null Sun 23 Dec 22:22:43 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 2prx-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prx-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prx-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-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/2prx-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-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 22:22:53 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/2prx-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-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 202 and 0 Target number of residues in the AU: 202 Target solvent content: 0.6281 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-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: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2560 target number of atoms Had to go as low as 0.55 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: 28.816 4.001 Wilson plot Bfac: 65.55 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2404 reflections ( 99.50 % complete ) and 0 restraints for refining 2836 atoms. Observations/parameters ratio is 0.21 ------------------------------------------------------ Starting model: R = 0.3153 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2449 (Rfree = 0.000) for 2836 atoms. Found 6 (13 requested) and removed 70 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 4.08 Search for helices and strands: 0 residues in 0 chains, 2790 seeds are put forward NCS extension: 0 residues added, 2790 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.210 Round 2: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.204 Round 3: 65 peptides, 14 chains. Longest chain 6 peptides. Score 0.234 Round 4: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.316 Round 5: 76 peptides, 13 chains. Longest chain 13 peptides. Score 0.335 Taking the results from Round 5 Chains 13, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 6130 restraints for refining 2310 atoms. 5891 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2557 (Rfree = 0.000) for 2310 atoms. Found 10 (10 requested) and removed 48 (5 requested) atoms. Cycle 2: After refmac, R = 0.2490 (Rfree = 0.000) for 2245 atoms. Found 10 (10 requested) and removed 26 (5 requested) atoms. Cycle 3: After refmac, R = 0.1801 (Rfree = 0.000) for 2200 atoms. Found 6 (10 requested) and removed 22 (5 requested) atoms. Cycle 4: After refmac, R = 0.2477 (Rfree = 0.000) for 2172 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 5: After refmac, R = 0.1839 (Rfree = 0.000) for 2144 atoms. Found 8 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.86 Search for helices and strands: 0 residues in 0 chains, 2191 seeds are put forward NCS extension: 0 residues added, 2191 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 7 peptides. Score 0.213 Round 2: 74 peptides, 15 chains. Longest chain 10 peptides. Score 0.266 Round 3: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.275 Round 4: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.273 Round 5: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 5 Chains 17, Residues 74, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4446 restraints for refining 1904 atoms. 4140 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2103 (Rfree = 0.000) for 1904 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 7: After refmac, R = 0.1858 (Rfree = 0.000) for 1877 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 8: After refmac, R = 0.1394 (Rfree = 0.000) for 1867 atoms. Found 4 (8 requested) and removed 16 (4 requested) atoms. Cycle 9: After refmac, R = 0.1235 (Rfree = 0.000) for 1851 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.1355 (Rfree = 0.000) for 1838 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.82 Search for helices and strands: 0 residues in 0 chains, 1893 seeds are put forward NCS extension: 0 residues added, 1893 seeds are put forward Round 1: 94 peptides, 21 chains. Longest chain 7 peptides. Score 0.233 Round 2: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.304 Round 3: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.342 Round 4: 106 peptides, 21 chains. Longest chain 8 peptides. Score 0.308 Round 5: 109 peptides, 20 chains. Longest chain 10 peptides. Score 0.351 Taking the results from Round 5 Chains 20, Residues 89, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4405 restraints for refining 1868 atoms. 4054 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2134 (Rfree = 0.000) for 1868 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 12: After refmac, R = 0.1632 (Rfree = 0.000) for 1839 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.1579 (Rfree = 0.000) for 1828 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.1626 (Rfree = 0.000) for 1822 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.1518 (Rfree = 0.000) for 1814 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 1879 seeds are put forward NCS extension: 0 residues added, 1879 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 7 peptides. Score 0.260 Round 2: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.346 Round 3: 107 peptides, 20 chains. Longest chain 8 peptides. Score 0.339 Round 4: 101 peptides, 17 chains. Longest chain 12 peptides. Score 0.379 Round 5: 106 peptides, 19 chains. Longest chain 8 peptides. Score 0.358 Taking the results from Round 4 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4460 restraints for refining 1928 atoms. 4119 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2056 (Rfree = 0.000) for 1928 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 17: After refmac, R = 0.1734 (Rfree = 0.000) for 1910 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.1663 (Rfree = 0.000) for 1899 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 19: After refmac, R = 0.1671 (Rfree = 0.000) for 1891 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 20: After refmac, R = 0.1538 (Rfree = 0.000) for 1881 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.78 Search for helices and strands: 0 residues in 0 chains, 1922 seeds are put forward NCS extension: 0 residues added, 1922 seeds are put forward Round 1: 92 peptides, 22 chains. Longest chain 6 peptides. Score 0.193 Round 2: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.364 Round 3: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.335 Round 4: 105 peptides, 19 chains. Longest chain 9 peptides. Score 0.352 Round 5: 110 peptides, 20 chains. Longest chain 9 peptides. Score 0.356 Taking the results from Round 2 Chains 19, Residues 88, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4363 restraints for refining 1911 atoms. 