Tue 25 Dec 19:27:55 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 2ouw-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-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/2ouw-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-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 ============================================================ Tue 25 Dec 19:28:05 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/2ouw-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-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 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-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.6-parrot-hancs.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 2445 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3680 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3393 (Rfree = 0.000) for 2445 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 4.00 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: 77 peptides, 17 chains. Longest chain 9 peptides. Score 0.238 Round 2: 112 peptides, 23 chains. Longest chain 9 peptides. Score 0.312 Round 3: 114 peptides, 24 chains. Longest chain 6 peptides. Score 0.297 Round 4: 122 peptides, 24 chains. Longest chain 9 peptides. Score 0.351 Round 5: 129 peptides, 25 chains. Longest chain 9 peptides. Score 0.369 Taking the results from Round 5 Chains 25, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4791 restraints for refining 1989 atoms. 4400 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2836 (Rfree = 0.000) for 1989 atoms. Found 10 (12 requested) and removed 21 (6 requested) atoms. Cycle 2: After refmac, R = 0.2775 (Rfree = 0.000) for 1957 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 3: After refmac, R = 0.2742 (Rfree = 0.000) for 1936 atoms. Found 12 (12 requested) and removed 72 (6 requested) atoms. Cycle 4: After refmac, R = 0.2782 (Rfree = 0.000) for 1874 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 5: After refmac, R = 0.2718 (Rfree = 0.000) for 1861 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.81 Search for helices and strands: 0 residues in 0 chains, 1963 seeds are put forward NCS extension: 0 residues added, 1963 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.225 Round 2: 80 peptides, 15 chains. Longest chain 7 peptides. Score 0.324 Round 3: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.340 Round 4: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.353 Round 5: 95 peptides, 18 chains. Longest chain 8 peptides. Score 0.339 Taking the results from Round 4 Chains 18, Residues 79, 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 1813 atoms. 4103 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2802 (Rfree = 0.000) for 1813 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2406 (Rfree = 0.000) for 1791 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2799 (Rfree = 0.000) for 1786 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2652 (Rfree = 0.000) for 1787 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2758 (Rfree = 0.000) for 1787 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.97 Search for helices and strands: 0 residues in 0 chains, 1882 seeds are put forward NCS extension: 0 residues added, 1882 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 8 peptides. Score 0.318 Round 2: 113 peptides, 21 chains. Longest chain 10 peptides. Score 0.375 Round 3: 123 peptides, 22 chains. Longest chain 10 peptides. Score 0.412 Round 4: 123 peptides, 21 chains. Longest chain 13 peptides. Score 0.438 Round 5: 126 peptides, 20 chains. Longest chain 12 peptides. Score 0.482 Taking the results from Round 5 Chains 21, Residues 106, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 3913 restraints for refining 1804 atoms. 3464 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2678 (Rfree = 0.000) for 1804 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 12: After refmac, R = 0.2143 (Rfree = 0.000) for 1780 atoms. Found 7 (11 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2296 (Rfree = 0.000) for 1776 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2382 (Rfree = 0.000) for 1777 atoms. Found 11 (11 requested) and removed 28 (5 requested) atoms. Cycle 15: After refmac, R = 0.2401 (Rfree = 0.000) for 1756 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.81 Search for helices and strands: 0 residues in 0 chains, 1847 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 1856 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 7 peptides. Score 0.249 Round 2: 115 peptides, 23 chains. Longest chain 8 peptides. Score 0.332 Round 3: 111 peptides, 21 chains. Longest chain 9 peptides. Score 0.362 Round 4: 116 peptides, 21 chains. Longest chain 16 peptides. Score 0.394 Round 5: 128 peptides, 23 chains. Longest chain 9 peptides. Score 0.416 Taking the results from Round 5 Chains 23, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4240 restraints for refining 1861 atoms. 3843 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2528 (Rfree = 0.000) for 1861 atoms. Found 11 (11 requested) and removed 28 (5 requested) atoms. Cycle 17: After refmac, R = 0.2490 (Rfree = 0.000) for 1830 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 18: After refmac, R = 0.2454 (Rfree = 0.000) for 1825 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 19: After refmac, R = 0.2467 (Rfree = 0.000) for 1817 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 20: After refmac, R = 0.2571 (Rfree = 0.000) for 1810 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.95 Search for helices and strands: 0 residues in 0 chains, 1917 seeds are put forward NCS extension: 0 residues added, 1917 seeds are put forward Round 1: 72 peptides, 17 chains. Longest chain 5 peptides. Score 0.199 Round 2: 98 peptides, 20 chains. Longest chain 7 peptides. Score 0.301 Round 3: 106 peptides, 21 chains. Longest chain 9 peptides. Score 0.328 Round 4: 105 peptides, 19 chains. Longest chain 8 peptides. Score 0.378 Round 5: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 5 Chains 18, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3346 reflections ( 99.79 % complete ) and 4458 restraints for refining 1874 atoms. 