null Sun 23 Dec 22:22:46 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 2pim-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pim-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pim-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-2.2-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/2pim-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-2.2-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 22:22:56 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/2pim-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-2.2-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 143 and 0 Target number of residues in the AU: 143 Target solvent content: 0.5376 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 141 Adjusted target solvent content: 0.54 Input MTZ file: 2pim-2.2-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: 177 Cell parameters: 111.771 111.771 46.411 90.000 90.000 120.000 Input sequence file: 2pim-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1128 target number of atoms Had to go as low as 0.45 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 1 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 Loops will be built when appropriate and at the last cycle Resolution range: 96.797 2.200 Wilson plot Bfac: 32.10 9093 reflections ( 99.81 % complete ) and 0 restraints for refining 1254 atoms. Observations/parameters ratio is 1.81 ------------------------------------------------------ Starting model: R = 0.3230 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2733 (Rfree = 0.000) for 1254 atoms. Found 32 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.39 2.27 Round 1: 107 peptides, 11 chains. Longest chain 20 peptides. Score 0.710 Round 2: 116 peptides, 9 chains. Longest chain 32 peptides. Score 0.796 Round 3: 120 peptides, 5 chains. Longest chain 58 peptides. Score 0.877 Round 4: 124 peptides, 5 chains. Longest chain 58 peptides. Score 0.887 Round 5: 124 peptides, 4 chains. Longest chain 58 peptides. Score 0.900 Taking the results from Round 5 Chains 5, Residues 120, Estimated correctness of the model 98.6 % 3 chains (103 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 81 A 4 chains (125 residues) following loop building 2 chains (108 residues) in sequence following loop building ------------------------------------------------------ 9093 reflections ( 99.81 % complete ) and 1187 restraints for refining 1087 atoms. 341 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3053 (Rfree = 0.000) for 1087 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 2: After refmac, R = 0.2718 (Rfree = 0.000) for 1084 atoms. Found 26 (27 requested) and removed 14 (14 requested) atoms. Cycle 3: After refmac, R = 0.2522 (Rfree = 0.000) for 1090 atoms. Found 18 (27 requested) and removed 14 (14 requested) atoms. Cycle 4: After refmac, R = 0.2370 (Rfree = 0.000) for 1087 atoms. Found 17 (26 requested) and removed 14 (14 requested) atoms. Cycle 5: After refmac, R = 0.2287 (Rfree = 0.000) for 1086 atoms. Found 8 (26 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.31 2.19 Round 1: 126 peptides, 3 chains. Longest chain 57 peptides. Score 0.916 Round 2: 127 peptides, 3 chains. Longest chain 76 peptides. Score 0.918 Round 3: 125 peptides, 4 chains. Longest chain 78 peptides. Score 0.902 Round 4: 127 peptides, 3 chains. Longest chain 76 peptides. Score 0.918 Round 5: 130 peptides, 3 chains. Longest chain 78 peptides. Score 0.923 Taking the results from Round 5 Chains 3, Residues 127, Estimated correctness of the model 99.1 % 3 chains (127 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 36 A Built loop between residues 57 A and 60 A 1 chains (131 residues) following loop building 1 chains (131 residues) in sequence following loop building ------------------------------------------------------ 9093 reflections ( 99.81 % complete ) and 1013 restraints for refining 1077 atoms. 56 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2445 (Rfree = 0.000) for 1077 atoms. Found 25 (25 requested) and removed 15 (14 requested) atoms. Cycle 7: After refmac, R = 0.2226 (Rfree = 0.000) for 1081 atoms. Found 25 (25 requested) and removed 14 (14 requested) atoms. Cycle 8: After refmac, R = 0.2077 (Rfree = 0.000) for 1091 atoms. Found 24 (24 requested) and removed 14 (14 requested) atoms. Cycle 9: After refmac, R = 0.2026 (Rfree = 0.000) for 1100 atoms. Found 24 (24 requested) and removed 16 (14 requested) atoms. Cycle 10: After refmac, R = 0.1983 (Rfree = 0.000) for 1107 atoms. Found 23 (23 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.32 2.20 Round 1: 130 peptides, 3 chains. Longest chain 66 peptides. Score 0.923 Round 2: 132 peptides, 2 chains. Longest chain 76 peptides. Score 0.937 Round 3: 131 peptides, 3 chains. Longest chain 66 peptides. Score 0.925 Round 4: 132 peptides, 1 chains. Longest chain 132 peptides. Score 0.947 Round 5: 131 peptides, 3 chains. Longest chain 90 peptides. Score 0.925 Taking the results from Round 4 Chains 1, Residues 131, Estimated correctness of the model 99.6 % 1 chains (131 residues) have been docked in sequence ------------------------------------------------------ 9093 reflections ( 99.81 % complete ) and 1041 restraints for refining 1077 atoms. 