null Mon 24 Dec 07:39:55 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 1zko-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1zko-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1zko-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-3.2-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/1zko-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-3.2-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 07:40:00 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/1zko-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-3.2-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 179 and 0 Target number of residues in the AU: 179 Target solvent content: 0.6031 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-3.2-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: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 2176 target number of atoms Had to go as low as 0.65 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: 47.500 3.200 Wilson plot Bfac: 53.76 4004 reflections ( 92.28 % complete ) and 0 restraints for refining 2400 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3666 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3522 (Rfree = 0.000) for 2400 atoms. Found 21 (21 requested) and removed 71 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 2380 seeds are put forward NCS extension: 0 residues added, 2380 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 8 peptides. Score 0.280 Round 2: 112 peptides, 25 chains. Longest chain 7 peptides. Score 0.255 Round 3: 119 peptides, 23 chains. Longest chain 10 peptides. Score 0.360 Round 4: 124 peptides, 22 chains. Longest chain 11 peptides. Score 0.420 Round 5: 135 peptides, 23 chains. Longest chain 11 peptides. Score 0.461 Taking the results from Round 5 Chains 23, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4518 restraints for refining 1987 atoms. 4093 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3006 (Rfree = 0.000) for 1987 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 2: After refmac, R = 0.2921 (Rfree = 0.000) for 1971 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.2849 (Rfree = 0.000) for 1961 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. Cycle 4: After refmac, R = 0.2853 (Rfree = 0.000) for 1948 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.2876 (Rfree = 0.000) for 1943 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.58 Search for helices and strands: 0 residues in 0 chains, 1991 seeds are put forward NCS extension: 0 residues added, 1991 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 8 peptides. Score 0.280 Round 2: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.394 Round 3: 133 peptides, 21 chains. Longest chain 17 peptides. Score 0.499 Round 4: 127 peptides, 23 chains. Longest chain 12 peptides. Score 0.412 Round 5: 120 peptides, 18 chains. Longest chain 16 peptides. Score 0.500 Taking the results from Round 5 Chains 18, Residues 102, Estimated correctness of the model 11.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4547 restraints for refining 1962 atoms. 4157 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2892 (Rfree = 0.000) for 1962 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 7: After refmac, R = 0.2698 (Rfree = 0.000) for 1967 atoms. Found 7 (17 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2797 (Rfree = 0.000) for 1958 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.2650 (Rfree = 0.000) for 1953 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.2538 (Rfree = 0.000) for 1949 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.59 Search for helices and strands: 0 residues in 0 chains, 1985 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 2011 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 8 peptides. Score 0.304 Round 2: 128 peptides, 22 chains. Longest chain 11 peptides. Score 0.444 Round 3: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.456 Round 4: 114 peptides, 18 chains. Longest chain 13 peptides. Score 0.464 Round 5: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.440 Taking the results from Round 4 Chains 18, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4579 restraints for refining 1955 atoms. 4213 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2801 (Rfree = 0.000) for 1955 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 12: After refmac, R = 0.2587 (Rfree = 0.000) for 1957 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2598 (Rfree = 0.000) for 1952 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.2458 (Rfree = 0.000) for 1945 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.2438 (Rfree = 0.000) for 1938 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.02 3.46 Search for helices and strands: 0 residues in 0 chains, 1968 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1983 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 12 peptides. Score 0.334 Round 2: 120 peptides, 22 chains. Longest chain 11 peptides. Score 0.394 Round 3: 119 peptides, 19 chains. Longest chain 16 peptides. Score 0.468 Round 4: 118 peptides, 18 chains. Longest chain 14 peptides. Score 0.488 Round 5: 121 peptides, 19 chains. Longest chain 14 peptides. Score 0.480 Taking the results from Round 4 Chains 18, Residues 100, Estimated correctness of the model 7.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4537 restraints for refining 1987 atoms. 4155 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2596 (Rfree = 0.000) for 1987 atoms. Found 11 (17 requested) and removed 12 (8 requested) atoms. Cycle 17: After refmac, R = 0.2581 (Rfree = 0.000) for 1981 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2478 (Rfree = 0.000) for 1978 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2400 (Rfree = 0.000) for 1970 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.2233 (Rfree = 0.000) for 1963 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 3.50 Search for helices and strands: 0 residues in 0 chains, 2005 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2019 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 7 peptides. Score 0.287 Round 2: 126 peptides, 22 chains. Longest chain 13 peptides. Score 0.432 Round 3: 126 peptides, 21 chains. Longest chain 12 peptides. Score 0.458 Round 4: 119 peptides, 21 chains. Longest chain 11 peptides. Score 0.415 Round 5: 116 peptides, 19 chains. Longest chain 10 peptides. Score 0.450 Taking the results from Round 3 Chains 21, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4426 restraints for refining 1970 atoms. 