Sun 23 Dec 23:54:55 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 2okf-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2okf-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2okf-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-4.0-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/2okf-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-4.0-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 23:54:59 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/2okf-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-4.0-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 188 and 0 Target number of residues in the AU: 188 Target solvent content: 0.6644 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-4.0-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: 59.870 59.870 73.240 90.000 90.000 120.000 Input sequence file: 2okf-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2240 target number of atoms Had to go as low as 0.75 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 4.005 Wilson plot Bfac: 86.99 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2457 reflections ( 99.43 % complete ) and 0 restraints for refining 2465 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3466 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3448 (Rfree = 0.000) for 2465 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.77 Search for helices and strands: 0 residues in 0 chains, 2493 seeds are put forward NCS extension: 0 residues added, 2493 seeds are put forward Round 1: 105 peptides, 25 chains. Longest chain 5 peptides. Score 0.198 Round 2: 129 peptides, 24 chains. Longest chain 11 peptides. Score 0.363 Round 3: 147 peptides, 26 chains. Longest chain 11 peptides. Score 0.413 Round 4: 151 peptides, 24 chains. Longest chain 11 peptides. Score 0.475 Round 5: 150 peptides, 24 chains. Longest chain 12 peptides. Score 0.470 Taking the results from Round 4 Chains 24, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4785 restraints for refining 2023 atoms. 4301 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2609 (Rfree = 0.000) for 2023 atoms. Found 3 (9 requested) and removed 23 (4 requested) atoms. Cycle 2: After refmac, R = 0.2556 (Rfree = 0.000) for 1969 atoms. Found 7 (9 requested) and removed 27 (4 requested) atoms. Cycle 3: After refmac, R = 0.2244 (Rfree = 0.000) for 1935 atoms. Found 3 (9 requested) and removed 13 (4 requested) atoms. Cycle 4: After refmac, R = 0.2355 (Rfree = 0.000) for 1914 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 5: After refmac, R = 0.2412 (Rfree = 0.000) for 1900 atoms. Found 4 (9 requested) and removed 19 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.69 Search for helices and strands: 0 residues in 0 chains, 1997 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 2006 seeds are put forward Round 1: 108 peptides, 25 chains. Longest chain 7 peptides. Score 0.217 Round 2: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.353 Round 3: 123 peptides, 24 chains. Longest chain 9 peptides. Score 0.329 Round 4: 122 peptides, 20 chains. Longest chain 15 peptides. Score 0.417 Round 5: 120 peptides, 18 chains. Longest chain 16 peptides. Score 0.452 Taking the results from Round 5 Chains 18, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4754 restraints for refining 2023 atoms. 4364 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2479 (Rfree = 0.000) for 2023 atoms. Found 4 (9 requested) and removed 28 (4 requested) atoms. Cycle 7: After refmac, R = 0.2047 (Rfree = 0.000) for 1981 atoms. Found 8 (9 requested) and removed 15 (4 requested) atoms. Cycle 8: After refmac, R = 0.2273 (Rfree = 0.000) for 1954 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 9: After refmac, R = 0.2031 (Rfree = 0.000) for 1934 atoms. Found 4 (9 requested) and removed 19 (4 requested) atoms. Cycle 10: After refmac, R = 0.2091 (Rfree = 0.000) for 1913 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.70 Search for helices and strands: 0 residues in 0 chains, 1998 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2022 seeds are put forward Round 1: 111 peptides, 24 chains. Longest chain 8 peptides. Score 0.260 Round 2: 117 peptides, 23 chains. Longest chain 8 peptides. Score 0.319 Round 3: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.382 Round 4: 130 peptides, 21 chains. Longest chain 11 peptides. Score 0.436 Round 5: 126 peptides, 21 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 4 Chains 21, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4667 restraints for refining 2013 atoms. 4252 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2100 (Rfree = 0.000) for 2013 atoms. Found 5 (9 requested) and removed 16 (4 requested) atoms. Cycle 12: After refmac, R = 0.2028 (Rfree = 0.000) for 1987 atoms. Found 7 (9 requested) and removed 21 (4 requested) atoms. Cycle 13: After refmac, R = 0.1731 (Rfree = 0.000) for 1967 atoms. Found 2 (9 requested) and removed 12 (4 requested) atoms. Cycle 14: After refmac, R = 0.1794 (Rfree = 0.000) for 1949 atoms. Found 2 (9 requested) and removed 10 (4 requested) atoms. Cycle 15: After refmac, R = 0.1775 (Rfree = 0.000) for 1933 atoms. Found 1 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 2000 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2016 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 7 peptides. Score 0.256 Round 2: 119 peptides, 22 chains. Longest chain 11 peptides. Score 0.354 Round 3: 122 peptides, 23 chains. Longest chain 10 peptides. Score 0.347 Round 4: 117 peptides, 22 chains. Longest chain 9 peptides. Score 0.343 Round 5: 128 peptides, 21 chains. Longest chain 10 peptides. Score 0.425 Taking the results from Round 5 Chains 21, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4615 restraints for refining 2022 atoms. 4208 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2623 (Rfree = 0.000) for 2022 atoms. Found 2 (9 requested) and removed 18 (4 requested) atoms. Cycle 17: After refmac, R = 0.2104 (Rfree = 0.000) for 1996 atoms. Found 4 (9 requested) and removed 12 (4 requested) atoms. Cycle 18: After refmac, R = 0.1992 (Rfree = 0.000) for 1981 atoms. Found 4 (9 requested) and removed 14 (4 requested) atoms. Cycle 19: After refmac, R = 0.1964 (Rfree = 0.000) for 1965 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.1724 (Rfree = 0.000) for 1960 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.72 Search for helices and strands: 0 residues in 0 chains, 2039 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2042 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 7 peptides. Score 0.274 Round 2: 123 peptides, 23 chains. Longest chain 12 peptides. Score 0.353 Round 3: 121 peptides, 21 chains. Longest chain 9 peptides. Score 0.389 Round 4: 115 peptides, 21 chains. Longest chain 10 peptides. Score 0.356 Round 5: 123 peptides, 22 chains. Longest chain 10 peptides. Score 0.376 Taking the results from Round 3 Chains 21, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4698 restraints for refining 2011 atoms. 