Hi everyone, I have run the ample for a 377 amino acids protein and generated 500 models. But I did not get any ensemble model and got error message that could not load any ensembles after running create_ensembles. I am here attaching the ample.log and debug.log file. Any one suggest me why this happened?
Thanks and regards
######################################################################### ######################################################################### ######################################################################### # CCP4: AMPLE - Ab Initio Modelling Molecular Replacement # ######################################################################### The authors of specific programs should be referenced where applicable: AMPLE: J. Bibby, R. M. Keegan, O. Mayans, M. D. Winn and D. J. Rigden. AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. (2012). Acta Cryst. D68, 1622-1631 [ doi:10.1107/S0907444912039194 ] CCP4: Collaborative Computational Project, Number 4. (1994), The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763 SHELX: "A short history of SHELX". Sheldrick, G.M. (2008). Acta Cryst. A64, 112-122 SCWRL: G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009). MaxCluster: http://www.sbg.bio.ic.ac.uk/maxcluster/ MOLREP: A.A.Vagin & A.Teplyakov (1997) J. Appl. Cryst. 30, 1022-1025 MrBUMP: R.M.Keegan and M.D.Winn (2007) Acta Cryst. D63, 447-457 PHASER: McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C. & Read, R.J. (2007) Phaser crystallographic software J. Appl. Cryst. 40, 658-674 REFMAC: G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) Refinement of Macromolecular Structures by the Maximum-Likelihood Method. Acta Cryst. D53, 240-255 SPICKER: Y. Zhang, J. Skolnick, SPICKER: Approach to clustering protein structures for near-native model selection, Journal of Computational Chemistry, 2004 25: 865-871 Theseus: THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures. Theobald, Douglas L. & Wuttke, Deborah S. (2006b) Bioinformatics 22(17):2171-2172 [Open Access] Supplementary Materials for Theobald and Wuttke 2006b. AMPLE version: 1.0.0 Invoked with command-line: /home/user1/Documents/destination/ccp4-6.5/bin/ample.py -mtz /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/fmt-c2221-vikram.mtz -fasta /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/fmtA.fasta -mr_sequence /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/fmtA.fasta -nmodels 500 -name MVD0 -run_dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i -nproc 1 -make_models True -rosetta_dir /home/user1/Downloads/rosetta_bin_linux_2016.32.58837_bundle -frags_3mers /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/aat000_03_05.200_v1_3 -frags_9mers /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/aat000_09_05.200_v1_3 -make_frags False -F F -SIGF SIGF -FREE FreeR_flag -early_terminate True -use_arpwarp False Running in directory: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9 Fasta is 377 amino acids long Using MTZ file: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/fmt-c2221-vikram.mtz Cannot find maxcluster binary in path so attempting to download it directory: /home/user1/.ample No ample rcdir found so creating in: /home/user1/.ample Attempting to download maxcluster binary from: http://www.sbg.bio.ic.ac.uk/~maxcluster/maxcluster64bit *** Cannot find shelxe executable in PATH - turning off use of SHELXE. *** SHELXE is recommended for the best chance of success. We recommend you install shelxe from: http://shelx.uni-ac.gwdg.de/SHELX/ and install it in your PATH so that AMPLE can use it. Using ROSETTA so checking options Rosetta version is: 3.6 NOT making Fragments Making Rosetta Models Rebuilding in Bucaneer Not rebuilding in ARP/wARP All needed programs are found, continuing Run ----- making Rosetta models-------- making 500 models... Checking pdbs in directory: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/models check_pdb_directory - pdb files all seem valid Ensembling models in directory: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir * Running SPICKER to cluster models * truncating at: 49.699237 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_100 truncating at: 39.252605 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_95 truncating at: 31.159337 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_90 truncating at: 27.050171 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_85 truncating at: 23.309889 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_80 truncating at: 20.874194 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_75 truncating at: 19.027473 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_70 truncating at: 17.406585 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_65 truncating at: 15.809747 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_60 truncating at: 14.641427 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_55 truncating at: 13.268672 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_50 truncating at: 12.065652 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_45 truncating at: 9.915939 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_40 truncating at: 9.056308 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_34 truncating at: 8.068462 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_29 truncating at: 7.189155 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_24 truncating at: 6.380863 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_19 truncating at: 5.512833 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_14 truncating at: 4.638785 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_9 truncating at: 3.716708 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_4 ********************************************************************** ******************** AMPLE ERROR ******************* ********************************************************************** Could not load any ensembles after running create_ensembles! ********************************************************************** More information may be found in the debug log file: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/debug.log If you believe that this is an error with AMPLE, please email: c...