null Sun 23 Dec 22:22:42 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vpz-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:43 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/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-hancs/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 88 and 0 Target number of residues in the AU: 88 Target solvent content: 0.6520 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-3.4-parrot-hancs.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-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1168 target number of atoms Had to go as low as 0.50 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 3.400 Wilson plot Bfac: 78.62 2008 reflections ( 98.14 % complete ) and 0 restraints for refining 1289 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3503 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3759 (Rfree = 0.000) for 1289 atoms. Found 6 (9 requested) and removed 93 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.88 4.32 Search for helices and strands: 0 residues in 0 chains, 1207 seeds are put forward NCS extension: 0 residues added, 1207 seeds are put forward Round 1: 24 peptides, 5 chains. Longest chain 6 peptides. Score 0.236 Round 2: 34 peptides, 7 chains. Longest chain 8 peptides. Score 0.259 Round 3: 41 peptides, 9 chains. Longest chain 8 peptides. Score 0.239 Round 4: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.291 Round 5: 47 peptides, 10 chains. Longest chain 8 peptides. Score 0.265 Taking the results from Round 4 Chains 10, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 2077 restraints for refining 909 atoms. 1931 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3428 (Rfree = 0.000) for 909 atoms. Found 2 (6 requested) and removed 50 (3 requested) atoms. Cycle 2: After refmac, R = 0.3465 (Rfree = 0.000) for 850 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 3: After refmac, R = 0.3139 (Rfree = 0.000) for 822 atoms. Found 2 (6 requested) and removed 12 (3 requested) atoms. Cycle 4: After refmac, R = 0.3192 (Rfree = 0.000) for 811 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.3271 (Rfree = 0.000) for 813 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.36 2.63 Search for helices and strands: 0 residues in 0 chains, 840 seeds are put forward NCS extension: 0 residues added, 840 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 7 peptides. Score 0.253 Round 2: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.302 Round 3: 58 peptides, 10 chains. Longest chain 13 peptides. Score 0.402 Round 4: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.433 Round 5: 69 peptides, 12 chains. Longest chain 12 peptides. Score 0.430 Taking the results from Round 4 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1673 restraints for refining 794 atoms. 1468 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3509 (Rfree = 0.000) for 794 atoms. Found 5 (5 requested) and removed 35 (2 requested) atoms. Cycle 7: After refmac, R = 0.3576 (Rfree = 0.000) for 755 atoms. Found 5 (5 requested) and removed 29 (2 requested) atoms. Cycle 8: After refmac, R = 0.3669 (Rfree = 0.000) for 727 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 9: After refmac, R = 0.3427 (Rfree = 0.000) for 713 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.3450 (Rfree = 0.000) for 711 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.02 4.48 Search for helices and strands: 0 residues in 0 chains, 752 seeds are put forward NCS extension: 0 residues added, 752 seeds are put forward Round 1: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.320 Round 2: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.448 Round 3: 62 peptides, 10 chains. Longest chain 8 peptides. Score 0.448 Round 4: 60 peptides, 9 chains. Longest chain 11 peptides. Score 0.474 Round 5: 64 peptides, 10 chains. Longest chain 11 peptides. Score 0.470 Taking the results from Round 4 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1624 restraints for refining 787 atoms. 1429 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3384 (Rfree = 0.000) for 787 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. Cycle 12: After refmac, R = 0.3055 (Rfree = 0.000) for 775 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 13: After refmac, R = 0.2962 (Rfree = 0.000) for 768 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.3328 (Rfree = 0.000) for 768 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.2963 (Rfree = 0.000) for 763 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 3.32 Search for helices and strands: 0 residues in 0 chains, 787 seeds are put forward NCS extension: 0 residues added, 787 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.274 Round 2: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.380 Round 3: 66 peptides, 11 chains. Longest chain 8 peptides. Score 0.444 Round 4: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.481 Round 5: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.452 Taking the results from Round 4 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1838 restraints for refining 850 atoms. 1591 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3146 (Rfree = 0.000) for 850 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 17: After refmac, R = 0.3011 (Rfree = 0.000) for 828 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.2920 (Rfree = 0.000) for 818 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2819 (Rfree = 0.000) for 818 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.3105 (Rfree = 0.000) for 815 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.85 Search for helices and strands: 0 residues in 0 chains, 850 seeds are put forward NCS extension: 0 residues added, 850 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 11 peptides. Score 0.352 Round 2: 62 peptides, 11 chains. Longest chain 12 peptides. Score 0.399 Round 3: 58 peptides, 10 chains. Longest chain 11 peptides. Score 0.402 Round 4: 69 peptides, 11 chains. Longest chain 12 peptides. Score 0.477 Round 5: 62 peptides, 9 chains. Longest chain 15 peptides. Score 0.495 Taking the results from Round 5 Chains 9, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 2025 restraints for refining 882 atoms. 