Mon 24 Dec 08:01:14 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 1vkm-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.2-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/1vkm-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.2-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 08:01:18 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/1vkm-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.2-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 1272 and 0 Target number of residues in the AU: 1272 Target solvent content: 0.5907 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-3.2-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: 19 Cell parameters: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.50 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: 75.160 3.200 Wilson plot Bfac: 48.83 Failed to save intermediate PDB 28485 reflections ( 99.98 % complete ) and 0 restraints for refining 15703 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3060 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2601 (Rfree = 0.000) for 15703 atoms. Found 128 (140 requested) and removed 166 (70 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 3.25 Search for helices and strands: 0 residues in 0 chains, 15982 seeds are put forward NCS extension: 0 residues added, 15982 seeds are put forward Round 1: 742 peptides, 151 chains. Longest chain 16 peptides. Score 0.314 Round 2: 923 peptides, 150 chains. Longest chain 16 peptides. Score 0.486 Round 3: 1056 peptides, 152 chains. Longest chain 27 peptides. Score 0.582 Round 4: 1069 peptides, 146 chains. Longest chain 21 peptides. Score 0.610 Round 5: 1097 peptides, 143 chains. Longest chain 28 peptides. Score 0.637 Taking the results from Round 5 Chains 152, Residues 954, Estimated correctness of the model 50.7 % 15 chains (166 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 27653 restraints for refining 13009 atoms. 23518 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2436 (Rfree = 0.000) for 13009 atoms. Found 89 (116 requested) and removed 128 (58 requested) atoms. Cycle 2: After refmac, R = 0.2304 (Rfree = 0.000) for 12864 atoms. Found 39 (116 requested) and removed 85 (58 requested) atoms. Cycle 3: After refmac, R = 0.2265 (Rfree = 0.000) for 12768 atoms. Found 38 (115 requested) and removed 71 (57 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2218 (Rfree = 0.000) for 12711 atoms. Found 36 (114 requested) and removed 75 (57 requested) atoms. Cycle 5: After refmac, R = 0.2183 (Rfree = 0.000) for 12644 atoms. Found 26 (113 requested) and removed 69 (56 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.95 3.24 Search for helices and strands: 0 residues in 0 chains, 13042 seeds are put forward NCS extension: 19 residues added (9 deleted due to clashes), 13061 seeds are put forward Round 1: 984 peptides, 151 chains. Longest chain 23 peptides. Score 0.532 Round 2: 1109 peptides, 146 chains. Longest chain 24 peptides. Score 0.636 Round 3: 1112 peptides, 140 chains. Longest chain 35 peptides. Score 0.655 Round 4: 1108 peptides, 139 chains. Longest chain 23 peptides. Score 0.655 Round 5: 1118 peptides, 137 chains. Longest chain 31 peptides. Score 0.667 Taking the results from Round 5 Chains 138, Residues 981, Estimated correctness of the model 57.9 % 8 chains (122 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 28241 restraints for refining 12956 atoms. 