null Sun 23 Dec 22:22:41 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 2gnr-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gnr-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gnr-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-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/2gnr-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-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 22:22:50 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/2gnr-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-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 196 and 0 Target number of residues in the AU: 196 Target solvent content: 0.6745 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.52 Input MTZ file: 2gnr-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: 91 Cell parameters: 75.160 75.160 115.370 90.000 90.000 90.000 Input sequence file: 2gnr-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2320 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 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: 75.160 4.000 Wilson plot Bfac: 95.39 3072 reflections ( 99.19 % complete ) and 0 restraints for refining 2584 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3514 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3577 (Rfree = 0.000) for 2584 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 2614 seeds are put forward NCS extension: 0 residues added, 2614 seeds are put forward Round 1: 106 peptides, 20 chains. Longest chain 11 peptides. Score 0.321 Round 2: 133 peptides, 22 chains. Longest chain 14 peptides. Score 0.415 Round 3: 151 peptides, 25 chains. Longest chain 16 peptides. Score 0.439 Round 4: 152 peptides, 21 chains. Longest chain 15 peptides. Score 0.522 Round 5: 158 peptides, 20 chains. Longest chain 17 peptides. Score 0.565 Taking the results from Round 5 Chains 20, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4929 restraints for refining 2094 atoms. 4397 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2703 (Rfree = 0.000) for 2094 atoms. Found 7 (9 requested) and removed 17 (4 requested) atoms. Cycle 2: After refmac, R = 0.2748 (Rfree = 0.000) for 2045 atoms. Found 6 (9 requested) and removed 14 (4 requested) atoms. Cycle 3: After refmac, R = 0.2835 (Rfree = 0.000) for 2020 atoms. Found 5 (9 requested) and removed 12 (4 requested) atoms. Cycle 4: After refmac, R = 0.2578 (Rfree = 0.000) for 1995 atoms. Found 5 (9 requested) and removed 12 (4 requested) atoms. Cycle 5: After refmac, R = 0.2717 (Rfree = 0.000) for 1968 atoms. Found 2 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 2065 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2080 seeds are put forward Round 1: 115 peptides, 24 chains. Longest chain 8 peptides. Score 0.277 Round 2: 126 peptides, 23 chains. Longest chain 14 peptides. Score 0.359 Round 3: 125 peptides, 20 chains. Longest chain 11 peptides. Score 0.419 Round 4: 129 peptides, 20 chains. Longest chain 14 peptides. Score 0.438 Round 5: 135 peptides, 20 chains. Longest chain 18 peptides. Score 0.466 Taking the results from Round 5 Chains 20, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4744 restraints for refining 1999 atoms. 4304 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2372 (Rfree = 0.000) for 1999 atoms. Found 4 (9 requested) and removed 15 (4 requested) atoms. Cycle 7: After refmac, R = 0.2229 (Rfree = 0.000) for 1974 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2162 (Rfree = 0.000) for 1959 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.2118 (Rfree = 0.000) for 1952 atoms. Found 1 (9 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2082 (Rfree = 0.000) for 1944 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 1999 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 2026 seeds are put forward Round 1: 103 peptides, 20 chains. Longest chain 7 peptides. Score 0.304 Round 2: 127 peptides, 20 chains. Longest chain 15 peptides. Score 0.429 Round 3: 129 peptides, 20 chains. Longest chain 14 peptides. Score 0.438 Round 4: 129 peptides, 21 chains. Longest chain 17 peptides. Score 0.417 Round 5: 134 peptides, 22 chains. Longest chain 11 peptides. Score 0.420 Taking the results from Round 3 Chains 20, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4730 restraints for refining 2010 atoms. 4314 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2489 (Rfree = 0.000) for 2010 atoms. Found 8 (9 requested) and removed 26 (4 requested) atoms. Cycle 12: After refmac, R = 0.2355 (Rfree = 0.000) for 1977 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 13: After refmac, R = 0.2215 (Rfree = 0.000) for 1958 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 14: After refmac, R = 0.2245 (Rfree = 0.000) for 1938 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 15: After refmac, R = 0.2310 (Rfree = 0.000) for 1923 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 1984 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2003 seeds are put forward Round 1: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.313 Round 2: 126 peptides, 18 chains. Longest chain 17 peptides. Score 0.466 Round 3: 127 peptides, 18 chains. Longest chain 18 peptides. Score 0.471 Round 4: 122 peptides, 18 chains. Longest chain 14 peptides. Score 0.447 Round 5: 132 peptides, 18 chains. Longest chain 18 peptides. Score 0.493 Taking the results from Round 5 Chains 18, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4259 restraints for refining 1922 atoms. 3821 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2311 (Rfree = 0.000) for 1922 atoms. Found 8 (9 requested) and removed 12 (4 requested) atoms. Cycle 17: After refmac, R = 0.2106 (Rfree = 0.000) for 1898 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.2179 (Rfree = 0.000) for 1886 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 19: After refmac, R = 0.2163 (Rfree = 0.000) for 1866 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 20: After refmac, R = 0.2111 (Rfree = 0.000) for 1853 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 1919 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1935 seeds are put forward Round 1: 99 peptides, 20 chains. Longest chain 9 peptides. Score 0.282 Round 2: 111 peptides, 20 chains. Longest chain 13 peptides. Score 0.348 Round 3: 122 peptides, 21 chains. Longest chain 12 peptides. Score 0.382 Round 4: 117 peptides, 17 chains. Longest chain 12 peptides. Score 0.445 Round 5: 122 peptides, 21 chains. Longest chain 9 peptides. Score 0.382 Taking the results from Round 4 Chains 17, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4459 restraints for refining 1952 atoms. 