Mon 24 Dec 07:59:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ooj-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ooj-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ooj-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:59:50 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/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-parrot-noncs/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 193 and 0 Target number of residues in the AU: 193 Target solvent content: 0.6226 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 282 Adjusted target solvent content: 0.45 Input MTZ file: 2ooj-3.4-parrot-noncs.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: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 2256 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 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: 53.043 3.400 Wilson plot Bfac: 61.81 4089 reflections ( 99.18 % complete ) and 0 restraints for refining 2501 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3610 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3647 (Rfree = 0.000) for 2501 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.40 Search for helices and strands: 0 residues in 0 chains, 2520 seeds are put forward NCS extension: 0 residues added, 2520 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 5 peptides. Score 0.211 Round 2: 105 peptides, 22 chains. Longest chain 8 peptides. Score 0.281 Round 3: 113 peptides, 23 chains. Longest chain 10 peptides. Score 0.306 Round 4: 128 peptides, 25 chains. Longest chain 11 peptides. Score 0.346 Round 5: 129 peptides, 24 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 5 Chains 24, Residues 105, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4794 restraints for refining 2052 atoms. 4376 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2949 (Rfree = 0.000) for 2052 atoms. Found 2 (15 requested) and removed 14 (7 requested) atoms. Cycle 2: After refmac, R = 0.3050 (Rfree = 0.000) for 2014 atoms. Found 13 (15 requested) and removed 31 (7 requested) atoms. Cycle 3: After refmac, R = 0.2765 (Rfree = 0.000) for 1987 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.2448 (Rfree = 0.000) for 1984 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 5: After refmac, R = 0.2516 (Rfree = 0.000) for 1973 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.52 Search for helices and strands: 0 residues in 0 chains, 2031 seeds are put forward NCS extension: 7 residues added (1 deleted due to clashes), 2038 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 10 peptides. Score 0.309 Round 2: 103 peptides, 18 chains. Longest chain 13 peptides. Score 0.375 Round 3: 109 peptides, 16 chains. Longest chain 13 peptides. Score 0.460 Round 4: 109 peptides, 17 chains. Longest chain 14 peptides. Score 0.435 Round 5: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.453 Taking the results from Round 3 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4675 restraints for refining 1989 atoms. 4286 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3025 (Rfree = 0.000) for 1989 atoms. Found 14 (15 requested) and removed 26 (7 requested) atoms. Cycle 7: After refmac, R = 0.2948 (Rfree = 0.000) for 1968 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 8: After refmac, R = 0.2882 (Rfree = 0.000) for 1949 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 9: After refmac, R = 0.2699 (Rfree = 0.000) for 1944 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.2369 (Rfree = 0.000) for 1935 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 1978 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1997 seeds are put forward Round 1: 109 peptides, 20 chains. Longest chain 12 peptides. Score 0.359 Round 2: 116 peptides, 19 chains. Longest chain 22 peptides. Score 0.425 Round 3: 121 peptides, 17 chains. Longest chain 19 peptides. Score 0.500 Round 4: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.400 Round 5: 123 peptides, 20 chains. Longest chain 13 peptides. Score 0.440 Taking the results from Round 3 Chains 17, Residues 104, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4495 restraints for refining 1967 atoms. 4069 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2762 (Rfree = 0.000) for 1967 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.2885 (Rfree = 0.000) for 1962 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2511 (Rfree = 0.000) for 1959 atoms. Found 10 (14 requested) and removed 18 (7 requested) atoms. Cycle 14: After refmac, R = 0.2523 (Rfree = 0.000) for 1947 atoms. Found 6 (14 requested) and removed 16 (7 requested) atoms. Cycle 15: After refmac, R = 0.2502 (Rfree = 0.000) for 1937 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 1960 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 1995 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 8 peptides. Score 0.299 Round 2: 130 peptides, 23 chains. Longest chain 11 peptides. Score 0.407 Round 3: 124 peptides, 20 chains. Longest chain 18 peptides. Score 0.446 Round 4: 124 peptides, 19 chains. Longest chain 15 peptides. Score 0.469 Round 5: 122 peptides, 18 chains. Longest chain 18 peptides. Score 0.482 Taking the results from Round 5 Chains 20, Residues 104, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4468 restraints for refining 2014 atoms. 4003 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2681 (Rfree = 0.000) for 2014 atoms. Found 9 (15 requested) and removed 16 (7 requested) atoms. Cycle 17: After refmac, R = 0.2905 (Rfree = 0.000) for 1992 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 18: After refmac, R = 0.2711 (Rfree = 0.000) for 1981 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.2444 (Rfree = 0.000) for 1980 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 20: After refmac, R = 0.2366 (Rfree = 0.000) for 1979 atoms. Found 13 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 2020 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2038 seeds are put forward Round 1: 101 peptides, 20 chains. Longest chain 12 peptides. Score 0.309 Round 2: 113 peptides, 19 chains. Longest chain 13 peptides. Score 0.408 Round 3: 118 peptides, 20 chains. Longest chain 14 peptides. Score 0.412 Round 4: 124 peptides, 22 chains. Longest chain 13 peptides. Score 0.397 Round 5: 128 peptides, 18 chains. Longest chain 12 peptides. Score 0.513 Taking the results from Round 5 Chains 18, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4794 restraints for refining 2052 atoms. 