24089 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2405 (Rfree = 0.000) for 12956 atoms. Found 77 (116 requested) and removed 119 (58 requested) atoms. Cycle 7: After refmac, R = 0.2236 (Rfree = 0.000) for 12878 atoms. Found 27 (115 requested) and removed 73 (57 requested) atoms. Cycle 8: After refmac, R = 0.2194 (Rfree = 0.000) for 12809 atoms. Found 34 (115 requested) and removed 69 (57 requested) atoms. Cycle 9: After refmac, R = 0.2124 (Rfree = 0.000) for 12760 atoms. Found 28 (114 requested) and removed 71 (57 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2077 (Rfree = 0.000) for 12696 atoms. Found 22 (114 requested) and removed 61 (57 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.96 3.25 Search for helices and strands: 0 residues in 0 chains, 13103 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 13122 seeds are put forward Round 1: 996 peptides, 144 chains. Longest chain 22 peptides. Score 0.564 Round 2: 1048 peptides, 132 chains. Longest chain 36 peptides. Score 0.637 Round 3: 1079 peptides, 130 chains. Longest chain 31 peptides. Score 0.662 Round 4: 1076 peptides, 133 chains. Longest chain 36 peptides. Score 0.652 Round 5: 1088 peptides, 129 chains. Longest chain 33 peptides. Score 0.670 Taking the results from Round 5 Chains 137, Residues 959, Estimated correctness of the model 58.5 % 14 chains (174 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 27923 restraints for refining 13013 atoms. 23673 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2333 (Rfree = 0.000) for 13013 atoms. Found 88 (116 requested) and removed 116 (58 requested) atoms. Cycle 12: After refmac, R = 0.2174 (Rfree = 0.000) for 12936 atoms. Found 32 (116 requested) and removed 75 (58 requested) atoms. Cycle 13: After refmac, R = 0.2125 (Rfree = 0.000) for 12861 atoms. Found 39 (115 requested) and removed 61 (57 requested) atoms. Cycle 14: After refmac, R = 0.2081 (Rfree = 0.000) for 12819 atoms. Found 36 (115 requested) and removed 59 (57 requested) atoms. Cycle 15: After refmac, R = 0.2026 (Rfree = 0.000) for 12784 atoms. Found 31 (114 requested) and removed 59 (57 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.00 3.30 Search for helices and strands: 0 residues in 0 chains, 13203 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 13225 seeds are put forward Round 1: 966 peptides, 151 chains. Longest chain 22 peptides. Score 0.517 Round 2: 1016 peptides, 137 chains. Longest chain 25 peptides. Score 0.601 Round 3: 1031 peptides, 134 chains. Longest chain 31 peptides. Score 0.620 Round 4: 1034 peptides, 127 chains. Longest chain 32 peptides. Score 0.643 Round 5: 1041 peptides, 135 chains. Longest chain 26 peptides. Score 0.624 Taking the results from Round 4 Chains 129, Residues 907, Estimated correctness of the model 52.1 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 29497 restraints for refining 13014 atoms. 25857 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2248 (Rfree = 0.000) for 13014 atoms. Found 91 (116 requested) and removed 74 (58 requested) atoms. Cycle 17: After refmac, R = 0.2150 (Rfree = 0.000) for 13007 atoms. Found 42 (116 requested) and removed 75 (58 requested) atoms. Cycle 18: After refmac, R = 0.2089 (Rfree = 0.000) for 12950 atoms. Found 37 (116 requested) and removed 67 (58 requested) atoms. Cycle 19: After refmac, R = 0.2020 (Rfree = 0.000) for 12904 atoms. Found 27 (115 requested) and removed 58 (57 requested) atoms. Cycle 20: After refmac, R = 0.1992 (Rfree = 0.000) for 12863 atoms. Found 25 (115 requested) and removed 58 (57 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 3.28 Search for helices and strands: 0 residues in 0 chains, 13232 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 13248 seeds are put forward Round 1: 929 peptides, 151 chains. Longest chain 17 peptides. Score 0.487 Round 2: 1017 peptides, 138 chains. Longest chain 20 peptides. Score 0.598 Round 3: 1013 peptides, 130 chains. Longest chain 20 peptides. Score 0.620 Round 4: 1042 peptides, 135 chains. Longest chain 26 peptides. Score 0.624 Round 5: 995 peptides, 127 chains. Longest chain 24 peptides. Score 0.617 Taking the results from Round 4 Chains 141, Residues 907, Estimated correctness of the model 47.4 % 11 chains (114 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 28542 restraints for refining 13015 atoms. 