null Sun 23 Dec 22:22:59 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okf-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okf-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-4.0-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 22:23:08 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-4.0-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 188 and 0 Target number of residues in the AU: 188 Target solvent content: 0.6644 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-4.0-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-4.0-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 4.005 Wilson plot Bfac: 86.99 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2457 reflections ( 99.43 % complete ) and 0 restraints for refining 2466 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3470 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3746 (Rfree = 0.000) for 2466 atoms. Found 7 (11 requested) and removed 26 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.83 Search for helices and strands: 0 residues in 0 chains, 2488 seeds are put forward NCS extension: 0 residues added, 2488 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.205 Round 2: 79 peptides, 14 chains. Longest chain 12 peptides. Score 0.323 Round 3: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.313 Round 4: 119 peptides, 22 chains. Longest chain 10 peptides. Score 0.354 Round 5: 119 peptides, 19 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 5 Chains 19, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4692 restraints for refining 1944 atoms. 4311 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2823 (Rfree = 0.000) for 1944 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 2: After refmac, R = 0.2401 (Rfree = 0.000) for 1909 atoms. Found 4 (9 requested) and removed 14 (4 requested) atoms. Cycle 3: After refmac, R = 0.2194 (Rfree = 0.000) for 1885 atoms. Found 6 (8 requested) and removed 18 (4 requested) atoms. Cycle 4: After refmac, R = 0.2257 (Rfree = 0.000) for 1862 atoms. Found 5 (8 requested) and removed 13 (4 requested) atoms. Cycle 5: After refmac, R = 0.2090 (Rfree = 0.000) for 1846 atoms. Found 3 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 1894 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1907 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.250 Round 2: 119 peptides, 21 chains. Longest chain 9 peptides. Score 0.378 Round 3: 120 peptides, 21 chains. Longest chain 11 peptides. Score 0.383 Round 4: 125 peptides, 20 chains. Longest chain 11 peptides. Score 0.432 Round 5: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.396 Taking the results from Round 4 Chains 20, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4190 restraints for refining 1865 atoms. 3790 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2410 (Rfree = 0.000) for 1865 atoms. Found 7 (8 requested) and removed 19 (4 requested) atoms. Cycle 7: After refmac, R = 0.2203 (Rfree = 0.000) for 1837 atoms. Found 2 (8 requested) and removed 19 (4 requested) atoms. Cycle 8: After refmac, R = 0.2109 (Rfree = 0.000) for 1808 atoms. Found 5 (8 requested) and removed 12 (4 requested) atoms. Cycle 9: After refmac, R = 0.1968 (Rfree = 0.000) for 1795 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.1940 (Rfree = 0.000) for 1778 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.65 Search for helices and strands: 0 residues in 0 chains, 1861 seeds are put forward NCS extension: 0 residues added, 1861 seeds are put forward Round 1: 117 peptides, 23 chains. Longest chain 11 peptides. Score 0.319 Round 2: 121 peptides, 21 chains. Longest chain 10 peptides. Score 0.389 Round 3: 121 peptides, 21 chains. Longest chain 10 peptides. Score 0.389 Round 4: 129 peptides, 23 chains. Longest chain 11 peptides. Score 0.385 Round 5: 120 peptides, 21 chains. Longest chain 9 peptides. Score 0.383 Taking the results from Round 3 Chains 21, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4256 restraints for refining 1863 atoms. 3877 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2440 (Rfree = 0.000) for 1863 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 12: After refmac, R = 0.2002 (Rfree = 0.000) for 1833 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.1955 (Rfree = 0.000) for 1819 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 14: After refmac, R = 0.1896 (Rfree = 0.000) for 1810 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.1797 (Rfree = 0.000) for 1798 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.69 Search for helices and strands: 0 residues in 0 chains, 1888 seeds are put forward NCS extension: 0 residues added, 1888 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 8 peptides. Score 0.290 Round 2: 137 peptides, 23 chains. Longest chain 14 peptides. Score 0.427 Round 3: 130 peptides, 22 chains. Longest chain 16 peptides. Score 0.413 Round 4: 128 peptides, 18 chains. Longest chain 13 peptides. Score 0.491 Round 5: 124 peptides, 20 chains. Longest chain 14 peptides. Score 0.427 Taking the results from Round 4 Chains 18, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4216 restraints for refining 1900 atoms. 3794 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2544 (Rfree = 0.000) for 1900 atoms. Found 8 (8 requested) and removed 34 (4 requested) atoms. Cycle 17: After refmac, R = 0.2136 (Rfree = 0.000) for 1858 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 18: After refmac, R = 0.1810 (Rfree = 0.000) for 1841 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. Cycle 19: After refmac, R = 0.1880 (Rfree = 0.000) for 1832 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 20: After refmac, R = 0.1708 (Rfree = 0.000) for 1823 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.73 Search for helices and strands: 0 residues in 0 chains, 1897 seeds are put forward NCS extension: 0 residues added, 1897 seeds are put forward Round 1: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.294 Round 2: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.342 Round 3: 139 peptides, 23 chains. Longest chain 13 peptides. Score 0.437 Round 4: 129 peptides, 23 chains. Longest chain 10 peptides. Score 0.385 Round 5: 127 peptides, 23 chains. Longest chain 12 peptides. Score 0.375 Taking the results from Round 3 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4251 restraints for refining 1935 atoms. 