4319 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1882 (Rfree = 0.000) for 2011 atoms. Found 4 (9 requested) and removed 19 (4 requested) atoms. Cycle 22: After refmac, R = 0.1833 (Rfree = 0.000) for 1993 atoms. Found 1 (9 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.1970 (Rfree = 0.000) for 1982 atoms. Found 1 (9 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.2037 (Rfree = 0.000) for 1965 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.1429 (Rfree = 0.000) for 1957 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.70 Search for helices and strands: 0 residues in 0 chains, 2024 seeds are put forward NCS extension: 0 residues added, 2024 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 9 peptides. Score 0.269 Round 2: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.352 Round 3: 119 peptides, 20 chains. Longest chain 16 peptides. Score 0.401 Round 4: 105 peptides, 19 chains. Longest chain 11 peptides. Score 0.348 Round 5: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.396 Taking the results from Round 3 Chains 20, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4525 restraints for refining 1976 atoms. 4149 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1895 (Rfree = 0.000) for 1976 atoms. Found 5 (9 requested) and removed 22 (4 requested) atoms. Cycle 27: After refmac, R = 0.2049 (Rfree = 0.000) for 1952 atoms. Found 4 (9 requested) and removed 18 (4 requested) atoms. Cycle 28: After refmac, R = 0.1838 (Rfree = 0.000) for 1933 atoms. Found 5 (9 requested) and removed 12 (4 requested) atoms. Cycle 29: After refmac, R = 0.1773 (Rfree = 0.000) for 1923 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 30: After refmac, R = 0.1657 (Rfree = 0.000) for 1914 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.74 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward NCS extension: 0 residues added, 1996 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 9 peptides. Score 0.272 Round 2: 104 peptides, 21 chains. Longest chain 9 peptides. Score 0.293 Round 3: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.365 Round 4: 111 peptides, 19 chains. Longest chain 10 peptides. Score 0.381 Round 5: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.361 Taking the results from Round 4 Chains 19, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4562 restraints for refining 1986 atoms. 4213 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2000 (Rfree = 0.000) for 1986 atoms. Found 4 (9 requested) and removed 20 (4 requested) atoms. Cycle 32: After refmac, R = 0.1901 (Rfree = 0.000) for 1962 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 33: After refmac, R = 0.1834 (Rfree = 0.000) for 1954 atoms. Found 6 (9 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.1718 (Rfree = 0.000) for 1946 atoms. Found 1 (9 requested) and removed 11 (4 requested) atoms. Cycle 35: After refmac, R = 0.1819 (Rfree = 0.000) for 1934 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.70 Search for helices and strands: 0 residues in 0 chains, 2008 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 2013 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 8 peptides. Score 0.214 Round 2: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.275 Round 3: 95 peptides, 20 chains. Longest chain 9 peptides. Score 0.264 Round 4: 102 peptides, 20 chains. Longest chain 9 peptides. Score 0.306 Round 5: 93 peptides, 18 chains. Longest chain 7 peptides. Score 0.303 Taking the results from Round 4 Chains 20, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4578 restraints for refining 2022 atoms. 4270 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2115 (Rfree = 0.000) for 2022 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 37: After refmac, R = 0.1982 (Rfree = 0.000) for 2003 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 38: After refmac, R = 0.1838 (Rfree = 0.000) for 1991 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 39: After refmac, R = 0.1722 (Rfree = 0.000) for 1982 atoms. Found 5 (9 requested) and removed 11 (4 requested) atoms. Cycle 40: After refmac, R = 0.1752 (Rfree = 0.000) for 1972 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.70 Search for helices and strands: 0 residues in 0 chains, 2040 seeds are put forward NCS extension: 0 residues added, 2040 seeds are put forward Round 1: 58 peptides, 14 chains. Longest chain 5 peptides. Score 0.182 Round 2: 71 peptides, 15 chains. Longest chain 7 peptides. Score 0.244 Round 3: 73 peptides, 15 chains. Longest chain 9 peptides. Score 0.258 Round 4: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.243 Round 5: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.279 Taking the results from Round 5 Chains 14, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.43 % complete ) and 4797 restraints for refining 2018 atoms. 4579 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1891 (Rfree = 0.000) for 2018 atoms. Found 5 (9 requested) and removed 14 (4 requested) atoms. Cycle 42: After refmac, R = 0.2043 (Rfree = 0.000) for 1997 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.1827 (Rfree = 0.000) for 1986 atoms. Found 2 (9 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.2047 (Rfree = 0.000) for 1976 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 45: After refmac, R = 0.1935 (Rfree = 0.000) for 1970 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.74 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward NCS extension: 0 residues added, 2036 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 6 peptides. Score 0.196 Round 2: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.292 Round 3: 61 peptides, 12 chains. Longest chain 8 peptides. Score 0.263 Round 4: 64 peptides, 14 chains. Longest chain 7 peptides. Score 0.225 Round 5: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.248 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 60, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2457 reflections ( 99.43 % complete ) and 4323 restraints for refining 1920 atoms. 4097 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1900 (Rfree = 0.000) for 1920 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1931 (Rfree = 0.000) for 1910 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1797 (Rfree = 0.000) for 1902 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1674 (Rfree = 0.000) for 1894 atoms. TimeTaking 25.9