Mon 24 Dec 07:52:37 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 2ooj-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ooj-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ooj-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-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/2ooj-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-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 07:52:41 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/2ooj-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-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 191 and 0 Target number of residues in the AU: 191 Target solvent content: 0.6265 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-3.6-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: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-3.6-parrot-noncs.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 3.600 Wilson plot Bfac: 64.40 3470 reflections ( 99.03 % complete ) and 0 restraints for refining 2508 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3599 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3719 (Rfree = 0.000) for 2508 atoms. Found 11 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 2516 seeds are put forward NCS extension: 0 residues added, 2516 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.218 Round 2: 60 peptides, 13 chains. Longest chain 6 peptides. Score 0.230 Round 3: 85 peptides, 17 chains. Longest chain 9 peptides. Score 0.288 Round 4: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.346 Round 5: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 5 Chains 17, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4908 restraints for refining 2044 atoms. 4617 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3425 (Rfree = 0.000) for 2044 atoms. Found 9 (13 requested) and removed 16 (6 requested) atoms. Cycle 2: After refmac, R = 0.3374 (Rfree = 0.000) for 2008 atoms. Found 7 (13 requested) and removed 15 (6 requested) atoms. Cycle 3: After refmac, R = 0.3247 (Rfree = 0.000) for 1983 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2736 (Rfree = 0.000) for 1963 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. Cycle 5: After refmac, R = 0.3127 (Rfree = 0.000) for 1946 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 1978 seeds are put forward NCS extension: 0 residues added, 1978 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 7 peptides. Score 0.218 Round 2: 103 peptides, 20 chains. Longest chain 9 peptides. Score 0.322 Round 3: 122 peptides, 21 chains. Longest chain 12 peptides. Score 0.410 Round 4: 111 peptides, 21 chains. Longest chain 9 peptides. Score 0.345 Round 5: 119 peptides, 19 chains. Longest chain 13 peptides. Score 0.442 Taking the results from Round 5 Chains 19, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4370 restraints for refining 1882 atoms. 3989 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2892 (Rfree = 0.000) for 1882 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.2794 (Rfree = 0.000) for 1859 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 8: After refmac, R = 0.2821 (Rfree = 0.000) for 1840 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 9: After refmac, R = 0.2692 (Rfree = 0.000) for 1823 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 10: After refmac, R = 0.2872 (Rfree = 0.000) for 1802 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 1872 seeds are put forward NCS extension: 0 residues added, 1872 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 9 peptides. Score 0.249 Round 2: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.365 Round 3: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.421 Round 4: 119 peptides, 20 chains. Longest chain 18 peptides. Score 0.418 Round 5: 126 peptides, 21 chains. Longest chain 10 peptides. Score 0.433 Taking the results from Round 5 Chains 21, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4153 restraints for refining 1899 atoms. 3754 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2899 (Rfree = 0.000) for 1899 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 12: After refmac, R = 0.2841 (Rfree = 0.000) for 1870 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 13: After refmac, R = 0.2716 (Rfree = 0.000) for 1853 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.2732 (Rfree = 0.000) for 1850 atoms. Found 8 (11 requested) and removed 11 (5 requested) atoms. Cycle 15: After refmac, R = 0.2820 (Rfree = 0.000) for 1835 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 1895 seeds are put forward NCS extension: 0 residues added, 1895 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 7 peptides. Score 0.210 Round 2: 98 peptides, 20 chains. Longest chain 8 peptides. Score 0.290 Round 3: 118 peptides, 23 chains. Longest chain 10 peptides. Score 0.336 Round 4: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.383 Round 5: 111 peptides, 19 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 5 Chains 19, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4427 restraints for refining 1928 atoms. 4078 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3010 (Rfree = 0.000) for 1928 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 17: After refmac, R = 0.2777 (Rfree = 0.000) for 1903 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 18: After refmac, R = 0.2952 (Rfree = 0.000) for 1891 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 19: After refmac, R = 0.2798 (Rfree = 0.000) for 1886 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 20: After refmac, R = 0.2703 (Rfree = 0.000) for 1879 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.44 Search for helices and strands: 0 residues in 0 chains, 1918 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 1929 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 8 peptides. Score 0.237 Round 2: 103 peptides, 20 chains. Longest chain 9 peptides. Score 0.322 Round 3: 113 peptides, 21 chains. Longest chain 9 peptides. Score 0.357 Round 4: 106 peptides, 20 chains. Longest chain 8 peptides. Score 0.341 Round 5: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.373 Taking the results from Round 5 Chains 19, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4338 restraints for refining 1917 atoms. 4005 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2855 (Rfree = 0.000) for 1917 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 22: After refmac, R = 0.2766 (Rfree = 0.000) for 1898 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 23: After refmac, R = 0.2961 (Rfree = 0.000) for 1890 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.2936 (Rfree = 0.000) for 1886 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.2864 (Rfree = 0.000) for 1886 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.57 Search for helices and strands: 0 residues in 0 chains, 1946 seeds are put forward NCS extension: 0 residues added, 1946 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 6 peptides. Score 0.204 Round 2: 98 peptides, 22 chains. Longest chain 6 peptides. Score 0.235 Round 3: 97 peptides, 18 chains. Longest chain 12 peptides. Score 0.338 Round 4: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.309 Round 5: 93 peptides, 18 chains. Longest chain 8 peptides. Score 0.312 Taking the results from Round 3 Chains 18, Residues 79, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4082 restraints for refining 1847 atoms. 3768 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2854 (Rfree = 0.000) for 1847 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 27: After refmac, R = 0.2908 (Rfree = 0.000) for 1825 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.2825 (Rfree = 0.000) for 1814 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.2875 (Rfree = 0.000) for 1810 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2925 (Rfree = 0.000) for 1812 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 1863 seeds are put forward NCS extension: 0 residues added, 1863 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 8 peptides. Score 0.211 Round 2: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.307 Round 3: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.285 Round 4: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.288 Round 5: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 5 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4175 restraints for refining 1829 atoms. 3921 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3079 (Rfree = 0.000) for 1829 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 32: After refmac, R = 0.2887 (Rfree = 0.000) for 1816 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.2781 (Rfree = 0.000) for 1812 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.2891 (Rfree = 0.000) for 1805 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 35: After refmac, R = 0.2931 (Rfree = 0.000) for 1802 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 1838 seeds are put forward NCS extension: 0 residues added, 1838 seeds are put forward Round 1: 62 peptides, 15 chains. Longest chain 5 peptides. Score 0.182 Round 2: 88 peptides, 19 chains. Longest chain 6 peptides. Score 0.251 Round 3: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.293 Round 4: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.272 Round 5: 88 peptides, 16 chains. Longest chain 8 peptides. Score 0.335 Taking the results from Round 5 Chains 16, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 3874 restraints for refining 1793 atoms. 3602 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2666 (Rfree = 0.000) for 1793 atoms. Found 6 (11 requested) and removed 20 (5 requested) atoms. Cycle 37: After refmac, R = 0.2594 (Rfree = 0.000) for 1776 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.2789 (Rfree = 0.000) for 1772 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2460 (Rfree = 0.000) for 1769 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2484 (Rfree = 0.000) for 1764 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.53 Search for helices and strands: 0 residues in 0 chains, 1798 seeds are put forward NCS extension: 0 residues added, 1798 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.205 Round 2: 79 peptides, 13 chains. Longest chain 8 peptides. Score 0.362 Round 3: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.354 Round 4: 93 peptides, 16 chains. Longest chain 9 peptides. Score 0.367 Round 5: 92 peptides, 17 chains. Longest chain 8 peptides. Score 0.333 Taking the results from Round 4 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 3854 restraints for refining 1762 atoms. 3562 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2925 (Rfree = 0.000) for 1762 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.3308 (Rfree = 0.000) for 1753 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 43: After refmac, R = 0.2838 (Rfree = 0.000) for 1741 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.2830 (Rfree = 0.000) for 1740 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.2588 (Rfree = 0.000) for 1739 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.52 Search for helices and strands: 0 residues in 0 chains, 1778 seeds are put forward NCS extension: 0 residues added, 1778 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.245 Round 2: 89 peptides, 17 chains. Longest chain 10 peptides. Score 0.314 Round 3: 91 peptides, 13 chains. Longest chain 12 peptides. Score 0.434 Round 4: 98 peptides, 17 chains. Longest chain 10 peptides. Score 0.371 Round 5: 83 peptides, 12 chains. Longest chain 11 peptides. Score 0.414 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 78, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2ooj-3_warpNtrace.pdb as input Building loops using Loopy2018 13 chains (78 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3470 reflections ( 99.03 % complete ) and 3839 restraints for refining 1790 atoms. 3495 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3046 (Rfree = 0.000) for 1790 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2893 (Rfree = 0.000) for 1784 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2855 (Rfree = 0.000) for 1776 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2665 (Rfree = 0.000) for 1766 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 27.23