null Sun 23 Dec 22:23:13 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 2okf-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okf-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okf-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-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/2okf-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-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 22:23:21 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/2okf-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-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 193 and 0 Target number of residues in the AU: 193 Target solvent content: 0.6554 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 280 Adjusted target solvent content: 0.50 Input MTZ file: 2okf-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: 144 Cell parameters: 59.870 59.870 73.240 90.000 90.000 120.000 Input sequence file: 2okf-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2240 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 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: 27.710 3.804 Wilson plot Bfac: 81.05 2872 reflections ( 99.45 % complete ) and 0 restraints for refining 2472 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3425 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3396 (Rfree = 0.000) for 2472 atoms. Found 9 (13 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.60 Search for helices and strands: 0 residues in 0 chains, 2496 seeds are put forward NCS extension: 0 residues added, 2496 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.265 Round 2: 125 peptides, 24 chains. Longest chain 9 peptides. Score 0.341 Round 3: 129 peptides, 22 chains. Longest chain 16 peptides. Score 0.408 Round 4: 139 peptides, 23 chains. Longest chain 12 peptides. Score 0.437 Round 5: 139 peptides, 21 chains. Longest chain 13 peptides. Score 0.480 Taking the results from Round 5 Chains 21, Residues 118, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4569 restraints for refining 2025 atoms. 4096 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2514 (Rfree = 0.000) for 2025 atoms. Found 5 (11 requested) and removed 27 (5 requested) atoms. Cycle 2: After refmac, R = 0.2267 (Rfree = 0.000) for 1981 atoms. Found 6 (10 requested) and removed 19 (5 requested) atoms. Cycle 3: After refmac, R = 0.2270 (Rfree = 0.000) for 1943 atoms. Found 2 (10 requested) and removed 23 (5 requested) atoms. Cycle 4: After refmac, R = 0.2133 (Rfree = 0.000) for 1913 atoms. Found 4 (10 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.1826 (Rfree = 0.000) for 1902 atoms. Found 4 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 1997 seeds are put forward NCS extension: 0 residues added, 1997 seeds are put forward Round 1: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.321 Round 2: 129 peptides, 23 chains. Longest chain 10 peptides. Score 0.385 Round 3: 133 peptides, 22 chains. Longest chain 11 peptides. Score 0.429 Round 4: 136 peptides, 21 chains. Longest chain 14 peptides. Score 0.466 Round 5: 141 peptides, 23 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 4 Chains 21, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4293 restraints for refining 1907 atoms. 3854 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2161 (Rfree = 0.000) for 1907 atoms. Found 2 (10 requested) and removed 20 (5 requested) atoms. Cycle 7: After refmac, R = 0.1816 (Rfree = 0.000) for 1867 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.1955 (Rfree = 0.000) for 1853 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 9: After refmac, R = 0.1924 (Rfree = 0.000) for 1840 atoms. Found 6 (10 requested) and removed 12 (5 requested) atoms. Cycle 10: After refmac, R = 0.1706 (Rfree = 0.000) for 1830 atoms. Found 1 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 1910 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1930 seeds are put forward Round 1: 115 peptides, 19 chains. Longest chain 15 peptides. Score 0.403 Round 2: 128 peptides, 19 chains. Longest chain 12 peptides. Score 0.470 Round 3: 138 peptides, 17 chains. Longest chain 21 peptides. Score 0.557 Round 4: 131 peptides, 17 chains. Longest chain 24 peptides. Score 0.526 Round 5: 141 peptides, 18 chains. Longest chain 21 peptides. Score 0.551 Taking the results from Round 3 Chains 17, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4041 restraints for refining 1887 atoms. 3574 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1987 (Rfree = 0.000) for 1887 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 12: After refmac, R = 0.1798 (Rfree = 0.000) for 1870 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.1889 (Rfree = 0.000) for 1856 atoms. Found 2 (10 requested) and removed 12 (5 requested) atoms. Cycle 14: After refmac, R = 0.1800 (Rfree = 0.000) for 1844 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.1767 (Rfree = 0.000) for 1836 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.57 Search for helices and strands: 0 residues in 0 chains, 1896 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 1935 seeds are put forward Round 1: 124 peptides, 23 chains. Longest chain 13 peptides. Score 0.358 Round 2: 143 peptides, 24 chains. Longest chain 19 peptides. Score 0.436 Round 3: 144 peptides, 21 chains. Longest chain 19 peptides. Score 0.504 Round 4: 149 peptides, 19 chains. Longest chain 21 peptides. Score 0.566 Round 5: 151 peptides, 22 chains. Longest chain 17 peptides. Score 0.516 Taking the results from Round 4 Chains 19, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4282 restraints for refining 1948 atoms. 3781 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1934 (Rfree = 0.000) for 1948 atoms. Found 6 (10 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.1930 (Rfree = 0.000) for 1929 atoms. Found 2 (10 requested) and removed 13 (5 requested) atoms. Cycle 18: After refmac, R = 0.1912 (Rfree = 0.000) for 1913 atoms. Found 5 (10 requested) and removed 12 (5 requested) atoms. Cycle 19: After refmac, R = 0.1949 (Rfree = 0.000) for 1904 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. Cycle 20: After refmac, R = 0.1649 (Rfree = 0.000) for 1896 atoms. Found 1 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 1960 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 1991 seeds are put forward Round 1: 121 peptides, 22 chains. Longest chain 19 peptides. Score 0.365 Round 2: 136 peptides, 21 chains. Longest chain 15 peptides. Score 0.466 Round 3: 132 peptides, 19 chains. Longest chain 20 peptides. Score 0.489 Round 4: 139 peptides, 21 chains. Longest chain 14 peptides. Score 0.480 Round 5: 143 peptides, 23 chains. Longest chain 20 peptides. Score 0.457 Taking the results from Round 3 Chains 19, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4530 restraints for refining 1992 atoms. 