null Mon 24 Dec 07:27:24 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 2p1a-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.6-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/2p1a-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.6-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 07:27:28 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/2p1a-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.6-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 195 and 0 Target number of residues in the AU: 195 Target solvent content: 0.6562 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.46 Input MTZ file: 2p1a-3.6-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: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 2464 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: 29.570 3.600 Wilson plot Bfac: 81.53 3840 reflections ( 99.43 % complete ) and 0 restraints for refining 2713 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3653 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3274 (Rfree = 0.000) for 2713 atoms. Found 16 (17 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.81 Search for helices and strands: 0 residues in 0 chains, 2772 seeds are put forward NCS extension: 0 residues added, 2772 seeds are put forward Round 1: 72 peptides, 13 chains. Longest chain 12 peptides. Score 0.306 Round 2: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.306 Round 3: 106 peptides, 20 chains. Longest chain 12 peptides. Score 0.327 Round 4: 115 peptides, 23 chains. Longest chain 8 peptides. Score 0.306 Round 5: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.308 Taking the results from Round 3 Chains 20, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 5499 restraints for refining 2233 atoms. 5175 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3155 (Rfree = 0.000) for 2233 atoms. Found 12 (14 requested) and removed 19 (7 requested) atoms. Cycle 2: After refmac, R = 0.2867 (Rfree = 0.000) for 2193 atoms. Found 13 (14 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.2415 (Rfree = 0.000) for 2169 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2302 (Rfree = 0.000) for 2155 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2269 (Rfree = 0.000) for 2144 atoms. Found 4 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2243 seeds are put forward NCS extension: 0 residues added, 2243 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.260 Round 2: 115 peptides, 22 chains. Longest chain 8 peptides. Score 0.330 Round 3: 107 peptides, 20 chains. Longest chain 9 peptides. Score 0.333 Round 4: 118 peptides, 18 chains. Longest chain 12 peptides. Score 0.439 Round 5: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.372 Taking the results from Round 4 Chains 18, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4545 restraints for refining 1983 atoms. 4163 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2516 (Rfree = 0.000) for 1983 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. Cycle 7: After refmac, R = 0.2402 (Rfree = 0.000) for 1957 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 8: After refmac, R = 0.2248 (Rfree = 0.000) for 1948 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.2310 (Rfree = 0.000) for 1934 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.1966 (Rfree = 0.000) for 1935 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.74 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2053 seeds are put forward Round 1: 103 peptides, 20 chains. Longest chain 9 peptides. Score 0.310 Round 2: 122 peptides, 21 chains. Longest chain 12 peptides. Score 0.392 Round 3: 132 peptides, 22 chains. Longest chain 15 peptides. Score 0.421 Round 4: 121 peptides, 18 chains. Longest chain 14 peptides. Score 0.454 Round 5: 125 peptides, 20 chains. Longest chain 13 peptides. Score 0.430 Taking the results from Round 4 Chains 18, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4447 restraints for refining 1976 atoms. 4053 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2185 (Rfree = 0.000) for 1976 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 12: After refmac, R = 0.2132 (Rfree = 0.000) for 1954 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.2046 (Rfree = 0.000) for 1947 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2070 (Rfree = 0.000) for 1936 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.1938 (Rfree = 0.000) for 1926 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2055 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 8 peptides. Score 0.284 Round 2: 117 peptides, 19 chains. Longest chain 11 peptides. Score 0.411 Round 3: 111 peptides, 18 chains. Longest chain 13 peptides. Score 0.403 Round 4: 126 peptides, 21 chains. Longest chain 14 peptides. Score 0.413 Round 5: 121 peptides, 21 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 4 Chains 21, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4414 restraints for refining 1993 atoms. 4015 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2238 (Rfree = 0.000) for 1993 atoms. Found 11 (12 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.2725 (Rfree = 0.000) for 1972 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.1923 (Rfree = 0.000) for 1959 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.1875 (Rfree = 0.000) for 1953 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2449 (Rfree = 0.000) for 1943 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 2044 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2064 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 7 peptides. Score 0.257 Round 2: 114 peptides, 20 chains. Longest chain 14 peptides. Score 0.372 Round 3: 117 peptides, 19 chains. Longest chain 10 peptides. Score 0.411 Round 4: 108 peptides, 17 chains. Longest chain 14 peptides. Score 0.410 Round 5: 111 peptides, 17 chains. Longest chain 18 peptides. Score 0.426 Taking the results from Round 5 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4468 restraints for refining 1986 atoms. 