null 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 2gno-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gno-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gno-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-3.8-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/2gno-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-3.8-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 22:22:51 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/2gno-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-3.8-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 191 and 0 Target number of residues in the AU: 191 Target solvent content: 0.6836 Checking the provided sequence file Detected sequence length: 305 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 305 Adjusted target solvent content: 0.49 Input MTZ file: 2gno-3.8-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: 79 Cell parameters: 135.560 135.560 35.560 90.000 90.000 90.000 Input sequence file: 2gno-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2440 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 Loops will be built when appropriate and at the last cycle Resolution range: 95.855 3.800 Wilson plot Bfac: 103.51 3335 reflections ( 98.79 % complete ) and 0 restraints for refining 2714 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3485 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3620 (Rfree = 0.000) for 2714 atoms. Found 7 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.95 Search for helices and strands: 0 residues in 0 chains, 2755 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.276 Round 2: 104 peptides, 20 chains. Longest chain 11 peptides. Score 0.310 Round 3: 126 peptides, 21 chains. Longest chain 14 peptides. Score 0.402 Round 4: 145 peptides, 25 chains. Longest chain 10 peptides. Score 0.410 Round 5: 147 peptides, 20 chains. Longest chain 17 peptides. Score 0.519 Taking the results from Round 5 Chains 20, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3335 reflections ( 98.79 % complete ) and 5060 restraints for refining 2162 atoms. 4572 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2843 (Rfree = 0.000) for 2162 atoms. Found 3 (11 requested) and removed 18 (5 requested) atoms. Cycle 2: After refmac, R = 0.2830 (Rfree = 0.000) for 2117 atoms. Found 2 (11 requested) and removed 16 (5 requested) atoms. Cycle 3: After refmac, R = 0.2391 (Rfree = 0.000) for 2083 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2396 (Rfree = 0.000) for 2063 atoms. Found 4 (11 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.2295 (Rfree = 0.000) for 2043 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 2135 seeds are put forward Round 1: 116 peptides, 25 chains. Longest chain 8 peptides. Score 0.260 Round 2: 135 peptides, 23 chains. Longest chain 10 peptides. Score 0.404 Round 3: 137 peptides, 23 chains. Longest chain 11 peptides. Score 0.413 Round 4: 138 peptides, 22 chains. Longest chain 16 peptides. Score 0.439 Round 5: 136 peptides, 20 chains. Longest chain 16 peptides. Score 0.470 Taking the results from Round 5 Chains 21, Residues 116, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3335 reflections ( 98.79 % complete ) and 4865 restraints for refining 2127 atoms. 4390 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2995 (Rfree = 0.000) for 2127 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 7: After refmac, R = 0.2376 (Rfree = 0.000) for 2090 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2171 (Rfree = 0.000) for 2068 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. Cycle 9: After refmac, R = 0.2640 (Rfree = 0.000) for 2055 atoms. Found 6 (11 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.2134 (Rfree = 0.000) for 2037 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.85 3.90 Search for helices and strands: 0 residues in 0 chains, 2112 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.294 Round 2: 137 peptides, 22 chains. Longest chain 11 peptides. Score 0.434 Round 3: 125 peptides, 22 chains. Longest chain 11 peptides. Score 0.375 Round 4: 123 peptides, 20 chains. Longest chain 11 peptides. Score 0.409 Round 5: 122 peptides, 20 chains. Longest chain 11 peptides. Score 0.404 Taking the results from Round 2 Chains 22, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3335 reflections ( 98.79 % complete ) and 4422 restraints for refining 2039 atoms. 3984 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2371 (Rfree = 0.000) for 2039 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 12: After refmac, R = 0.2344 (Rfree = 0.000) for 2019 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2196 (Rfree = 0.000) for 2014 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2315 (Rfree = 0.000) for 2008 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2389 (Rfree = 0.000) for 1988 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.88 3.93 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward Round 1: 112 peptides, 25 chains. Longest chain 6 peptides. Score 0.237 Round 2: 130 peptides, 25 chains. Longest chain 14 peptides. Score 0.335 Round 3: 137 peptides, 25 chains. Longest chain 14 peptides. Score 0.371 Round 4: 131 peptides, 22 chains. Longest chain 14 peptides. Score 0.405 Round 5: 140 peptides, 27 chains. Longest chain 9 peptides. Score 0.343 Taking the results from Round 4 Chains 22, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3335 reflections ( 98.79 % complete ) and 4811 restraints for refining 2089 atoms. 4397 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2453 (Rfree = 0.000) for 2089 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.2737 (Rfree = 0.000) for 2075 atoms. Found 9 (11 requested) and removed 16 (5 requested) atoms. Cycle 18: After refmac, R = 0.2812 (Rfree = 0.000) for 2049 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2592 (Rfree = 0.000) for 2028 atoms. Found 3 (11 requested) and removed 13 (5 requested) atoms. Cycle 20: After refmac, R = 0.2501 (Rfree = 0.000) for 2003 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.86 3.91 Search for helices and strands: 0 residues in 0 chains, 2105 seeds are put forward Round 1: 103 peptides, 23 chains. Longest chain 6 peptides. Score 0.233 Round 2: 131 peptides, 26 chains. Longest chain 11 peptides. Score 0.318 Round 3: 127 peptides, 24 chains. Longest chain 12 peptides. Score 0.341 Round 4: 120 peptides, 21 chains. Longest chain 13 peptides. Score 0.372 Round 5: 127 peptides, 22 chains. Longest chain 10 peptides. Score 0.385 Taking the results from Round 5 Chains 22, Residues 105, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3335 reflections ( 98.79 % complete ) and 4693 restraints for refining 2085 atoms. 