@stfc.ac.uk providing as much information as you can about how you ran the program. Please include the debug logfile with your email: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/debug.log
2016-10-22 00:22:56,702 - root - INFO - ######################################################################### ######################################################################### ######################################################################### # CCP4: AMPLE - Ab Initio Modelling Molecular Replacement # ######################################################################### The authors of specific programs should be referenced where applicable: AMPLE: J. Bibby, R. M. Keegan, O. Mayans, M. D. Winn and D. J. Rigden. AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. (2012). Acta Cryst. D68, 1622-1631 [ doi:10.1107/S0907444912039194 ] CCP4: Collaborative Computational Project, Number 4. (1994), The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763 SHELX: "A short history of SHELX". Sheldrick, G.M. (2008). Acta Cryst. A64, 112-122 SCWRL: G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009). MaxCluster: http://www.sbg.bio.ic.ac.uk/maxcluster/ MOLREP: A.A.Vagin & A.Teplyakov (1997) J. Appl. Cryst. 30, 1022-1025 MrBUMP: R.M.Keegan and M.D.Winn (2007) Acta Cryst. D63, 447-457 PHASER: McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C. & Read, R.J. (2007) Phaser crystallographic software J. Appl. Cryst. 40, 658-674 REFMAC: G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) Refinement of Macromolecular Structures by the Maximum-Likelihood Method. Acta Cryst. D53, 240-255 SPICKER: Y. Zhang, J. Skolnick, SPICKER: Approach to clustering protein structures for near-native model selection, Journal of Computational Chemistry, 2004 25: 865-871 Theseus: THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures. Theobald, Douglas L. & Wuttke, Deborah S. (2006b) Bioinformatics 22(17):2171-2172 [Open Access] Supplementary Materials for Theobald and Wuttke 2006b. 2016-10-22 00:22:56,702 - root - INFO - AMPLE version: 1.0.0 2016-10-22 00:22:56,702 - root - INFO - Invoked with command-line: /home/user1/Documents/destination/ccp4-6.5/bin/ample.py -mtz /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/fmt-c2221-vikram.mtz -fasta /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/fmtA.fasta -mr_sequence /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/fmtA.fasta -nmodels 500 -name MVD0 -run_dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i -nproc 1 -make_models True -rosetta_dir /home/user1/Downloads/rosetta_bin_linux_2016.32.58837_bundle -frags_3mers /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/aat000_03_05.200_v1_3 -frags_9mers /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/aat000_09_05.200_v1_3 -make_frags False -F F -SIGF SIGF -FREE FreeR_flag -early_terminate True -use_arpwarp False 2016-10-22 00:22:56,702 - root - INFO - Running in directory: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9 2016-10-22 00:22:56,706 - root - DEBUG - Parsing FASTA file 2016-10-22 00:22:56,707 - root - INFO - Fasta is 377 amino acids long 2016-10-22 00:22:56,769 - root - INFO - Using MTZ file: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/fmt-c2221-vikram.mtz 2016-10-22 00:22:56,770 - root - DEBUG - Looking for executable: maxcluster 2016-10-22 00:22:56,770 - root - DEBUG - Checking paths: ['/home/user1/Documents/destination/ccp4-6.5/share/dbccp4i/bin', '/home/user1/Documents/destination/arp_warp_7.5/bin/bin-x86_64-Linux', '/home/user1/Documents/destination/ccp4-6.5/etc', '/home/user1/Documents/destination/ccp4-6.5/bin', '/home/user1/Documents/destination/ccp4-6.5/share/xia2/Applications', '/usr/local/phenix-1.10.1-2155/build/bin', '/usr/lib64/qt-3.3/bin', '/usr/local/bin', '/usr/local/sbin', '/usr/bin', '/usr/sbin', '/bin', '/sbin', '/home/programs/cns_solve_1.3/bin', '/home/user1/.local/bin', '/home/user1/bin', '/home/programs/cns_solve_1.3/bin', '/home/user1/.ample'] 2016-10-22 00:22:56,770 - root - INFO - Cannot find maxcluster binary in path so attempting to download it directory: /home/user1/.ample 2016-10-22 00:22:56,770 - root - INFO - No ample rcdir found so creating in: /home/user1/.ample 2016-10-22 00:22:56,817 - root - INFO - Attempting to download maxcluster binary from: http://www.sbg.bio.ic.ac.uk/~maxcluster/maxcluster64bit 2016-10-22 00:23:05,701 - root - DEBUG - Looking for executable: spicker 2016-10-22 00:23:05,701 - root - DEBUG - Checking paths: ['/home/user1/Documents/destination/ccp4-6.5/share/dbccp4i/bin', '/home/user1/Documents/destination/arp_warp_7.5/bin/bin-x86_64-Linux', '/home/user1/Documents/destination/ccp4-6.5/etc', '/home/user1/Documents/destination/ccp4-6.5/bin', '/home/user1/Documents/destination/ccp4-6.5/share/xia2/Applications', '/usr/local/phenix-1.10.1-2155/build/bin', '/usr/lib64/qt-3.3/bin', '/usr/local/bin', '/usr/local/sbin', '/usr/bin', '/usr/sbin', '/bin', '/sbin', '/home/programs/cns_solve_1.3/bin', '/home/user1/.local/bin', '/home/user1/bin', '/home/programs/cns_solve_1.3/bin'] 2016-10-22 00:23:05,701 - root - DEBUG - Found executable spicker in directory /home/user1/Documents/destination/ccp4-6.5/bin 2016-10-22 00:23:05,701 - root - DEBUG - find_exe found executable: /home/user1/Documents/destination/ccp4-6.5/bin/spicker 2016-10-22 00:23:05,701 - root - DEBUG - Looking for executable: theseus 2016-10-22 00:23:05,701 - root - DEBUG - Checking paths: ['/home/user1/Documents/destination/ccp4-6.5/share/dbccp4i/bin', '/home/user1/Documents/destination/arp_warp_7.5/bin/bin-x86_64-Linux', '/home/user1/Documents/destination/ccp4-6.5/etc', '/home/user1/Documents/destination/ccp4-6.5/bin', '/home/user1/Documents/destination/ccp4-6.5/share/xia2/Applications', '/usr/local/phenix-1.10.1-2155/build/bin', '/usr/lib64/qt-3.3/bin', '/usr/local/bin', '/usr/local/sbin', '/usr/bin', '/usr/sbin', '/bin', '/sbin', '/home/programs/cns_solve_1.3/bin', '/home/user1/.local/bin', '/home/user1/bin', '/home/programs/cns_solve_1.3/bin'] 2016-10-22 00:23:05,702 - root - DEBUG - Found executable theseus in directory /home/user1/Documents/destination/ccp4-6.5/bin 2016-10-22 00:23:05,702 - root - DEBUG - find_exe found executable: /home/user1/Documents/destination/ccp4-6.5/bin/theseus 2016-10-22 00:23:05,702 - root - DEBUG - Looking for executable: shelxe 2016-10-22 00:23:05,702 - root - DEBUG - Checking paths: ['/home/user1/Documents/destination/ccp4-6.5/share/dbccp4i/bin', '/home/user1/Documents/destination/arp_warp_7.5/bin/bin-x86_64-Linux', '/home/user1/Documents/destination/ccp4-6.5/etc', '/home/user1/Documents/destination/ccp4-6.5/bin', '/home/user1/Documents/destination/ccp4-6.5/share/xia2/Applications', '/usr/local/phenix-1.10.1-2155/build/bin', '/usr/lib64/qt-3.3/bin', '/usr/local/bin', '/usr/local/sbin', '/usr/bin', '/usr/sbin', '/bin', '/sbin', '/home/programs/cns_solve_1.3/bin', '/home/user1/.local/bin', '/home/user1/bin', '/home/programs/cns_solve_1.3/bin'] 2016-10-22 00:23:05,702 - root - WARNING - *** Cannot find shelxe executable in PATH - turning off use of SHELXE. *** SHELXE is recommended for the best chance of success. We recommend you install shelxe from: http://shelx.uni-ac.gwdg.de/SHELX/ and install it in your PATH so that AMPLE can use it. 2016-10-22 00:23:05,702 - root - INFO - Using ROSETTA so checking options 2016-10-22 00:23:05,702 - root - DEBUG - Version file for Rosetta not found - checking to see if its 3.5 or 3.6 2016-10-22 00:23:05,702 - root - INFO - Rosetta version is: 3.6 2016-10-22 00:23:05,704 - root - INFO - NOT making Fragments 2016-10-22 00:23:05,704 - root - INFO - Making Rosetta Models 2016-10-22 00:23:05,704 - root - INFO - Rebuilding in Bucaneer 2016-10-22 00:23:05,704 - root - INFO - Not rebuilding in ARP/wARP 2016-10-22 00:23:05,705 - root - INFO - All needed programs are found, continuing Run 2016-10-22 00:23:05,705 - root - DEBUG - Parameters Used in this Run F : F FREE : FreeR_flag LGA : None ROSETTA_cluster : None SIGF : SIGF alignment_file : None all_atom : True ample_log : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/AMPLE.log ample_version : 1.0.0 arpwarp_cycles : 10 benchmark_mode : False blast_dir : None buccaneer_cycles : 5 ccp4_jobid : None cluster_method : spicker constraints_file : None debug : False devel_mode : None domain_all_chains_pdb : None domain_termini_distance : 0 dry_run : False early_terminate : True ensembles_dir : None fast_protein_cluster_exe : None fasta : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/MVD0_.fasta fasta_length : 377 frags_3mers : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/aat000_03_05.200_v1_3 frags_9mers : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/aat000_09_05.200_v1_3 homologs : False ideal_helices : False import_ensembles : False import_models : False improve_template : None make_frags : False make_models : True max_array_jobs : None max_ensemble_models : 30 maxcluster_exe : /home/user1/.ample/maxcluster missing_domain : False models : None models_dir : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/models molrep_only : False mr_keys : [] mr_sequence : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/ample_21_oct_2016/fmtA.fasta mrbump_programs : ['phaser'] mtz : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/fmt-c2221-vikram.mtz name : MVD0_ native_pdb : None nmasu : 0 nmodels : 500 nmr_model_in : None nmr_process : None nmr_remodel : False nmr_remodel_fasta : None nproc : 1 nr : None num_clusters : 1 output_pdb : ample_output.pdb percent : 5 phaser_kill : 360 phaser_only : True phenix_exe : None psipred_ss2 : None purge : False quick_mode : None rcdir : /home/user1/.ample results_path : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/resultsd.pkl rg_reweight : None rosetta_AbinitioRelax : None rosetta_db : None rosetta_dir : /home/user1/Downloads/rosetta_bin_linux_2016.32.58837_bundle rosetta_fragments_exe : None rosetta_version : None run_dir : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i scwrl_exe : None sequence : SIALIFHRLQTKTHSIDPIHKETKLSDNEKYLVDRNKEKVAPSKLKEVYNSKDPKYKKIDKYLQSSLFNGSVAIYENGKLKMSKGYGYQDFEKGIKNTPNTMFLIGSAQKFSTGLLLKQLEEEHKININDPVSKYLPWFKTSKPIPLKDLMLHQSGLYKYKSSKDYKNLDQAVKAIQKRGIDPKKYKKHMYNDGNYLVLAKVIEEVTGKSYAENYYTKIGDPLKLQHTAFYDEQPFKKYLAKGYAYNSTGLSFLRPNILDQYYGAGNLYMTPTDMGKLITQIQQYKLFSPKITNPLLHEFGTKKYPDEYRYGFYAKPTLNRLNGGFFGQVFTVYYNDKYVVVLALNVKGNNEVRIKHIYNDILKQNKPYNTKGVIVQ sf_cif : None shelx_cycles : 15 shelxe_exe : shelxe shelxe_rebuild : False shelxe_rebuild_arpwarp : False shelxe_rebuild_buccaneer : False spicker_exe : /home/user1/Documents/destination/ccp4-6.5/bin/spicker split_mr : False submit_array : True submit_cluster : False submit_max_array : None submit_qtype : None submit_queue : None theseus_exe : /home/user1/Documents/destination/ccp4-6.5/bin/theseus top_model_only : False transmembrane : False transmembrane_lipofile : None transmembrane_octopusfile : None transmembrane_spanfile : None truncation_method : percent truncation_pruning : none use_arpwarp : False use_buccaneer : True use_homs : True use_scwrl : False use_shelxe : False webserver_uri : None work_dir : /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9 2016-10-22 00:23:05,705 - root - INFO - ----- making Rosetta models-------- 2016-10-22 00:23:05,705 - root - INFO - making 500 models... 2016-10-22 00:23:05,705 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/modelling Running command: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/modelling/job_0/model_0.sh 2016-10-22 00:23:05,706 - root - DEBUG - Logfile is: model_0.log 2016-10-29 18:25:21,676 - root - INFO - Checking pdbs in directory: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/models 2016-10-29 18:25:31,296 - root - INFO - check_pdb_directory - pdb files all seem valid 2016-10-29 18:25:31,301 - root - INFO - Ensembling models in directory: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir 2016-10-29 18:25:31,301 - root - INFO - * Running SPICKER to cluster models * 2016-10-29 18:25:31,301 - root - DEBUG - Running spicker in directory: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/spicker 2016-10-29 18:26:02,003 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/spicker Running command: /home/user1/Documents/destination/ccp4-6.5/bin/spicker 2016-10-29 18:26:02,004 - root - DEBUG - Logfile is: spicker.log 2016-10-29 18:26:03,773 - root - DEBUG - Processing spicker output file: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/spicker/str.txt 2016-10-29 18:26:03,774 - root - DEBUG - ---- Spicker Results ---- Cluster: 1 * number of models: 2 * files are listed in file: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/spicker/spicker_cluster_1.list * centroid model is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/models/model_176.pdb Cluster: 2 * number of models: 2 Cluster: 3 * number of models: 1 Cluster: 4 * number of models: 1 Cluster: 5 * number of models: 1 Cluster: 6 * number of models: 1 Cluster: 7 * number of models: 1 Cluster: 8 * number of models: 1 Cluster: 9 * number of models: 1 Cluster: 10 * number of models: 1 2016-10-29 18:26:03,775 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/Documents/destination/ccp4-6.5/bin/theseus -a0 -r theseus ../../models/model_176.pdb ../../models/model_350.pdb 2016-10-29 18:26:03,775 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/theseus.log 2016-10-29 18:26:03,899 - root - INFO - truncating at: 49.699237 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_100 2016-10-29 18:26:03,961 - root - INFO - truncating at: 39.252605 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_95 2016-10-29 18:26:04,021 - root - INFO - truncating at: 31.159337 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_90 2016-10-29 18:26:04,081 - root - INFO - truncating at: 27.050171 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_85 2016-10-29 18:26:04,143 - root - INFO - truncating at: 23.309889 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_80 2016-10-29 18:26:04,204 - root - INFO - truncating at: 20.874194 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_75 2016-10-29 18:26:04,264 - root - INFO - truncating at: 19.027473 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_70 2016-10-29 18:26:04,323 - root - INFO - truncating at: 17.406585 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_65 2016-10-29 18:26:04,380 - root - INFO - truncating at: 15.809747 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_60 2016-10-29 18:26:04,436 - root - INFO - truncating at: 14.641427 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_55 2016-10-29 18:26:04,491 - root - INFO - truncating at: 13.268672 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_50 2016-10-29 18:26:04,545 - root - INFO - truncating at: 12.065652 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_45 2016-10-29 18:26:04,598 - root - INFO - truncating at: 9.915939 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_40 2016-10-29 18:26:04,649 - root - INFO - truncating at: 9.056308 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_34 2016-10-29 18:26:04,699 - root - INFO - truncating at: 8.068462 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_29 2016-10-29 18:26:04,748 - root - INFO - truncating at: 7.189155 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_24 2016-10-29 18:26:04,796 - root - INFO - truncating at: 6.380863 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_19 2016-10-29 18:26:04,843 - root - INFO - truncating at: 5.512833 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_14 2016-10-29 18:26:04,888 - root - INFO - truncating at: 4.638785 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_9 2016-10-29 18:26:04,931 - root - INFO - truncating