Sun 23 Dec 22:22:44 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 2owp-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2owp-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2owp-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-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/2owp-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-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 22:22:53 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/2owp-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-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 321 and 0 Target number of residues in the AU: 321 Target solvent content: 0.6008 Checking the provided sequence file Detected sequence length: 129 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 258 Adjusted target solvent content: 0.68 Input MTZ file: 2owp-3.2-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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 1.10 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: 29.899 3.200 Wilson plot Bfac: 52.66 7504 reflections ( 99.15 % complete ) and 0 restraints for refining 2281 atoms. Observations/parameters ratio is 0.82 ------------------------------------------------------ Starting model: R = 0.3444 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3372 (Rfree = 0.000) for 2281 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 2.63 Search for helices and strands: 0 residues in 0 chains, 2335 seeds are put forward NCS extension: 0 residues added, 2335 seeds are put forward Round 1: 171 peptides, 23 chains. Longest chain 14 peptides. Score 0.491 Round 2: 222 peptides, 24 chains. Longest chain 28 peptides. Score 0.630 Round 3: 228 peptides, 20 chains. Longest chain 32 peptides. Score 0.691 Round 4: 216 peptides, 19 chains. Longest chain 25 peptides. Score 0.674 Round 5: 224 peptides, 18 chains. Longest chain 46 peptides. Score 0.703 Taking the results from Round 5 Chains 20, Residues 206, Estimated correctness of the model 65.8 % 4 chains (101 residues) have been docked in sequence Building loops using Loopy2018 20 chains (206 residues) following loop building 4 chains (101 residues) in sequence following loop building ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 2971 restraints for refining 1968 atoms. 1763 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3231 (Rfree = 0.000) for 1968 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 2: After refmac, R = 0.3084 (Rfree = 0.000) for 1918 atoms. Found 15 (17 requested) and removed 16 (8 requested) atoms. Cycle 3: After refmac, R = 0.3009 (Rfree = 0.000) for 1899 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 4: After refmac, R = 0.2903 (Rfree = 0.000) for 1885 atoms. Found 15 (16 requested) and removed 14 (8 requested) atoms. Cycle 5: After refmac, R = 0.2791 (Rfree = 0.000) for 1883 atoms. Found 1 (15 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.43 Search for helices and strands: 0 residues in 0 chains, 1937 seeds are put forward NCS extension: 50 residues added (8 deleted due to clashes), 1987 seeds are put forward Round 1: 214 peptides, 24 chains. Longest chain 33 peptides. Score 0.608 Round 2: 213 peptides, 18 chains. Longest chain 30 peptides. Score 0.678 Round 3: 209 peptides, 19 chains. Longest chain 35 peptides. Score 0.657 Round 4: 214 peptides, 17 chains. Longest chain 42 peptides. Score 0.692 Round 5: 197 peptides, 17 chains. Longest chain 42 peptides. Score 0.651 Taking the results from Round 4 Chains 20, Residues 197, Estimated correctness of the model 63.5 % 6 chains (101 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 2983 restraints for refining 1915 atoms. 1811 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3200 (Rfree = 0.000) for 1915 atoms. Found 15 (15 requested) and removed 23 (8 requested) atoms. Cycle 7: After refmac, R = 0.3025 (Rfree = 0.000) for 1889 atoms. Found 15 (15 requested) and removed 18 (8 requested) atoms. Cycle 8: After refmac, R = 0.2906 (Rfree = 0.000) for 1881 atoms. Found 6 (14 requested) and removed 12 (8 requested) atoms. Cycle 9: After refmac, R = 0.2846 (Rfree = 0.000) for 1866 atoms. Found 4 (14 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.2804 (Rfree = 0.000) for 1856 atoms. Found 5 (14 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 2.53 Search for helices and strands: 0 residues in 0 chains, 1900 seeds are put forward NCS extension: 41 residues added (3 deleted due to clashes), 1941 seeds are put forward Round 1: 194 peptides, 24 chains. Longest chain 21 peptides. Score 0.550 Round 2: 203 peptides, 19 chains. Longest chain 40 peptides. Score 0.642 Round 3: 207 peptides, 18 chains. Longest chain 31 peptides. Score 0.664 Round 4: 210 peptides, 16 chains. Longest chain 35 peptides. Score 0.694 Round 5: 205 peptides, 18 chains. Longest chain 32 peptides. Score 0.659 Taking the results from Round 4 Chains 18, Residues 194, Estimated correctness of the model 63.9 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3411 restraints for refining 1884 atoms. 