null Sun 23 Dec 22:22:44 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 2b8m-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-3.8-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/2b8m-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-3.8-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 22:22:52 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/2b8m-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-3.8-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 79 and 0 Target number of residues in the AU: 79 Target solvent content: 0.6253 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 117 Adjusted target solvent content: 0.45 Input MTZ file: 2b8m-3.8-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: 152 Cell parameters: 50.280 50.280 78.170 90.000 90.000 120.000 Input sequence file: 2b8m-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 936 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.086 3.803 Wilson plot Bfac: 62.49 1255 reflections ( 99.13 % complete ) and 0 restraints for refining 1036 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3227 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2275 (Rfree = 0.000) for 1036 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 1047 seeds are put forward Round 1: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.423 Round 2: 76 peptides, 9 chains. Longest chain 17 peptides. Score 0.680 Round 3: 73 peptides, 6 chains. Longest chain 22 peptides. Score 0.764 Round 4: 75 peptides, 8 chains. Longest chain 15 peptides. Score 0.709 Round 5: 79 peptides, 7 chains. Longest chain 22 peptides. Score 0.771 Taking the results from Round 5 Chains 7, Residues 72, Estimated correctness of the model 63.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 99.13 % complete ) and 1774 restraints for refining 846 atoms. 1493 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2288 (Rfree = 0.000) for 846 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 2: After refmac, R = 0.2239 (Rfree = 0.000) for 821 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 3: After refmac, R = 0.2199 (Rfree = 0.000) for 814 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 4: After refmac, R = 0.2038 (Rfree = 0.000) for 809 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 5: After refmac, R = 0.1966 (Rfree = 0.000) for 806 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 847 seeds are put forward Round 1: 58 peptides, 10 chains. Longest chain 12 peptides. Score 0.436 Round 2: 75 peptides, 10 chains. Longest chain 23 peptides. Score 0.630 Round 3: 85 peptides, 10 chains. Longest chain 29 peptides. Score 0.715 Round 4: 82 peptides, 9 chains. Longest chain 14 peptides. Score 0.727 Round 5: 81 peptides, 10 chains. Longest chain 18 peptides. Score 0.684 Taking the results from Round 4 Chains 9, Residues 73, Estimated correctness of the model 49.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 99.13 % complete ) and 1749 restraints for refining 818 atoms. 1466 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2571 (Rfree = 0.000) for 818 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 7: After refmac, R = 0.2356 (Rfree = 0.000) for 809 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.2189 (Rfree = 0.000) for 805 atoms. Found 0 (3 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.2135 (Rfree = 0.000) for 797 atoms. Found 1 (3 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.2078 (Rfree = 0.000) for 791 atoms. Found 1 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.60 Search for helices and strands: 0 residues in 0 chains, 812 seeds are put forward Round 1: 61 peptides, 10 chains. Longest chain 13 peptides. Score 0.475 Round 2: 69 peptides, 9 chains. Longest chain 17 peptides. Score 0.615 Round 3: 71 peptides, 10 chains. Longest chain 13 peptides. Score 0.590 Round 4: 67 peptides, 8 chains. Longest chain 13 peptides. Score 0.639 Round 5: 72 peptides, 11 chains. Longest chain 13 peptides. Score 0.554 Taking the results from Round 4 Chains 8, Residues 59, Estimated correctness of the model 16.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 99.13 % complete ) and 1973 restraints for refining 845 atoms. 1745 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2372 (Rfree = 0.000) for 845 atoms. Found 1 (3 requested) and removed 5 (2 requested) atoms. Cycle 12: After refmac, R = 0.2096 (Rfree = 0.000) for 835 atoms. Found 2 (3 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.2000 (Rfree = 0.000) for 832 atoms. Found 1 (3 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2149 (Rfree = 0.000) for 830 atoms. Found 2 (3 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.2020 (Rfree = 0.000) for 825 atoms. Found 1 (3 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.66 Search for helices and strands: 0 residues in 0 chains, 841 seeds are put forward Round 1: 60 peptides, 11 chains. Longest chain 11 peptides. Score 0.406 Round 2: 68 peptides, 11 chains. Longest chain 16 peptides. Score 0.508 Round 3: 63 peptides, 9 chains. Longest chain 12 peptides. Score 0.551 Round 4: 78 peptides, 10 chains. Longest chain 13 peptides. Score 0.658 Round 5: 80 peptides, 10 chains. Longest chain 23 peptides. Score 0.675 Taking the results from Round 5 Chains 10, Residues 70, Estimated correctness of the model 30.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 99.13 % complete ) and 1868 restraints for refining 846 atoms. 1598 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2186 (Rfree = 0.000) for 846 atoms. Found 1 (3 requested) and removed 4 (2 requested) atoms. Cycle 17: After refmac, R = 0.2186 (Rfree = 0.000) for 836 atoms. Found 3 (3 requested) and removed 4 (2 requested) atoms. Cycle 18: After refmac, R = 0.2156 (Rfree = 0.000) for 834 atoms. Found 0 (3 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.2149 (Rfree = 0.000) for 831 atoms. Found 0 (3 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.2062 (Rfree = 0.000) for 828 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 849 seeds are put forward Round 1: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.410 Round 2: 63 peptides, 10 chains. Longest chain 11 peptides. Score 0.500 Round 3: 69 peptides, 10 chains. Longest chain 16 peptides. Score 0.569 Round 4: 66 peptides, 9 chains. Longest chain 15 peptides. Score 0.584 Round 5: 66 peptides, 10 chains. Longest chain 13 peptides. Score 0.535 Taking the results from Round 4 Chains 9, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 99.13 % complete ) and 1995 restraints for refining 846 atoms. 