3810 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2073 (Rfree = 0.000) for 1935 atoms. Found 8 (9 requested) and removed 18 (4 requested) atoms. Cycle 22: After refmac, R = 0.2032 (Rfree = 0.000) for 1912 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.2027 (Rfree = 0.000) for 1891 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.1871 (Rfree = 0.000) for 1887 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. Cycle 25: After refmac, R = 0.1948 (Rfree = 0.000) for 1877 atoms. Found 6 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.75 Search for helices and strands: 0 residues in 0 chains, 1938 seeds are put forward NCS extension: 0 residues added, 1938 seeds are put forward Round 1: 103 peptides, 23 chains. Longest chain 7 peptides. Score 0.236 Round 2: 115 peptides, 22 chains. Longest chain 9 peptides. Score 0.332 Round 3: 114 peptides, 18 chains. Longest chain 15 peptides. Score 0.421 Round 4: 104 peptides, 20 chains. Longest chain 10 peptides. Score 0.318 Round 5: 107 peptides, 19 chains. Longest chain 9 peptides. Score 0.359 Taking the results from Round 3 Chains 18, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4350 restraints for refining 1931 atoms. 3984 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2251 (Rfree = 0.000) for 1931 atoms. Found 9 (9 requested) and removed 26 (4 requested) atoms. Cycle 27: After refmac, R = 0.2206 (Rfree = 0.000) for 1897 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 28: After refmac, R = 0.2051 (Rfree = 0.000) for 1879 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.2080 (Rfree = 0.000) for 1866 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 30: After refmac, R = 0.1998 (Rfree = 0.000) for 1856 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.81 Search for helices and strands: 0 residues in 0 chains, 1923 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1945 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 6 peptides. Score 0.236 Round 2: 94 peptides, 18 chains. Longest chain 7 peptides. Score 0.309 Round 3: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.319 Round 4: 107 peptides, 18 chains. Longest chain 11 peptides. Score 0.383 Round 5: 109 peptides, 17 chains. Longest chain 13 peptides. Score 0.418 Taking the results from Round 5 Chains 17, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4438 restraints for refining 1965 atoms. 4087 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2176 (Rfree = 0.000) for 1965 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 32: After refmac, R = 0.2018 (Rfree = 0.000) for 1949 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 33: After refmac, R = 0.2111 (Rfree = 0.000) for 1934 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 34: After refmac, R = 0.1925 (Rfree = 0.000) for 1921 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.1780 (Rfree = 0.000) for 1913 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.76 Search for helices and strands: 0 residues in 0 chains, 2000 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2014 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.266 Round 2: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.315 Round 3: 80 peptides, 14 chains. Longest chain 9 peptides. Score 0.329 Round 4: 90 peptides, 15 chains. Longest chain 11 peptides. Score 0.362 Round 5: 104 peptides, 17 chains. Longest chain 10 peptides. Score 0.391 Taking the results from Round 5 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4454 restraints for refining 1971 atoms. 4123 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2274 (Rfree = 0.000) for 1971 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 37: After refmac, R = 0.1992 (Rfree = 0.000) for 1953 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 38: After refmac, R = 0.1923 (Rfree = 0.000) for 1943 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 39: After refmac, R = 0.1915 (Rfree = 0.000) for 1934 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.1734 (Rfree = 0.000) for 1930 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.71 Search for helices and strands: 0 residues in 0 chains, 1994 seeds are put forward NCS extension: 0 residues added, 1994 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 6 peptides. Score 0.229 Round 2: 73 peptides, 14 chains. Longest chain 7 peptides. Score 0.285 Round 3: 72 peptides, 12 chains. Longest chain 9 peptides. Score 0.335 Round 4: 79 peptides, 13 chains. Longest chain 9 peptides. Score 0.350 Round 5: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.344 Taking the results from Round 4 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4594 restraints for refining 1944 atoms. 4343 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1957 (Rfree = 0.000) for 1944 atoms. Found 4 (9 requested) and removed 18 (4 requested) atoms. Cycle 42: After refmac, R = 0.2021 (Rfree = 0.000) for 1927 atoms. Found 8 (9 requested) and removed 17 (4 requested) atoms. Cycle 43: After refmac, R = 0.1923 (Rfree = 0.000) for 1917 atoms. Found 7 (9 requested) and removed 12 (4 requested) atoms. Cycle 44: After refmac, R = 0.2010 (Rfree = 0.000) for 1907 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 45: After refmac, R = 0.1867 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.72 Search for helices and strands: 0 residues in 0 chains, 1962 seeds are put forward NCS extension: 0 residues added, 1962 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.243 Round 2: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.342 Round 3: 89 peptides, 16 chains. Longest chain 10 peptides. Score 0.330 Round 4: 96 peptides, 16 chains. Longest chain 9 peptides. Score 0.371 Round 5: 97 peptides, 17 chains. Longest chain 9 peptides. Score 0.352 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 80, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2457 reflections ( 99.43 % complete ) and 4183 restraints for refining 1868 atoms. 3879 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1967 (Rfree = 0.000) for 1868 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1885 (Rfree = 0.000) for 1854 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1967 (Rfree = 0.000) for 1846 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1641 (Rfree = 0.000) for 1839 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:37 GMT 2018 Job finished. TimeTaking 33.64 Used memory is bytes: 19517736