Sun 23 Dec 22:22:49 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 2ooj-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-4.0-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/2ooj-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-4.0-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 22:22:58 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/2ooj-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-4.0-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 185 and 0 Target number of residues in the AU: 185 Target solvent content: 0.6382 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-4.0-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: 19 Cell parameters: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2256 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: 53.043 4.000 Wilson plot Bfac: 70.85 2539 reflections ( 98.68 % complete ) and 0 restraints for refining 2487 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3774 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3561 (Rfree = 0.000) for 2487 atoms. Found 8 (11 requested) and removed 110 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 2400 seeds are put forward NCS extension: 0 residues added, 2400 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.242 Round 2: 88 peptides, 16 chains. Longest chain 12 peptides. Score 0.335 Round 3: 95 peptides, 18 chains. Longest chain 15 peptides. Score 0.325 Round 4: 100 peptides, 17 chains. Longest chain 15 peptides. Score 0.383 Round 5: 86 peptides, 14 chains. Longest chain 11 peptides. Score 0.378 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 ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5142 restraints for refining 2037 atoms. 4827 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3478 (Rfree = 0.000) for 2037 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 2: After refmac, R = 0.3304 (Rfree = 0.000) for 2025 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.3232 (Rfree = 0.000) for 2015 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 4: After refmac, R = 0.3187 (Rfree = 0.000) for 2012 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.3156 (Rfree = 0.000) for 2008 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward NCS extension: 0 residues added, 2038 seeds are put forward Round 1: 81 peptides, 19 chains. Longest chain 7 peptides. Score 0.203 Round 2: 105 peptides, 22 chains. Longest chain 9 peptides. Score 0.281 Round 3: 90 peptides, 19 chains. Longest chain 8 peptides. Score 0.265 Round 4: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.336 Round 5: 92 peptides, 17 chains. Longest chain 8 peptides. Score 0.333 Taking the results from Round 4 Chains 19, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5252 restraints for refining 2037 atoms. 4943 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3162 (Rfree = 0.000) for 2037 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. Cycle 7: After refmac, R = 0.3032 (Rfree = 0.000) for 2030 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2953 (Rfree = 0.000) for 2024 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2900 (Rfree = 0.000) for 2018 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.2866 (Rfree = 0.000) for 2012 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 2047 seeds are put forward NCS extension: 0 residues added, 2047 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 12 peptides. Score 0.277 Round 2: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.272 Round 3: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.307 Round 4: 89 peptides, 15 chains. Longest chain 15 peptides. Score 0.369 Round 5: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 4 Chains 15, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5156 restraints for refining 2028 atoms. 4875 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3062 (Rfree = 0.000) for 2028 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.2888 (Rfree = 0.000) for 2023 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 13: After refmac, R = 0.2792 (Rfree = 0.000) for 2021 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2743 (Rfree = 0.000) for 2013 atoms. Found 0 (9 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.2704 (Rfree = 0.000) for 2004 atoms. Found 0 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 2032 seeds are put forward NCS extension: 0 residues added, 2032 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 8 peptides. Score 0.225 Round 2: 102 peptides, 19 chains. Longest chain 12 peptides. Score 0.342 Round 3: 92 peptides, 16 chains. Longest chain 17 peptides. Score 0.360 Round 4: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.371 Round 5: 97 peptides, 15 chains. Longest chain 17 peptides. Score 0.417 Taking the results from Round 5 Chains 15, Residues 82, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5098 restraints for refining 2036 atoms. 4768 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2842 (Rfree = 0.000) for 2036 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 17: After refmac, R = 0.2701 (Rfree = 0.000) for 2034 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.3040 (Rfree = 0.000) for 2033 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.2900 (Rfree = 0.000) for 2016 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2849 (Rfree = 0.000) for 2014 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.81 Search for helices and strands: 0 residues in 0 chains, 2041 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2066 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 8 peptides. Score 0.241 Round 2: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.329 Round 3: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.356 Round 4: 89 peptides, 17 chains. Longest chain 8 peptides. Score 0.314 Round 5: 89 peptides, 15 chains. Longest chain 9 peptides. Score 0.369 Taking the results from Round 5 Chains 15, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5199 restraints for refining 2037 atoms. 