84 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2355 (Rfree = 0.000) for 1077 atoms. Found 22 (22 requested) and removed 14 (14 requested) atoms. Cycle 12: After refmac, R = 0.2128 (Rfree = 0.000) for 1084 atoms. Found 22 (22 requested) and removed 14 (14 requested) atoms. Cycle 13: After refmac, R = 0.2036 (Rfree = 0.000) for 1090 atoms. Found 21 (21 requested) and removed 14 (14 requested) atoms. Cycle 14: After refmac, R = 0.1988 (Rfree = 0.000) for 1097 atoms. Found 21 (21 requested) and removed 16 (14 requested) atoms. Cycle 15: After refmac, R = 0.1924 (Rfree = 0.000) for 1100 atoms. Found 20 (20 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.30 2.18 Round 1: 131 peptides, 2 chains. Longest chain 67 peptides. Score 0.935 Round 2: 131 peptides, 1 chains. Longest chain 131 peptides. Score 0.945 Round 3: 129 peptides, 3 chains. Longest chain 65 peptides. Score 0.921 Round 4: 130 peptides, 2 chains. Longest chain 101 peptides. Score 0.934 Round 5: 130 peptides, 2 chains. Longest chain 114 peptides. Score 0.934 Taking the results from Round 2 Chains 1, Residues 130, Estimated correctness of the model 99.5 % 1 chains (130 residues) have been docked in sequence ------------------------------------------------------ 9093 reflections ( 99.81 % complete ) and 1037 restraints for refining 1077 atoms. 88 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2241 (Rfree = 0.000) for 1077 atoms. Found 20 (20 requested) and removed 15 (14 requested) atoms. Cycle 17: After refmac, R = 0.2043 (Rfree = 0.000) for 1080 atoms. Found 19 (19 requested) and removed 14 (14 requested) atoms. Cycle 18: After refmac, R = 0.1954 (Rfree = 0.000) for 1084 atoms. Found 18 (18 requested) and removed 15 (14 requested) atoms. Cycle 19: After refmac, R = 0.1909 (Rfree = 0.000) for 1086 atoms. Found 18 (18 requested) and removed 15 (14 requested) atoms. Cycle 20: After refmac, R = 0.1898 (Rfree = 0.000) for 1089 atoms. Found 17 (17 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.30 2.18 Round 1: 131 peptides, 2 chains. Longest chain 67 peptides. Score 0.935 Round 2: 130 peptides, 2 chains. Longest chain 79 peptides. Score 0.934 Round 3: 125 peptides, 2 chains. Longest chain 82 peptides. Score 0.926 Round 4: 130 peptides, 3 chains. Longest chain 76 peptides. Score 0.923 Round 5: 132 peptides, 2 chains. Longest chain 67 peptides. Score 0.937 Taking the results from Round 5 Chains 2, Residues 130, Estimated correctness of the model 99.4 % 2 chains (130 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 73 A 1 chains (132 residues) following loop building 1 chains (132 residues) in sequence following loop building ------------------------------------------------------ 9093 reflections ( 99.81 % complete ) and 1022 restraints for refining 1077 atoms. 57 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2310 (Rfree = 0.000) for 1077 atoms. Found 17 (17 requested) and removed 15 (14 requested) atoms. Cycle 22: After refmac, R = 0.2097 (Rfree = 0.000) for 1077 atoms. Found 16 (16 requested) and removed 14 (14 requested) atoms. Cycle 23: After refmac, R = 0.1986 (Rfree = 0.000) for 1078 atoms. Found 16 (16 requested) and removed 14 (14 requested) atoms. Cycle 24: After refmac, R = 0.1918 (Rfree = 0.000) for 1080 atoms. Found 15 (15 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.1887 (Rfree = 0.000) for 1081 atoms. Found 15 (15 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.29 2.17 Round 1: 132 peptides, 2 chains. Longest chain 78 peptides. Score 0.937 Round 2: 132 peptides, 2 chains. Longest chain 78 peptides. Score 0.937 Round 3: 132 peptides, 2 chains. Longest chain 78 peptides. Score 0.937 Round 4: 129 peptides, 4 chains. Longest chain 66 peptides. Score 0.910 Round 5: 126 peptides, 5 chains. Longest chain 57 peptides. Score 0.891 Taking the results from Round 3 Chains 2, Residues 130, Estimated correctness of the model 99.4 % 2 chains (130 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A 1 chains (132 residues) following loop building 1 chains (132 residues) in sequence following loop building ------------------------------------------------------ 9093 reflections ( 99.81 % complete ) and 1022 restraints for refining 1077 atoms. 57 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2276 (Rfree = 0.000) for 1077 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 27: After refmac, R = 0.2059 (Rfree = 0.000) for 1076 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 28: After refmac, R = 0.1988 (Rfree = 0.000) for 1075 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 29: After refmac, R = 0.1933 (Rfree = 0.000) for 1074 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.1898 (Rfree = 0.000) for 1074 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.31 2.19 Round 1: 130 peptides, 3 chains. Longest chain 65 peptides. Score 0.923 Round 2: 132 peptides, 2 chains. Longest chain 78 peptides. Score 0.937 Round 3: 127 peptides, 6 chains. Longest chain 58 peptides. Score 0.880 Round 4: 132 peptides, 2 chains. Longest chain 78 peptides. Score 0.937 Round 5: 129 peptides, 3 chains. Longest chain 79 peptides. Score 0.921 Taking the results from Round 4 Chains 2, Residues 130, Estimated correctness of the model 99.4 % 2 chains (130 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A 1 chains (132 residues) following loop building 1 chains (132 residues) in sequence following loop building ------------------------------------------------------ 9093 reflections ( 99.81 % complete ) and 1017 restraints for refining 1077 atoms. 