at: 3.716708 in directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_4 2016-10-29 18:26:04,972 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:04,972 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,052 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,052 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,052 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_100 SKIPPING 2016-10-29 18:26:05,052 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,053 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,053 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_100 SKIPPING 2016-10-29 18:26:05,053 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,053 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,053 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_100 SKIPPING 2016-10-29 18:26:05,053 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,053 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,127 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,127 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,127 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_95 SKIPPING 2016-10-29 18:26:05,127 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,127 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,127 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_95 SKIPPING 2016-10-29 18:26:05,127 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,127 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,127 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_95 SKIPPING 2016-10-29 18:26:05,127 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,127 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,193 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,193 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,193 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_90 SKIPPING 2016-10-29 18:26:05,193 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,193 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,193 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_90 SKIPPING 2016-10-29 18:26:05,193 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,193 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,193 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_90 SKIPPING 2016-10-29 18:26:05,194 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,194 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,251 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,252 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,252 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_85 SKIPPING 2016-10-29 18:26:05,252 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,252 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,252 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_85 SKIPPING 2016-10-29 18:26:05,252 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,252 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,252 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_85 SKIPPING 2016-10-29 18:26:05,252 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,252 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,303 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,304 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,304 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_80 SKIPPING 2016-10-29 18:26:05,304 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,304 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,304 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_80 SKIPPING 2016-10-29 18:26:05,304 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,304 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,304 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_80 SKIPPING 2016-10-29 18:26:05,304 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,304 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,350 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,350 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,350 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_75 SKIPPING 2016-10-29 18:26:05,350 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,350 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,350 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_75 SKIPPING 2016-10-29 18:26:05,350 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,350 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,350 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_75 SKIPPING 2016-10-29 18:26:05,351 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,351 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,389 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,389 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,389 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_70 SKIPPING 2016-10-29 18:26:05,389 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,390 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,390 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_70 SKIPPING 2016-10-29 18:26:05,390 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,390 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,390 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_70 SKIPPING 2016-10-29 18:26:05,390 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,390 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,424 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,424 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,424 