null Sun 23 Dec 22:22:53 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 2o1q-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-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/2o1q-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-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 22:23:03 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/2o1q-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-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 166 and 0 Target number of residues in the AU: 166 Target solvent content: 0.6485 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: 0.39 Input MTZ file: 2o1q-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-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: 56.142 4.002 Wilson plot Bfac: 76.90 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2457 reflections ( 99.59 % complete ) and 0 restraints for refining 2584 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3577 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3222 (Rfree = 0.000) for 2584 atoms. Found 12 (12 requested) and removed 44 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 4.10 Search for helices and strands: 0 residues in 0 chains, 2577 seeds are put forward NCS extension: 0 residues added, 2577 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 6 peptides. Score 0.214 Round 2: 95 peptides, 19 chains. Longest chain 10 peptides. Score 0.306 Round 3: 107 peptides, 21 chains. Longest chain 8 peptides. Score 0.330 Round 4: 118 peptides, 23 chains. Longest chain 10 peptides. Score 0.347 Round 5: 117 peptides, 21 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 5 Chains 21, Residues 96, Estimated correctness of the model 0.0 % 6 chains (26 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4776 restraints for refining 2094 atoms. 4341 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2599 (Rfree = 0.000) for 2094 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 2: After refmac, R = 0.2370 (Rfree = 0.000) for 2045 atoms. Found 6 (9 requested) and removed 12 (4 requested) atoms. Cycle 3: After refmac, R = 0.2247 (Rfree = 0.000) for 2027 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 4: After refmac, R = 0.2249 (Rfree = 0.000) for 2012 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2138 (Rfree = 0.000) for 2005 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 4.19 Search for helices and strands: 0 residues in 0 chains, 2045 seeds are put forward NCS extension: 0 residues added, 2045 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 6 peptides. Score 0.234 Round 2: 119 peptides, 23 chains. Longest chain 10 peptides. Score 0.353 Round 3: 126 peptides, 21 chains. Longest chain 15 peptides. Score 0.448 Round 4: 124 peptides, 23 chains. Longest chain 8 peptides. Score 0.385 Round 5: 126 peptides, 21 chains. Longest chain 10 peptides. Score 0.448 Taking the results from Round 5 Chains 21, Residues 105, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4596 restraints for refining 2017 atoms. 4158 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2183 (Rfree = 0.000) for 2017 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 7: After refmac, R = 0.1945 (Rfree = 0.000) for 1988 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 8: After refmac, R = 0.1476 (Rfree = 0.000) for 1966 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.1413 (Rfree = 0.000) for 1957 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.1286 (Rfree = 0.000) for 1952 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 4.21 Search for helices and strands: 0 residues in 0 chains, 1984 seeds are put forward NCS extension: 0 residues added, 1984 seeds are put forward Round 1: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.357 Round 2: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.431 Round 3: 129 peptides, 22 chains. Longest chain 12 peptides. Score 0.441 Round 4: 127 peptides, 23 chains. Longest chain 14 peptides. Score 0.403 Round 5: 123 peptides, 21 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 3 Chains 22, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4537 restraints for refining 1990 atoms. 4131 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2123 (Rfree = 0.000) for 1990 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 12: After refmac, R = 0.2189 (Rfree = 0.000) for 1969 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 13: After refmac, R = 0.2145 (Rfree = 0.000) for 1950 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2179 (Rfree = 0.000) for 1939 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.2141 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 4.20 Search for helices and strands: 0 residues in 0 chains, 1992 seeds are put forward NCS extension: 0 residues added, 1992 seeds are put forward Round 1: 79 peptides, 19 chains. Longest chain 5 peptides. Score 0.190 Round 2: 101 peptides, 21 chains. Longest chain 7 peptides. Score 0.289 Round 3: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.326 Round 4: 106 peptides, 19 chains. Longest chain 9 peptides. Score 0.378 Round 5: 110 peptides, 18 chains. Longest chain 15 peptides. Score 0.430 Taking the results from Round 5 Chains 18, Residues 92, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4439 restraints for refining 1952 atoms. 4075 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2037 (Rfree = 0.000) for 1952 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 17: After refmac, R = 0.1923 (Rfree = 0.000) for 1931 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 18: After refmac, R = 0.1944 (Rfree = 0.000) for 1917 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.1267 (Rfree = 0.000) for 1904 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.1155 (Rfree = 0.000) for 1894 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 4.05 Search for helices and strands: 0 residues in 0 chains, 1929 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1951 seeds are put forward Round 1: 77 peptides, 18 chains. Longest chain 5 peptides. Score 0.205 Round 2: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.362 Round 3: 110 peptides, 20 chains. Longest chain 9 peptides. Score 0.377 Round 4: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.389 Round 5: 98 peptides, 17 chains. Longest chain 9 peptides. Score 0.382 Taking the results from Round 4 Chains 20, Residues 92, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4252 restraints for refining 1935 atoms. 