Sun 23 Dec 23:53:45 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prx-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-3.8-parrot-mrncs ############### 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 23:53:49 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/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-3.8-parrot-mrncs/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 208 and 0 Target number of residues in the AU: 208 Target solvent content: 0.6171 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-3.8-parrot-mrncs.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-3.8-parrot-mrncs.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 3.801 Wilson plot Bfac: 59.98 2800 reflections ( 99.57 % complete ) and 0 restraints for refining 2835 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3199 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3159 (Rfree = 0.000) for 2835 atoms. Found 15 (15 requested) and removed 77 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.98 Search for helices and strands: 0 residues in 0 chains, 2792 seeds are put forward NCS extension: 0 residues added, 2792 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.216 Round 2: 66 peptides, 15 chains. Longest chain 7 peptides. Score 0.211 Round 3: 73 peptides, 14 chains. Longest chain 12 peptides. Score 0.288 Round 4: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.302 Round 5: 96 peptides, 19 chains. Longest chain 10 peptides. Score 0.298 Taking the results from Round 4 Chains 17, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 5827 restraints for refining 2293 atoms. 5560 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2439 (Rfree = 0.000) for 2293 atoms. Found 8 (12 requested) and removed 56 (6 requested) atoms. Cycle 2: After refmac, R = 0.2420 (Rfree = 0.000) for 2235 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 3: After refmac, R = 0.2355 (Rfree = 0.000) for 2209 atoms. Found 12 (12 requested) and removed 37 (6 requested) atoms. Cycle 4: After refmac, R = 0.2468 (Rfree = 0.000) for 2166 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 5: After refmac, R = 0.1989 (Rfree = 0.000) for 2150 atoms. Found 6 (11 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 2176 seeds are put forward NCS extension: 0 residues added, 2176 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.203 Round 2: 94 peptides, 18 chains. Longest chain 11 peptides. Score 0.312 Round 3: 104 peptides, 20 chains. Longest chain 10 peptides. Score 0.321 Round 4: 108 peptides, 21 chains. Longest chain 11 peptides. Score 0.320 Round 5: 101 peptides, 20 chains. Longest chain 11 peptides. Score 0.303 Taking the results from Round 3 Chains 20, Residues 84, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4585 restraints for refining 1975 atoms. 4246 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2055 (Rfree = 0.000) for 1975 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 7: After refmac, R = 0.2114 (Rfree = 0.000) for 1956 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 8: After refmac, R = 0.1884 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 9: After refmac, R = 0.2127 (Rfree = 0.000) for 1924 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 10: After refmac, R = 0.2045 (Rfree = 0.000) for 1911 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.73 Search for helices and strands: 0 residues in 0 chains, 1947 seeds are put forward NCS extension: 0 residues added, 1947 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.218 Round 2: 93 peptides, 18 chains. Longest chain 13 peptides. Score 0.306 Round 3: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.297 Round 4: 89 peptides, 19 chains. Longest chain 7 peptides. Score 0.254 Round 5: 92 peptides, 16 chains. Longest chain 12 peptides. Score 0.352 Taking the results from Round 5 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4430 restraints for refining 1861 atoms. 4131 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1911 (Rfree = 0.000) for 1861 atoms. Found 4 (10 requested) and removed 30 (5 requested) atoms. Cycle 12: After refmac, R = 0.1964 (Rfree = 0.000) for 1825 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.1780 (Rfree = 0.000) for 1823 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.1613 (Rfree = 0.000) for 1827 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.1479 (Rfree = 0.000) for 1821 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.82 Search for helices and strands: 0 residues in 0 chains, 1864 seeds are put forward NCS extension: 0 residues added, 1864 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 12 peptides. Score 0.266 Round 2: 96 peptides, 17 chains. Longest chain 8 peptides. Score 0.350 Round 3: 107 peptides, 19 chains. Longest chain 15 peptides. Score 0.364 Round 4: 105 peptides, 17 chains. Longest chain 11 peptides. Score 0.402 Round 5: 105 peptides, 18 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 4 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4344 restraints for refining 1890 atoms. 3966 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1673 (Rfree = 0.000) for 1890 atoms. Found 6 (10 requested) and removed 11 (5 requested) atoms. Cycle 17: After refmac, R = 0.1648 (Rfree = 0.000) for 1880 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.1478 (Rfree = 0.000) for 1879 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.1542 (Rfree = 0.000) for 1870 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1448 (Rfree = 0.000) for 1868 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 1915 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1927 seeds are put forward Round 1: 106 peptides, 23 chains. Longest chain 10 peptides. Score 0.257 Round 2: 116 peptides, 20 chains. Longest chain 14 peptides. Score 0.390 Round 3: 128 peptides, 22 chains. Longest chain 12 peptides. Score 0.409 Round 4: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.365 Round 5: 123 peptides, 20 chains. Longest chain 14 peptides. Score 0.428 Taking the results from Round 5 Chains 20, Residues 103, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4431 restraints for refining 1967 atoms. 