   62    5.231    2.826    4.610
converged  2.40157747 244351
  9  -53.607  -35.614  -54.906   63    4.120    2.826    4.333
converged  2.76985812 232100
 10  -28.509  -10.986  -54.905   63    6.041    2.826    4.333
standard     trials: 177450 accepts:   8574 %:   4.83 e/trial:   0.00051
-----------------------------------------------------
Starting score3 moves...
kk,score3,low_score,rms_err,low_rms,rms_min,naccept
  0  -17.927  -17.927    4.333    4.333    2.826 11800[/color]

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