4109 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2028 (Rfree = 0.000) for 1986 atoms. Found 10 (12 requested) and removed 17 (6 requested) atoms. Cycle 22: After refmac, R = 0.1819 (Rfree = 0.000) for 1970 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.1861 (Rfree = 0.000) for 1958 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.1799 (Rfree = 0.000) for 1956 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1760 (Rfree = 0.000) for 1954 atoms. Found 9 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 2024 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2050 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.271 Round 2: 113 peptides, 21 chains. Longest chain 11 peptides. Score 0.343 Round 3: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.350 Round 4: 99 peptides, 17 chains. Longest chain 11 peptides. Score 0.361 Round 5: 91 peptides, 14 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 5 Chains 14, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4706 restraints for refining 2029 atoms. 4412 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2107 (Rfree = 0.000) for 2029 atoms. Found 7 (13 requested) and removed 14 (6 requested) atoms. Cycle 27: After refmac, R = 0.1977 (Rfree = 0.000) for 2016 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2058 (Rfree = 0.000) for 2007 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 29: After refmac, R = 0.2270 (Rfree = 0.000) for 2008 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.2134 (Rfree = 0.000) for 1999 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 2084 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 11 peptides. Score 0.244 Round 2: 97 peptides, 19 chains. Longest chain 11 peptides. Score 0.300 Round 3: 95 peptides, 17 chains. Longest chain 8 peptides. Score 0.338 Round 4: 100 peptides, 17 chains. Longest chain 12 peptides. Score 0.367 Round 5: 98 peptides, 17 chains. Longest chain 14 peptides. Score 0.356 Taking the results from Round 4 Chains 17, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4638 restraints for refining 2026 atoms. 4323 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1884 (Rfree = 0.000) for 2026 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.1902 (Rfree = 0.000) for 2018 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 33: After refmac, R = 0.1667 (Rfree = 0.000) for 2017 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 34: After refmac, R = 0.1587 (Rfree = 0.000) for 2016 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1688 (Rfree = 0.000) for 2011 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 2114 seeds are put forward NCS extension: 0 residues added, 2114 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 9 peptides. Score 0.283 Round 2: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.344 Round 3: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.352 Round 4: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.313 Round 5: 103 peptides, 17 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 5 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4963 restraints for refining 2120 atoms. 4636 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1823 (Rfree = 0.000) for 2120 atoms. Found 8 (13 requested) and removed 19 (6 requested) atoms. Cycle 37: After refmac, R = 0.1672 (Rfree = 0.000) for 2102 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2222 (Rfree = 0.000) for 2093 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.1812 (Rfree = 0.000) for 2086 atoms. Found 1 (13 requested) and removed 11 (6 requested) atoms. Cycle 40: After refmac, R = 0.1926 (Rfree = 0.000) for 2072 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 3.69 Search for helices and strands: 0 residues in 0 chains, 2145 seeds are put forward NCS extension: 0 residues added, 2145 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 6 peptides. Score 0.233 Round 2: 95 peptides, 20 chains. Longest chain 9 peptides. Score 0.263 Round 3: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.275 Round 4: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.323 Round 5: 99 peptides, 17 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 5 Chains 17, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4947 restraints for refining 2135 atoms. 4636 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2050 (Rfree = 0.000) for 2135 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.1897 (Rfree = 0.000) for 2123 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.1868 (Rfree = 0.000) for 2114 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.1974 (Rfree = 0.000) for 2109 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.1608 (Rfree = 0.000) for 2112 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 2193 seeds are put forward NCS extension: 0 residues added, 2193 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.205 Round 2: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.297 Round 3: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.297 Round 4: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.281 Round 5: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.307 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 66, 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 2p1a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3840 reflections ( 99.43 % complete ) and 5000 restraints for refining 2123 atoms. 4751 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2446 (Rfree = 0.000) for 2123 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1645 (Rfree = 0.000) for 2106 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2288 (Rfree = 0.000) for 2100 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1734 (Rfree = 0.000) for 2091 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:56:08 GMT 2018 Job finished. TimeTaking 28.74 Used memory is bytes: 19863576