null Sun 23 Dec 22:23:10 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pim-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pim-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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/2pim-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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 ============================================================ Sun 23 Dec 22:23:20 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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 113 and 0 Target number of residues in the AU: 113 Target solvent content: 0.6346 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-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: 177 Cell parameters: 111.771 111.771 46.411 90.000 90.000 120.000 Input sequence file: 2pim-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1128 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 Loops will be built when appropriate and at the last cycle Resolution range: 96.797 3.601 Wilson plot Bfac: 68.42 2197 reflections ( 99.23 % complete ) and 0 restraints for refining 1261 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3326 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3456 (Rfree = 0.000) for 1261 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 1270 seeds are put forward Round 1: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.393 Round 2: 88 peptides, 10 chains. Longest chain 20 peptides. Score 0.623 Round 3: 85 peptides, 10 chains. Longest chain 17 peptides. Score 0.602 Round 4: 94 peptides, 9 chains. Longest chain 23 peptides. Score 0.690 Round 5: 96 peptides, 10 chains. Longest chain 20 peptides. Score 0.674 Taking the results from Round 4 Chains 11, Residues 85, Estimated correctness of the model 46.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2197 reflections ( 99.23 % complete ) and 2072 restraints for refining 1022 atoms. 1721 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2617 (Rfree = 0.000) for 1022 atoms. Found 4 (6 requested) and removed 17 (3 requested) atoms. Cycle 2: After refmac, R = 0.2422 (Rfree = 0.000) for 983 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.2334 (Rfree = 0.000) for 971 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. Cycle 4: After refmac, R = 0.2282 (Rfree = 0.000) for 961 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2285 (Rfree = 0.000) for 945 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 1002 seeds are put forward Round 1: 90 peptides, 13 chains. Longest chain 14 peptides. Score 0.538 Round 2: 93 peptides, 11 chains. Longest chain 22 peptides. Score 0.626 Round 3: 88 peptides, 11 chains. Longest chain 17 peptides. Score 0.591 Round 4: 92 peptides, 9 chains. Longest chain 19 peptides. Score 0.678 Round 5: 91 peptides, 8 chains. Longest chain 25 peptides. Score 0.701 Taking the results from Round 5 Chains 10, Residues 83, Estimated correctness of the model 49.9 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2197 reflections ( 99.23 % complete ) and 2047 restraints for refining 987 atoms. 1701 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2475 (Rfree = 0.000) for 987 atoms. Found 6 (6 requested) and removed 26 (3 requested) atoms. Cycle 7: After refmac, R = 0.2439 (Rfree = 0.000) for 962 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 8: After refmac, R = 0.2348 (Rfree = 0.000) for 948 atoms. Found 4 (6 requested) and removed 11 (3 requested) atoms. Cycle 9: After refmac, R = 0.2175 (Rfree = 0.000) for 939 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.1994 (Rfree = 0.000) for 937 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 973 seeds are put forward Round 1: 83 peptides, 12 chains. Longest chain 13 peptides. Score 0.517 Round 2: 90 peptides, 10 chains. Longest chain 17 peptides. Score 0.636 Round 3: 101 peptides, 11 chains. Longest chain 28 peptides. Score 0.676 Round 4: 106 peptides, 11 chains. Longest chain 34 peptides. Score 0.705 Round 5: 97 peptides, 11 chains. Longest chain 18 peptides. Score 0.652 Taking the results from Round 4 Chains 11, Residues 95, Estimated correctness of the model 51.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2197 reflections ( 99.23 % complete ) and 2065 restraints for refining 1013 atoms. 1696 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2445 (Rfree = 0.000) for 1013 atoms. Found 4 (5 requested) and removed 32 (3 requested) atoms. Cycle 12: After refmac, R = 0.2191 (Rfree = 0.000) for 977 atoms. Found 5 (5 requested) and removed 19 (3 requested) atoms. Cycle 13: After refmac, R = 0.2018 (Rfree = 0.000) for 958 atoms. Found 5 (5 requested) and removed 18 (3 requested) atoms. Cycle 14: After refmac, R = 0.2129 (Rfree = 0.000) for 944 atoms. Found 5 (5 requested) and removed 18 (3 requested) atoms. Cycle 15: After refmac, R = 0.1973 (Rfree = 0.000) for 930 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 973 seeds are put forward Round 1: 78 peptides, 14 chains. Longest chain 12 peptides. Score 0.397 Round 2: 90 peptides, 11 chains. Longest chain 21 peptides. Score 0.605 Round 3: 84 peptides, 11 chains. Longest chain 14 peptides. Score 0.561 Round 4: 81 peptides, 10 chains. Longest chain 20 peptides. Score 0.572 Round 5: 91 peptides, 12 chains. Longest chain 16 peptides. Score 0.580 Taking the results from Round 2 Chains 12, Residues 79, Estimated correctness of the model 16.5 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2197 reflections ( 99.23 % complete ) and 1890 restraints for refining 967 atoms. 