Sun 23 Dec 23:58:01 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 2ooj-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ooj-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ooj-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.8-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/2ooj-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.8-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 23:58:05 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/2ooj-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.8-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: 0.6323 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-3.8-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: 19 Cell parameters: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-3.8-parrot-mrncs.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 3.800 Wilson plot Bfac: 66.95 2963 reflections ( 98.87 % complete ) and 0 restraints for refining 2487 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3703 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2905 (Rfree = 0.000) for 2487 atoms. Found 8 (13 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 2502 seeds are put forward NCS extension: 0 residues added, 2502 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 7 peptides. Score 0.205 Round 2: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.271 Round 3: 87 peptides, 17 chains. Longest chain 11 peptides. Score 0.301 Round 4: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.312 Round 5: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.350 Taking the results from Round 5 Chains 15, Residues 71, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5125 restraints for refining 2041 atoms. 4850 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2633 (Rfree = 0.000) for 2041 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 2: After refmac, R = 0.2448 (Rfree = 0.000) for 2009 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 3: After refmac, R = 0.2378 (Rfree = 0.000) for 1997 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 4: After refmac, R = 0.2385 (Rfree = 0.000) for 1990 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2337 (Rfree = 0.000) for 1982 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 2021 seeds are put forward NCS extension: 0 residues added, 2021 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 11 peptides. Score 0.282 Round 2: 117 peptides, 23 chains. Longest chain 11 peptides. Score 0.330 Round 3: 110 peptides, 22 chains. Longest chain 12 peptides. Score 0.313 Round 4: 116 peptides, 24 chains. Longest chain 8 peptides. Score 0.298 Round 5: 111 peptides, 20 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 5 Chains 20, Residues 91, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5138 restraints for refining 2019 atoms. 4790 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2465 (Rfree = 0.000) for 2019 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 7: After refmac, R = 0.2373 (Rfree = 0.000) for 2007 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 8: After refmac, R = 0.2263 (Rfree = 0.000) for 2000 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2202 (Rfree = 0.000) for 1989 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2166 (Rfree = 0.000) for 1983 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 2018 seeds are put forward NCS extension: 0 residues added, 2018 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 7 peptides. Score 0.239 Round 2: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.347 Round 3: 106 peptides, 17 chains. Longest chain 14 peptides. Score 0.418 Round 4: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.402 Round 5: 105 peptides, 16 chains. Longest chain 13 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 ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4961 restraints for refining 2031 atoms. 4621 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2640 (Rfree = 0.000) for 2031 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 12: After refmac, R = 0.2452 (Rfree = 0.000) for 2024 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.2356 (Rfree = 0.000) for 2018 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.2310 (Rfree = 0.000) for 2013 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.2263 (Rfree = 0.000) for 2007 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 2024 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2041 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 7 peptides. Score 0.281 Round 2: 98 peptides, 17 chains. Longest chain 13 peptides. Score 0.371 Round 3: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.379 Round 4: 100 peptides, 18 chains. Longest chain 11 peptides. Score 0.356 Round 5: 100 peptides, 17 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 5 Chains 17, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5115 restraints for refining 2041 atoms. 4800 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2747 (Rfree = 0.000) for 2041 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.2615 (Rfree = 0.000) for 2042 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.2560 (Rfree = 0.000) for 2032 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2530 (Rfree = 0.000) for 2026 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2508 (Rfree = 0.000) for 2022 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.60 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward NCS extension: 0 residues added, 2055 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 7 peptides. Score 0.218 Round 2: 104 peptides, 18 chains. Longest chain 13 peptides. Score 0.381 Round 3: 105 peptides, 19 chains. Longest chain 10 peptides. Score 0.361 Round 4: 105 peptides, 19 chains. Longest chain 10 peptides. Score 0.361 Round 5: 113 peptides, 20 chains. Longest chain 11 peptides. Score 0.383 Taking the results from Round 5 Chains 20, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5091 restraints for refining 2041 atoms. 