Sun 23 Dec 22:23:10 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-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/2ooj-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-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 22:23:19 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-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 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-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-3.8-parrot-hancs.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 Failed to save intermediate PDB 2963 reflections ( 98.87 % complete ) and 0 restraints for refining 2487 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3705 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2876 (Rfree = 0.000) for 2487 atoms. Found 5 (13 requested) and removed 47 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.41 Search for helices and strands: 0 residues in 0 chains, 2464 seeds are put forward NCS extension: 0 residues added, 2464 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 6 peptides. Score 0.218 Round 2: 100 peptides, 18 chains. Longest chain 11 peptides. Score 0.356 Round 3: 95 peptides, 16 chains. Longest chain 17 peptides. Score 0.379 Round 4: 112 peptides, 18 chains. Longest chain 12 peptides. Score 0.427 Round 5: 109 peptides, 19 chains. Longest chain 10 peptides. Score 0.385 Taking the results from Round 4 Chains 19, Residues 94, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4762 restraints for refining 2041 atoms. 4379 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2918 (Rfree = 0.000) for 2041 atoms. Found 6 (11 requested) and removed 24 (5 requested) atoms. Cycle 2: After refmac, R = 0.2810 (Rfree = 0.000) for 2014 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 3: After refmac, R = 0.2764 (Rfree = 0.000) for 2006 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2730 (Rfree = 0.000) for 1997 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2709 (Rfree = 0.000) for 1990 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 2016 seeds are put forward NCS extension: 0 residues added, 2016 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 7 peptides. Score 0.276 Round 2: 106 peptides, 20 chains. Longest chain 9 peptides. Score 0.341 Round 3: 111 peptides, 20 chains. Longest chain 11 peptides. Score 0.371 Round 4: 114 peptides, 20 chains. Longest chain 10 peptides. Score 0.389 Round 5: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.422 Taking the results from Round 5 Chains 18, Residues 93, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4967 restraints for refining 2028 atoms. 4589 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2827 (Rfree = 0.000) for 2028 atoms. Found 5 (11 requested) and removed 11 (5 requested) atoms. Cycle 7: After refmac, R = 0.2729 (Rfree = 0.000) for 2015 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.2684 (Rfree = 0.000) for 2009 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.2677 (Rfree = 0.000) for 2001 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.2666 (Rfree = 0.000) for 1993 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 2030 seeds are put forward NCS extension: 0 residues added, 2030 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 10 peptides. Score 0.270 Round 2: 108 peptides, 20 chains. Longest chain 14 peptides. Score 0.353 Round 3: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.356 Round 4: 101 peptides, 17 chains. Longest chain 17 peptides. Score 0.389 Round 5: 114 peptides, 19 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 19, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4997 restraints for refining 2041 atoms. 4636 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2832 (Rfree = 0.000) for 2041 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 12: After refmac, R = 0.2739 (Rfree = 0.000) for 2038 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 13: After refmac, R = 0.2689 (Rfree = 0.000) for 2034 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.2655 (Rfree = 0.000) for 2031 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2638 (Rfree = 0.000) for 2022 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward NCS extension: 0 residues added, 2060 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 10 peptides. Score 0.270 Round 2: 112 peptides, 20 chains. Longest chain 11 peptides. Score 0.377 Round 3: 122 peptides, 21 chains. Longest chain 14 peptides. Score 0.410 Round 4: 122 peptides, 21 chains. Longest chain 12 peptides. Score 0.410 Round 5: 109 peptides, 18 chains. Longest chain 13 peptides. Score 0.410 Taking the results from Round 5 Chains 18, Residues 91, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5074 restraints for refining 2041 atoms. 4715 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2900 (Rfree = 0.000) for 2041 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 17: After refmac, R = 0.2806 (Rfree = 0.000) for 2034 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2756 (Rfree = 0.000) for 2031 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2726 (Rfree = 0.000) for 2021 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2693 (Rfree = 0.000) for 2015 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.65 Search for helices and strands: 0 residues in 0 chains, 2037 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2052 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 9 peptides. Score 0.314 Round 2: 101 peptides, 16 chains. Longest chain 11 peptides. Score 0.415 Round 3: 98 peptides, 17 chains. Longest chain 10 peptides. Score 0.371 Round 4: 112 peptides, 17 chains. Longest chain 12 peptides. Score 0.452 Round 5: 108 peptides, 18 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 4 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5024 restraints for refining 2030 atoms. 