4007 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1691 (Rfree = 0.000) for 1967 atoms. Found 9 (10 requested) and removed 13 (5 requested) atoms. Cycle 22: After refmac, R = 0.1552 (Rfree = 0.000) for 1950 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.1441 (Rfree = 0.000) for 1944 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.1367 (Rfree = 0.000) for 1940 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1335 (Rfree = 0.000) for 1934 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 2005 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2028 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.273 Round 2: 110 peptides, 19 chains. Longest chain 11 peptides. Score 0.381 Round 3: 109 peptides, 17 chains. Longest chain 16 peptides. Score 0.424 Round 4: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.404 Round 5: 109 peptides, 15 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 5 Chains 15, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4698 restraints for refining 1999 atoms. 4337 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1890 (Rfree = 0.000) for 1999 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.2013 (Rfree = 0.000) for 1977 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 28: After refmac, R = 0.1731 (Rfree = 0.000) for 1965 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 29: After refmac, R = 0.1355 (Rfree = 0.000) for 1955 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.1265 (Rfree = 0.000) for 1948 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 1977 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 2018 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 9 peptides. Score 0.239 Round 2: 108 peptides, 18 chains. Longest chain 11 peptides. Score 0.394 Round 3: 111 peptides, 18 chains. Longest chain 10 peptides. Score 0.411 Round 4: 110 peptides, 18 chains. Longest chain 14 peptides. Score 0.405 Round 5: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 3 Chains 18, Residues 93, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4546 restraints for refining 1995 atoms. 4168 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1853 (Rfree = 0.000) for 1995 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 32: After refmac, R = 0.1595 (Rfree = 0.000) for 1979 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 33: After refmac, R = 0.1314 (Rfree = 0.000) for 1976 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.1212 (Rfree = 0.000) for 1971 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 35: After refmac, R = 0.1177 (Rfree = 0.000) for 1965 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 2005 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2016 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 7 peptides. Score 0.268 Round 2: 108 peptides, 21 chains. Longest chain 15 peptides. Score 0.320 Round 3: 121 peptides, 22 chains. Longest chain 14 peptides. Score 0.370 Round 4: 106 peptides, 20 chains. Longest chain 10 peptides. Score 0.333 Round 5: 98 peptides, 18 chains. Longest chain 11 peptides. Score 0.336 Taking the results from Round 3 Chains 22, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4929 restraints for refining 2048 atoms. 4555 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1796 (Rfree = 0.000) for 2048 atoms. Found 11 (11 requested) and removed 35 (5 requested) atoms. Cycle 37: After refmac, R = 0.1640 (Rfree = 0.000) for 2020 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.1652 (Rfree = 0.000) for 2014 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 39: After refmac, R = 0.1391 (Rfree = 0.000) for 2002 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.1688 (Rfree = 0.000) for 1999 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 2042 seeds are put forward NCS extension: 0 residues added, 2042 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.241 Round 2: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.310 Round 3: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.318 Round 4: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.318 Round 5: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.330 Taking the results from Round 5 Chains 15, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4963 restraints for refining 2022 atoms. 4702 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1543 (Rfree = 0.000) for 2022 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.1852 (Rfree = 0.000) for 2015 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.1696 (Rfree = 0.000) for 2011 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 44: After refmac, R = 0.1689 (Rfree = 0.000) for 2002 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 45: After refmac, R = 0.1734 (Rfree = 0.000) for 1997 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.76 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 0 residues added, 2035 seeds are put forward Round 1: 76 peptides, 18 chains. Longest chain 5 peptides. Score 0.195 Round 2: 74 peptides, 16 chains. Longest chain 8 peptides. Score 0.238 Round 3: 74 peptides, 15 chains. Longest chain 9 peptides. Score 0.266 Round 4: 79 peptides, 17 chains. Longest chain 8 peptides. Score 0.243 Round 5: 79 peptides, 16 chains. Longest chain 10 peptides. Score 0.271 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 63, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2800 reflections ( 99.57 % complete ) and 4748 restraints for refining 1996 atoms. 4512 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1962 (Rfree = 0.000) for 1996 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1843 (Rfree = 0.000) for 1983 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1657 (Rfree = 0.000) for 1974 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1031 (Rfree = 0.000) for 1962 atoms. TimeTaking 25.18