4739 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2835 (Rfree = 0.000) for 2041 atoms. Found 9 (11 requested) and removed 12 (5 requested) atoms. Cycle 22: After refmac, R = 0.2680 (Rfree = 0.000) for 2036 atoms. Found 0 (11 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.2630 (Rfree = 0.000) for 2027 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2585 (Rfree = 0.000) for 2023 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2555 (Rfree = 0.000) for 2020 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward NCS extension: 0 residues added, 2055 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 11 peptides. Score 0.307 Round 2: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.336 Round 3: 98 peptides, 17 chains. Longest chain 13 peptides. Score 0.371 Round 4: 110 peptides, 18 chains. Longest chain 13 peptides. Score 0.416 Round 5: 97 peptides, 13 chains. Longest chain 13 peptides. Score 0.468 Taking the results from Round 5 Chains 13, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5021 restraints for refining 2041 atoms. 4698 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2596 (Rfree = 0.000) for 2041 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 27: After refmac, R = 0.2437 (Rfree = 0.000) for 2037 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2369 (Rfree = 0.000) for 2033 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2336 (Rfree = 0.000) for 2029 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2311 (Rfree = 0.000) for 2025 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 2064 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2070 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 8 peptides. Score 0.274 Round 2: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.335 Round 3: 93 peptides, 15 chains. Longest chain 9 peptides. Score 0.393 Round 4: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.320 Round 5: 94 peptides, 16 chains. Longest chain 9 peptides. Score 0.373 Taking the results from Round 3 Chains 15, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5028 restraints for refining 2016 atoms. 4731 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2406 (Rfree = 0.000) for 2016 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2289 (Rfree = 0.000) for 2010 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2233 (Rfree = 0.000) for 2006 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2203 (Rfree = 0.000) for 1999 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2185 (Rfree = 0.000) for 1995 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 2033 seeds are put forward NCS extension: 0 residues added, 2033 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.244 Round 2: 91 peptides, 19 chains. Longest chain 7 peptides. Score 0.272 Round 3: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.278 Round 4: 98 peptides, 19 chains. Longest chain 7 peptides. Score 0.317 Round 5: 90 peptides, 18 chains. Longest chain 9 peptides. Score 0.293 Taking the results from Round 4 Chains 19, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5120 restraints for refining 2041 atoms. 4823 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2365 (Rfree = 0.000) for 2041 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 37: After refmac, R = 0.2267 (Rfree = 0.000) for 2036 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.2244 (Rfree = 0.000) for 2028 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2184 (Rfree = 0.000) for 2023 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.2162 (Rfree = 0.000) for 2018 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.72 Search for helices and strands: 0 residues in 0 chains, 2053 seeds are put forward NCS extension: 0 residues added, 2053 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 7 peptides. Score 0.239 Round 2: 99 peptides, 20 chains. Longest chain 8 peptides. Score 0.297 Round 3: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.318 Round 4: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.355 Round 5: 86 peptides, 16 chains. Longest chain 8 peptides. Score 0.322 Taking the results from Round 4 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5237 restraints for refining 2041 atoms. 4990 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2391 (Rfree = 0.000) for 2041 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.2305 (Rfree = 0.000) for 2035 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2280 (Rfree = 0.000) for 2029 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2271 (Rfree = 0.000) for 2024 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2260 (Rfree = 0.000) for 2020 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.61 Search for helices and strands: 0 residues in 0 chains, 2043 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2054 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 6 peptides. Score 0.232 Round 2: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.277 Round 3: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.318 Round 4: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.327 Round 5: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.291 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 64, 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 2ooj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2963 reflections ( 98.87 % complete ) and 5078 restraints for refining 2013 atoms. 4836 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2307 (Rfree = 0.000) for 2013 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2213 (Rfree = 0.000) for 2007 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2216 (Rfree = 0.000) for 2001 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2226 (Rfree = 0.000) for 1996 atoms. TimeTaking 26.17