4136 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2497 (Rfree = 0.000) for 1874 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 22: After refmac, R = 0.2575 (Rfree = 0.000) for 1851 atoms. Found 11 (11 requested) and removed 30 (5 requested) atoms. Cycle 23: After refmac, R = 0.2779 (Rfree = 0.000) for 1830 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 24: After refmac, R = 0.2726 (Rfree = 0.000) for 1812 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 25: After refmac, R = 0.2848 (Rfree = 0.000) for 1807 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.67 Search for helices and strands: 0 residues in 0 chains, 1901 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1904 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 8 peptides. Score 0.222 Round 2: 84 peptides, 18 chains. Longest chain 7 peptides. Score 0.260 Round 3: 85 peptides, 17 chains. Longest chain 6 peptides. Score 0.298 Round 4: 92 peptides, 18 chains. Longest chain 7 peptides. Score 0.318 Round 5: 86 peptides, 17 chains. Longest chain 7 peptides. Score 0.306 Taking the results from Round 4 Chains 18, Residues 74, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3346 reflections ( 99.79 % complete ) and 4179 restraints for refining 1832 atoms. 3878 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2652 (Rfree = 0.000) for 1832 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 27: After refmac, R = 0.2784 (Rfree = 0.000) for 1818 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 28: After refmac, R = 0.2672 (Rfree = 0.000) for 1809 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 29: After refmac, R = 0.2651 (Rfree = 0.000) for 1803 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2603 (Rfree = 0.000) for 1801 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 1887 seeds are put forward NCS extension: 0 residues added, 1887 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.246 Round 2: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.324 Round 3: 89 peptides, 18 chains. Longest chain 10 peptides. Score 0.297 Round 4: 85 peptides, 16 chains. Longest chain 10 peptides. Score 0.329 Round 5: 78 peptides, 14 chains. Longest chain 12 peptides. Score 0.340 Taking the results from Round 5 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3346 reflections ( 99.79 % complete ) and 4350 restraints for refining 1864 atoms. 4108 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2794 (Rfree = 0.000) for 1864 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2572 (Rfree = 0.000) for 1856 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.2447 (Rfree = 0.000) for 1854 atoms. Found 9 (11 requested) and removed 10 (5 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2574 (Rfree = 0.000) for 1852 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 35: After refmac, R = 0.2407 (Rfree = 0.000) for 1852 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.86 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: 62 peptides, 15 chains. Longest chain 5 peptides. Score 0.184 Round 2: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.300 Round 3: 74 peptides, 15 chains. Longest chain 9 peptides. Score 0.279 Round 4: 73 peptides, 14 chains. Longest chain 14 peptides. Score 0.304 Round 5: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.294 Taking the results from Round 4 Chains 15, Residues 59, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4407 restraints for refining 1891 atoms. 4153 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2996 (Rfree = 0.000) for 1891 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2994 (Rfree = 0.000) for 1872 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 38: After refmac, R = 0.3116 (Rfree = 0.000) for 1863 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 39: After refmac, R = 0.3078 (Rfree = 0.000) for 1852 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.3156 (Rfree = 0.000) for 1849 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 1922 seeds are put forward NCS extension: 0 residues added, 1922 seeds are put forward Round 1: 24 peptides, 5 chains. Longest chain 7 peptides. Score 0.218 Round 2: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.205 Round 3: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.214 Round 4: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.315 Round 5: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.304 Taking the results from Round 4 Chains 10, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 3856 restraints for refining 1734 atoms. 3678 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2892 (Rfree = 0.000) for 1734 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 42: After refmac, R = 0.2923 (Rfree = 0.000) for 1734 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 43: After refmac, R = 0.2777 (Rfree = 0.000) for 1733 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2806 (Rfree = 0.000) for 1736 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.2801 (Rfree = 0.000) for 1738 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.84 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward NCS extension: 0 residues added, 1818 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 6 peptides. Score 0.195 Round 2: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.260 Round 3: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.288 Round 4: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.280 Round 5: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.270 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 47, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2ouw-3_warpNtrace.pdb as input Building loops using Loopy2018 11 chains (47 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3346 reflections ( 99.79 % complete ) and 3660 restraints for refining 1686 atoms. 3459 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2587 (Rfree = 0.000) for 1686 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2636 (Rfree = 0.000) for 1678 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2818 (Rfree = 0.000) for 1671 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2678 (Rfree = 0.000) for 1665 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 46.66