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 2okf-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okf-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okf-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-3.4-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/2okf-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-3.4-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 22:22:52 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/2okf-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-3.4-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 205 and 0 Target number of residues in the AU: 205 Target solvent content: 0.6340 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 280 Adjusted target solvent content: 0.50 Input MTZ file: 2okf-3.4-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: 59.870 59.870 73.240 90.000 90.000 120.000 Input sequence file: 2okf-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2240 target number of atoms Had to go as low as 0.70 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: 27.710 3.400 Wilson plot Bfac: 68.65 4027 reflections ( 99.58 % complete ) and 0 restraints for refining 2468 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3329 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2705 (Rfree = 0.000) for 2468 atoms. Found 9 (18 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 2512 seeds are put forward NCS extension: 0 residues added, 2512 seeds are put forward Round 1: 134 peptides, 24 chains. Longest chain 11 peptides. Score 0.389 Round 2: 170 peptides, 27 chains. Longest chain 12 peptides. Score 0.503 Round 3: 167 peptides, 23 chains. Longest chain 16 peptides. Score 0.566 Round 4: 174 peptides, 24 chains. Longest chain 20 peptides. Score 0.577 Round 5: 177 peptides, 25 chains. Longest chain 16 peptides. Score 0.571 Taking the results from Round 4 Chains 25, Residues 150, Estimated correctness of the model 21.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.58 % complete ) and 4398 restraints for refining 2037 atoms. 3764 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2364 (Rfree = 0.000) for 2037 atoms. Found 11 (15 requested) and removed 17 (7 requested) atoms. Cycle 2: After refmac, R = 0.2096 (Rfree = 0.000) for 1998 atoms. Found 9 (15 requested) and removed 14 (7 requested) atoms. Cycle 3: After refmac, R = 0.1982 (Rfree = 0.000) for 1986 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.1981 (Rfree = 0.000) for 1970 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.1922 (Rfree = 0.000) for 1956 atoms. Found 1 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.25 Search for helices and strands: 0 residues in 0 chains, 2014 seeds are put forward NCS extension: 8 residues added (7 deleted due to clashes), 2022 seeds are put forward Round 1: 136 peptides, 26 chains. Longest chain 11 peptides. Score 0.355 Round 2: 158 peptides, 22 chains. Longest chain 14 peptides. Score 0.547 Round 3: 182 peptides, 26 chains. Longest chain 15 peptides. Score 0.573 Round 4: 188 peptides, 27 chains. Longest chain 19 peptides. Score 0.580 Round 5: 180 peptides, 24 chains. Longest chain 22 peptides. Score 0.600 Taking the results from Round 5 Chains 24, Residues 156, Estimated correctness of the model 28.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.58 % complete ) and 4305 restraints for refining 1990 atoms. 3705 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2319 (Rfree = 0.000) for 1990 atoms. Found 4 (15 requested) and removed 15 (7 requested) atoms. Cycle 7: After refmac, R = 0.2147 (Rfree = 0.000) for 1971 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 8: After refmac, R = 0.2113 (Rfree = 0.000) for 1960 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. Cycle 9: After refmac, R = 0.2109 (Rfree = 0.000) for 1945 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.2023 (Rfree = 0.000) for 1935 atoms. Found 0 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.24 Search for helices and strands: 0 residues in 0 chains, 2000 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 2028 seeds are put forward Round 1: 161 peptides, 24 chains. Longest chain 17 peptides. Score 0.521 Round 2: 177 peptides, 24 chains. Longest chain 18 peptides. Score 0.589 Round 3: 183 peptides, 26 chains. Longest chain 18 peptides. Score 0.577 Round 4: 177 peptides, 23 chains. Longest chain 19 peptides. Score 0.606 Round 5: 181 peptides, 23 chains. Longest chain 19 peptides. Score 0.621 Taking the results from Round 5 Chains 25, Residues 158, Estimated correctness of the model 35.4 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.58 % complete ) and 4290 restraints for refining 2037 atoms. 3618 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2594 (Rfree = 0.000) for 2037 atoms. Found 10 (15 requested) and removed 11 (7 requested) atoms. Cycle 12: After refmac, R = 0.2292 (Rfree = 0.000) for 2030 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2204 (Rfree = 0.000) for 2017 atoms. Found 0 (15 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.2152 (Rfree = 0.000) for 2008 atoms. Found 2 (15 requested) and removed 13 (7 requested) atoms. Cycle 15: After refmac, R = 0.2065 (Rfree = 0.000) for 1995 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.27 Search for helices and strands: 0 residues in 0 chains, 2040 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 2065 seeds are put forward Round 1: 149 peptides, 26 chains. Longest chain 12 peptides. Score 0.423 Round 2: 164 peptides, 26 chains. Longest chain 17 peptides. Score 0.495 Round 3: 173 peptides, 23 chains. Longest chain 21 peptides. Score 0.590 Round 4: 163 peptides, 25 chains. Longest chain 18 peptides. Score 0.511 Round 5: 161 peptides, 22 chains. Longest chain 18 peptides. Score 0.559 Taking the results from Round 3 Chains 23, Residues 150, Estimated correctness of the model 25.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.58 % complete ) and 4455 restraints for refining 2037 atoms. 3878 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2144 (Rfree = 0.000) for 2037 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. Cycle 17: After refmac, R = 0.2013 (Rfree = 0.000) for 2021 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. Cycle 18: After refmac, R = 0.1900 (Rfree = 0.000) for 2012 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 19: After refmac, R = 0.1953 (Rfree = 0.000) for 2004 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.1942 (Rfree = 0.000) for 1998 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 2060 seeds are put forward Round 1: 150 peptides, 28 chains. Longest chain 14 peptides. Score 0.384 Round 2: 161 peptides, 24 chains. Longest chain 19 peptides. Score 0.521 Round 3: 157 peptides, 25 chains. Longest chain 15 peptides. Score 0.483 Round 4: 153 peptides, 22 chains. Longest chain 14 peptides. Score 0.525 Round 5: 160 peptides, 24 chains. Longest chain 16 peptides. Score 0.517 Taking the results from Round 4 Chains 23, Residues 131, Estimated correctness of the model 2.3 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.58 % complete ) and 4459 restraints for refining 2037 atoms. 