Sun 23 Dec 22:22:52 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 1vkm-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-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/1vkm-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-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 22:23:02 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/1vkm-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-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 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-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: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.55 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 28485 reflections ( 99.98 % complete ) and 0 restraints for refining 15820 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.2926 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2538 (Rfree = 0.000) for 15820 atoms. Found 75 (141 requested) and removed 242 (70 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.93 3.22 Search for helices and strands: 0 residues in 0 chains, 16031 seeds are put forward NCS extension: 0 residues added, 16031 seeds are put forward Round 1: 899 peptides, 169 chains. Longest chain 16 peptides. Score 0.393 Round 2: 1048 peptides, 151 chains. Longest chain 23 peptides. Score 0.580 Round 3: 1139 peptides, 143 chains. Longest chain 25 peptides. Score 0.663 Round 4: 1197 peptides, 130 chains. Longest chain 35 peptides. Score 0.727 Round 5: 1211 peptides, 131 chains. Longest chain 32 peptides. Score 0.732 Taking the results from Round 5 Chains 140, Residues 1080, Estimated correctness of the model 71.7 % 12 chains (161 residues) have been docked in sequence Building loops using Loopy2018 140 chains (1080 residues) following loop building 12 chains (161 residues) in sequence following loop building ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 26826 restraints for refining 13003 atoms. 22098 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2445 (Rfree = 0.000) for 13003 atoms. Found 79 (116 requested) and removed 113 (58 requested) atoms. Cycle 2: After refmac, R = 0.2311 (Rfree = 0.000) for 12836 atoms. Found 39 (114 requested) and removed 88 (58 requested) atoms. Cycle 3: After refmac, R = 0.2271 (Rfree = 0.000) for 12718 atoms. Found 39 (109 requested) and removed 72 (57 requested) atoms. Cycle 4: After refmac, R = 0.2214 (Rfree = 0.000) for 12655 atoms. Found 32 (106 requested) and removed 64 (56 requested) atoms. Cycle 5: After refmac, R = 0.2168 (Rfree = 0.000) for 12586 atoms. Found 27 (104 requested) and removed 64 (56 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.95 3.24 Search for helices and strands: 0 residues in 0 chains, 12952 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 12962 seeds are put forward Round 1: 1121 peptides, 135 chains. Longest chain 42 peptides. Score 0.674 Round 2: 1213 peptides, 125 chains. Longest chain 34 peptides. Score 0.746 Round 3: 1262 peptides, 127 chains. Longest chain 35 peptides. Score 0.764 Round 4: 1266 peptides, 124 chains. Longest chain 44 peptides. Score 0.771 Round 5: 1249 peptides, 120 chains. Longest chain 29 peptides. Score 0.772 Taking the results from Round 5 Chains 129, Residues 1129, Estimated correctness of the model 78.9 % 16 chains (250 residues) have been docked in sequence Building loops using Loopy2018 129 chains (1129 residues) following loop building 16 chains (250 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 28485 reflections ( 99.98 % complete ) and 26267 restraints for refining 13014 atoms. 