4270 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2536 (Rfree = 0.000) for 2085 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 22: After refmac, R = 0.2532 (Rfree = 0.000) for 2059 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 23: After refmac, R = 0.2838 (Rfree = 0.000) for 2039 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 24: After refmac, R = 0.3012 (Rfree = 0.000) for 2016 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 25: After refmac, R = 0.2226 (Rfree = 0.000) for 1989 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.88 Search for helices and strands: 0 residues in 0 chains, 2080 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 6 peptides. Score 0.230 Round 2: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.294 Round 3: 83 peptides, 15 chains. Longest chain 11 peptides. Score 0.313 Round 4: 98 peptides, 18 chains. Longest chain 8 peptides. Score 0.324 Round 5: 105 peptides, 19 chains. Longest chain 9 peptides. Score 0.338 Taking the results from Round 5 Chains 19, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3335 reflections ( 98.79 % complete ) and 4365 restraints for refining 1943 atoms. 4040 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2759 (Rfree = 0.000) for 1943 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.2696 (Rfree = 0.000) for 1922 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 28: After refmac, R = 0.2187 (Rfree = 0.000) for 1907 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1982 (Rfree = 0.000) for 1904 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.1732 (Rfree = 0.000) for 1893 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.84 3.89 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 9 peptides. Score 0.259 Round 2: 104 peptides, 20 chains. Longest chain 7 peptides. Score 0.310 Round 3: 109 peptides, 17 chains. Longest chain 11 peptides. Score 0.405 Round 4: 110 peptides, 19 chains. Longest chain 11 peptides. Score 0.365 Round 5: 117 peptides, 19 chains. Longest chain 11 peptides. Score 0.401 Taking the results from Round 3 Chains 17, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3335 reflections ( 98.79 % complete ) and 4254 restraints for refining 1929 atoms. 3903 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2114 (Rfree = 0.000) for 1929 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 32: After refmac, R = 0.2154 (Rfree = 0.000) for 1922 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2655 (Rfree = 0.000) for 1921 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 34: After refmac, R = 0.1930 (Rfree = 0.000) for 1914 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2172 (Rfree = 0.000) for 1907 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.91 3.96 Search for helices and strands: 0 residues in 0 chains, 1980 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 9 peptides. Score 0.264 Round 2: 101 peptides, 18 chains. Longest chain 13 peptides. Score 0.340 Round 3: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.300 Round 4: 88 peptides, 17 chains. Longest chain 11 peptides. Score 0.292 Round 5: 87 peptides, 17 chains. Longest chain 10 peptides. Score 0.286 Taking the results from Round 2 Chains 18, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3335 reflections ( 98.79 % complete ) and 4088 restraints for refining 1878 atoms. 3774 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2368 (Rfree = 0.000) for 1878 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.1959 (Rfree = 0.000) for 1868 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.1738 (Rfree = 0.000) for 1869 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.1792 (Rfree = 0.000) for 1863 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1646 (Rfree = 0.000) for 1861 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.88 Search for helices and strands: 0 residues in 0 chains, 1946 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 10 peptides. Score 0.243 Round 2: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.328 Round 3: 95 peptides, 14 chains. Longest chain 17 peptides. Score 0.403 Round 4: 90 peptides, 14 chains. Longest chain 11 peptides. Score 0.376 Round 5: 83 peptides, 12 chains. Longest chain 16 peptides. Score 0.388 Taking the results from Round 3 Chains 14, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3335 reflections ( 98.79 % complete ) and 4257 restraints for refining 1924 atoms. 3947 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2019 (Rfree = 0.000) for 1924 atoms. Found 7 (10 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.1777 (Rfree = 0.000) for 1917 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.2036 (Rfree = 0.000) for 1917 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1869 (Rfree = 0.000) for 1917 atoms. Found 8 (10 requested) and removed 23 (5 requested) atoms. Cycle 45: After refmac, R = 0.1777 (Rfree = 0.000) for 1897 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.88 Search for helices and strands: 0 residues in 0 chains, 1956 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 11 peptides. Score 0.226 Round 2: 89 peptides, 17 chains. Longest chain 11 peptides. Score 0.298 Round 3: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.292 Round 4: 89 peptides, 16 chains. Longest chain 10 peptides. Score 0.322 Round 5: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.273 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 73, 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 2gno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3335 reflections ( 98.79 % complete ) and 4459 restraints for refining 1966 atoms. 4183 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2360 (Rfree = 0.000) for 1966 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2342 (Rfree = 0.000) for 1952 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2366 (Rfree = 0.000) for 1940 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2131 (Rfree = 0.000) for 1930 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:45 GMT 2018 Job finished. TimeTaking 44.04 Used memory is bytes: 20649936