1776 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2200 (Rfree = 0.000) for 846 atoms. Found 3 (3 requested) and removed 3 (2 requested) atoms. Cycle 22: After refmac, R = 0.2066 (Rfree = 0.000) for 846 atoms. Found 1 (3 requested) and removed 3 (2 requested) atoms. Cycle 23: After refmac, R = 0.1972 (Rfree = 0.000) for 843 atoms. Found 1 (3 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.1914 (Rfree = 0.000) for 841 atoms. Found 0 (3 requested) and removed 3 (2 requested) atoms. Cycle 25: After refmac, R = 0.1889 (Rfree = 0.000) for 838 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 850 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 11 peptides. Score 0.393 Round 2: 68 peptides, 11 chains. Longest chain 13 peptides. Score 0.508 Round 3: 63 peptides, 8 chains. Longest chain 17 peptides. Score 0.599 Round 4: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.469 Round 5: 65 peptides, 7 chains. Longest chain 21 peptides. Score 0.664 Taking the results from Round 5 Chains 7, Residues 58, Estimated correctness of the model 26.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 99.13 % complete ) and 2007 restraints for refining 846 atoms. 1782 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1976 (Rfree = 0.000) for 846 atoms. Found 3 (3 requested) and removed 8 (2 requested) atoms. Cycle 27: After refmac, R = 0.1822 (Rfree = 0.000) for 834 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Cycle 28: After refmac, R = 0.1752 (Rfree = 0.000) for 829 atoms. Found 1 (3 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.1661 (Rfree = 0.000) for 826 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.1674 (Rfree = 0.000) for 823 atoms. Found 1 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 851 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.297 Round 2: 61 peptides, 9 chains. Longest chain 11 peptides. Score 0.528 Round 3: 63 peptides, 11 chains. Longest chain 11 peptides. Score 0.446 Round 4: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.450 Round 5: 50 peptides, 6 chains. Longest chain 14 peptides. Score 0.556 Taking the results from Round 5 Chains 6, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 99.13 % complete ) and 2072 restraints for refining 846 atoms. 1902 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2083 (Rfree = 0.000) for 846 atoms. Found 0 (3 requested) and removed 3 (2 requested) atoms. Cycle 32: After refmac, R = 0.1906 (Rfree = 0.000) for 835 atoms. Found 1 (3 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.1755 (Rfree = 0.000) for 832 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.2105 (Rfree = 0.000) for 828 atoms. Found 2 (3 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.1690 (Rfree = 0.000) for 827 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 853 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.290 Round 2: 61 peptides, 10 chains. Longest chain 11 peptides. Score 0.475 Round 3: 64 peptides, 9 chains. Longest chain 12 peptides. Score 0.562 Round 4: 70 peptides, 10 chains. Longest chain 14 peptides. Score 0.580 Round 5: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.558 Taking the results from Round 4 Chains 10, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 99.13 % complete ) and 1955 restraints for refining 846 atoms. 1725 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2305 (Rfree = 0.000) for 846 atoms. Found 3 (3 requested) and removed 4 (2 requested) atoms. Cycle 37: After refmac, R = 0.1996 (Rfree = 0.000) for 842 atoms. Found 0 (3 requested) and removed 6 (2 requested) atoms. Cycle 38: After refmac, R = 0.1852 (Rfree = 0.000) for 836 atoms. Found 1 (3 requested) and removed 4 (2 requested) atoms. Cycle 39: After refmac, R = 0.1872 (Rfree = 0.000) for 832 atoms. Found 0 (3 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.1788 (Rfree = 0.000) for 828 atoms. Found 1 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 853 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.279 Round 2: 54 peptides, 10 chains. Longest chain 12 peptides. Score 0.382 Round 3: 54 peptides, 9 chains. Longest chain 12 peptides. Score 0.440 Round 4: 56 peptides, 7 chains. Longest chain 15 peptides. Score 0.573 Round 5: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.450 Taking the results from Round 4 Chains 7, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 99.13 % complete ) and 1954 restraints for refining 846 atoms. 1765 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1969 (Rfree = 0.000) for 846 atoms. Found 3 (3 requested) and removed 3 (2 requested) atoms. Cycle 42: After refmac, R = 0.1741 (Rfree = 0.000) for 845 atoms. Found 1 (3 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.1640 (Rfree = 0.000) for 841 atoms. Found 2 (3 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.1577 (Rfree = 0.000) for 839 atoms. Found 1 (3 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.1530 (Rfree = 0.000) for 838 atoms. Found 1 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.61 Search for helices and strands: 0 residues in 0 chains, 854 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 7 peptides. Score 0.219 Round 2: 49 peptides, 9 chains. Longest chain 10 peptides. Score 0.371 Round 3: 51 peptides, 8 chains. Longest chain 12 peptides. Score 0.458 Round 4: 56 peptides, 10 chains. Longest chain 7 peptides. Score 0.410 Round 5: 58 peptides, 8 chains. Longest chain 12 peptides. Score 0.544 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 50, 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 2b8m-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1255 reflections ( 99.13 % complete ) and 2015 restraints for refining 846 atoms. 1823 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1818 (Rfree = 0.000) for 846 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1658 (Rfree = 0.000) for 841 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1632 (Rfree = 0.000) for 837 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1614 (Rfree = 0.000) for 833 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:23 GMT 2018 Job finished. TimeTaking 22.65 Used memory is bytes: 10556592