21010 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2410 (Rfree = 0.000) for 13014 atoms. Found 64 (104 requested) and removed 101 (58 requested) atoms. Cycle 7: After refmac, R = 0.2275 (Rfree = 0.000) for 12928 atoms. Found 40 (102 requested) and removed 69 (58 requested) atoms. Cycle 8: After refmac, R = 0.2172 (Rfree = 0.000) for 12865 atoms. Found 27 (99 requested) and removed 64 (57 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2117 (Rfree = 0.000) for 12805 atoms. Found 17 (97 requested) and removed 58 (57 requested) atoms. Cycle 10: After refmac, R = 0.2062 (Rfree = 0.000) for 12747 atoms. Found 13 (93 requested) and removed 60 (57 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.97 3.26 Search for helices and strands: 0 residues in 0 chains, 13091 seeds are put forward NCS extension: 12 residues added (13 deleted due to clashes), 13103 seeds are put forward Round 1: 1131 peptides, 139 chains. Longest chain 27 peptides. Score 0.669 Round 2: 1235 peptides, 133 chains. Longest chain 34 peptides. Score 0.739 Round 3: 1224 peptides, 127 chains. Longest chain 26 peptides. Score 0.747 Round 4: 1218 peptides, 134 chains. Longest chain 36 peptides. Score 0.728 Round 5: 1224 peptides, 124 chains. Longest chain 42 peptides. Score 0.753 Taking the results from Round 5 Chains 134, Residues 1100, Estimated correctness of the model 75.6 % 15 chains (230 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 A and 137 A 133 chains (1107 residues) following loop building 14 chains (239 residues) in sequence following loop building ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 26582 restraints for refining 13013 atoms. 21599 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2426 (Rfree = 0.000) for 13013 atoms. Found 81 (93 requested) and removed 112 (58 requested) atoms. Cycle 12: After refmac, R = 0.2294 (Rfree = 0.000) for 12945 atoms. Found 39 (90 requested) and removed 74 (58 requested) atoms. Cycle 13: After refmac, R = 0.2229 (Rfree = 0.000) for 12892 atoms. Found 31 (87 requested) and removed 63 (57 requested) atoms. Cycle 14: After refmac, R = 0.2146 (Rfree = 0.000) for 12851 atoms. Found 18 (85 requested) and removed 60 (57 requested) atoms. Cycle 15: After refmac, R = 0.2135 (Rfree = 0.000) for 12796 atoms. Found 14 (82 requested) and removed 59 (57 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 3.28 Search for helices and strands: 0 residues in 0 chains, 13122 seeds are put forward NCS extension: 17 residues added (23 deleted due to clashes), 13139 seeds are put forward Round 1: 1037 peptides, 138 chains. Longest chain 23 peptides. Score 0.612 Round 2: 1129 peptides, 127 chains. Longest chain 27 peptides. Score 0.699 Round 3: 1153 peptides, 131 chains. Longest chain 28 peptides. Score 0.702 Round 4: 1165 peptides, 131 chains. Longest chain 27 peptides. Score 0.708 Round 5: 1124 peptides, 128 chains. Longest chain 31 peptides. Score 0.694 Taking the results from Round 4 Chains 133, Residues 1034, Estimated correctness of the model 66.9 % 16 chains (215 residues) have been docked in sequence Building loops using Loopy2018 133 chains (1034 residues) following loop building 16 chains (215 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 28485 reflections ( 99.98 % complete ) and 26892 restraints for refining 13014 atoms. 22139 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2376 (Rfree = 0.000) for 13014 atoms. Found 70 (81 requested) and removed 97 (58 requested) atoms. Cycle 17: After refmac, R = 0.2238 (Rfree = 0.000) for 12957 atoms. Found 32 (79 requested) and removed 67 (58 requested) atoms. Cycle 18: After refmac, R = 0.2163 (Rfree = 0.000) for 12896 atoms. Found 23 (76 requested) and removed 59 (57 requested) atoms. Cycle 19: After refmac, R = 0.2118 (Rfree = 0.000) for 12848 atoms. Found 24 (74 requested) and removed 59 (57 requested) atoms. Cycle 20: After refmac, R = 0.2073 (Rfree = 0.000) for 12807 atoms. Found 25 (71 requested) and removed 57 (57 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.95 3.24 Search for helices and strands: 0 residues in 0 chains, 13166 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 13182 seeds are put forward Round 1: 1040 peptides, 150 chains. Longest chain 19 peptides. Score 0.577 Round 2: 1150 peptides, 140 chains. Longest chain 23 peptides. Score 0.677 Round 3: 1149 peptides, 134 chains. Longest chain 24 peptides. Score 0.692 Round 4: 1127 peptides, 133 chains. Longest chain 26 peptides. Score 0.682 Round 5: 1137 peptides, 135 chains. Longest chain 22 peptides. Score 0.683 Taking the results from Round 3 Chains 140, Residues 1015, Estimated correctness of the model 63.5 % 11 chains (134 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 27890 restraints for refining 13015 atoms. 