1822 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3043 (Rfree = 0.000) for 882 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 22: After refmac, R = 0.2917 (Rfree = 0.000) for 867 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.2815 (Rfree = 0.000) for 864 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.3429 (Rfree = 0.000) for 858 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 25: After refmac, R = 0.2737 (Rfree = 0.000) for 851 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.72 Search for helices and strands: 0 residues in 0 chains, 872 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 896 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.278 Round 2: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.418 Round 3: 60 peptides, 11 chains. Longest chain 11 peptides. Score 0.376 Round 4: 66 peptides, 12 chains. Longest chain 11 peptides. Score 0.396 Round 5: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.480 Taking the results from Round 5 Chains 10, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1924 restraints for refining 897 atoms. 1714 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2890 (Rfree = 0.000) for 897 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. Cycle 27: After refmac, R = 0.2906 (Rfree = 0.000) for 887 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.2681 (Rfree = 0.000) for 884 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2642 (Rfree = 0.000) for 882 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 30: After refmac, R = 0.2567 (Rfree = 0.000) for 880 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.81 Search for helices and strands: 0 residues in 0 chains, 898 seeds are put forward NCS extension: 0 residues added, 898 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 6 peptides. Score 0.263 Round 2: 54 peptides, 10 chains. Longest chain 10 peptides. Score 0.355 Round 3: 56 peptides, 8 chains. Longest chain 14 peptides. Score 0.479 Round 4: 55 peptides, 9 chains. Longest chain 14 peptides. Score 0.418 Round 5: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.379 Taking the results from Round 3 Chains 8, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1954 restraints for refining 874 atoms. 1770 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2954 (Rfree = 0.000) for 874 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.3186 (Rfree = 0.000) for 866 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.3064 (Rfree = 0.000) for 865 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 34: After refmac, R = 0.2631 (Rfree = 0.000) for 856 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2914 (Rfree = 0.000) for 856 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.77 Search for helices and strands: 0 residues in 0 chains, 880 seeds are put forward NCS extension: 0 residues added, 880 seeds are put forward Round 1: 44 peptides, 8 chains. Longest chain 8 peptides. Score 0.337 Round 2: 51 peptides, 9 chains. Longest chain 10 peptides. Score 0.370 Round 3: 50 peptides, 8 chains. Longest chain 10 peptides. Score 0.411 Round 4: 60 peptides, 11 chains. Longest chain 11 peptides. Score 0.376 Round 5: 46 peptides, 6 chains. Longest chain 13 peptides. Score 0.468 Taking the results from Round 5 Chains 6, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1848 restraints for refining 840 atoms. 1694 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2813 (Rfree = 0.000) for 840 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.2519 (Rfree = 0.000) for 835 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.2374 (Rfree = 0.000) for 834 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2491 (Rfree = 0.000) for 831 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.2723 (Rfree = 0.000) for 828 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.80 3.12 Search for helices and strands: 0 residues in 0 chains, 851 seeds are put forward NCS extension: 0 residues added, 851 seeds are put forward Round 1: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.315 Round 2: 48 peptides, 7 chains. Longest chain 12 peptides. Score 0.439 Round 3: 44 peptides, 7 chains. Longest chain 13 peptides. Score 0.392 Round 4: 43 peptides, 6 chains. Longest chain 11 peptides. Score 0.434 Round 5: 50 peptides, 7 chains. Longest chain 13 peptides. Score 0.462 Taking the results from Round 5 Chains 7, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1801 restraints for refining 831 atoms. 1636 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2840 (Rfree = 0.000) for 831 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 42: After refmac, R = 0.2882 (Rfree = 0.000) for 824 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 43: After refmac, R = 0.3467 (Rfree = 0.000) for 822 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.2880 (Rfree = 0.000) for 816 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.3460 (Rfree = 0.000) for 816 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.86 Search for helices and strands: 0 residues in 0 chains, 833 seeds are put forward NCS extension: 0 residues added, 833 seeds are put forward Round 1: 40 peptides, 7 chains. Longest chain 8 peptides. Score 0.341 Round 2: 50 peptides, 9 chains. Longest chain 11 peptides. Score 0.358 Round 3: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.362 Round 4: 47 peptides, 7 chains. Longest chain 13 peptides. Score 0.428 Round 5: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.320 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 40, 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. 2008 reflections ( 98.14 % complete ) and 1820 restraints for refining 846 atoms. 1667 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2909 (Rfree = 0.000) for 846 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2745 (Rfree = 0.000) for 840 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2481 (Rfree = 0.000) for 837 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2496 (Rfree = 0.000) for 834 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:17:36 GMT 2018 Job finished. TimeTaking 54.91 Used memory is bytes: 10495992