24682 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2216 (Rfree = 0.000) for 13015 atoms. Found 63 (116 requested) and removed 84 (58 requested) atoms. Cycle 22: After refmac, R = 0.2131 (Rfree = 0.000) for 12957 atoms. Found 41 (116 requested) and removed 63 (58 requested) atoms. Cycle 23: After refmac, R = 0.2055 (Rfree = 0.000) for 12917 atoms. Found 30 (116 requested) and removed 60 (58 requested) atoms. Cycle 24: After refmac, R = 0.2016 (Rfree = 0.000) for 12878 atoms. Found 29 (115 requested) and removed 57 (57 requested) atoms. Cycle 25: After refmac, R = 0.1963 (Rfree = 0.000) for 12842 atoms. Found 40 (115 requested) and removed 58 (57 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.96 3.25 Search for helices and strands: 0 residues in 0 chains, 13233 seeds are put forward NCS extension: 17 residues added (11 deleted due to clashes), 13250 seeds are put forward Round 1: 902 peptides, 149 chains. Longest chain 20 peptides. Score 0.472 Round 2: 974 peptides, 134 chains. Longest chain 27 peptides. Score 0.580 Round 3: 989 peptides, 134 chains. Longest chain 27 peptides. Score 0.591 Round 4: 961 peptides, 136 chains. Longest chain 21 peptides. Score 0.564 Round 5: 969 peptides, 135 chains. Longest chain 20 peptides. Score 0.573 Taking the results from Round 3 Chains 140, Residues 855, Estimated correctness of the model 38.6 % 10 chains (108 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 28853 restraints for refining 13014 atoms. 25210 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2175 (Rfree = 0.000) for 13014 atoms. Found 62 (116 requested) and removed 89 (58 requested) atoms. Cycle 27: After refmac, R = 0.2071 (Rfree = 0.000) for 12966 atoms. Found 34 (116 requested) and removed 64 (58 requested) atoms. Cycle 28: After refmac, R = 0.2023 (Rfree = 0.000) for 12922 atoms. Found 29 (116 requested) and removed 60 (58 requested) atoms. Cycle 29: After refmac, R = 0.1979 (Rfree = 0.000) for 12882 atoms. Found 27 (115 requested) and removed 58 (57 requested) atoms. Cycle 30: After refmac, R = 0.1926 (Rfree = 0.000) for 12843 atoms. Found 31 (115 requested) and removed 58 (57 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.95 3.24 Search for helices and strands: 0 residues in 0 chains, 13182 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 13199 seeds are put forward Round 1: 797 peptides, 132 chains. Longest chain 20 peptides. Score 0.444 Round 2: 908 peptides, 135 chains. Longest chain 20 peptides. Score 0.527 Round 3: 898 peptides, 125 chains. Longest chain 24 peptides. Score 0.553 Round 4: 922 peptides, 125 chains. Longest chain 19 peptides. Score 0.571 Round 5: 886 peptides, 123 chains. Longest chain 23 peptides. Score 0.551 Taking the results from Round 4 Chains 128, Residues 797, Estimated correctness of the model 33.0 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 28485 reflections ( 99.98 % complete ) and 29807 restraints for refining 13015 atoms. 26596 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2099 (Rfree = 0.000) for 13015 atoms. Found 54 (116 requested) and removed 69 (58 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2028 (Rfree = 0.000) for 12987 atoms. Found 35 (116 requested) and removed 61 (58 requested) atoms. Cycle 33: After refmac, R = 0.2001 (Rfree = 0.000) for 12954 atoms. Found 30 (116 requested) and removed 61 (58 requested) atoms. Cycle 34: After refmac, R = 0.1962 (Rfree = 0.000) for 12918 atoms. Found 24 (115 requested) and removed 59 (57 requested) atoms. Cycle 35: After refmac, R = 0.1947 (Rfree = 0.000) for 12875 atoms. Found 29 (115 requested) and removed 57 (57 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.97 3.26 Search for helices and strands: 0 residues in 0 chains, 13238 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 13266 seeds are put forward Round 1: 762 peptides, 138 chains. Longest chain 14 peptides. Score 0.387 Round 2: 856 peptides, 129 chains. Longest chain 18 peptides. Score 0.506 Round 3: 862 peptides, 124 chains. Longest chain 19 peptides. Score 0.529 Round 4: 882 peptides, 130 chains. Longest chain 20 peptides. Score 0.523 Round 5: 856 peptides, 116 chains. Longest chain 20 peptides. Score 0.552 Taking the results from Round 5 Chains 120, Residues 740, Estimated correctness of the model 27.5 % 5 chains (57 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 29723 restraints for refining 13015 atoms. 