Sun 23 Dec 22:22:49 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-3.2-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 22:22:59 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-3.2-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: 0.5826 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-3.2-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-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 936 target number of atoms Had to go as low as 0.70 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 3.200 Wilson plot Bfac: 45.00 2065 reflections ( 99.37 % complete ) and 0 restraints for refining 1043 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3067 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2544 (Rfree = 0.000) for 1043 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.89 3.09 Search for helices and strands: 0 residues in 0 chains, 1054 seeds are put forward Round 1: 62 peptides, 8 chains. Longest chain 11 peptides. Score 0.589 Round 2: 71 peptides, 10 chains. Longest chain 18 peptides. Score 0.590 Round 3: 76 peptides, 9 chains. Longest chain 17 peptides. Score 0.680 Round 4: 83 peptides, 9 chains. Longest chain 20 peptides. Score 0.734 Round 5: 79 peptides, 8 chains. Longest chain 18 peptides. Score 0.739 Taking the results from Round 5 Chains 8, Residues 71, Estimated correctness of the model 73.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.37 % complete ) and 1600 restraints for refining 855 atoms. 1247 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2597 (Rfree = 0.000) for 855 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 2: After refmac, R = 0.2308 (Rfree = 0.000) for 844 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 3: After refmac, R = 0.2396 (Rfree = 0.000) for 840 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2242 (Rfree = 0.000) for 837 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.2356 (Rfree = 0.000) for 831 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.98 3.19 Search for helices and strands: 0 residues in 0 chains, 857 seeds are put forward Round 1: 75 peptides, 9 chains. Longest chain 21 peptides. Score 0.671 Round 2: 76 peptides, 8 chains. Longest chain 21 peptides. Score 0.717 Round 3: 82 peptides, 8 chains. Longest chain 21 peptides. Score 0.760 Round 4: 88 peptides, 6 chains. Longest chain 24 peptides. Score 0.845 Round 5: 87 peptides, 7 chains. Longest chain 21 peptides. Score 0.817 Taking the results from Round 4 Chains 7, Residues 82, Estimated correctness of the model 89.6 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.37 % complete ) and 1574 restraints for refining 855 atoms. 1192 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2251 (Rfree = 0.000) for 855 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 7: After refmac, R = 0.2387 (Rfree = 0.000) for 844 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.1985 (Rfree = 0.000) for 842 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.2220 (Rfree = 0.000) for 840 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.1863 (Rfree = 0.000) for 834 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.90 3.10 Search for helices and strands: 0 residues in 0 chains, 849 seeds are put forward Round 1: 73 peptides, 9 chains. Longest chain 13 peptides. Score 0.653 Round 2: 81 peptides, 5 chains. Longest chain 38 peptides. Score 0.838 Round 3: 81 peptides, 9 chains. Longest chain 16 peptides. Score 0.720 Round 4: 83 peptides, 6 chains. Longest chain 29 peptides. Score 0.822 Round 5: 85 peptides, 7 chains. Longest chain 24 peptides. Score 0.806 Taking the results from Round 2 Chains 6, Residues 76, Estimated correctness of the model 88.7 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.37 % complete ) and 1471 restraints for refining 854 atoms. 1045 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2357 (Rfree = 0.000) for 854 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2127 (Rfree = 0.000) for 848 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.1981 (Rfree = 0.000) for 839 atoms. Found 5 (5 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.2096 (Rfree = 0.000) for 840 atoms. Found 3 (5 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1931 (Rfree = 0.000) for 835 atoms. Found 1 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.87 3.07 Search for helices and strands: 0 residues in 0 chains, 859 seeds are put forward Round 1: 76 peptides, 9 chains. Longest chain 12 peptides. Score 0.680 Round 2: 85 peptides, 7 chains. Longest chain 24 peptides. Score 0.806 Round 3: 83 peptides, 7 chains. Longest chain 32 peptides. Score 0.795 Round 4: 88 peptides, 7 chains. Longest chain 35 peptides. Score 0.821 Round 5: 77 peptides, 9 chains. Longest chain 14 peptides. Score 0.688 Taking the results from Round 4 Chains 8, Residues 81, Estimated correctness of the model 86.5 % 1 chains (33 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.37 % complete ) and 1388 restraints for refining 855 atoms. 923 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3157 (Rfree = 0.000) for 855 atoms. Found 5 (5 requested) and removed 10 (3 requested) atoms. Cycle 17: After refmac, R = 0.2350 (Rfree = 0.000) for 840 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2654 (Rfree = 0.000) for 835 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2065 (Rfree = 0.000) for 833 atoms. Found 4 (5 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1964 (Rfree = 0.000) for 831 atoms. Found 3 (4 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.98 3.19 Search for helices and strands: 0 residues in 0 chains, 842 seeds are put forward Round 1: 71 peptides, 8 chains. Longest chain 17 peptides. Score 0.676 Round 2: 72 peptides, 8 chains. Longest chain 14 peptides. Score 0.685 Round 3: 77 peptides, 7 chains. Longest chain 16 peptides. Score 0.758 Round 4: 83 peptides, 8 chains. Longest chain 15 peptides. Score 0.766 Round 5: 84 peptides, 9 chains. Longest chain 19 peptides. Score 0.741 Taking the results from Round 4 Chains 8, Residues 75, Estimated correctness of the model 77.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.37 % complete ) and 1839 restraints for refining 855 atoms. 