null Mon 24 Dec 00:25:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vpz-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.6-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.6-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:26:01 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.6-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 85 and 0 Target number of residues in the AU: 85 Target solvent content: 0.6639 Checking the provided sequence file Detected sequence length: 73 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 146 Adjusted target solvent content: 0.42 Input MTZ file: 1vpz-3.6-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 20 Cell parameters: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1168 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 24.580 3.601 Wilson plot Bfac: 86.64 1697 reflections ( 97.87 % complete ) and 0 restraints for refining 1296 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3622 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2839 (Rfree = 0.000) for 1296 atoms. Found 2 (8 requested) and removed 119 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 4.08 Search for helices and strands: 0 residues in 0 chains, 1192 seeds are put forward NCS extension: 0 residues added, 1192 seeds are put forward Round 1: 22 peptides, 5 chains. Longest chain 6 peptides. Score 0.203 Round 2: 31 peptides, 7 chains. Longest chain 6 peptides. Score 0.214 Round 3: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.242 Round 4: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.273 Round 5: 31 peptides, 6 chains. Longest chain 6 peptides. Score 0.278 Taking the results from Round 5 Chains 6, Residues 25, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2767 restraints for refining 1057 atoms. 2673 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3258 (Rfree = 0.000) for 1057 atoms. Found 4 (6 requested) and removed 54 (3 requested) atoms. Cycle 2: After refmac, R = 0.3158 (Rfree = 0.000) for 1005 atoms. Found 3 (6 requested) and removed 10 (3 requested) atoms. Cycle 3: After refmac, R = 0.3080 (Rfree = 0.000) for 995 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.3057 (Rfree = 0.000) for 989 atoms. Found 1 (6 requested) and removed 8 (3 requested) atoms. Cycle 5: After refmac, R = 0.3053 (Rfree = 0.000) for 982 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.91 Search for helices and strands: 0 residues in 0 chains, 991 seeds are put forward NCS extension: 0 residues added, 991 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.183 Round 2: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.242 Round 3: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.280 Round 4: 46 peptides, 9 chains. Longest chain 7 peptides. Score 0.307 Round 5: 46 peptides, 8 chains. Longest chain 8 peptides. Score 0.362 Taking the results from Round 5 Chains 8, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2301 restraints for refining 949 atoms. 2157 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3315 (Rfree = 0.000) for 949 atoms. Found 3 (6 requested) and removed 35 (3 requested) atoms. Cycle 7: After refmac, R = 0.3158 (Rfree = 0.000) for 916 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 8: After refmac, R = 0.3072 (Rfree = 0.000) for 912 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.3026 (Rfree = 0.000) for 905 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2970 (Rfree = 0.000) for 904 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.02 2.25 Search for helices and strands: 0 residues in 0 chains, 905 seeds are put forward NCS extension: 0 residues added, 905 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 8 peptides. Score 0.238 Round 2: 48 peptides, 10 chains. Longest chain 6 peptides. Score 0.278 Round 3: 52 peptides, 10 chains. Longest chain 7 peptides. Score 0.330 Round 4: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.330 Round 5: 53 peptides, 10 chains. Longest chain 11 peptides. Score 0.342 Taking the results from Round 5 Chains 10, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2234 restraints for refining 934 atoms. 