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_65 SKIPPING 2016-10-29 18:26:05,424 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,424 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,424 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_65 SKIPPING 2016-10-29 18:26:05,424 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,424 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,424 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_65 SKIPPING 2016-10-29 18:26:05,424 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,424 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,452 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,453 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,453 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_60 SKIPPING 2016-10-29 18:26:05,453 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,453 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,453 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_60 SKIPPING 2016-10-29 18:26:05,453 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,453 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,453 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_60 SKIPPING 2016-10-29 18:26:05,453 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,453 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,477 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,478 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,478 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_55 SKIPPING 2016-10-29 18:26:05,478 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,478 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,478 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_55 SKIPPING 2016-10-29 18:26:05,478 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,478 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,478 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_55 SKIPPING 2016-10-29 18:26:05,478 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,478 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,499 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,499 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,499 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_50 SKIPPING 2016-10-29 18:26:05,499 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,499 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,499 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_50 SKIPPING 2016-10-29 18:26:05,499 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,499 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,499 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_50 SKIPPING 2016-10-29 18:26:05,500 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,500 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,517 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,517 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,517 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_45 SKIPPING 2016-10-29 18:26:05,517 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,517 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,517 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_45 SKIPPING 2016-10-29 18:26:05,518 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,518 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,518 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_45 SKIPPING 2016-10-29 18:26:05,518 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,518 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,533 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,533 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,533 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_40 SKIPPING 2016-10-29 18:26:05,533 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,533 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,533 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_40 SKIPPING 2016-10-29 18:26:05,533 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,533 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,533 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_40 SKIPPING 2016-10-29 18:26:05,533 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,533 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,545 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,546 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,546 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_34 SKIPPING 2016-10-29 18:26:05,546 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,546 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,546 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_34 SKIPPING 2016-10-29 18:26:05,546 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,546 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,546 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_34 SKIPPING 2016-10-29 18:26:05,546 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,546 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,563 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,563 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,563 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_29 SKIPPING 2016-10-29 18:26:05,563 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,563 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,563 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_29 SKIPPING 2016-10-29 18:26:05,564 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,564 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,564 