23496 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2242 (Rfree = 0.000) for 13015 atoms. Found 57 (70 requested) and removed 80 (58 requested) atoms. Cycle 22: After refmac, R = 0.2166 (Rfree = 0.000) for 12969 atoms. Found 29 (70 requested) and removed 64 (58 requested) atoms. Cycle 23: After refmac, R = 0.2124 (Rfree = 0.000) for 12918 atoms. Found 23 (70 requested) and removed 59 (58 requested) atoms. Cycle 24: After refmac, R = 0.2076 (Rfree = 0.000) for 12875 atoms. Found 28 (69 requested) and removed 59 (57 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2059 (Rfree = 0.000) for 12839 atoms. Found 10 (69 requested) and removed 58 (57 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.97 3.26 Search for helices and strands: 0 residues in 0 chains, 13153 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 13167 seeds are put forward Round 1: 979 peptides, 142 chains. Longest chain 23 peptides. Score 0.558 Round 2: 1092 peptides, 132 chains. Longest chain 26 peptides. Score 0.665 Round 3: 1045 peptides, 129 chains. Longest chain 22 peptides. Score 0.644 Round 4: 1082 peptides, 127 chains. Longest chain 24 peptides. Score 0.672 Round 5: 1054 peptides, 133 chains. Longest chain 20 peptides. Score 0.638 Taking the results from Round 4 Chains 133, Residues 955, Estimated correctness of the model 59.0 % 8 chains (68 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 28833 restraints for refining 13014 atoms. 24949 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2218 (Rfree = 0.000) for 13014 atoms. Found 55 (70 requested) and removed 72 (58 requested) atoms. Cycle 27: After refmac, R = 0.2143 (Rfree = 0.000) for 12984 atoms. Found 45 (70 requested) and removed 62 (58 requested) atoms. Cycle 28: After refmac, R = 0.2067 (Rfree = 0.000) for 12955 atoms. Found 26 (70 requested) and removed 59 (58 requested) atoms. Cycle 29: After refmac, R = 0.2015 (Rfree = 0.000) for 12915 atoms. Found 30 (69 requested) and removed 58 (57 requested) atoms. Cycle 30: After refmac, R = 0.1997 (Rfree = 0.000) for 12876 atoms. Found 25 (69 requested) and removed 57 (57 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.97 3.26 Search for helices and strands: 0 residues in 0 chains, 13221 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 13242 seeds are put forward Round 1: 875 peptides, 137 chains. Longest chain 18 peptides. Score 0.493 Round 2: 994 peptides, 134 chains. Longest chain 19 peptides. Score 0.595 Round 3: 1003 peptides, 124 chains. Longest chain 21 peptides. Score 0.631 Round 4: 995 peptides, 126 chains. Longest chain 22 peptides. Score 0.620 Round 5: 995 peptides, 122 chains. Longest chain 23 peptides. Score 0.632 Taking the results from Round 5 Chains 123, Residues 873, Estimated correctness of the model 49.4 % 7 chains (89 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 28877 restraints for refining 13013 atoms. 25226 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2189 (Rfree = 0.000) for 13013 atoms. Found 70 (70 requested) and removed 74 (58 requested) atoms. Cycle 32: After refmac, R = 0.2113 (Rfree = 0.000) for 12989 atoms. Found 54 (70 requested) and removed 66 (58 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2044 (Rfree = 0.000) for 12969 atoms. Found 40 (70 requested) and removed 58 (58 requested) atoms. Cycle 34: After refmac, R = 0.1991 (Rfree = 0.000) for 12942 atoms. Found 25 (70 requested) and removed 58 (58 requested) atoms. Cycle 35: After refmac, R = 0.1948 (Rfree = 0.000) for 12903 atoms. Found 26 (69 requested) and removed 57 (57 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.98 3.27 Search for helices and strands: 0 residues in 0 chains, 13213 seeds are put forward NCS extension: 23 residues added (7 deleted due to clashes), 13236 seeds are put forward Round 1: 861 peptides, 134 chains. Longest chain 18 peptides. Score 0.492 Round 2: 951 peptides, 131 chains. Longest chain 21 peptides. Score 0.573 Round 3: 972 peptides, 132 chains. Longest chain 25 peptides. Score 0.585 Round 4: 986 peptides, 133 chains. Longest chain 21 peptides. Score 0.592 Round 5: 971 peptides, 133 chains. Longest chain 16 peptides. Score 0.581 Taking the results from Round 4 Chains 134, Residues 853, Estimated correctness of the model 38.9 % 7 chains (73 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 29041 restraints for refining 13014 atoms. 