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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prx-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prx-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-3.8-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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-3.8-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 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-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-3.8-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 3.801 Wilson plot Bfac: 59.98 2800 reflections ( 99.57 % complete ) and 0 restraints for refining 2839 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3193 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2930 (Rfree = 0.000) for 2839 atoms. Found 15 (15 requested) and removed 74 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 2799 seeds are put forward NCS extension: 0 residues added, 2799 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 5 peptides. Score 0.190 Round 2: 89 peptides, 19 chains. Longest chain 11 peptides. Score 0.254 Round 3: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.302 Round 4: 107 peptides, 19 chains. Longest chain 9 peptides. Score 0.364 Round 5: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 4 Chains 19, Residues 88, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 5646 restraints for refining 2278 atoms. 5278 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2473 (Rfree = 0.000) for 2278 atoms. Found 12 (12 requested) and removed 48 (6 requested) atoms. Cycle 2: After refmac, R = 0.2500 (Rfree = 0.000) for 2208 atoms. Found 10 (12 requested) and removed 32 (6 requested) atoms. Cycle 3: After refmac, R = 0.1958 (Rfree = 0.000) for 2166 atoms. Found 5 (12 requested) and removed 15 (6 requested) atoms. Cycle 4: After refmac, R = 0.1873 (Rfree = 0.000) for 2146 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.2009 (Rfree = 0.000) for 2126 atoms. Found 5 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.71 Search for helices and strands: 0 residues in 0 chains, 2169 seeds are put forward NCS extension: 0 residues added, 2169 seeds are put forward Round 1: 72 peptides, 17 chains. Longest chain 6 peptides. Score 0.195 Round 2: 103 peptides, 21 chains. Longest chain 11 peptides. Score 0.290 Round 3: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.341 Round 4: 101 peptides, 18 chains. Longest chain 11 peptides. Score 0.354 Round 5: 105 peptides, 18 chains. Longest chain 13 peptides. Score 0.377 Taking the results from Round 5 Chains 18, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4951 restraints for refining 2059 atoms. 4621 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2267 (Rfree = 0.000) for 2059 atoms. Found 9 (11 requested) and removed 23 (5 requested) atoms. Cycle 7: After refmac, R = 0.2059 (Rfree = 0.000) for 2036 atoms. Found 4 (11 requested) and removed 26 (5 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2019 (Rfree = 0.000) for 2011 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.1992 (Rfree = 0.000) for 2004 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.1971 (Rfree = 0.000) for 2002 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.77 Search for helices and strands: 0 residues in 0 chains, 2046 seeds are put forward NCS extension: 0 residues added, 2046 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.245 Round 2: 101 peptides, 19 chains. Longest chain 12 peptides. Score 0.329 Round 3: 100 peptides, 18 chains. Longest chain 8 peptides. Score 0.348 Round 4: 118 peptides, 22 chains. Longest chain 8 peptides. Score 0.353 Round 5: 113 peptides, 17 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 5 Chains 17, Residues 96, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4877 restraints for refining 2091 atoms. 4457 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1968 (Rfree = 0.000) for 2091 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 12: After refmac, R = 0.1781 (Rfree = 0.000) for 2062 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.1731 (Rfree = 0.000) for 2052 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.1739 (Rfree = 0.000) for 2044 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.1757 (Rfree = 0.000) for 2039 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2090 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 7 peptides. Score 0.260 Round 2: 115 peptides, 22 chains. Longest chain 10 peptides. Score 0.336 Round 3: 111 peptides, 21 chains. Longest chain 9 peptides. Score 0.337 Round 4: 117 peptides, 21 chains. Longest chain 10 peptides. Score 0.372 Round 5: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.324 Taking the results from Round 4 Chains 21, Residues 96, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4978 restraints for refining 2122 atoms. 4583 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1876 (Rfree = 0.000) for 2122 atoms. Found 9 (11 requested) and removed 15 (5 requested) atoms. Cycle 17: After refmac, R = 0.1751 (Rfree = 0.000) for 2109 atoms. Found 5 (11 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.1694 (Rfree = 0.000) for 2099 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.1682 (Rfree = 0.000) for 2095 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1669 (Rfree = 0.000) for 2091 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 2150 seeds are put forward NCS extension: 0 residues added, 2150 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 10 peptides. Score 0.272 Round 2: 100 peptides, 19 chains. Longest chain 11 peptides. Score 0.323 Round 3: 99 peptides, 19 chains. Longest chain 11 peptides. Score 0.317 Round 4: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.344 Round 5: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.340 Taking the results from Round 4 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 5218 restraints for refining 2133 atoms. 