4015 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1808 (Rfree = 0.000) for 1911 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 22: After refmac, R = 0.1652 (Rfree = 0.000) for 1892 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.1730 (Rfree = 0.000) for 1890 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 24: After refmac, R = 0.1628 (Rfree = 0.000) for 1879 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.1180 (Rfree = 0.000) for 1873 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.84 Search for helices and strands: 0 residues in 0 chains, 1930 seeds are put forward NCS extension: 0 residues added, 1930 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 6 peptides. Score 0.216 Round 2: 88 peptides, 15 chains. Longest chain 12 peptides. Score 0.355 Round 3: 101 peptides, 17 chains. Longest chain 15 peptides. Score 0.379 Round 4: 96 peptides, 16 chains. Longest chain 15 peptides. Score 0.376 Round 5: 103 peptides, 17 chains. Longest chain 15 peptides. Score 0.391 Taking the results from Round 5 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4444 restraints for refining 1918 atoms. 4095 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1950 (Rfree = 0.000) for 1918 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 27: After refmac, R = 0.1686 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 28: After refmac, R = 0.1227 (Rfree = 0.000) for 1891 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 29: After refmac, R = 0.1089 (Rfree = 0.000) for 1884 atoms. Found 1 (8 requested) and removed 11 (4 requested) atoms. Cycle 30: After refmac, R = 0.1063 (Rfree = 0.000) for 1867 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.73 Search for helices and strands: 0 residues in 0 chains, 1907 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 1931 seeds are put forward Round 1: 83 peptides, 18 chains. Longest chain 11 peptides. Score 0.242 Round 2: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.320 Round 3: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.358 Round 4: 97 peptides, 16 chains. Longest chain 18 peptides. Score 0.382 Round 5: 99 peptides, 18 chains. Longest chain 10 peptides. Score 0.342 Taking the results from Round 4 Chains 16, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4580 restraints for refining 1966 atoms. 4272 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1631 (Rfree = 0.000) for 1966 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 32: After refmac, R = 0.1626 (Rfree = 0.000) for 1954 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 33: After refmac, R = 0.1646 (Rfree = 0.000) for 1949 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 34: After refmac, R = 0.1336 (Rfree = 0.000) for 1942 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1438 (Rfree = 0.000) for 1942 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 1982 seeds are put forward NCS extension: 0 residues added, 1982 seeds are put forward Round 1: 72 peptides, 17 chains. Longest chain 6 peptides. Score 0.195 Round 2: 88 peptides, 19 chains. Longest chain 7 peptides. Score 0.248 Round 3: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.283 Round 4: 93 peptides, 16 chains. Longest chain 14 peptides. Score 0.358 Round 5: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.263 Taking the results from Round 4 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4692 restraints for refining 1995 atoms. 4383 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1712 (Rfree = 0.000) for 1995 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 37: After refmac, R = 0.1180 (Rfree = 0.000) for 1968 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.1066 (Rfree = 0.000) for 1960 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.1297 (Rfree = 0.000) for 1958 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.1001 (Rfree = 0.000) for 1956 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.74 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward NCS extension: 0 residues added, 1996 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 8 peptides. Score 0.250 Round 2: 103 peptides, 19 chains. Longest chain 12 peptides. Score 0.341 Round 3: 110 peptides, 20 chains. Longest chain 14 peptides. Score 0.356 Round 4: 115 peptides, 20 chains. Longest chain 15 peptides. Score 0.385 Round 5: 115 peptides, 22 chains. Longest chain 10 peptides. Score 0.336 Taking the results from Round 4 Chains 20, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4500 restraints for refining 1984 atoms. 4140 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1781 (Rfree = 0.000) for 1984 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 42: After refmac, R = 0.1678 (Rfree = 0.000) for 1967 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 43: After refmac, R = 0.1449 (Rfree = 0.000) for 1957 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.1418 (Rfree = 0.000) for 1954 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 45: After refmac, R = 0.1346 (Rfree = 0.000) for 1948 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.76 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2012 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.232 Round 2: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.283 Round 3: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.340 Round 4: 96 peptides, 18 chains. Longest chain 10 peptides. Score 0.324 Round 5: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.350 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 79, 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 2prx-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2404 reflections ( 99.50 % complete ) and 4737 restraints for refining 2016 atoms. 4438 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1735 (Rfree = 0.000) for 2016 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1646 (Rfree = 0.000) for 2002 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1622 (Rfree = 0.000) for 1994 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1491 (Rfree = 0.000) for 1985 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:38 GMT 2018 Job finished. TimeTaking 33.92 Used memory is bytes: 21349656