4661 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2773 (Rfree = 0.000) for 2030 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 22: After refmac, R = 0.2610 (Rfree = 0.000) for 2024 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2538 (Rfree = 0.000) for 2018 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2502 (Rfree = 0.000) for 2013 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2453 (Rfree = 0.000) for 2007 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 2026 seeds are put forward NCS extension: 0 residues added, 2026 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 6 peptides. Score 0.229 Round 2: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.342 Round 3: 97 peptides, 14 chains. Longest chain 15 peptides. Score 0.443 Round 4: 103 peptides, 16 chains. Longest chain 20 peptides. Score 0.426 Round 5: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 3 Chains 14, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5178 restraints for refining 2041 atoms. 4860 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2514 (Rfree = 0.000) for 2041 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 27: After refmac, R = 0.2442 (Rfree = 0.000) for 2032 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2396 (Rfree = 0.000) for 2030 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2391 (Rfree = 0.000) for 2021 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2370 (Rfree = 0.000) for 2018 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.61 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 2076 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 8 peptides. Score 0.245 Round 2: 104 peptides, 19 chains. Longest chain 10 peptides. Score 0.355 Round 3: 100 peptides, 14 chains. Longest chain 13 peptides. Score 0.460 Round 4: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.389 Round 5: 109 peptides, 18 chains. Longest chain 10 peptides. Score 0.410 Taking the results from Round 3 Chains 14, Residues 86, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5079 restraints for refining 2038 atoms. 4725 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2555 (Rfree = 0.000) for 2038 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 32: After refmac, R = 0.2459 (Rfree = 0.000) for 2037 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2428 (Rfree = 0.000) for 2030 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2400 (Rfree = 0.000) for 2026 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2383 (Rfree = 0.000) for 2020 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 2047 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2063 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 8 peptides. Score 0.261 Round 2: 92 peptides, 17 chains. Longest chain 8 peptides. Score 0.333 Round 3: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.330 Round 4: 101 peptides, 16 chains. Longest chain 11 peptides. Score 0.415 Round 5: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.355 Taking the results from Round 4 Chains 16, Residues 85, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5209 restraints for refining 2041 atoms. 4879 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2520 (Rfree = 0.000) for 2041 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.2444 (Rfree = 0.000) for 2037 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.2424 (Rfree = 0.000) for 2030 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2384 (Rfree = 0.000) for 2026 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2372 (Rfree = 0.000) for 2020 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.61 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: 97 peptides, 21 chains. Longest chain 8 peptides. Score 0.256 Round 2: 114 peptides, 22 chains. Longest chain 9 peptides. Score 0.338 Round 3: 103 peptides, 18 chains. Longest chain 9 peptides. Score 0.375 Round 4: 102 peptides, 19 chains. Longest chain 8 peptides. Score 0.342 Round 5: 104 peptides, 20 chains. Longest chain 9 peptides. Score 0.328 Taking the results from Round 3 Chains 18, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5148 restraints for refining 2041 atoms. 4826 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2507 (Rfree = 0.000) for 2041 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2428 (Rfree = 0.000) for 2040 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2385 (Rfree = 0.000) for 2035 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.2354 (Rfree = 0.000) for 2031 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2310 (Rfree = 0.000) for 2027 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.63 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 0 residues added, 2048 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.242 Round 2: 101 peptides, 19 chains. Longest chain 8 peptides. Score 0.336 Round 3: 97 peptides, 16 chains. Longest chain 9 peptides. Score 0.391 Round 4: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.333 Round 5: 86 peptides, 15 chains. Longest chain 9 peptides. Score 0.350 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 81, 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 5193 restraints for refining 2041 atoms. 4885 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2451 (Rfree = 0.000) for 2041 atoms. Found 0 (11 requested) and removed 4 (5 requested) atoms. Cycle 47: After refmac, R = 0.2365 (Rfree = 0.000) for 2036 atoms. Found 0 (11 requested) and removed 4 (5 requested) atoms. Cycle 48: After refmac, R = 0.2326 (Rfree = 0.000) for 2032 atoms. Found 0 (11 requested) and removed 1 (5 requested) atoms. Cycle 49: After refmac, R = 0.2300 (Rfree = 0.000) for 2030 atoms. Found 0 (11 requested) and removed 1 (5 requested) atoms. Writing output files ... TimeTaking 33.8