Sun 23 Dec 22:23:14 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 1vk4-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk4-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.8-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/1vk4-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.8-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 22:23:22 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/1vk4-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk4-3.8-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 190 and 0 Target number of residues in the AU: 190 Target solvent content: 0.6394 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: 1vk4-3.8-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: 19 Cell parameters: 43.308 68.545 96.054 90.000 90.000 90.000 Input sequence file: 1vk4-3.8-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 3.800 Wilson plot Bfac: 70.63 3047 reflections ( 98.96 % complete ) and 0 restraints for refining 2637 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3099 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3287 (Rfree = 0.000) for 2637 atoms. Found 14 (14 requested) and removed 70 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.92 Search for helices and strands: 0 residues in 0 chains, 2611 seeds are put forward Round 1: 104 peptides, 23 chains. Longest chain 7 peptides. Score 0.246 Round 2: 146 peptides, 28 chains. Longest chain 12 peptides. Score 0.373 Round 3: 150 peptides, 27 chains. Longest chain 11 peptides. Score 0.418 Round 4: 144 peptides, 25 chains. Longest chain 14 peptides. Score 0.431 Round 5: 155 peptides, 23 chains. Longest chain 14 peptides. Score 0.529 Taking the results from Round 5 Chains 24, Residues 132, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3047 reflections ( 98.96 % complete ) and 4710 restraints for refining 2121 atoms. 4151 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2605 (Rfree = 0.000) for 2121 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 2: After refmac, R = 0.2636 (Rfree = 0.000) for 2056 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 3: After refmac, R = 0.3009 (Rfree = 0.000) for 2020 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. Cycle 4: After refmac, R = 0.2671 (Rfree = 0.000) for 1998 atoms. Found 5 (11 requested) and removed 13 (5 requested) atoms. Cycle 5: After refmac, R = 0.2256 (Rfree = 0.000) for 1980 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.83 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward Round 1: 119 peptides, 23 chains. Longest chain 10 peptides. Score 0.338 Round 2: 151 peptides, 28 chains. Longest chain 12 peptides. Score 0.400 Round 3: 139 peptides, 24 chains. Longest chain 10 peptides. Score 0.427 Round 4: 140 peptides, 22 chains. Longest chain 14 peptides. Score 0.478 Round 5: 150 peptides, 23 chains. Longest chain 14 peptides. Score 0.506 Taking the results from Round 5 Chains 23, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3047 reflections ( 98.96 % complete ) and 4422 restraints for refining 1944 atoms. 3937 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2584 (Rfree = 0.000) for 1944 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 7: After refmac, R = 0.2286 (Rfree = 0.000) for 1932 atoms. Found 3 (10 requested) and removed 207 (5 requested) atoms. Cycle 8: After refmac, R = 0.2593 (Rfree = 0.000) for 1726 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.2168 (Rfree = 0.000) for 1718 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2192 (Rfree = 0.000) for 1713 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.90 Search for helices and strands: 0 residues in 0 chains, 1796 seeds are put forward Round 1: 146 peptides, 29 chains. Longest chain 9 peptides. Score 0.349 Round 2: 150 peptides, 27 chains. Longest chain 11 peptides. Score 0.418 Round 3: 148 peptides, 23 chains. Longest chain 17 peptides. Score 0.496 Round 4: 154 peptides, 25 chains. Longest chain 11 peptides. Score 0.483 Round 5: 153 peptides, 26 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 3 Chains 23, Residues 125, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3047 reflections ( 98.96 % complete ) and 4133 restraints for refining 1940 atoms. 3630 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2450 (Rfree = 0.000) for 1940 atoms. Found 7 (10 requested) and removed 18 (5 requested) atoms. Cycle 12: After refmac, R = 0.2071 (Rfree = 0.000) for 1922 atoms. Found 4 (10 requested) and removed 12 (5 requested) atoms. Cycle 13: After refmac, R = 0.1945 (Rfree = 0.000) for 1910 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.1940 (Rfree = 0.000) for 1903 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2065 (Rfree = 0.000) for 1896 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 1956 seeds are put forward Round 1: 138 peptides, 26 chains. Longest chain 10 peptides. Score 0.375 Round 2: 156 peptides, 25 chains. Longest chain 14 peptides. Score 0.493 Round 3: 155 peptides, 24 chains. Longest chain 17 peptides. Score 0.509 Round 4: 162 peptides, 22 chains. Longest chain 20 peptides. Score 0.581 Round 5: 157 peptides, 22 chains. Longest chain 19 peptides. Score 0.559 Taking the results from Round 4 Chains 22, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3047 reflections ( 98.96 % complete ) and 4486 restraints for refining 2042 atoms. 3948 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2418 (Rfree = 0.000) for 2042 atoms. Found 6 (11 requested) and removed 22 (5 requested) atoms. Cycle 17: After refmac, R = 0.2054 (Rfree = 0.000) for 2020 atoms. Found 2 (11 requested) and removed 13 (5 requested) atoms. Cycle 18: After refmac, R = 0.2312 (Rfree = 0.000) for 2002 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 19: After refmac, R = 0.2041 (Rfree = 0.000) for 1995 atoms. Found 10 (10 requested) and removed 37 (5 requested) atoms. Cycle 20: After refmac, R = 0.1981 (Rfree = 0.000) for 1960 atoms. Found 6 (10 requested) and removed 48 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.75 Search for helices and strands: 0 residues in 0 chains, 1994 seeds are put forward Round 1: 108 peptides, 22 chains. Longest chain 9 peptides. Score 0.297 Round 2: 135 peptides, 25 chains. Longest chain 11 peptides. Score 0.382 Round 3: 131 peptides, 22 chains. Longest chain 12 peptides. Score 0.430 Round 4: 136 peptides, 24 chains. Longest chain 11 peptides. Score 0.411 Round 5: 133 peptides, 20 chains. Longest chain 13 peptides. Score 0.486 Taking the results from Round 5 Chains 22, Residues 113, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3047 reflections ( 98.96 % complete ) and 4511 restraints for refining 2092 atoms. 