2453 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3083 (Rfree = 0.000) for 1884 atoms. Found 14 (14 requested) and removed 16 (8 requested) atoms. Cycle 12: After refmac, R = 0.2888 (Rfree = 0.000) for 1872 atoms. Found 12 (14 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2851 (Rfree = 0.000) for 1869 atoms. Found 14 (14 requested) and removed 16 (8 requested) atoms. Cycle 14: After refmac, R = 0.2768 (Rfree = 0.000) for 1865 atoms. Found 9 (14 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.2780 (Rfree = 0.000) for 1858 atoms. Found 9 (14 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 2.43 Search for helices and strands: 0 residues in 0 chains, 1930 seeds are put forward NCS extension: 34 residues added (4 deleted due to clashes), 1964 seeds are put forward Round 1: 196 peptides, 21 chains. Longest chain 25 peptides. Score 0.597 Round 2: 212 peptides, 22 chains. Longest chain 29 peptides. Score 0.628 Round 3: 209 peptides, 17 chains. Longest chain 30 peptides. Score 0.680 Round 4: 221 peptides, 19 chains. Longest chain 31 peptides. Score 0.686 Round 5: 221 peptides, 19 chains. Longest chain 31 peptides. Score 0.686 Taking the results from Round 5 Chains 21, Residues 202, Estimated correctness of the model 62.2 % 3 chains (61 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3170 restraints for refining 1884 atoms. 2131 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3042 (Rfree = 0.000) for 1884 atoms. Found 14 (14 requested) and removed 21 (8 requested) atoms. Cycle 17: After refmac, R = 0.2941 (Rfree = 0.000) for 1857 atoms. Found 7 (14 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2854 (Rfree = 0.000) for 1844 atoms. Found 6 (14 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.2792 (Rfree = 0.000) for 1833 atoms. Found 8 (14 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.2744 (Rfree = 0.000) for 1821 atoms. Found 12 (14 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.04 2.37 Search for helices and strands: 0 residues in 0 chains, 1886 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 1913 seeds are put forward Round 1: 192 peptides, 25 chains. Longest chain 16 peptides. Score 0.530 Round 2: 205 peptides, 21 chains. Longest chain 28 peptides. Score 0.622 Round 3: 213 peptides, 23 chains. Longest chain 27 peptides. Score 0.618 Round 4: 213 peptides, 17 chains. Longest chain 43 peptides. Score 0.690 Round 5: 205 peptides, 18 chains. Longest chain 21 peptides. Score 0.659 Taking the results from Round 4 Chains 18, Residues 196, Estimated correctness of the model 63.0 % 3 chains (70 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3163 restraints for refining 1884 atoms. 2116 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3065 (Rfree = 0.000) for 1884 atoms. Found 14 (14 requested) and removed 16 (8 requested) atoms. Cycle 22: After refmac, R = 0.2862 (Rfree = 0.000) for 1866 atoms. Found 14 (14 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.2757 (Rfree = 0.000) for 1863 atoms. Found 5 (14 requested) and removed 12 (8 requested) atoms. Cycle 24: After refmac, R = 0.2698 (Rfree = 0.000) for 1851 atoms. Found 7 (14 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2688 (Rfree = 0.000) for 1848 atoms. Found 6 (14 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 2.53 Search for helices and strands: 0 residues in 0 chains, 1895 seeds are put forward NCS extension: 36 residues added (12 deleted due to clashes), 1931 seeds are put forward Round 1: 205 peptides, 25 chains. Longest chain 23 peptides. Score 0.570 Round 2: 212 peptides, 20 chains. Longest chain 31 peptides. Score 0.652 Round 3: 210 peptides, 16 chains. Longest chain 32 peptides. Score 0.694 Round 4: 212 peptides, 21 chains. Longest chain 31 peptides. Score 0.640 Round 5: 209 peptides, 20 chains. Longest chain 26 peptides. Score 0.645 Taking the results from Round 3 Chains 16, Residues 194, Estimated correctness of the model 63.9 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3633 restraints for refining 1883 atoms. 2774 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3012 (Rfree = 0.000) for 1883 atoms. Found 14 (14 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.3062 (Rfree = 0.000) for 1876 atoms. Found 14 (14 requested) and removed 13 (8 requested) atoms. Cycle 28: After refmac, R = 0.3043 (Rfree = 0.000) for 1868 atoms. Found 14 (14 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.2915 (Rfree = 0.000) for 1867 atoms. Found 14 (14 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.2901 (Rfree = 0.000) for 1868 atoms. Found 6 (14 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 2.61 Search for helices and strands: 0 residues in 0 chains, 1921 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 1940 seeds are put forward Round 1: 194 peptides, 24 chains. Longest chain 19 peptides. Score 0.550 Round 2: 203 peptides, 20 chains. Longest chain 26 peptides. Score 0.629 Round 3: 204 peptides, 22 chains. Longest chain 22 peptides. Score 0.606 Round 4: 216 peptides, 22 chains. Longest chain 25 peptides. Score 0.638 Round 5: 210 peptides, 19 chains. Longest chain 33 peptides. Score 0.659 Taking the results from Round 5 Chains 21, Residues 191, Estimated correctness of the model 56.0 % 3 chains (58 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3241 restraints for refining 1883 atoms. 