Sun 23 Dec 22:22:49 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 2ash-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ash-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ash-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.4-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/2ash-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.4-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 22:22:58 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/2ash-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.4-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 1136 and 0 Target number of residues in the AU: 1136 Target solvent content: 0.6503 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-3.4-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.85 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: 103.605 3.400 Wilson plot Bfac: 78.27 23968 reflections ( 99.79 % complete ) and 0 restraints for refining 13499 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3298 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2854 (Rfree = 0.000) for 13499 atoms. Found 101 (101 requested) and removed 84 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 13779 seeds are put forward NCS extension: 0 residues added, 13779 seeds are put forward Round 1: 633 peptides, 116 chains. Longest chain 16 peptides. Score 0.347 Round 2: 825 peptides, 130 chains. Longest chain 16 peptides. Score 0.466 Round 3: 872 peptides, 128 chains. Longest chain 18 peptides. Score 0.511 Round 4: 887 peptides, 121 chains. Longest chain 20 peptides. Score 0.547 Round 5: 922 peptides, 123 chains. Longest chain 30 peptides. Score 0.566 Taking the results from Round 5 Chains 126, Residues 799, Estimated correctness of the model 17.2 % 7 chains (68 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 23968 reflections ( 99.79 % complete ) and 24014 restraints for refining 11081 atoms. 20679 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2462 (Rfree = 0.000) for 11081 atoms. Found 67 (83 requested) and removed 60 (41 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2424 (Rfree = 0.000) for 10910 atoms. Found 60 (83 requested) and removed 54 (41 requested) atoms. Cycle 3: After refmac, R = 0.2178 (Rfree = 0.000) for 10828 atoms. Found 44 (82 requested) and removed 47 (41 requested) atoms. Cycle 4: After refmac, R = 0.2099 (Rfree = 0.000) for 10766 atoms. Found 36 (81 requested) and removed 51 (40 requested) atoms. Cycle 5: After refmac, R = 0.2029 (Rfree = 0.000) for 10723 atoms. Found 31 (81 requested) and removed 46 (40 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 11138 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 11166 seeds are put forward Round 1: 799 peptides, 135 chains. Longest chain 15 peptides. Score 0.425 Round 2: 896 peptides, 127 chains. Longest chain 20 peptides. Score 0.533 Round 3: 878 peptides, 117 chains. Longest chain 17 peptides. Score 0.553 Round 4: 903 peptides, 110 chains. Longest chain 22 peptides. Score 0.594 Round 5: 896 peptides, 112 chains. Longest chain 28 peptides. Score 0.583 Taking the results from Round 4 Chains 115, Residues 793, Estimated correctness of the model 26.7 % 9 chains (102 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 23820 restraints for refining 11084 atoms. 20378 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2257 (Rfree = 0.000) for 11084 atoms. Found 80 (83 requested) and removed 60 (41 requested) atoms. Cycle 7: After refmac, R = 0.2096 (Rfree = 0.000) for 11017 atoms. Found 41 (83 requested) and removed 47 (41 requested) atoms. Cycle 8: After refmac, R = 0.2023 (Rfree = 0.000) for 10974 atoms. Found 29 (83 requested) and removed 48 (41 requested) atoms. Cycle 9: After refmac, R = 0.1959 (Rfree = 0.000) for 10927 atoms. Found 32 (82 requested) and removed 46 (41 requested) atoms. Cycle 10: After refmac, R = 0.1919 (Rfree = 0.000) for 10890 atoms. Found 27 (82 requested) and removed 48 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 11267 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 11283 seeds are put forward Round 1: 793 peptides, 131 chains. Longest chain 15 peptides. Score 0.435 Round 2: 864 peptides, 124 chains. Longest chain 20 peptides. Score 0.519 Round 3: 904 peptides, 123 chains. Longest chain 22 peptides. Score 0.553 Round 4: 905 peptides, 119 chains. Longest chain 25 peptides. Score 0.567 Round 5: 922 peptides, 120 chains. Longest chain 32 peptides. Score 0.576 Taking the results from Round 5 Chains 123, Residues 802, Estimated correctness of the model 20.7 % 4 chains (65 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24346 restraints for refining 11085 atoms. 