4918 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2908 (Rfree = 0.000) for 2037 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.2777 (Rfree = 0.000) for 2034 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.2688 (Rfree = 0.000) for 2030 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2657 (Rfree = 0.000) for 2026 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2612 (Rfree = 0.000) for 2021 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.83 Search for helices and strands: 0 residues in 0 chains, 2065 seeds are put forward NCS extension: 0 residues added, 2065 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.244 Round 2: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.284 Round 3: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.337 Round 4: 85 peptides, 16 chains. Longest chain 11 peptides. Score 0.316 Round 5: 86 peptides, 16 chains. Longest chain 13 peptides. Score 0.322 Taking the results from Round 3 Chains 15, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5288 restraints for refining 2037 atoms. 5027 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2660 (Rfree = 0.000) for 2037 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 27: After refmac, R = 0.2527 (Rfree = 0.000) for 2037 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2484 (Rfree = 0.000) for 2030 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2607 (Rfree = 0.000) for 2026 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.2499 (Rfree = 0.000) for 2020 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.87 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 0 residues added, 2050 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 6 peptides. Score 0.230 Round 2: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.329 Round 3: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.344 Round 4: 92 peptides, 17 chains. Longest chain 8 peptides. Score 0.333 Round 5: 88 peptides, 16 chains. Longest chain 13 peptides. Score 0.335 Taking the results from Round 3 Chains 15, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5279 restraints for refining 2037 atoms. 5014 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2735 (Rfree = 0.000) for 2037 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2588 (Rfree = 0.000) for 2037 atoms. Found 1 (9 requested) and removed 7 (4 requested) atoms. Cycle 33: After refmac, R = 0.2534 (Rfree = 0.000) for 2029 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2413 (Rfree = 0.000) for 2024 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2375 (Rfree = 0.000) for 2024 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.86 Search for helices and strands: 0 residues in 0 chains, 2059 seeds are put forward NCS extension: 0 residues added, 2059 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 10 peptides. Score 0.265 Round 2: 83 peptides, 18 chains. Longest chain 7 peptides. Score 0.246 Round 3: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.242 Round 4: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.251 Round 5: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.281 Taking the results from Round 5 Chains 13, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5365 restraints for refining 2037 atoms. 5162 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2446 (Rfree = 0.000) for 2037 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2396 (Rfree = 0.000) for 2033 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2423 (Rfree = 0.000) for 2028 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2323 (Rfree = 0.000) for 2026 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2311 (Rfree = 0.000) for 2022 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.89 Search for helices and strands: 0 residues in 0 chains, 2052 seeds are put forward NCS extension: 0 residues added, 2052 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 7 peptides. Score 0.229 Round 2: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.255 Round 3: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.224 Round 4: 58 peptides, 12 chains. Longest chain 8 peptides. Score 0.247 Round 5: 61 peptides, 12 chains. Longest chain 7 peptides. Score 0.269 Taking the results from Round 5 Chains 12, Residues 49, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5366 restraints for refining 2022 atoms. 5168 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2421 (Rfree = 0.000) for 2022 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2318 (Rfree = 0.000) for 2019 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2256 (Rfree = 0.000) for 2016 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2272 (Rfree = 0.000) for 2012 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2234 (Rfree = 0.000) for 2008 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.89 Search for helices and strands: 0 residues in 0 chains, 2061 seeds are put forward NCS extension: 0 residues added, 2061 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.228 Round 2: 74 peptides, 15 chains. Longest chain 7 peptides. Score 0.271 Round 3: 74 peptides, 15 chains. Longest chain 7 peptides. Score 0.271 Round 4: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.277 Round 5: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.331 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 2ooj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2539 reflections ( 98.68 % complete ) and 5168 restraints for refining 2027 atoms. 4911 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2540 (Rfree = 0.000) for 2027 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2440 (Rfree = 0.000) for 2021 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2582 (Rfree = 0.000) for 2016 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2479 (Rfree = 0.000) for 2010 atoms. TimeTaking 33.33