3916 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2024 (Rfree = 0.000) for 2037 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. Cycle 22: After refmac, R = 0.1862 (Rfree = 0.000) for 2028 atoms. Found 1 (15 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.1768 (Rfree = 0.000) for 2013 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.1862 (Rfree = 0.000) for 2005 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1780 (Rfree = 0.000) for 1995 atoms. Found 0 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 2039 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2047 seeds are put forward Round 1: 124 peptides, 20 chains. Longest chain 13 peptides. Score 0.427 Round 2: 136 peptides, 21 chains. Longest chain 14 peptides. Score 0.466 Round 3: 138 peptides, 20 chains. Longest chain 15 peptides. Score 0.496 Round 4: 145 peptides, 22 chains. Longest chain 18 peptides. Score 0.488 Round 5: 144 peptides, 21 chains. Longest chain 15 peptides. Score 0.504 Taking the results from Round 5 Chains 21, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.58 % complete ) and 4731 restraints for refining 2037 atoms. 4260 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1949 (Rfree = 0.000) for 2037 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.1767 (Rfree = 0.000) for 2032 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.1800 (Rfree = 0.000) for 2022 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.1798 (Rfree = 0.000) for 2013 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1746 (Rfree = 0.000) for 2008 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 2058 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 2072 seeds are put forward Round 1: 122 peptides, 22 chains. Longest chain 12 peptides. Score 0.371 Round 2: 133 peptides, 21 chains. Longest chain 16 peptides. Score 0.451 Round 3: 138 peptides, 21 chains. Longest chain 14 peptides. Score 0.475 Round 4: 129 peptides, 17 chains. Longest chain 18 peptides. Score 0.517 Round 5: 134 peptides, 21 chains. Longest chain 12 peptides. Score 0.456 Taking the results from Round 4 Chains 17, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.58 % complete ) and 4673 restraints for refining 2036 atoms. 4242 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1939 (Rfree = 0.000) for 2036 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. Cycle 32: After refmac, R = 0.1886 (Rfree = 0.000) for 2026 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.1684 (Rfree = 0.000) for 2021 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1724 (Rfree = 0.000) for 2013 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1683 (Rfree = 0.000) for 2008 atoms. Found 1 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 2072 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 2098 seeds are put forward Round 1: 105 peptides, 19 chains. Longest chain 11 peptides. Score 0.348 Round 2: 122 peptides, 18 chains. Longest chain 11 peptides. Score 0.462 Round 3: 123 peptides, 19 chains. Longest chain 12 peptides. Score 0.445 Round 4: 122 peptides, 17 chains. Longest chain 13 peptides. Score 0.484 Round 5: 132 peptides, 18 chains. Longest chain 13 peptides. Score 0.510 Taking the results from Round 5 Chains 18, Residues 114, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.58 % complete ) and 4411 restraints for refining 2037 atoms. 3898 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1914 (Rfree = 0.000) for 2037 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Cycle 37: After refmac, R = 0.1764 (Rfree = 0.000) for 2027 atoms. Found 9 (15 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.1676 (Rfree = 0.000) for 2027 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.1664 (Rfree = 0.000) for 2020 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1642 (Rfree = 0.000) for 2015 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.29 Search for helices and strands: 0 residues in 0 chains, 2064 seeds are put forward NCS extension: 9 residues added (5 deleted due to clashes), 2073 seeds are put forward Round 1: 114 peptides, 20 chains. Longest chain 14 peptides. Score 0.374 Round 2: 123 peptides, 20 chains. Longest chain 14 peptides. Score 0.422 Round 3: 119 peptides, 17 chains. Longest chain 14 peptides. Score 0.469 Round 4: 128 peptides, 20 chains. Longest chain 14 peptides. Score 0.448 Round 5: 119 peptides, 18 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 3 Chains 17, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.58 % complete ) and 4624 restraints for refining 2035 atoms. 4233 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1877 (Rfree = 0.000) for 2035 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.1851 (Rfree = 0.000) for 2031 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.1756 (Rfree = 0.000) for 2026 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1696 (Rfree = 0.000) for 2021 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1704 (Rfree = 0.000) for 2014 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.30 Search for helices and strands: 0 residues in 0 chains, 2069 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 2085 seeds are put forward Round 1: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.354 Round 2: 106 peptides, 15 chains. Longest chain 14 peptides. Score 0.449 Round 3: 116 peptides, 16 chains. Longest chain 16 peptides. Score 0.477 Round 4: 123 peptides, 17 chains. Longest chain 14 peptides. Score 0.489 Round 5: 111 peptides, 14 chains. Longest chain 16 peptides. Score 0.497 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 97, 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 2okf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4027 reflections ( 99.58 % complete ) and 4659 restraints for refining 2037 atoms. 4285 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2016 (Rfree = 0.000) for 2037 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1893 (Rfree = 0.000) for 2030 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2084 (Rfree = 0.000) for 2018 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1859 (Rfree = 0.000) for 2010 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:04:50 GMT 2018 Job finished. TimeTaking 42.12