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_29 SKIPPING 2016-10-29 18:26:05,564 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,564 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,576 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,577 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,577 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_24 SKIPPING 2016-10-29 18:26:05,577 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,577 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,577 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_24 SKIPPING 2016-10-29 18:26:05,577 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,577 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,577 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_24 SKIPPING 2016-10-29 18:26:05,577 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,578 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,586 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,587 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,587 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_19 SKIPPING 2016-10-29 18:26:05,587 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,587 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,587 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_19 SKIPPING 2016-10-29 18:26:05,587 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,587 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,587 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_19 SKIPPING 2016-10-29 18:26:05,588 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,588 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,594 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,594 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,594 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_14 SKIPPING 2016-10-29 18:26:05,594 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,595 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,595 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_14 SKIPPING 2016-10-29 18:26:05,595 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,595 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,595 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_14 SKIPPING 2016-10-29 18:26:05,595 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,595 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,600 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,600 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,600 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_9 SKIPPING 2016-10-29 18:26:05,600 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,600 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,600 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_9 SKIPPING 2016-10-29 18:26:05,600 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,601 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,601 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_9 SKIPPING 2016-10-29 18:26:05,601 - root - DEBUG - In directory /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1 Running command: /home/user1/.ample/maxcluster -l /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/files.list -L 4 -rmsd -d 1000 -bb -C0 2016-10-29 18:26:05,601 - root - DEBUG - Logfile is: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/maxcluster.log 2016-10-29 18:26:05,605 - root - DEBUG - subclustering files under radius: 1 2016-10-29 18:26:05,605 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,605 - root - DEBUG - Clustered fewer than 2 files using radius 1 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_4 SKIPPING 2016-10-29 18:26:05,605 - root - DEBUG - subclustering files under radius: 2 2016-10-29 18:26:05,605 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,605 - root - DEBUG - Clustered fewer than 2 files using radius 2 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_4 SKIPPING 2016-10-29 18:26:05,605 - root - DEBUG - subclustering files under radius: 3 2016-10-29 18:26:05,605 - root - DEBUG - Clustered 1 files 2016-10-29 18:26:05,605 - root - DEBUG - Clustered fewer than 2 files using radius 3 - in truncation dir /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/ensemble_workdir/truncate_1/tlevel_4 SKIPPING 2016-10-29 18:26:05,605 - root - CRITICAL - ********************************************************************** ******************** AMPLE ERROR ******************* ********************************************************************** Could not load any ensembles after running create_ensembles! ********************************************************************** More information may be found in the debug log file: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/debug.log If you believe that this is an error with AMPLE, please email: c...@stfc.ac.uk providing as much information as you can about how you ran the program. Please include the debug logfile with your email: /home/user1/Documents/projects/FmtA/Fmt_vik/ccp4i/AMPLE_9/debug.log 2016-10-29 18:26:05,606 - root - DEBUG - AMPLE EXITING AT... 2016-10-29 18:26:05,606 - root - DEBUG - File "/home/user1/Documents/destination/ccp4-6.5/bin/ample.py", line 994, in <module> main() File "/home/user1/Documents/destination/ccp4-6.5/bin/ample.py", line 899, in main ample_exit.exit(msg) File "/home/user1/Documents/destination/ccp4-6.5/share/ample/python/ample_exit.py", line 46, in exit ample_tb=traceback.extract_stack()