1547 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2179 (Rfree = 0.000) for 855 atoms. Found 4 (4 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.1926 (Rfree = 0.000) for 852 atoms. Found 4 (4 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.1841 (Rfree = 0.000) for 850 atoms. Found 3 (4 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.1816 (Rfree = 0.000) for 850 atoms. Found 2 (4 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1755 (Rfree = 0.000) for 849 atoms. Found 2 (4 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.96 3.16 Search for helices and strands: 0 residues in 0 chains, 865 seeds are put forward Round 1: 72 peptides, 7 chains. Longest chain 15 peptides. Score 0.722 Round 2: 85 peptides, 8 chains. Longest chain 22 peptides. Score 0.778 Round 3: 91 peptides, 8 chains. Longest chain 20 peptides. Score 0.812 Round 4: 93 peptides, 9 chains. Longest chain 20 peptides. Score 0.796 Round 5: 85 peptides, 9 chains. Longest chain 27 peptides. Score 0.748 Taking the results from Round 3 Chains 9, Residues 83, Estimated correctness of the model 85.2 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.37 % complete ) and 1566 restraints for refining 855 atoms. 1179 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2216 (Rfree = 0.000) for 855 atoms. Found 2 (4 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.2464 (Rfree = 0.000) for 852 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.1729 (Rfree = 0.000) for 850 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.1754 (Rfree = 0.000) for 849 atoms. Found 3 (3 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1856 (Rfree = 0.000) for 848 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.92 3.12 Search for helices and strands: 0 residues in 0 chains, 861 seeds are put forward Round 1: 81 peptides, 9 chains. Longest chain 15 peptides. Score 0.720 Round 2: 82 peptides, 8 chains. Longest chain 24 peptides. Score 0.760 Round 3: 84 peptides, 8 chains. Longest chain 25 peptides. Score 0.772 Round 4: 81 peptides, 10 chains. Longest chain 15 peptides. Score 0.684 Round 5: 77 peptides, 8 chains. Longest chain 15 peptides. Score 0.724 Taking the results from Round 3 Chains 8, Residues 76, Estimated correctness of the model 78.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.37 % complete ) and 1805 restraints for refining 855 atoms. 1509 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2191 (Rfree = 0.000) for 855 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. Cycle 32: After refmac, R = 0.1915 (Rfree = 0.000) for 853 atoms. Found 2 (3 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.1779 (Rfree = 0.000) for 850 atoms. Found 3 (3 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.1799 (Rfree = 0.000) for 847 atoms. Found 3 (3 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.1887 (Rfree = 0.000) for 846 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.94 3.14 Search for helices and strands: 0 residues in 0 chains, 856 seeds are put forward Round 1: 73 peptides, 10 chains. Longest chain 14 peptides. Score 0.611 Round 2: 76 peptides, 10 chains. Longest chain 14 peptides. Score 0.640 Round 3: 70 peptides, 6 chains. Longest chain 22 peptides. Score 0.743 Round 4: 72 peptides, 8 chains. Longest chain 20 peptides. Score 0.685 Round 5: 68 peptides, 8 chains. Longest chain 22 peptides. Score 0.649 Taking the results from Round 3 Chains 6, Residues 64, Estimated correctness of the model 73.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.37 % complete ) and 1861 restraints for refining 855 atoms. 1611 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2075 (Rfree = 0.000) for 855 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.1822 (Rfree = 0.000) for 855 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.1699 (Rfree = 0.000) for 855 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.1620 (Rfree = 0.000) for 855 atoms. Found 2 (3 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.1583 (Rfree = 0.000) for 854 atoms. Found 1 (3 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.92 3.12 Search for helices and strands: 0 residues in 0 chains, 865 seeds are put forward Round 1: 72 peptides, 10 chains. Longest chain 13 peptides. Score 0.601 Round 2: 70 peptides, 7 chains. Longest chain 14 peptides. Score 0.707 Round 3: 71 peptides, 7 chains. Longest chain 25 peptides. Score 0.714 Round 4: 68 peptides, 7 chains. Longest chain 22 peptides. Score 0.690 Round 5: 77 peptides, 6 chains. Longest chain 37 peptides. Score 0.789 Taking the results from Round 5 Chains 6, Residues 71, Estimated correctness of the model 81.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2065 reflections ( 99.37 % complete ) and 1814 restraints for refining 855 atoms. 1536 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2003 (Rfree = 0.000) for 855 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. Cycle 42: After refmac, R = 0.1894 (Rfree = 0.000) for 854 atoms. Found 2 (3 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.1760 (Rfree = 0.000) for 852 atoms. Found 0 (3 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1738 (Rfree = 0.000) for 849 atoms. Found 2 (3 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1622 (Rfree = 0.000) for 848 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.95 3.15 Search for helices and strands: 0 residues in 0 chains, 867 seeds are put forward Round 1: 63 peptides, 8 chains. Longest chain 14 peptides. Score 0.599 Round 2: 62 peptides, 8 chains. Longest chain 16 peptides. Score 0.589 Round 3: 71 peptides, 9 chains. Longest chain 14 peptides. Score 0.635 Round 4: 60 peptides, 7 chains. Longest chain 16 peptides. Score 0.615 Round 5: 58 peptides, 8 chains. Longest chain 16 peptides. Score 0.544 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 62, Estimated correctness of the model 50.2 % 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. 2065 reflections ( 99.37 % complete ) and 1878 restraints for refining 855 atoms. 1639 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1989 (Rfree = 0.000) for 855 atoms. Found 0 (3 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1787 (Rfree = 0.000) for 850 atoms. Found 0 (3 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1808 (Rfree = 0.000) for 847 atoms. Found 0 (3 requested) and removed 1 (3 requested) atoms. Cycle 49: After refmac, R = 0.1717 (Rfree = 0.000) for 846 atoms. TimeTaking 23.82