2072 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3331 (Rfree = 0.000) for 934 atoms. Found 5 (5 requested) and removed 35 (2 requested) atoms. Cycle 12: After refmac, R = 0.3159 (Rfree = 0.000) for 902 atoms. Found 4 (5 requested) and removed 7 (2 requested) atoms. Cycle 13: After refmac, R = 0.3026 (Rfree = 0.000) for 898 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.2956 (Rfree = 0.000) for 896 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.2892 (Rfree = 0.000) for 895 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.46 2.74 Search for helices and strands: 0 residues in 0 chains, 906 seeds are put forward NCS extension: 0 residues added, 906 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.195 Round 2: 52 peptides, 11 chains. Longest chain 6 peptides. Score 0.276 Round 3: 52 peptides, 11 chains. Longest chain 8 peptides. Score 0.276 Round 4: 45 peptides, 8 chains. Longest chain 10 peptides. Score 0.349 Round 5: 39 peptides, 8 chains. Longest chain 8 peptides. Score 0.270 Taking the results from Round 4 Chains 8, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2152 restraints for refining 929 atoms. 2012 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3174 (Rfree = 0.000) for 929 atoms. Found 3 (5 requested) and removed 16 (2 requested) atoms. Cycle 17: After refmac, R = 0.3038 (Rfree = 0.000) for 916 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 18: After refmac, R = 0.2913 (Rfree = 0.000) for 912 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. Cycle 19: After refmac, R = 0.2864 (Rfree = 0.000) for 905 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.2824 (Rfree = 0.000) for 901 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.82 Search for helices and strands: 0 residues in 0 chains, 909 seeds are put forward NCS extension: 0 residues added, 909 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 5 peptides. Score 0.227 Round 2: 41 peptides, 8 chains. Longest chain 8 peptides. Score 0.297 Round 3: 42 peptides, 9 chains. Longest chain 8 peptides. Score 0.253 Round 4: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.265 Round 5: 46 peptides, 9 chains. Longest chain 7 peptides. Score 0.307 Taking the results from Round 5 Chains 9, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2139 restraints for refining 912 atoms. 2000 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2951 (Rfree = 0.000) for 912 atoms. Found 5 (5 requested) and removed 39 (2 requested) atoms. Cycle 22: After refmac, R = 0.2747 (Rfree = 0.000) for 877 atoms. Found 3 (5 requested) and removed 12 (2 requested) atoms. Cycle 23: After refmac, R = 0.2684 (Rfree = 0.000) for 868 atoms. Found 1 (5 requested) and removed 11 (2 requested) atoms. Cycle 24: After refmac, R = 0.2702 (Rfree = 0.000) for 858 atoms. Found 3 (5 requested) and removed 19 (2 requested) atoms. Cycle 25: After refmac, R = 0.2614 (Rfree = 0.000) for 841 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.75 Search for helices and strands: 0 residues in 0 chains, 865 seeds are put forward NCS extension: 0 residues added, 865 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 6 peptides. Score 0.239 Round 2: 44 peptides, 9 chains. Longest chain 8 peptides. Score 0.280 Round 3: 48 peptides, 10 chains. Longest chain 6 peptides. Score 0.278 Round 4: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.304 Round 5: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.249 Taking the results from Round 4 Chains 10, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2008 restraints for refining 883 atoms. 1858 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2885 (Rfree = 0.000) for 883 atoms. Found 3 (5 requested) and removed 28 (2 requested) atoms. Cycle 27: After refmac, R = 0.2772 (Rfree = 0.000) for 857 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 28: After refmac, R = 0.2775 (Rfree = 0.000) for 853 atoms. Found 4 (5 requested) and removed 11 (2 requested) atoms. Cycle 29: After refmac, R = 0.2729 (Rfree = 0.000) for 845 atoms. Found 4 (5 requested) and removed 9 (2 requested) atoms. Cycle 30: After refmac, R = 0.2682 (Rfree = 0.000) for 839 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.87 Search for helices and strands: 0 residues in 0 chains, 853 seeds are put forward NCS extension: 0 residues added, 853 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.183 Round 2: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.227 Round 3: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.278 Round 4: 36 peptides, 7 chains. Longest chain 7 peptides. Score 0.287 Round 5: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.315 Taking the results from Round 5 Chains 7, Residues 31, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2019 restraints for refining 873 atoms. 