2260 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3395 (Rfree = 0.000) for 1883 atoms. Found 14 (14 requested) and removed 19 (8 requested) atoms. Cycle 32: After refmac, R = 0.3178 (Rfree = 0.000) for 1862 atoms. Found 14 (14 requested) and removed 15 (8 requested) atoms. Cycle 33: After refmac, R = 0.3157 (Rfree = 0.000) for 1852 atoms. Found 14 (14 requested) and removed 13 (8 requested) atoms. Cycle 34: After refmac, R = 0.3107 (Rfree = 0.000) for 1846 atoms. Found 14 (14 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.2929 (Rfree = 0.000) for 1845 atoms. Found 3 (14 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 2.51 Search for helices and strands: 0 residues in 0 chains, 1907 seeds are put forward NCS extension: 23 residues added (7 deleted due to clashes), 1930 seeds are put forward Round 1: 187 peptides, 24 chains. Longest chain 17 peptides. Score 0.529 Round 2: 218 peptides, 22 chains. Longest chain 30 peptides. Score 0.644 Round 3: 210 peptides, 23 chains. Longest chain 26 peptides. Score 0.610 Round 4: 205 peptides, 19 chains. Longest chain 25 peptides. Score 0.647 Round 5: 218 peptides, 22 chains. Longest chain 22 peptides. Score 0.644 Taking the results from Round 4 Chains 24, Residues 186, Estimated correctness of the model 53.1 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3433 restraints for refining 1882 atoms. 2522 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3316 (Rfree = 0.000) for 1882 atoms. Found 14 (14 requested) and removed 19 (8 requested) atoms. Cycle 37: After refmac, R = 0.3343 (Rfree = 0.000) for 1871 atoms. Found 14 (14 requested) and removed 24 (8 requested) atoms. Cycle 38: After refmac, R = 0.3319 (Rfree = 0.000) for 1856 atoms. Found 14 (14 requested) and removed 20 (8 requested) atoms. Cycle 39: After refmac, R = 0.3270 (Rfree = 0.000) for 1848 atoms. Found 14 (14 requested) and removed 12 (8 requested) atoms. Cycle 40: After refmac, R = 0.3077 (Rfree = 0.000) for 1848 atoms. Found 14 (14 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 2.68 Search for helices and strands: 0 residues in 0 chains, 1926 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 1937 seeds are put forward Round 1: 182 peptides, 23 chains. Longest chain 20 peptides. Score 0.527 Round 2: 190 peptides, 20 chains. Longest chain 21 peptides. Score 0.593 Round 3: 190 peptides, 19 chains. Longest chain 32 peptides. Score 0.607 Round 4: 190 peptides, 17 chains. Longest chain 31 peptides. Score 0.633 Round 5: 203 peptides, 18 chains. Longest chain 40 peptides. Score 0.654 Taking the results from Round 5 Chains 22, Residues 185, Estimated correctness of the model 54.8 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3465 restraints for refining 1884 atoms. 2570 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3491 (Rfree = 0.000) for 1884 atoms. Found 14 (14 requested) and removed 26 (8 requested) atoms. Cycle 42: After refmac, R = 0.3493 (Rfree = 0.000) for 1861 atoms. Found 14 (14 requested) and removed 19 (8 requested) atoms. Cycle 43: After refmac, R = 0.3468 (Rfree = 0.000) for 1846 atoms. Found 14 (14 requested) and removed 23 (8 requested) atoms. Cycle 44: After refmac, R = 0.3404 (Rfree = 0.000) for 1834 atoms. Found 14 (14 requested) and removed 17 (8 requested) atoms. Cycle 45: After refmac, R = 0.3418 (Rfree = 0.000) for 1822 atoms. Found 14 (14 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 2.45 Search for helices and strands: 0 residues in 0 chains, 1882 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 1922 seeds are put forward Round 1: 154 peptides, 23 chains. Longest chain 14 peptides. Score 0.432 Round 2: 180 peptides, 23 chains. Longest chain 19 peptides. Score 0.521 Round 3: 176 peptides, 22 chains. Longest chain 19 peptides. Score 0.523 Round 4: 162 peptides, 20 chains. Longest chain 20 peptides. Score 0.507 Round 5: 166 peptides, 19 chains. Longest chain 18 peptides. Score 0.535 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 147, Estimated correctness of the model 22.4 % 2 chains (22 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2owp-3_warpNtrace.pdb as input Building loops using Loopy2018 21 chains (147 residues) following loop building 2 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7504 reflections ( 99.15 % complete ) and 3750 restraints for refining 1884 atoms. 3080 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3450 (Rfree = 0.000) for 1884 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.3516 (Rfree = 0.000) for 1860 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.3358 (Rfree = 0.000) for 1847 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.3229 (Rfree = 0.000) for 1836 atoms. TimeTaking 47.43