4027 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2641 (Rfree = 0.000) for 1970 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.2416 (Rfree = 0.000) for 1973 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2318 (Rfree = 0.000) for 1968 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2298 (Rfree = 0.000) for 1963 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2220 (Rfree = 0.000) for 1956 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 3.56 Search for helices and strands: 0 residues in 0 chains, 1991 seeds are put forward NCS extension: 9 residues added (2 deleted due to clashes), 2000 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 7 peptides. Score 0.254 Round 2: 105 peptides, 21 chains. Longest chain 10 peptides. Score 0.322 Round 3: 117 peptides, 23 chains. Longest chain 10 peptides. Score 0.347 Round 4: 116 peptides, 23 chains. Longest chain 10 peptides. Score 0.340 Round 5: 101 peptides, 20 chains. Longest chain 10 peptides. Score 0.323 Taking the results from Round 3 Chains 23, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4613 restraints for refining 1977 atoms. 4260 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2536 (Rfree = 0.000) for 1977 atoms. Found 10 (17 requested) and removed 10 (8 requested) atoms. Cycle 27: After refmac, R = 0.2595 (Rfree = 0.000) for 1970 atoms. Found 13 (17 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2809 (Rfree = 0.000) for 1972 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.2897 (Rfree = 0.000) for 1965 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 30: After refmac, R = 0.2843 (Rfree = 0.000) for 1956 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 3.47 Search for helices and strands: 0 residues in 0 chains, 2025 seeds are put forward NCS extension: 0 residues added, 2025 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.248 Round 2: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.346 Round 3: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.360 Round 4: 94 peptides, 15 chains. Longest chain 14 peptides. Score 0.421 Round 5: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.372 Taking the results from Round 4 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4272 restraints for refining 1936 atoms. 3928 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3137 (Rfree = 0.000) for 1936 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 32: After refmac, R = 0.2707 (Rfree = 0.000) for 1926 atoms. Found 16 (17 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2828 (Rfree = 0.000) for 1929 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 34: After refmac, R = 0.2614 (Rfree = 0.000) for 1928 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2701 (Rfree = 0.000) for 1933 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.85 4.41 Search for helices and strands: 0 residues in 0 chains, 1983 seeds are put forward NCS extension: 0 residues added, 1983 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.268 Round 2: 73 peptides, 13 chains. Longest chain 12 peptides. Score 0.337 Round 3: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.332 Round 4: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.341 Round 5: 95 peptides, 18 chains. Longest chain 8 peptides. Score 0.340 Taking the results from Round 4 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4774 restraints for refining 1982 atoms. 4532 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2805 (Rfree = 0.000) for 1982 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 37: After refmac, R = 0.2832 (Rfree = 0.000) for 1979 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 38: After refmac, R = 0.2836 (Rfree = 0.000) for 1978 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 39: After refmac, R = 0.2824 (Rfree = 0.000) for 1979 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.2904 (Rfree = 0.000) for 1983 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.71 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2044 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 9 peptides. Score 0.248 Round 2: 63 peptides, 13 chains. Longest chain 9 peptides. Score 0.260 Round 3: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.327 Round 4: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.307 Round 5: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 5 Chains 14, Residues 65, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4563 restraints for refining 1954 atoms. 4293 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3124 (Rfree = 0.000) for 1954 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 42: After refmac, R = 0.3059 (Rfree = 0.000) for 1947 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2971 (Rfree = 0.000) for 1947 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 44: After refmac, R = 0.3037 (Rfree = 0.000) for 1944 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.2780 (Rfree = 0.000) for 1946 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 3.47 Search for helices and strands: 0 residues in 0 chains, 1976 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1985 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 6 peptides. Score 0.237 Round 2: 72 peptides, 14 chains. Longest chain 10 peptides. Score 0.297 Round 3: 74 peptides, 14 chains. Longest chain 10 peptides. Score 0.312 Round 4: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.278 Round 5: 83 peptides, 15 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 68, 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 1zko-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4004 reflections ( 92.28 % complete ) and 4189 restraints for refining 1859 atoms. 3932 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2863 (Rfree = 0.000) for 1859 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.3041 (Rfree = 0.000) for 1844 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.3137 (Rfree = 0.000) for 1829 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2927 (Rfree = 0.000) for 1818 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:07:17 GMT 2018 Job finished. TimeTaking 27.37 Used memory is bytes: 7325552