4097 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1997 (Rfree = 0.000) for 1992 atoms. Found 7 (10 requested) and removed 16 (5 requested) atoms. Cycle 22: After refmac, R = 0.1983 (Rfree = 0.000) for 1972 atoms. Found 5 (10 requested) and removed 14 (5 requested) atoms. Cycle 23: After refmac, R = 0.1457 (Rfree = 0.000) for 1959 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.1485 (Rfree = 0.000) for 1952 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1918 (Rfree = 0.000) for 1944 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.51 Search for helices and strands: 0 residues in 0 chains, 2014 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 2035 seeds are put forward Round 1: 115 peptides, 23 chains. Longest chain 13 peptides. Score 0.308 Round 2: 126 peptides, 20 chains. Longest chain 13 peptides. Score 0.438 Round 3: 138 peptides, 20 chains. Longest chain 18 peptides. Score 0.496 Round 4: 133 peptides, 19 chains. Longest chain 18 peptides. Score 0.494 Round 5: 131 peptides, 19 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 3 Chains 20, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4476 restraints for refining 2026 atoms. 4024 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1875 (Rfree = 0.000) for 2026 atoms. Found 7 (11 requested) and removed 25 (5 requested) atoms. Cycle 27: After refmac, R = 0.1914 (Rfree = 0.000) for 1998 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 28: After refmac, R = 0.1636 (Rfree = 0.000) for 1989 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.1890 (Rfree = 0.000) for 1985 atoms. Found 9 (10 requested) and removed 10 (5 requested) atoms. Cycle 30: After refmac, R = 0.1692 (Rfree = 0.000) for 1982 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.62 Search for helices and strands: 0 residues in 0 chains, 2066 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2085 seeds are put forward Round 1: 120 peptides, 23 chains. Longest chain 9 peptides. Score 0.336 Round 2: 125 peptides, 18 chains. Longest chain 13 peptides. Score 0.477 Round 3: 119 peptides, 18 chains. Longest chain 19 peptides. Score 0.447 Round 4: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.414 Round 5: 114 peptides, 20 chains. Longest chain 9 peptides. Score 0.374 Taking the results from Round 2 Chains 18, Residues 107, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4397 restraints for refining 2026 atoms. 3950 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1677 (Rfree = 0.000) for 2026 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 32: After refmac, R = 0.1723 (Rfree = 0.000) for 2017 atoms. Found 3 (11 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.1849 (Rfree = 0.000) for 2006 atoms. Found 6 (11 requested) and removed 12 (5 requested) atoms. Cycle 34: After refmac, R = 0.1630 (Rfree = 0.000) for 1995 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.1756 (Rfree = 0.000) for 1992 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 2075 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2090 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.301 Round 2: 108 peptides, 20 chains. Longest chain 10 peptides. Score 0.341 Round 3: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.378 Round 4: 122 peptides, 19 chains. Longest chain 11 peptides. Score 0.440 Round 5: 112 peptides, 18 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 4 Chains 19, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4724 restraints for refining 2026 atoms. 4331 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2317 (Rfree = 0.000) for 2026 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.1787 (Rfree = 0.000) for 2019 atoms. Found 10 (11 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.1730 (Rfree = 0.000) for 2018 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.1817 (Rfree = 0.000) for 2015 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.1604 (Rfree = 0.000) for 2009 atoms. Found 4 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.56 Search for helices and strands: 0 residues in 0 chains, 2078 seeds are put forward NCS extension: 0 residues added, 2078 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.321 Round 2: 103 peptides, 17 chains. Longest chain 11 peptides. Score 0.386 Round 3: 107 peptides, 18 chains. Longest chain 12 peptides. Score 0.383 Round 4: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.370 Round 5: 102 peptides, 16 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 5 Chains 16, Residues 86, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4682 restraints for refining 2026 atoms. 4301 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1993 (Rfree = 0.000) for 2026 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. Cycle 42: After refmac, R = 0.1940 (Rfree = 0.000) for 2021 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.1723 (Rfree = 0.000) for 2017 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1876 (Rfree = 0.000) for 2008 atoms. Found 9 (11 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.1726 (Rfree = 0.000) for 2002 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 2044 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2055 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 9 peptides. Score 0.225 Round 2: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.291 Round 3: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.285 Round 4: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.342 Round 5: 88 peptides, 16 chains. Longest chain 9 peptides. Score 0.325 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 75, 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 2okf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2872 reflections ( 99.45 % complete ) and 4847 restraints for refining 2026 atoms. 4563 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2158 (Rfree = 0.000) for 2026 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1921 (Rfree = 0.000) for 2013 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1891 (Rfree = 0.000) for 2006 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = (Rfree = 0.000) for 1998 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:05:38 GMT 2018 Job finished. TimeTaking 42.42 Used memory is bytes: 12216384