Mon 24 Dec 08:05:05 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 2ouw-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-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/2ouw-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-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 08:05:09 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/2ouw-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-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 158 and 0 Target number of residues in the AU: 158 Target solvent content: 0.6521 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 2208 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 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: 108.355 3.601 Wilson plot Bfac: 79.25 3346 reflections ( 99.79 % complete ) and 0 restraints for refining 2447 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3669 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3462 (Rfree = 0.000) for 2447 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 4.06 Search for helices and strands: 0 residues in 0 chains, 2507 seeds are put forward NCS extension: 0 residues added, 2507 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 6 peptides. Score 0.238 Round 2: 101 peptides, 19 chains. Longest chain 11 peptides. Score 0.351 Round 3: 108 peptides, 19 chains. Longest chain 13 peptides. Score 0.398 Round 4: 111 peptides, 19 chains. Longest chain 13 peptides. Score 0.417 Round 5: 112 peptides, 17 chains. Longest chain 15 peptides. Score 0.476 Taking the results from Round 5 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4750 restraints for refining 2001 atoms. 4387 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3049 (Rfree = 0.000) for 2001 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 2: After refmac, R = 0.2868 (Rfree = 0.000) for 1969 atoms. Found 12 (12 requested) and removed 59 (6 requested) atoms. Cycle 3: After refmac, R = 0.2759 (Rfree = 0.000) for 1907 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 4: After refmac, R = 0.2616 (Rfree = 0.000) for 1884 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 5: After refmac, R = 0.2722 (Rfree = 0.000) for 1874 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.75 Search for helices and strands: 0 residues in 0 chains, 1958 seeds are put forward NCS extension: 0 residues added, 1958 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 8 peptides. Score 0.222 Round 2: 94 peptides, 19 chains. Longest chain 8 peptides. Score 0.302 Round 3: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.315 Round 4: 106 peptides, 20 chains. Longest chain 8 peptides. Score 0.356 Round 5: 108 peptides, 20 chains. Longest chain 10 peptides. Score 0.370 Taking the results from Round 5 Chains 20, Residues 88, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4336 restraints for refining 1840 atoms. 3973 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2899 (Rfree = 0.000) for 1840 atoms. Found 11 (11 requested) and removed 28 (5 requested) atoms. Cycle 7: After refmac, R = 0.2938 (Rfree = 0.000) for 1809 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 8: After refmac, R = 0.2935 (Rfree = 0.000) for 1797 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.2760 (Rfree = 0.000) for 1787 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.2864 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.99 Search for helices and strands: 0 residues in 0 chains, 1877 seeds are put forward NCS extension: 0 residues added, 1877 seeds are put forward Round 1: 105 peptides, 24 chains. Longest chain 7 peptides. Score 0.233 Round 2: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.380 Round 3: 113 peptides, 20 chains. Longest chain 8 peptides. Score 0.402 Round 4: 116 peptides, 22 chains. Longest chain 8 peptides. Score 0.367 Round 5: 122 peptides, 22 chains. Longest chain 9 peptides. Score 0.405 Taking the results from Round 5 Chains 22, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4188 restraints for refining 1843 atoms. 3810 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2497 (Rfree = 0.000) for 1843 atoms. Found 9 (11 requested) and removed 20 (5 requested) atoms. Cycle 12: After refmac, R = 0.2440 (Rfree = 0.000) for 1821 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 13: After refmac, R = 0.3064 (Rfree = 0.000) for 1811 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 14: After refmac, R = 0.2510 (Rfree = 0.000) for 1800 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.2482 (Rfree = 0.000) for 1793 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.92 Search for helices and strands: 0 residues in 0 chains, 1910 seeds are put forward NCS extension: 0 residues added, 1910 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 8 peptides. Score 0.260 Round 2: 99 peptides, 18 chains. Longest chain 10 peptides. Score 0.366 Round 3: 94 peptides, 16 chains. Longest chain 10 peptides. Score 0.391 Round 4: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.366 Round 5: 96 peptides, 16 chains. Longest chain 12 peptides. Score 0.404 Taking the results from Round 5 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4277 restraints for refining 1861 atoms. 3958 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2646 (Rfree = 0.000) for 1861 atoms. Found 11 (11 requested) and removed 35 (5 requested) atoms. Cycle 17: After refmac, R = 0.2728 (Rfree = 0.000) for 1833 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 18: After refmac, R = 0.2417 (Rfree = 0.000) for 1823 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.2453 (Rfree = 0.000) for 1819 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2260 (Rfree = 0.000) for 1819 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.92 Search for helices and strands: 0 residues in 0 chains, 1892 seeds are put forward NCS extension: 0 residues added, 1892 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.294 Round 2: 113 peptides, 23 chains. Longest chain 7 peptides. Score 0.319 Round 3: 118 peptides, 23 chains. Longest chain 10 peptides. Score 0.352 Round 4: 122 peptides, 25 chains. Longest chain 8 peptides. Score 0.323 Round 5: 105 peptides, 20 chains. Longest chain 8 peptides. Score 0.350 Taking the results from Round 3 Chains 23, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4337 restraints for refining 1896 atoms. 3980 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2320 (Rfree = 0.000) for 1896 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 22: After refmac, R = 0.2439 (Rfree = 0.000) for 1875 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 23: After refmac, R = 0.2386 (Rfree = 0.000) for 1876 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.2400 (Rfree = 0.000) for 1873 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.2452 (Rfree = 0.000) for 1873 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 1968 seeds are put forward NCS extension: 0 residues added, 1968 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 6 peptides. Score 0.230 Round 2: 107 peptides, 20 chains. Longest chain 8 peptides. Score 0.363 Round 3: 118 peptides, 21 chains. Longest chain 10 peptides. Score 0.407 Round 4: 111 peptides, 20 chains. Longest chain 9 peptides. Score 0.389 Round 5: 106 peptides, 18 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 5 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4406 restraints for refining 1947 atoms. 4072 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2749 (Rfree = 0.000) for 1947 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 27: After refmac, R = 0.2604 (Rfree = 0.000) for 1924 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 28: After refmac, R = 0.2584 (Rfree = 0.000) for 1917 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 29: After refmac, R = 0.2479 (Rfree = 0.000) for 1905 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 30: After refmac, R = 0.2427 (Rfree = 0.000) for 1900 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 2002 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 2009 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.268 Round 2: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.318 Round 3: 90 peptides, 19 chains. Longest chain 9 peptides. Score 0.274 Round 4: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.325 Round 5: 89 peptides, 17 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 5 Chains 17, Residues 72, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4411 restraints for refining 1913 atoms. 4127 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2522 (Rfree = 0.000) for 1913 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 32: After refmac, R = 0.2598 (Rfree = 0.000) for 1909 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.2617 (Rfree = 0.000) for 1907 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2538 (Rfree = 0.000) for 1910 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 35: After refmac, R = 0.2537 (Rfree = 0.000) for 1909 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.86 Search for helices and strands: 0 residues in 0 chains, 1997 seeds are put forward NCS extension: 0 residues added, 1997 seeds are put forward Round 1: 71 peptides, 17 chains. Longest chain 5 peptides. Score 0.191 Round 2: 75 peptides, 13 chains. Longest chain 12 peptides. Score 0.350 Round 3: 81 peptides, 15 chains. Longest chain 13 peptides. Score 0.331 Round 4: 81 peptides, 14 chains. Longest chain 13 peptides. Score 0.361 Round 5: 78 peptides, 13 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 5 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4401 restraints for refining 1893 atoms. 4154 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2746 (Rfree = 0.000) for 1893 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.2865 (Rfree = 0.000) for 1885 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 38: After refmac, R = 0.2949 (Rfree = 0.000) for 1882 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.2996 (Rfree = 0.000) for 1876 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 40: After refmac, R = 0.2609 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 1957 seeds are put forward NCS extension: 0 residues added, 1957 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 9 peptides. Score 0.253 Round 2: 69 peptides, 12 chains. Longest chain 12 peptides. Score 0.338 Round 3: 71 peptides, 14 chains. Longest chain 7 peptides. Score 0.289 Round 4: 69 peptides, 12 chains. Longest chain 12 peptides. Score 0.338 Round 5: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.304 Taking the results from Round 4 Chains 12, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 3935 restraints for refining 1753 atoms. 3719 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2933 (Rfree = 0.000) for 1753 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2765 (Rfree = 0.000) for 1748 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.2975 (Rfree = 0.000) for 1742 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.2916 (Rfree = 0.000) for 1743 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.2762 (Rfree = 0.000) for 1745 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 4.00 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward NCS extension: 0 residues added, 1805 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 7 peptides. Score 0.194 Round 2: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.262 Round 3: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.296 Round 4: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.266 Round 5: 66 peptides, 12 chains. Longest chain 11 peptides. Score 0.316 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 54, 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 2ouw-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3346 reflections ( 99.79 % complete ) and 3764 restraints for refining 1684 atoms. 3560 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2991 (Rfree = 0.000) for 1684 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3025 (Rfree = 0.000) for 1673 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2815 (Rfree = 0.000) for 1665 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2924 (Rfree = 0.000) for 1656 atoms. TimeTaking 29.95