null Tue 25 Dec 19:27:57 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 1vk4-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.6-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/1vk4-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.6-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 ============================================================ Tue 25 Dec 19:28:07 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/1vk4-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.6-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 200 and 0 Target number of residues in the AU: 200 Target solvent content: 0.6204 Checking the provided sequence file Detected sequence length: 298 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 298 Adjusted target solvent content: 0.43 Input MTZ file: 1vk4-3.6-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: 19 Cell parameters: 43.308 68.545 96.054 90.000 90.000 90.000 Input sequence file: 1vk4-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2384 target number of atoms Had to go as low as 0.60 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 Loops will be built when appropriate and at the last cycle Resolution range: 55.795 3.600 Wilson plot Bfac: 61.14 3559 reflections ( 99.11 % complete ) and 0 restraints for refining 2639 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3044 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3123 (Rfree = 0.000) for 2639 atoms. Found 16 (16 requested) and removed 64 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.73 Search for helices and strands: 0 residues in 0 chains, 2645 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 9 peptides. Score 0.280 Round 2: 114 peptides, 20 chains. Longest chain 11 peptides. Score 0.384 Round 3: 133 peptides, 23 chains. Longest chain 11 peptides. Score 0.418 Round 4: 130 peptides, 22 chains. Longest chain 13 peptides. Score 0.425 Round 5: 156 peptides, 24 chains. Longest chain 15 peptides. Score 0.514 Taking the results from Round 5 Chains 24, Residues 132, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3559 reflections ( 99.11 % complete ) and 4540 restraints for refining 2095 atoms. 4012 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2684 (Rfree = 0.000) for 2095 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 2: After refmac, R = 0.2337 (Rfree = 0.000) for 2068 atoms. Found 8 (13 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2382 (Rfree = 0.000) for 2045 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2446 (Rfree = 0.000) for 2032 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.2060 (Rfree = 0.000) for 2024 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.65 Search for helices and strands: 0 residues in 0 chains, 2094 seeds are put forward Round 1: 115 peptides, 21 chains. Longest chain 9 peptides. Score 0.365 Round 2: 144 peptides, 24 chains. Longest chain 12 peptides. Score 0.454 Round 3: 151 peptides, 24 chains. Longest chain 12 peptides. Score 0.489 Round 4: 151 peptides, 21 chains. Longest chain 16 peptides. Score 0.552 Round 5: 165 peptides, 26 chains. Longest chain 15 peptides. Score 0.515 Taking the results from Round 4 Chains 22, Residues 130, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3559 reflections ( 99.11 % complete ) and 4325 restraints for refining 1989 atoms. 3795 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2346 (Rfree = 0.000) for 1989 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 7: After refmac, R = 0.2337 (Rfree = 0.000) for 1974 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 8: After refmac, R = 0.2373 (Rfree = 0.000) for 1958 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 9: After refmac, R = 0.1997 (Rfree = 0.000) for 1951 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.1917 (Rfree = 0.000) for 1950 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.69 Search for helices and strands: 0 residues in 0 chains, 2021 seeds are put forward Round 1: 137 peptides, 25 chains. Longest chain 15 peptides. Score 0.393 Round 2: 163 peptides, 30 chains. Longest chain 8 peptides. Score 0.420 Round 3: 166 peptides, 26 chains. Longest chain 15 peptides. Score 0.520 Round 4: 165 peptides, 25 chains. Longest chain 19 peptides. Score 0.535 Round 5: 180 peptides, 28 chains. Longest chain 15 peptides. Score 0.545 Taking the results from Round 5 Chains 28, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3559 reflections ( 99.11 % complete ) and 4437 restraints for refining 2030 atoms. 