4372 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2536 (Rfree = 0.000) for 2052 atoms. Found 10 (15 requested) and removed 16 (7 requested) atoms. Cycle 22: After refmac, R = 0.2555 (Rfree = 0.000) for 2035 atoms. Found 10 (15 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.2664 (Rfree = 0.000) for 2023 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 24: After refmac, R = 0.2514 (Rfree = 0.000) for 2017 atoms. Found 14 (15 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2441 (Rfree = 0.000) for 2013 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2071 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 7 peptides. Score 0.255 Round 2: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.379 Round 3: 105 peptides, 19 chains. Longest chain 10 peptides. Score 0.361 Round 4: 114 peptides, 19 chains. Longest chain 10 peptides. Score 0.414 Round 5: 120 peptides, 17 chains. Longest chain 19 peptides. Score 0.495 Taking the results from Round 5 Chains 19, Residues 103, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4609 restraints for refining 2047 atoms. 4183 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2648 (Rfree = 0.000) for 2047 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 27: After refmac, R = 0.2265 (Rfree = 0.000) for 2036 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.2308 (Rfree = 0.000) for 2030 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.2248 (Rfree = 0.000) for 2030 atoms. Found 14 (15 requested) and removed 11 (7 requested) atoms. Cycle 30: After refmac, R = 0.2147 (Rfree = 0.000) for 2029 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.42 Search for helices and strands: 0 residues in 0 chains, 2083 seeds are put forward NCS extension: 0 residues added, 2083 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.272 Round 2: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.323 Round 3: 111 peptides, 19 chains. Longest chain 12 peptides. Score 0.396 Round 4: 110 peptides, 17 chains. Longest chain 11 peptides. Score 0.441 Round 5: 115 peptides, 18 chains. Longest chain 11 peptides. Score 0.444 Taking the results from Round 5 Chains 19, Residues 97, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4781 restraints for refining 2052 atoms. 4376 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2137 (Rfree = 0.000) for 2052 atoms. Found 10 (15 requested) and removed 12 (7 requested) atoms. Cycle 32: After refmac, R = 0.2360 (Rfree = 0.000) for 2044 atoms. Found 11 (15 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.2281 (Rfree = 0.000) for 2039 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.2290 (Rfree = 0.000) for 2038 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.1857 (Rfree = 0.000) for 2027 atoms. Found 0 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.41 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: 102 peptides, 23 chains. Longest chain 8 peptides. Score 0.235 Round 2: 115 peptides, 24 chains. Longest chain 9 peptides. Score 0.292 Round 3: 126 peptides, 22 chains. Longest chain 15 peptides. Score 0.409 Round 4: 110 peptides, 21 chains. Longest chain 7 peptides. Score 0.339 Round 5: 120 peptides, 21 chains. Longest chain 8 peptides. Score 0.399 Taking the results from Round 3 Chains 22, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4548 restraints for refining 1991 atoms. 4154 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2595 (Rfree = 0.000) for 1991 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 37: After refmac, R = 0.2596 (Rfree = 0.000) for 1985 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 38: After refmac, R = 0.2328 (Rfree = 0.000) for 1983 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.1916 (Rfree = 0.000) for 1977 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.1856 (Rfree = 0.000) for 1972 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.51 Search for helices and strands: 0 residues in 0 chains, 2004 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2022 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 9 peptides. Score 0.266 Round 2: 102 peptides, 18 chains. Longest chain 15 peptides. Score 0.369 Round 3: 108 peptides, 19 chains. Longest chain 15 peptides. Score 0.379 Round 4: 100 peptides, 16 chains. Longest chain 14 peptides. Score 0.409 Round 5: 105 peptides, 16 chains. Longest chain 16 peptides. Score 0.438 Taking the results from Round 5 Chains 16, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4509 restraints for refining 1959 atoms. 4169 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2227 (Rfree = 0.000) for 1959 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 42: After refmac, R = 0.1950 (Rfree = 0.000) for 1943 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.1900 (Rfree = 0.000) for 1932 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1733 (Rfree = 0.000) for 1926 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1739 (Rfree = 0.000) for 1923 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 1952 seeds are put forward NCS extension: 0 residues added, 1952 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 7 peptides. Score 0.289 Round 2: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.399 Round 3: 101 peptides, 16 chains. Longest chain 12 peptides. Score 0.415 Round 4: 104 peptides, 16 chains. Longest chain 13 peptides. Score 0.432 Round 5: 104 peptides, 14 chains. Longest chain 20 peptides. Score 0.482 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 90, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 2ooj-3_warpNtrace.pdb as input Building loops using Loopy2018 15 chains (90 residues) following loop building 3 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4089 reflections ( 99.18 % complete ) and 4438 restraints for refining 1990 atoms. 4050 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1984 (Rfree = 0.000) for 1990 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2141 (Rfree = 0.000) for 1983 atoms. Found 0 (14 requested) and removed 2 (7 requested) atoms. Cycle 48: After refmac, R = 0.2277 (Rfree = 0.000) for 1977 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2075 (Rfree = 0.000) for 1967 atoms. TimeTaking 25.85