1902 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2824 (Rfree = 0.000) for 873 atoms. Found 2 (5 requested) and removed 46 (2 requested) atoms. Cycle 32: After refmac, R = 0.2789 (Rfree = 0.000) for 828 atoms. Found 1 (5 requested) and removed 9 (2 requested) atoms. Cycle 33: After refmac, R = 0.2764 (Rfree = 0.000) for 820 atoms. Found 0 (5 requested) and removed 8 (2 requested) atoms. Cycle 34: After refmac, R = 0.2750 (Rfree = 0.000) for 812 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2729 (Rfree = 0.000) for 809 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.86 Search for helices and strands: 0 residues in 0 chains, 809 seeds are put forward NCS extension: 0 residues added, 809 seeds are put forward Round 1: 23 peptides, 5 chains. Longest chain 7 peptides. Score 0.220 Round 2: 30 peptides, 6 chains. Longest chain 6 peptides. Score 0.263 Round 3: 32 peptides, 7 chains. Longest chain 5 peptides. Score 0.229 Round 4: 32 peptides, 6 chains. Longest chain 7 peptides. Score 0.292 Round 5: 38 peptides, 7 chains. Longest chain 8 peptides. Score 0.315 Taking the results from Round 5 Chains 7, Residues 31, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2008 restraints for refining 871 atoms. 1891 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2876 (Rfree = 0.000) for 871 atoms. Found 3 (5 requested) and removed 29 (2 requested) atoms. Cycle 37: After refmac, R = 0.2732 (Rfree = 0.000) for 844 atoms. Found 4 (5 requested) and removed 16 (2 requested) atoms. Cycle 38: After refmac, R = 0.2719 (Rfree = 0.000) for 829 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.2693 (Rfree = 0.000) for 830 atoms. Found 2 (5 requested) and removed 11 (2 requested) atoms. Cycle 40: After refmac, R = 0.2671 (Rfree = 0.000) for 819 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.92 Search for helices and strands: 0 residues in 0 chains, 847 seeds are put forward NCS extension: 0 residues added, 847 seeds are put forward Round 1: 26 peptides, 6 chains. Longest chain 5 peptides. Score 0.200 Round 2: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.224 Round 3: 47 peptides, 10 chains. Longest chain 8 peptides. Score 0.265 Round 4: 43 peptides, 9 chains. Longest chain 7 peptides. Score 0.267 Round 5: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.280 Taking the results from Round 5 Chains 9, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2032 restraints for refining 869 atoms. 1901 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3045 (Rfree = 0.000) for 869 atoms. Found 3 (5 requested) and removed 40 (2 requested) atoms. Cycle 42: After refmac, R = 0.3024 (Rfree = 0.000) for 832 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 43: After refmac, R = 0.2941 (Rfree = 0.000) for 831 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.2876 (Rfree = 0.000) for 830 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.2819 (Rfree = 0.000) for 827 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.95 4.40 Search for helices and strands: 0 residues in 0 chains, 839 seeds are put forward NCS extension: 0 residues added, 839 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 7 peptides. Score 0.242 Round 2: 39 peptides, 7 chains. Longest chain 11 peptides. Score 0.328 Round 3: 37 peptides, 7 chains. Longest chain 10 peptides. Score 0.301 Round 4: 31 peptides, 5 chains. Longest chain 10 peptides. Score 0.340 Round 5: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.278 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 26, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vpz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1697 reflections ( 97.87 % complete ) and 1945 restraints for refining 842 atoms. 1846 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3130 (Rfree = 0.000) for 842 atoms. Found 0 (5 requested) and removed 0 (2 requested) atoms. Cycle 47: After refmac, R = 0.2963 (Rfree = 0.000) for 842 atoms. Found 0 (5 requested) and removed 0 (2 requested) atoms. Cycle 48: After refmac, R = 0.2853 (Rfree = 0.000) for 842 atoms. Found 0 (5 requested) and removed 0 (2 requested) atoms. Cycle 49: After refmac, R = 0.2823 (Rfree = 0.000) for 842 atoms. Found 0 (5 requested) and removed 0 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:42:08 GMT 2018 Job finished. TimeTaking 16.17 Used memory is bytes: 19499968