26712 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2127 (Rfree = 0.000) for 13015 atoms. Found 73 (116 requested) and removed 70 (58 requested) atoms. Cycle 37: After refmac, R = 0.2045 (Rfree = 0.000) for 13012 atoms. Found 48 (116 requested) and removed 64 (58 requested) atoms. Cycle 38: After refmac, R = 0.1974 (Rfree = 0.000) for 12990 atoms. Found 32 (116 requested) and removed 59 (58 requested) atoms. Cycle 39: After refmac, R = 0.1935 (Rfree = 0.000) for 12957 atoms. Found 31 (116 requested) and removed 59 (58 requested) atoms. Cycle 40: After refmac, R = 0.1907 (Rfree = 0.000) for 12921 atoms. Found 41 (116 requested) and removed 58 (58 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.97 3.26 Search for helices and strands: 0 residues in 0 chains, 13254 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 13279 seeds are put forward Round 1: 714 peptides, 133 chains. Longest chain 11 peptides. Score 0.362 Round 2: 838 peptides, 136 chains. Longest chain 20 peptides. Score 0.465 Round 3: 821 peptides, 130 chains. Longest chain 19 peptides. Score 0.472 Round 4: 807 peptides, 124 chains. Longest chain 20 peptides. Score 0.483 Round 5: 802 peptides, 122 chains. Longest chain 25 peptides. Score 0.486 Taking the results from Round 5 Chains 124, Residues 680, Estimated correctness of the model 6.7 % 7 chains (43 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 30435 restraints for refining 13015 atoms. 27728 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2055 (Rfree = 0.000) for 13015 atoms. Found 63 (116 requested) and removed 67 (58 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1976 (Rfree = 0.000) for 12995 atoms. Found 44 (116 requested) and removed 58 (58 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 43: After refmac, R = 0.1946 (Rfree = 0.000) for 12973 atoms. Found 50 (116 requested) and removed 59 (58 requested) atoms. Cycle 44: After refmac, R = 0.1886 (Rfree = 0.000) for 12961 atoms. Found 55 (116 requested) and removed 60 (58 requested) atoms. Cycle 45: After refmac, R = 0.1855 (Rfree = 0.000) for 12943 atoms. Found 40 (116 requested) and removed 59 (58 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 3.30 Search for helices and strands: 0 residues in 0 chains, 13263 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 13275 seeds are put forward Round 1: 692 peptides, 129 chains. Longest chain 17 peptides. Score 0.357 Round 2: 764 peptides, 122 chains. Longest chain 18 peptides. Score 0.453 Round 3: 781 peptides, 123 chains. Longest chain 17 peptides. Score 0.464 Round 4: 774 peptides, 122 chains. Longest chain 18 peptides. Score 0.462 Round 5: 773 peptides, 116 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 119, Residues 657, Estimated correctness of the model 6.1 % 6 chains (54 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 119 chains (657 residues) following loop building 6 chains (54 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 28485 reflections ( 99.98 % complete ) and 30324 restraints for refining 13015 atoms. 27699 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1966 (Rfree = 0.000) for 13015 atoms. Found 0 (116 requested) and removed 53 (58 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1976 (Rfree = 0.000) for 12951 atoms. Found 0 (116 requested) and removed 32 (58 requested) atoms. Cycle 48: After refmac, R = 0.1935 (Rfree = 0.000) for 12911 atoms. Found 0 (115 requested) and removed 35 (57 requested) atoms. Cycle 49: After refmac, R = 0.1885 (Rfree = 0.000) for 12870 atoms. Found 0 (115 requested) and removed 31 (57 requested) atoms. Writing output files ... TimeTaking 129.93