3866 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1988 (Rfree = 0.000) for 1935 atoms. Found 8 (9 requested) and removed 15 (4 requested) atoms. Cycle 22: After refmac, R = 0.2025 (Rfree = 0.000) for 1914 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.2181 (Rfree = 0.000) for 1906 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 24: After refmac, R = 0.2353 (Rfree = 0.000) for 1890 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 25: After refmac, R = 0.1977 (Rfree = 0.000) for 1883 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.99 Search for helices and strands: 0 residues in 0 chains, 1921 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1924 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 7 peptides. Score 0.233 Round 2: 97 peptides, 20 chains. Longest chain 7 peptides. Score 0.290 Round 3: 95 peptides, 18 chains. Longest chain 7 peptides. Score 0.334 Round 4: 97 peptides, 18 chains. Longest chain 10 peptides. Score 0.348 Round 5: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.341 Taking the results from Round 4 Chains 18, Residues 79, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4276 restraints for refining 1922 atoms. 3949 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2151 (Rfree = 0.000) for 1922 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 27: After refmac, R = 0.2124 (Rfree = 0.000) for 1910 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 28: After refmac, R = 0.2072 (Rfree = 0.000) for 1900 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.1950 (Rfree = 0.000) for 1900 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.1507 (Rfree = 0.000) for 1899 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 4.04 Search for helices and strands: 0 residues in 0 chains, 1926 seeds are put forward NCS extension: 0 residues added, 1926 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 7 peptides. Score 0.233 Round 2: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.331 Round 3: 100 peptides, 19 chains. Longest chain 8 peptides. Score 0.339 Round 4: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.367 Round 5: 100 peptides, 18 chains. Longest chain 8 peptides. Score 0.367 Taking the results from Round 5 Chains 18, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4349 restraints for refining 1910 atoms. 4039 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2260 (Rfree = 0.000) for 1910 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 32: After refmac, R = 0.2286 (Rfree = 0.000) for 1887 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2273 (Rfree = 0.000) for 1883 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.1951 (Rfree = 0.000) for 1884 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 35: After refmac, R = 0.2052 (Rfree = 0.000) for 1877 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.99 Search for helices and strands: 0 residues in 0 chains, 1928 seeds are put forward NCS extension: 0 residues added, 1928 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 7 peptides. Score 0.231 Round 2: 84 peptides, 17 chains. Longest chain 10 peptides. Score 0.287 Round 3: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.310 Round 4: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.354 Round 5: 80 peptides, 13 chains. Longest chain 13 peptides. Score 0.379 Taking the results from Round 5 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4288 restraints for refining 1897 atoms. 3976 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2109 (Rfree = 0.000) for 1897 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 37: After refmac, R = 0.2099 (Rfree = 0.000) for 1873 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 38: After refmac, R = 0.2280 (Rfree = 0.000) for 1865 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 39: After refmac, R = 0.1939 (Rfree = 0.000) for 1847 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.2081 (Rfree = 0.000) for 1841 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 4.12 Search for helices and strands: 0 residues in 0 chains, 1875 seeds are put forward NCS extension: 0 residues added, 1875 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.220 Round 2: 59 peptides, 13 chains. Longest chain 6 peptides. Score 0.226 Round 3: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.253 Round 4: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.282 Round 5: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.315 Taking the results from Round 5 Chains 11, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4017 restraints for refining 1776 atoms. 3824 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2098 (Rfree = 0.000) for 1776 atoms. Found 8 (8 requested) and removed 34 (4 requested) atoms. Cycle 42: After refmac, R = 0.2363 (Rfree = 0.000) for 1747 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.1997 (Rfree = 0.000) for 1733 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 44: After refmac, R = 0.2245 (Rfree = 0.000) for 1724 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.2165 (Rfree = 0.000) for 1722 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 4.10 Search for helices and strands: 0 residues in 0 chains, 1755 seeds are put forward NCS extension: 0 residues added, 1755 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 6 peptides. Score 0.199 Round 2: 73 peptides, 15 chains. Longest chain 6 peptides. Score 0.269 Round 3: 64 peptides, 13 chains. Longest chain 6 peptides. Score 0.265 Round 4: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.273 Round 5: 71 peptides, 14 chains. Longest chain 7 peptides. Score 0.285 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 57, 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 2o1q-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2457 reflections ( 99.59 % complete ) and 3633 restraints for refining 1687 atoms. 3419 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2358 (Rfree = 0.000) for 1687 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2054 (Rfree = 0.000) for 1677 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2263 (Rfree = 0.000) for 1669 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1963 (Rfree = 0.000) for 1661 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:55:18 GMT 2018 Job finished. TimeTaking 32.42 Used memory is bytes: 21012528