20998 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2238 (Rfree = 0.000) for 11085 atoms. Found 67 (83 requested) and removed 57 (41 requested) atoms. Cycle 12: After refmac, R = 0.2014 (Rfree = 0.000) for 11037 atoms. Found 31 (83 requested) and removed 44 (41 requested) atoms. Cycle 13: After refmac, R = 0.1979 (Rfree = 0.000) for 10990 atoms. Found 24 (83 requested) and removed 46 (41 requested) atoms. Cycle 14: After refmac, R = 0.1954 (Rfree = 0.000) for 10952 atoms. Found 27 (82 requested) and removed 44 (41 requested) atoms. Cycle 15: After refmac, R = 0.1939 (Rfree = 0.000) for 10919 atoms. Found 28 (82 requested) and removed 45 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 11248 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11263 seeds are put forward Round 1: 792 peptides, 133 chains. Longest chain 21 peptides. Score 0.427 Round 2: 898 peptides, 126 chains. Longest chain 27 peptides. Score 0.538 Round 3: 903 peptides, 120 chains. Longest chain 26 peptides. Score 0.562 Round 4: 880 peptides, 115 chains. Longest chain 30 peptides. Score 0.561 Round 5: 851 peptides, 115 chains. Longest chain 22 peptides. Score 0.540 Taking the results from Round 3 Chains 128, Residues 783, Estimated correctness of the model 15.8 % 9 chains (100 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 23829 restraints for refining 11086 atoms. 20443 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2151 (Rfree = 0.000) for 11086 atoms. Found 70 (83 requested) and removed 58 (41 requested) atoms. Cycle 17: After refmac, R = 0.2015 (Rfree = 0.000) for 11037 atoms. Found 28 (83 requested) and removed 50 (41 requested) atoms. Cycle 18: After refmac, R = 0.1951 (Rfree = 0.000) for 10983 atoms. Found 20 (83 requested) and removed 42 (41 requested) atoms. Cycle 19: After refmac, R = 0.1919 (Rfree = 0.000) for 10936 atoms. Found 24 (82 requested) and removed 44 (41 requested) atoms. Cycle 20: After refmac, R = 0.1891 (Rfree = 0.000) for 10903 atoms. Found 23 (82 requested) and removed 44 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 11226 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 11249 seeds are put forward Round 1: 721 peptides, 120 chains. Longest chain 23 peptides. Score 0.413 Round 2: 836 peptides, 115 chains. Longest chain 34 peptides. Score 0.528 Round 3: 848 peptides, 115 chains. Longest chain 35 peptides. Score 0.538 Round 4: 876 peptides, 115 chains. Longest chain 32 peptides. Score 0.559 Round 5: 916 peptides, 118 chains. Longest chain 23 peptides. Score 0.578 Taking the results from Round 5 Chains 122, Residues 798, Estimated correctness of the model 21.3 % 6 chains (51 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24477 restraints for refining 11084 atoms. 21252 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2150 (Rfree = 0.000) for 11084 atoms. Found 58 (83 requested) and removed 51 (41 requested) atoms. Cycle 22: After refmac, R = 0.1957 (Rfree = 0.000) for 11030 atoms. Found 34 (83 requested) and removed 44 (41 requested) atoms. Cycle 23: After refmac, R = 0.1908 (Rfree = 0.000) for 10994 atoms. Found 25 (83 requested) and removed 48 (41 requested) atoms. Cycle 24: After refmac, R = 0.1847 (Rfree = 0.000) for 10947 atoms. Found 23 (82 requested) and removed 42 (41 requested) atoms. Cycle 25: After refmac, R = 0.1810 (Rfree = 0.000) for 10905 atoms. Found 13 (82 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 11269 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11289 seeds are put forward Round 1: 760 peptides, 133 chains. Longest chain 15 peptides. Score 0.398 Round 2: 819 peptides, 117 chains. Longest chain 35 peptides. Score 0.508 Round 3: 832 peptides, 121 chains. Longest chain 18 peptides. Score 0.504 Round 4: 830 peptides, 113 chains. Longest chain 22 peptides. Score 0.531 Round 5: 846 peptides, 116 chains. Longest chain 30 peptides. Score 0.533 Taking the results from Round 5 Chains 116, Residues 730, Estimated correctness of the model 5.3 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 23968 reflections ( 99.79 % complete ) and 25152 restraints for refining 11084 atoms. 22257 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2088 (Rfree = 0.000) for 11084 atoms. Found 60 (83 requested) and removed 48 (41 requested) atoms. Cycle 27: After refmac, R = 0.1958 (Rfree = 0.000) for 11055 atoms. Found 36 (83 requested) and removed 44 (41 requested) atoms. Cycle 28: After refmac, R = 0.1937 (Rfree = 0.000) for 11027 atoms. Found 33 (83 requested) and removed 44 (41 requested) atoms. Cycle 29: After refmac, R = 0.1871 (Rfree = 0.000) for 11000 atoms. Found 22 (83 requested) and removed 47 (41 requested) atoms. Cycle 30: After refmac, R = 0.1830 (Rfree = 0.000) for 10963 atoms. Found 31 (82 requested) and removed 49 (41 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 11343 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 11363 seeds are put forward Round 1: 716 peptides, 127 chains. Longest chain 18 peptides. Score 0.381 Round 2: 779 peptides, 117 chains. Longest chain 29 peptides. Score 0.475 Round 3: 799 peptides, 112 chains. Longest chain 17 peptides. Score 0.510 Round 4: 816 peptides, 113 chains. Longest chain 28 peptides. Score 0.520 Round 5: 827 peptides, 112 chains. Longest chain 19 peptides. Score 0.532 Taking the results from Round 5 Chains 113, Residues 715, Estimated correctness of the model 4.9 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25113 restraints for refining 11084 atoms. 