25531 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2146 (Rfree = 0.000) for 13014 atoms. Found 64 (70 requested) and removed 73 (58 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2071 (Rfree = 0.000) for 12993 atoms. Found 37 (70 requested) and removed 61 (58 requested) atoms. Cycle 38: After refmac, R = 0.2016 (Rfree = 0.000) for 12957 atoms. Found 40 (70 requested) and removed 60 (58 requested) atoms. Cycle 39: After refmac, R = 0.1947 (Rfree = 0.000) for 12928 atoms. Found 33 (70 requested) and removed 58 (58 requested) atoms. Cycle 40: After refmac, R = 0.1918 (Rfree = 0.000) for 12895 atoms. Found 22 (69 requested) and removed 57 (57 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.97 3.26 Search for helices and strands: 0 residues in 0 chains, 13198 seeds are put forward NCS extension: 13 residues added (9 deleted due to clashes), 13211 seeds are put forward Round 1: 843 peptides, 139 chains. Longest chain 18 peptides. Score 0.458 Round 2: 958 peptides, 137 chains. Longest chain 21 peptides. Score 0.559 Round 3: 924 peptides, 133 chains. Longest chain 19 peptides. Score 0.546 Round 4: 919 peptides, 132 chains. Longest chain 20 peptides. Score 0.546 Round 5: 891 peptides, 122 chains. Longest chain 24 peptides. Score 0.558 Taking the results from Round 2 Chains 138, Residues 821, Estimated correctness of the model 29.5 % 8 chains (85 residues) have been docked in sequence ------------------------------------------------------ 28485 reflections ( 99.98 % complete ) and 29208 restraints for refining 13015 atoms. 25797 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2029 (Rfree = 0.000) for 13015 atoms. Found 57 (70 requested) and removed 71 (58 requested) atoms. Cycle 42: After refmac, R = 0.1991 (Rfree = 0.000) for 12985 atoms. Found 29 (70 requested) and removed 59 (58 requested) atoms. Cycle 43: After refmac, R = 0.1969 (Rfree = 0.000) for 12948 atoms. Found 25 (70 requested) and removed 58 (58 requested) atoms. Cycle 44: After refmac, R = 0.1917 (Rfree = 0.000) for 12908 atoms. Found 20 (69 requested) and removed 58 (57 requested) atoms. Cycle 45: After refmac, R = 0.1905 (Rfree = 0.000) for 12861 atoms. Found 24 (69 requested) and removed 58 (57 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.96 3.25 Search for helices and strands: 0 residues in 0 chains, 13181 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 13201 seeds are put forward Round 1: 843 peptides, 147 chains. Longest chain 17 peptides. Score 0.427 Round 2: 903 peptides, 132 chains. Longest chain 24 peptides. Score 0.533 Round 3: 881 peptides, 133 chains. Longest chain 16 peptides. Score 0.512 Round 4: 901 peptides, 134 chains. Longest chain 23 peptides. Score 0.525 Round 5: 861 peptides, 127 chains. Longest chain 21 peptides. Score 0.517 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 134, Residues 771, Estimated correctness of the model 21.7 % 6 chains (55 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 134 chains (771 residues) following loop building 6 chains (55 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 28485 reflections ( 99.98 % complete ) and 29383 restraints for refining 13015 atoms. 26256 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1970 (Rfree = 0.000) for 13015 atoms. Found 0 (70 requested) and removed 36 (58 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1972 (Rfree = 0.000) for 12963 atoms. Found 0 (70 requested) and removed 16 (58 requested) atoms. Cycle 48: After refmac, R = 0.1934 (Rfree = 0.000) for 12939 atoms. Found 0 (70 requested) and removed 15 (58 requested) atoms. Cycle 49: After refmac, R = 0.1918 (Rfree = 0.000) for 12919 atoms. TimeTaking 147.15