4076 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2510 (Rfree = 0.000) for 1952 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 22: After refmac, R = 0.2440 (Rfree = 0.000) for 1934 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 23: After refmac, R = 0.2174 (Rfree = 0.000) for 1915 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 24: After refmac, R = 0.2240 (Rfree = 0.000) for 1911 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 25: After refmac, R = 0.2062 (Rfree = 0.000) for 1897 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 1981 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1997 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 8 peptides. Score 0.268 Round 2: 106 peptides, 21 chains. Longest chain 9 peptides. Score 0.297 Round 3: 115 peptides, 20 chains. Longest chain 9 peptides. Score 0.369 Round 4: 131 peptides, 20 chains. Longest chain 12 peptides. Score 0.448 Round 5: 137 peptides, 19 chains. Longest chain 15 peptides. Score 0.496 Taking the results from Round 5 Chains 19, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4406 restraints for refining 1974 atoms. 3953 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2401 (Rfree = 0.000) for 1974 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.1999 (Rfree = 0.000) for 1960 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.2214 (Rfree = 0.000) for 1945 atoms. Found 6 (9 requested) and removed 12 (4 requested) atoms. Cycle 29: After refmac, R = 0.2313 (Rfree = 0.000) for 1932 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 30: After refmac, R = 0.2226 (Rfree = 0.000) for 1920 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 1986 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2006 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 8 peptides. Score 0.234 Round 2: 116 peptides, 19 chains. Longest chain 10 peptides. Score 0.396 Round 3: 122 peptides, 19 chains. Longest chain 9 peptides. Score 0.426 Round 4: 130 peptides, 19 chains. Longest chain 15 peptides. Score 0.464 Round 5: 132 peptides, 20 chains. Longest chain 15 peptides. Score 0.453 Taking the results from Round 4 Chains 19, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4605 restraints for refining 2009 atoms. 4180 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2762 (Rfree = 0.000) for 2009 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 32: After refmac, R = 0.2175 (Rfree = 0.000) for 1992 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 33: After refmac, R = 0.2354 (Rfree = 0.000) for 1979 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 34: After refmac, R = 0.2078 (Rfree = 0.000) for 1962 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2160 (Rfree = 0.000) for 1954 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 2000 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2017 seeds are put forward Round 1: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.288 Round 2: 129 peptides, 22 chains. Longest chain 19 peptides. Score 0.396 Round 3: 123 peptides, 22 chains. Longest chain 12 peptides. Score 0.365 Round 4: 109 peptides, 19 chains. Longest chain 12 peptides. Score 0.360 Round 5: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.369 Taking the results from Round 2 Chains 22, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4436 restraints for refining 1956 atoms. 4030 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2111 (Rfree = 0.000) for 1956 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 37: After refmac, R = 0.2284 (Rfree = 0.000) for 1937 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.2104 (Rfree = 0.000) for 1924 atoms. Found 6 (9 requested) and removed 15 (4 requested) atoms. Cycle 39: After refmac, R = 0.1836 (Rfree = 0.000) for 1909 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.1931 (Rfree = 0.000) for 1896 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.87 3.77 Search for helices and strands: 0 residues in 0 chains, 1949 seeds are put forward NCS extension: 0 residues added, 1949 seeds are put forward Round 1: 88 peptides, 20 chains. Longest chain 6 peptides. Score 0.217 Round 2: 114 peptides, 21 chains. Longest chain 18 peptides. Score 0.341 Round 3: 115 peptides, 22 chains. Longest chain 9 peptides. Score 0.323 Round 4: 123 peptides, 24 chains. Longest chain 8 peptides. Score 0.321 Round 5: 118 peptides, 23 chains. Longest chain 8 peptides. Score 0.317 Taking the results from Round 2 Chains 22, Residues 93, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4272 restraints for refining 1905 atoms. 3895 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2417 (Rfree = 0.000) for 1905 atoms. Found 7 (9 requested) and removed 14 (4 requested) atoms. Cycle 42: After refmac, R = 0.2161 (Rfree = 0.000) for 1886 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.2295 (Rfree = 0.000) for 1882 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 44: After refmac, R = 0.2188 (Rfree = 0.000) for 1873 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 45: After refmac, R = 0.2223 (Rfree = 0.000) for 1871 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.86 3.76 Search for helices and strands: 0 residues in 0 chains, 1914 seeds are put forward NCS extension: 0 residues added, 1914 seeds are put forward Round 1: 93 peptides, 20 chains. Longest chain 7 peptides. Score 0.247 Round 2: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.323 Round 3: 109 peptides, 21 chains. Longest chain 7 peptides. Score 0.314 Round 4: 105 peptides, 20 chains. Longest chain 10 peptides. Score 0.315 Round 5: 104 peptides, 20 chains. Longest chain 9 peptides. Score 0.310 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 83, 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 2gnr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3072 reflections ( 99.19 % complete ) and 4387 restraints for refining 1916 atoms. 4074 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2574 (Rfree = 0.000) for 1916 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2006 (Rfree = 0.000) for 1905 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1911 (Rfree = 0.000) for 1894 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2110 (Rfree = 0.000) for 1885 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:05:06 GMT 2018 Job finished. TimeTaking 42.43 Used memory is bytes: 9208248