3857 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2656 (Rfree = 0.000) for 2030 atoms. Found 12 (13 requested) and removed 19 (6 requested) atoms. Cycle 12: After refmac, R = 0.2289 (Rfree = 0.000) for 2012 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 13: After refmac, R = 0.1975 (Rfree = 0.000) for 2006 atoms. Found 1 (12 requested) and removed 19 (6 requested) atoms. Cycle 14: After refmac, R = 0.1973 (Rfree = 0.000) for 1986 atoms. Found 4 (12 requested) and removed 16 (6 requested) atoms. Cycle 15: After refmac, R = 0.2041 (Rfree = 0.000) for 1974 atoms. Found 7 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.68 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 11 peptides. Score 0.352 Round 2: 147 peptides, 24 chains. Longest chain 14 peptides. Score 0.469 Round 3: 151 peptides, 26 chains. Longest chain 12 peptides. Score 0.446 Round 4: 158 peptides, 25 chains. Longest chain 13 peptides. Score 0.502 Round 5: 153 peptides, 25 chains. Longest chain 10 peptides. Score 0.478 Taking the results from Round 4 Chains 25, Residues 133, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3559 reflections ( 99.11 % complete ) and 4637 restraints for refining 2101 atoms. 4091 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2341 (Rfree = 0.000) for 2101 atoms. Found 10 (13 requested) and removed 18 (6 requested) atoms. Cycle 17: After refmac, R = 0.2177 (Rfree = 0.000) for 2080 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 18: After refmac, R = 0.2039 (Rfree = 0.000) for 2055 atoms. Found 11 (13 requested) and removed 13 (6 requested) atoms. Cycle 19: After refmac, R = 0.1922 (Rfree = 0.000) for 2044 atoms. Found 6 (13 requested) and removed 11 (6 requested) atoms. Cycle 20: After refmac, R = 0.1791 (Rfree = 0.000) for 2031 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.59 Search for helices and strands: 0 residues in 0 chains, 2111 seeds are put forward Round 1: 124 peptides, 24 chains. Longest chain 13 peptides. Score 0.343 Round 2: 159 peptides, 24 chains. Longest chain 13 peptides. Score 0.528 Round 3: 158 peptides, 23 chains. Longest chain 13 peptides. Score 0.543 Round 4: 161 peptides, 25 chains. Longest chain 15 peptides. Score 0.517 Round 5: 162 peptides, 26 chains. Longest chain 14 peptides. Score 0.501 Taking the results from Round 3 Chains 23, Residues 135, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3559 reflections ( 99.11 % complete ) and 4584 restraints for refining 2111 atoms. 4015 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2172 (Rfree = 0.000) for 2111 atoms. Found 9 (13 requested) and removed 30 (6 requested) atoms. Cycle 22: After refmac, R = 0.2022 (Rfree = 0.000) for 2073 atoms. Found 10 (13 requested) and removed 19 (6 requested) atoms. Cycle 23: After refmac, R = 0.1537 (Rfree = 0.000) for 2058 atoms. Found 6 (13 requested) and removed 12 (6 requested) atoms. Cycle 24: After refmac, R = 0.1578 (Rfree = 0.000) for 2050 atoms. Found 4 (13 requested) and removed 13 (6 requested) atoms. Cycle 25: After refmac, R = 0.1882 (Rfree = 0.000) for 2038 atoms. Found 9 (13 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.59 Search for helices and strands: 0 residues in 0 chains, 2091 seeds are put forward Round 1: 122 peptides, 22 chains. Longest chain 12 peptides. Score 0.381 Round 2: 127 peptides, 21 chains. Longest chain 10 peptides. Score 0.432 Round 3: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.392 Round 4: 137 peptides, 20 chains. Longest chain 12 peptides. Score 0.506 Round 5: 139 peptides, 23 chains. Longest chain 11 peptides. Score 0.450 Taking the results from Round 4 Chains 21, Residues 117, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3559 reflections ( 99.11 % complete ) and 4768 restraints for refining 2133 atoms. 4288 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2339 (Rfree = 0.000) for 2133 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 27: After refmac, R = 0.2103 (Rfree = 0.000) for 2113 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2009 (Rfree = 0.000) for 2107 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1754 (Rfree = 0.000) for 2107 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.1818 (Rfree = 0.000) for 2101 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.51 Search for helices and strands: 0 residues in 0 chains, 2175 seeds are put forward Round 1: 113 peptides, 23 chains. Longest chain 11 peptides. Score 0.302 Round 2: 129 peptides, 24 chains. Longest chain 10 peptides. Score 0.372 Round 3: 126 peptides, 24 chains. Longest chain 11 peptides. Score 0.355 Round 4: 129 peptides, 21 chains. Longest chain 11 peptides. Score 0.443 Round 5: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 4 Chains 21, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3559 reflections ( 99.11 % complete ) and 5076 restraints for refining 2161 atoms. 