22240 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2101 (Rfree = 0.000) for 11084 atoms. Found 71 (83 requested) and removed 45 (41 requested) atoms. Cycle 32: After refmac, R = 0.1977 (Rfree = 0.000) for 11074 atoms. Found 28 (83 requested) and removed 42 (41 requested) atoms. Cycle 33: After refmac, R = 0.1956 (Rfree = 0.000) for 11043 atoms. Found 35 (83 requested) and removed 45 (41 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1909 (Rfree = 0.000) for 11017 atoms. Found 36 (83 requested) and removed 43 (41 requested) atoms. Cycle 35: After refmac, R = 0.1869 (Rfree = 0.000) for 10994 atoms. Found 44 (83 requested) and removed 44 (41 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 11351 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11368 seeds are put forward Round 1: 698 peptides, 126 chains. Longest chain 14 peptides. Score 0.368 Round 2: 809 peptides, 129 chains. Longest chain 21 peptides. Score 0.456 Round 3: 814 peptides, 117 chains. Longest chain 40 peptides. Score 0.504 Round 4: 830 peptides, 118 chains. Longest chain 37 peptides. Score 0.513 Round 5: 792 peptides, 117 chains. Longest chain 24 peptides. Score 0.486 Taking the results from Round 4 Chains 119, Residues 712, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25109 restraints for refining 11082 atoms. 22248 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2063 (Rfree = 0.000) for 11082 atoms. Found 60 (83 requested) and removed 46 (41 requested) atoms. Cycle 37: After refmac, R = 0.1953 (Rfree = 0.000) for 11055 atoms. Found 55 (83 requested) and removed 44 (41 requested) atoms. Cycle 38: After refmac, R = 0.1895 (Rfree = 0.000) for 11039 atoms. Found 39 (83 requested) and removed 43 (41 requested) atoms. Cycle 39: After refmac, R = 0.1857 (Rfree = 0.000) for 11023 atoms. Found 40 (83 requested) and removed 44 (41 requested) atoms. Cycle 40: After refmac, R = 0.1813 (Rfree = 0.000) for 11000 atoms. Found 30 (83 requested) and removed 46 (41 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 11387 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11403 seeds are put forward Round 1: 675 peptides, 128 chains. Longest chain 15 peptides. Score 0.338 Round 2: 796 peptides, 121 chains. Longest chain 31 peptides. Score 0.475 Round 3: 814 peptides, 124 chains. Longest chain 29 peptides. Score 0.479 Round 4: 790 peptides, 116 chains. Longest chain 23 peptides. Score 0.488 Round 5: 792 peptides, 114 chains. Longest chain 19 peptides. Score 0.497 Taking the results from Round 5 Chains 115, Residues 678, Estimated correctness of the model 0.0 % 6 chains (42 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25009 restraints for refining 11086 atoms. 22269 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2058 (Rfree = 0.000) for 11086 atoms. Found 83 (83 requested) and removed 50 (41 requested) atoms. Cycle 42: After refmac, R = 0.1939 (Rfree = 0.000) for 11083 atoms. Found 40 (83 requested) and removed 44 (41 requested) atoms. Cycle 43: After refmac, R = 0.1894 (Rfree = 0.000) for 11062 atoms. Found 38 (83 requested) and removed 49 (41 requested) atoms. Cycle 44: After refmac, R = 0.1805 (Rfree = 0.000) for 11036 atoms. Found 32 (83 requested) and removed 45 (41 requested) atoms. Cycle 45: After refmac, R = 0.1764 (Rfree = 0.000) for 11015 atoms. Found 22 (83 requested) and removed 43 (41 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 11365 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11382 seeds are put forward Round 1: 678 peptides, 128 chains. Longest chain 13 peptides. Score 0.341 Round 2: 767 peptides, 121 chains. Longest chain 14 peptides. Score 0.450 Round 3: 752 peptides, 117 chains. Longest chain 28 peptides. Score 0.452 Round 4: 749 peptides, 114 chains. Longest chain 18 peptides. Score 0.461 Round 5: 771 peptides, 117 chains. Longest chain 20 peptides. Score 0.469 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 118, Residues 654, Estimated correctness of the model 0.0 % 6 chains (42 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2ash-3_warpNtrace.pdb as input Building loops using Loopy2018 118 chains (654 residues) following loop building 6 chains (42 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23968 reflections ( 99.79 % complete ) and 25526 restraints for refining 11086 atoms. 22886 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1985 (Rfree = 0.000) for 11086 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Cycle 47: After refmac, R = 0.1945 (Rfree = 0.000) for 11018 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Cycle 48: After refmac, R = 0.1865 (Rfree = 0.000) for 10954 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Cycle 49: After refmac, R = 0.1823 (Rfree = 0.000) for 10898 atoms. TimeTaking 143.8