4025 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2851 (Rfree = 0.000) for 2092 atoms. Found 11 (11 requested) and removed 31 (5 requested) atoms. Cycle 22: After refmac, R = 0.2345 (Rfree = 0.000) for 2054 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 23: After refmac, R = 0.2209 (Rfree = 0.000) for 2036 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 24: After refmac, R = 0.2181 (Rfree = 0.000) for 2027 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 25: After refmac, R = 0.2010 (Rfree = 0.000) for 2021 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.90 Search for helices and strands: 0 residues in 0 chains, 2086 seeds are put forward Round 1: 110 peptides, 22 chains. Longest chain 10 peptides. Score 0.310 Round 2: 127 peptides, 25 chains. Longest chain 10 peptides. Score 0.336 Round 3: 129 peptides, 23 chains. Longest chain 10 peptides. Score 0.396 Round 4: 129 peptides, 23 chains. Longest chain 10 peptides. Score 0.396 Round 5: 136 peptides, 25 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 4 Chains 23, Residues 106, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3047 reflections ( 98.96 % complete ) and 4723 restraints for refining 2111 atoms. 4301 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2459 (Rfree = 0.000) for 2111 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 27: After refmac, R = 0.2275 (Rfree = 0.000) for 2093 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 28: After refmac, R = 0.1982 (Rfree = 0.000) for 2079 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 29: After refmac, R = 0.2111 (Rfree = 0.000) for 2068 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 30: After refmac, R = 0.1919 (Rfree = 0.000) for 2056 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 2126 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 7 peptides. Score 0.269 Round 2: 115 peptides, 21 chains. Longest chain 11 peptides. Score 0.365 Round 3: 117 peptides, 20 chains. Longest chain 12 peptides. Score 0.401 Round 4: 118 peptides, 21 chains. Longest chain 8 peptides. Score 0.382 Round 5: 113 peptides, 19 chains. Longest chain 12 peptides. Score 0.403 Taking the results from Round 5 Chains 19, Residues 94, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3047 reflections ( 98.96 % complete ) and 4826 restraints for refining 2086 atoms. 4438 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2163 (Rfree = 0.000) for 2086 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 32: After refmac, R = 0.2063 (Rfree = 0.000) for 2071 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 33: After refmac, R = 0.2032 (Rfree = 0.000) for 2066 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.1453 (Rfree = 0.000) for 2060 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. Cycle 35: After refmac, R = 0.1468 (Rfree = 0.000) for 2055 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 2100 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 5 peptides. Score 0.209 Round 2: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.342 Round 3: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.317 Round 4: 89 peptides, 15 chains. Longest chain 13 peptides. Score 0.365 Round 5: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.350 Taking the results from Round 4 Chains 15, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3047 reflections ( 98.96 % complete ) and 4964 restraints for refining 2077 atoms. 4683 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1930 (Rfree = 0.000) for 2077 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.2353 (Rfree = 0.000) for 2068 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 38: After refmac, R = 0.1749 (Rfree = 0.000) for 2044 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.1939 (Rfree = 0.000) for 2043 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 40: After refmac, R = 0.1977 (Rfree = 0.000) for 2043 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.80 Search for helices and strands: 0 residues in 0 chains, 2093 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 8 peptides. Score 0.220 Round 2: 80 peptides, 16 chains. Longest chain 12 peptides. Score 0.280 Round 3: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.267 Round 4: 93 peptides, 16 chains. Longest chain 10 peptides. Score 0.362 Round 5: 95 peptides, 16 chains. Longest chain 14 peptides. Score 0.374 Taking the results from Round 5 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3047 reflections ( 98.96 % complete ) and 4615 restraints for refining 2036 atoms. 4303 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1815 (Rfree = 0.000) for 2036 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.1836 (Rfree = 0.000) for 2027 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2085 (Rfree = 0.000) for 2024 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.1901 (Rfree = 0.000) for 2021 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1821 (Rfree = 0.000) for 2019 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 2067 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.205 Round 2: 77 peptides, 17 chains. Longest chain 9 peptides. Score 0.231 Round 3: 76 peptides, 15 chains. Longest chain 10 peptides. Score 0.282 Round 4: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.282 Round 5: 73 peptides, 16 chains. Longest chain 8 peptides. Score 0.232 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 61, 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 1vk4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3047 reflections ( 98.96 % complete ) and 4715 restraints for refining 2009 atoms. 4486 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2192 (Rfree = 0.000) for 2009 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1834 (Rfree = 0.000) for 1998 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1672 (Rfree = 0.000) for 1991 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1377 (Rfree = 0.000) for 1982 atoms. TimeTaking 32.18