4665 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2077 (Rfree = 0.000) for 2161 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.1891 (Rfree = 0.000) for 2143 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.1761 (Rfree = 0.000) for 2136 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.1864 (Rfree = 0.000) for 2135 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 35: After refmac, R = 0.1694 (Rfree = 0.000) for 2137 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.57 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward Round 1: 105 peptides, 24 chains. Longest chain 6 peptides. Score 0.226 Round 2: 127 peptides, 24 chains. Longest chain 9 peptides. Score 0.361 Round 3: 116 peptides, 22 chains. Longest chain 8 peptides. Score 0.346 Round 4: 111 peptides, 19 chains. Longest chain 10 peptides. Score 0.391 Round 5: 112 peptides, 19 chains. Longest chain 10 peptides. Score 0.397 Taking the results from Round 5 Chains 19, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3559 reflections ( 99.11 % complete ) and 5107 restraints for refining 2161 atoms. 4754 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1986 (Rfree = 0.000) for 2161 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 37: After refmac, R = 0.1845 (Rfree = 0.000) for 2158 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.1949 (Rfree = 0.000) for 2160 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1756 (Rfree = 0.000) for 2164 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1855 (Rfree = 0.000) for 2164 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.58 Search for helices and strands: 0 residues in 0 chains, 2214 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 9 peptides. Score 0.212 Round 2: 95 peptides, 21 chains. Longest chain 8 peptides. Score 0.241 Round 3: 114 peptides, 22 chains. Longest chain 9 peptides. Score 0.334 Round 4: 115 peptides, 21 chains. Longest chain 11 peptides. Score 0.365 Round 5: 122 peptides, 23 chains. Longest chain 9 peptides. Score 0.356 Taking the results from Round 4 Chains 21, Residues 94, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3559 reflections ( 99.11 % complete ) and 5059 restraints for refining 2148 atoms. 4693 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2132 (Rfree = 0.000) for 2148 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 42: After refmac, R = 0.1896 (Rfree = 0.000) for 2135 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.1812 (Rfree = 0.000) for 2129 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.1741 (Rfree = 0.000) for 2126 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.1255 (Rfree = 0.000) for 2127 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.57 Search for helices and strands: 0 residues in 0 chains, 2198 seeds are put forward Round 1: 96 peptides, 22 chains. Longest chain 6 peptides. Score 0.221 Round 2: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.305 Round 3: 114 peptides, 22 chains. Longest chain 10 peptides. Score 0.334 Round 4: 109 peptides, 19 chains. Longest chain 12 peptides. Score 0.380 Round 5: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.361 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 90, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 1vk4-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (90 residues) following loop building 2 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3559 reflections ( 99.11 % complete ) and 4859 restraints for refining 2161 atoms. 4443 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1771 (Rfree = 0.000) for 2161 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1914 (Rfree = 0.000) for 2143 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2004 (Rfree = 0.000) for 2135 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1685 (Rfree = 0.000) for 2124 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:10:14 GMT 2018 Job finished. TimeTaking 42.28 Used memory is bytes: 6326120