4923 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1767 (Rfree = 0.000) for 2133 atoms. Found 7 (11 requested) and removed 25 (5 requested) atoms. Cycle 22: After refmac, R = 0.1648 (Rfree = 0.000) for 2108 atoms. Found 8 (11 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.1590 (Rfree = 0.000) for 2101 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.1571 (Rfree = 0.000) for 2097 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1549 (Rfree = 0.000) for 2092 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.74 Search for helices and strands: 0 residues in 0 chains, 2140 seeds are put forward NCS extension: 0 residues added, 2140 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.263 Round 2: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.384 Round 3: 111 peptides, 19 chains. Longest chain 13 peptides. Score 0.387 Round 4: 114 peptides, 21 chains. Longest chain 15 peptides. Score 0.355 Round 5: 109 peptides, 18 chains. Longest chain 14 peptides. Score 0.400 Taking the results from Round 5 Chains 18, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 5059 restraints for refining 2128 atoms. 4713 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1805 (Rfree = 0.000) for 2128 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 27: After refmac, R = 0.1792 (Rfree = 0.000) for 2116 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 28: After refmac, R = 0.1469 (Rfree = 0.000) for 2105 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.1559 (Rfree = 0.000) for 2099 atoms. Found 7 (11 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.1903 (Rfree = 0.000) for 2090 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.69 Search for helices and strands: 0 residues in 0 chains, 2139 seeds are put forward NCS extension: 0 residues added, 2139 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 6 peptides. Score 0.256 Round 2: 91 peptides, 19 chains. Longest chain 6 peptides. Score 0.267 Round 3: 101 peptides, 18 chains. Longest chain 8 peptides. Score 0.354 Round 4: 102 peptides, 18 chains. Longest chain 10 peptides. Score 0.360 Round 5: 112 peptides, 19 chains. Longest chain 10 peptides. Score 0.392 Taking the results from Round 5 Chains 19, Residues 93, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4825 restraints for refining 2110 atoms. 4442 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1681 (Rfree = 0.000) for 2110 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 32: After refmac, R = 0.1683 (Rfree = 0.000) for 2086 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 33: After refmac, R = 0.1292 (Rfree = 0.000) for 2078 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.1165 (Rfree = 0.000) for 2064 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.1151 (Rfree = 0.000) for 2057 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.74 Search for helices and strands: 0 residues in 0 chains, 2100 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2112 seeds are put forward Round 1: 101 peptides, 22 chains. Longest chain 8 peptides. Score 0.251 Round 2: 109 peptides, 19 chains. Longest chain 10 peptides. Score 0.375 Round 3: 106 peptides, 18 chains. Longest chain 10 peptides. Score 0.383 Round 4: 106 peptides, 18 chains. Longest chain 12 peptides. Score 0.383 Round 5: 99 peptides, 17 chains. Longest chain 9 peptides. Score 0.368 Taking the results from Round 4 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4923 restraints for refining 2124 atoms. 4589 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1765 (Rfree = 0.000) for 2124 atoms. Found 11 (11 requested) and removed 21 (5 requested) atoms. Cycle 37: After refmac, R = 0.1691 (Rfree = 0.000) for 2107 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 38: After refmac, R = 0.1717 (Rfree = 0.000) for 2098 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 39: After refmac, R = 0.1690 (Rfree = 0.000) for 2084 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 40: After refmac, R = 0.1105 (Rfree = 0.000) for 2070 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.77 Search for helices and strands: 0 residues in 0 chains, 2107 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 2114 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 9 peptides. Score 0.260 Round 2: 83 peptides, 16 chains. Longest chain 7 peptides. Score 0.297 Round 3: 92 peptides, 17 chains. Longest chain 9 peptides. Score 0.326 Round 4: 98 peptides, 18 chains. Longest chain 9 peptides. Score 0.336 Round 5: 90 peptides, 17 chains. Longest chain 7 peptides. Score 0.314 Taking the results from Round 4 Chains 18, Residues 80, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2800 reflections ( 99.57 % complete ) and 4555 restraints for refining 2035 atoms. 4222 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1661 (Rfree = 0.000) for 2035 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 42: After refmac, R = 0.1757 (Rfree = 0.000) for 2023 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 43: After refmac, R = 0.1162 (Rfree = 0.000) for 2016 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.1133 (Rfree = 0.000) for 2010 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.1142 (Rfree = 0.000) for 2004 atoms. Found 1 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 2049 seeds are put forward NCS extension: 0 residues added, 2049 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.249 Round 2: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.336 Round 3: 79 peptides, 13 chains. Longest chain 9 peptides. Score 0.354 Round 4: 84 peptides, 14 chains. Longest chain 10 peptides. Score 0.357 Round 5: 83 peptides, 12 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 71, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 12 % 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 4622 restraints for refining 2015 atoms. 4339 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1448 (Rfree = 0.000) for 2015 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1387 (Rfree = 0.000) for 2009 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1543 (Rfree = 0.000) for 2003 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1293 (Rfree = 0.000) for 1997 atoms. TimeTaking 34.38