52 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2255 (Rfree = 0.000) for 1077 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 32: After refmac, R = 0.2043 (Rfree = 0.000) for 1076 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.1946 (Rfree = 0.000) for 1076 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 34: After refmac, R = 0.1902 (Rfree = 0.000) for 1076 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.1862 (Rfree = 0.000) for 1076 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.29 2.17 Round 1: 129 peptides, 3 chains. Longest chain 64 peptides. Score 0.921 Round 2: 130 peptides, 3 chains. Longest chain 76 peptides. Score 0.923 Round 3: 131 peptides, 2 chains. Longest chain 66 peptides. Score 0.935 Round 4: 129 peptides, 3 chains. Longest chain 66 peptides. Score 0.921 Round 5: 128 peptides, 3 chains. Longest chain 61 peptides. Score 0.920 Taking the results from Round 3 Chains 3, Residues 129, Estimated correctness of the model 99.4 % 2 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 A and 72 A 1 chains (130 residues) following loop building 1 chains (130 residues) in sequence following loop building ------------------------------------------------------ 9093 reflections ( 99.81 % complete ) and 1034 restraints for refining 1077 atoms. 85 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2243 (Rfree = 0.000) for 1077 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 37: After refmac, R = 0.2059 (Rfree = 0.000) for 1074 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 38: After refmac, R = 0.1968 (Rfree = 0.000) for 1074 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 39: After refmac, R = 0.1891 (Rfree = 0.000) for 1073 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.1880 (Rfree = 0.000) for 1073 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.30 2.18 Round 1: 130 peptides, 3 chains. Longest chain 66 peptides. Score 0.923 Round 2: 131 peptides, 1 chains. Longest chain 131 peptides. Score 0.945 Round 3: 128 peptides, 4 chains. Longest chain 76 peptides. Score 0.908 Round 4: 130 peptides, 3 chains. Longest chain 78 peptides. Score 0.923 Round 5: 130 peptides, 3 chains. Longest chain 66 peptides. Score 0.923 Taking the results from Round 2 Chains 1, Residues 130, Estimated correctness of the model 99.5 % 1 chains (130 residues) have been docked in sequence ------------------------------------------------------ 9093 reflections ( 99.81 % complete ) and 1036 restraints for refining 1077 atoms. 87 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2170 (Rfree = 0.000) for 1077 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 42: After refmac, R = 0.1994 (Rfree = 0.000) for 1075 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 43: After refmac, R = 0.1905 (Rfree = 0.000) for 1075 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 44: After refmac, R = 0.1872 (Rfree = 0.000) for 1075 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.1859 (Rfree = 0.000) for 1075 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.32 2.20 Round 1: 129 peptides, 2 chains. Longest chain 78 peptides. Score 0.932 Round 2: 131 peptides, 2 chains. Longest chain 67 peptides. Score 0.935 Round 3: 129 peptides, 2 chains. Longest chain 76 peptides. Score 0.932 Round 4: 129 peptides, 4 chains. Longest chain 65 peptides. Score 0.910 Round 5: 131 peptides, 2 chains. Longest chain 70 peptides. Score 0.935 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 129, Estimated correctness of the model 99.4 % 2 chains (129 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 74 A and 77 A 1 chains (131 residues) following loop building 1 chains (131 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 9093 reflections ( 99.81 % complete ) and 957 restraints for refining 949 atoms. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2595 (Rfree = 0.000) for 949 atoms. Found 6 (12 requested) and removed 0 (12 requested) atoms. Cycle 47: After refmac, R = 0.2414 (Rfree = 0.000) for 949 atoms. Found 2 (12 requested) and removed 0 (12 requested) atoms. Cycle 48: After refmac, R = 0.2300 (Rfree = 0.000) for 949 atoms. Found 4 (12 requested) and removed 0 (12 requested) atoms. Cycle 49: After refmac, R = 0.2227 (Rfree = 0.000) for 949 atoms. Found 3 (12 requested) and removed 1 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:33 GMT 2018 Job finished. TimeTaking 33.78 Used memory is bytes: 13071152