1552 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2502 (Rfree = 0.000) for 967 atoms. Found 5 (5 requested) and removed 9 (3 requested) atoms. Cycle 17: After refmac, R = 0.2354 (Rfree = 0.000) for 947 atoms. Found 5 (5 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.2338 (Rfree = 0.000) for 932 atoms. Found 5 (5 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2328 (Rfree = 0.000) for 931 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 20: After refmac, R = 0.2083 (Rfree = 0.000) for 927 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 962 seeds are put forward Round 1: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.418 Round 2: 94 peptides, 10 chains. Longest chain 20 peptides. Score 0.662 Round 3: 95 peptides, 11 chains. Longest chain 35 peptides. Score 0.639 Round 4: 91 peptides, 8 chains. Longest chain 30 peptides. Score 0.701 Round 5: 92 peptides, 11 chains. Longest chain 15 peptides. Score 0.619 Taking the results from Round 4 Chains 8, Residues 83, Estimated correctness of the model 49.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2197 reflections ( 99.23 % complete ) and 2087 restraints for refining 993 atoms. 1763 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2759 (Rfree = 0.000) for 993 atoms. Found 5 (5 requested) and removed 23 (3 requested) atoms. Cycle 22: After refmac, R = 0.2460 (Rfree = 0.000) for 966 atoms. Found 5 (5 requested) and removed 11 (3 requested) atoms. Cycle 23: After refmac, R = 0.2295 (Rfree = 0.000) for 957 atoms. Found 3 (5 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.2317 (Rfree = 0.000) for 948 atoms. Found 4 (4 requested) and removed 7 (3 requested) atoms. Cycle 25: After refmac, R = 0.1961 (Rfree = 0.000) for 943 atoms. Found 4 (4 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 982 seeds are put forward Round 1: 85 peptides, 12 chains. Longest chain 15 peptides. Score 0.534 Round 2: 85 peptides, 11 chains. Longest chain 16 peptides. Score 0.568 Round 3: 91 peptides, 12 chains. Longest chain 20 peptides. Score 0.580 Round 4: 90 peptides, 12 chains. Longest chain 16 peptides. Score 0.572 Round 5: 84 peptides, 11 chains. Longest chain 18 peptides. Score 0.561 Taking the results from Round 3 Chains 12, Residues 79, Estimated correctness of the model 6.6 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2197 reflections ( 99.23 % complete ) and 2022 restraints for refining 1007 atoms. 1690 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2279 (Rfree = 0.000) for 1007 atoms. Found 4 (4 requested) and removed 24 (3 requested) atoms. Cycle 27: After refmac, R = 0.2116 (Rfree = 0.000) for 987 atoms. Found 4 (4 requested) and removed 15 (3 requested) atoms. Cycle 28: After refmac, R = 0.2071 (Rfree = 0.000) for 967 atoms. Found 1 (4 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2161 (Rfree = 0.000) for 958 atoms. Found 4 (4 requested) and removed 13 (3 requested) atoms. Cycle 30: After refmac, R = 0.1905 (Rfree = 0.000) for 947 atoms. Found 2 (4 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 991 seeds are put forward Round 1: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.409 Round 2: 78 peptides, 12 chains. Longest chain 13 peptides. Score 0.475 Round 3: 82 peptides, 11 chains. Longest chain 16 peptides. Score 0.545 Round 4: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.461 Round 5: 82 peptides, 10 chains. Longest chain 13 peptides. Score 0.580 Taking the results from Round 5 Chains 11, Residues 72, Estimated correctness of the model 6.6 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2197 reflections ( 99.23 % complete ) and 2073 restraints for refining 1023 atoms. 1731 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2712 (Rfree = 0.000) for 1023 atoms. Found 4 (4 requested) and removed 12 (3 requested) atoms. Cycle 32: After refmac, R = 0.2449 (Rfree = 0.000) for 1003 atoms. Found 4 (4 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.2423 (Rfree = 0.000) for 997 atoms. Found 4 (4 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.2318 (Rfree = 0.000) for 992 atoms. Found 4 (4 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.2270 (Rfree = 0.000) for 989 atoms. Found 4 (4 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 1012 seeds are put forward Round 1: 84 peptides, 14 chains. Longest chain 13 peptides. