Sun 23 Dec 22:23:14 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.6-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 22:23:22 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.6-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 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-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-3.6-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 3.600 Wilson plot Bfac: 64.40 3470 reflections ( 99.03 % complete ) and 0 restraints for refining 2501 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3687 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3731 (Rfree = 0.000) for 2501 atoms. Found 12 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 2520 seeds are put forward NCS extension: 0 residues added, 2520 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.215 Round 2: 88 peptides, 18 chains. Longest chain 7 peptides. Score 0.280 Round 3: 99 peptides, 20 chains. Longest chain 8 peptides. Score 0.297 Round 4: 113 peptides, 20 chains. Longest chain 9 peptides. Score 0.383 Round 5: 111 peptides, 19 chains. Longest chain 10 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 4875 restraints for refining 2045 atoms. 4526 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3219 (Rfree = 0.000) for 2045 atoms. Found 10 (13 requested) and removed 17 (6 requested) atoms. Cycle 2: After refmac, R = 0.3343 (Rfree = 0.000) for 2014 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 3: After refmac, R = 0.3104 (Rfree = 0.000) for 1990 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.3138 (Rfree = 0.000) for 1977 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 5: After refmac, R = 0.3140 (Rfree = 0.000) for 1961 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.51 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2015 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.262 Round 2: 110 peptides, 20 chains. Longest chain 12 peptides. Score 0.365 Round 3: 105 peptides, 17 chains. Longest chain 17 peptides. Score 0.412 Round 4: 115 peptides, 17 chains. Longest chain 15 peptides. Score 0.468 Round 5: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.420 Taking the results from Round 4 Chains 17, Residues 98, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4186 restraints for refining 1867 atoms. 3798 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3061 (Rfree = 0.000) for 1867 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 7: After refmac, R = 0.3014 (Rfree = 0.000) for 1843 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 8: After refmac, R = 0.3055 (Rfree = 0.000) for 1823 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2936 (Rfree = 0.000) for 1808 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.2998 (Rfree = 0.000) for 1801 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 1862 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 1883 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 6 peptides. Score 0.249 Round 2: 108 peptides, 21 chains. Longest chain 10 peptides. Score 0.327 Round 3: 131 peptides, 21 chains. Longest chain 14 peptides. Score 0.460 Round 4: 120 peptides, 21 chains. Longest chain 10 peptides. Score 0.399 Round 5: 123 peptides, 19 chains. Longest chain 17 peptides. Score 0.464 Taking the results from Round 5 Chains 19, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4030 restraints for refining 1815 atoms. 3633 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3056 (Rfree = 0.000) for 1815 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 12: After refmac, R = 0.2863 (Rfree = 0.000) for 1801 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.2719 (Rfree = 0.000) for 1792 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2839 (Rfree = 0.000) for 1790 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 15: After refmac, R = 0.2708 (Rfree = 0.000) for 1782 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 1855 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 1879 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 8 peptides. Score 0.268 Round 2: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.323 Round 3: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.377 Round 4: 103 peptides, 16 chains. Longest chain 12 peptides. Score 0.426 Round 5: 110 peptides, 18 chains. Longest chain 12 peptides. Score 0.416 Taking the results from Round 4 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4099 restraints for refining 1838 atoms. 3744 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2963 (Rfree = 0.000) for 1838 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 17: After refmac, R = 0.2961 (Rfree = 0.000) for 1816 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.2890 (Rfree = 0.000) for 1803 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.2729 (Rfree = 0.000) for 1797 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2809 (Rfree = 0.000) for 1792 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1846 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 9 peptides. Score 0.250 Round 2: 108 peptides, 20 chains. Longest chain 11 peptides. Score 0.353 Round 3: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.416 Round 4: 114 peptides, 19 chains. Longest chain 11 peptides. Score 0.414 Round 5: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 3 Chains 21, Residues 102, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 3819 restraints for refining 1776 atoms. 3412 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2880 (Rfree = 0.000) for 1776 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 22: After refmac, R = 0.2821 (Rfree = 0.000) for 1774 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 23: After refmac, R = 0.2716 (Rfree = 0.000) for 1761 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2647 (Rfree = 0.000) for 1756 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 25: After refmac, R = 0.2828 (Rfree = 0.000) for 1751 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.42 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward NCS extension: 0 residues added, 1816 seeds are put forward Round 1: 92 peptides, 21 chains. Longest chain 6 peptides. Score 0.223 Round 2: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.316 Round 3: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.309 Round 4: 114 peptides, 19 chains. Longest chain 18 peptides. Score 0.414 Round 5: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.389 Taking the results from Round 4 Chains 19, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4283 restraints for refining 1934 atoms. 3922 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2945 (Rfree = 0.000) for 1934 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 27: After refmac, R = 0.2860 (Rfree = 0.000) for 1912 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.2687 (Rfree = 0.000) for 1901 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.2563 (Rfree = 0.000) for 1891 atoms. Found 3 (12 requested) and removed 25 (6 requested) atoms. Cycle 30: After refmac, R = 0.2606 (Rfree = 0.000) for 1866 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 1915 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 1944 seeds are put forward Round 1: 74 peptides, 18 chains. Longest chain 5 peptides. Score 0.182 Round 2: 94 peptides, 18 chains. Longest chain 10 peptides. Score 0.319 Round 3: 91 peptides, 17 chains. Longest chain 12 peptides. Score 0.327 Round 4: 97 peptides, 18 chains. Longest chain 10 peptides. Score 0.338 Round 5: 105 peptides, 18 chains. Longest chain 12 peptides. Score 0.387 Taking the results from Round 5 Chains 18, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4219 restraints for refining 1860 atoms. 3889 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3000 (Rfree = 0.000) for 1860 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 32: After refmac, R = 0.2946 (Rfree = 0.000) for 1852 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.2813 (Rfree = 0.000) for 1847 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.3181 (Rfree = 0.000) for 1842 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 35: After refmac, R = 0.2913 (Rfree = 0.000) for 1834 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 1868 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1886 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 6 peptides. Score 0.218 Round 2: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.293 Round 3: 89 peptides, 15 chains. Longest chain 9 peptides. Score 0.369 Round 4: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.306 Round 5: 87 peptides, 14 chains. Longest chain 10 peptides. Score 0.384 Taking the results from Round 5 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 4120 restraints for refining 1847 atoms. 3842 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2964 (Rfree = 0.000) for 1847 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 37: After refmac, R = 0.2878 (Rfree = 0.000) for 1839 atoms. Found 6 (11 requested) and removed 15 (5 requested) atoms. Cycle 38: After refmac, R = 0.2895 (Rfree = 0.000) for 1826 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 39: After refmac, R = 0.2885 (Rfree = 0.000) for 1823 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.3090 (Rfree = 0.000) for 1819 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 1878 seeds are put forward NCS extension: 0 residues added, 1878 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.203 Round 2: 63 peptides, 12 chains. Longest chain 7 peptides. Score 0.284 Round 3: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.294 Round 4: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.286 Round 5: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.279 Taking the results from Round 3 Chains 11, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.03 % complete ) and 3648 restraints for refining 1714 atoms. 3463 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3117 (Rfree = 0.000) for 1714 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.2985 (Rfree = 0.000) for 1706 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 43: After refmac, R = 0.3004 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.3186 (Rfree = 0.000) for 1696 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.2815 (Rfree = 0.000) for 1694 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 1724 seeds are put forward NCS extension: 0 residues added, 1724 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 7 peptides. Score 0.218 Round 2: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.257 Round 3: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.242 Round 4: 73 peptides, 14 chains. Longest chain 11 peptides. Score 0.293 Round 5: 63 peptides, 12 chains. Longest chain 7 peptides. Score 0.284 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 59, 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. 3470 reflections ( 99.03 % complete ) and 3402 restraints for refining 1669 atoms. 3180 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2892 (Rfree = 0.000) for 1669 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2860 (Rfree = 0.000) for 1657 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2783 (Rfree = 0.000) for 1646 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3008 (Rfree = 0.000) for 1639 atoms. TimeTaking 31.92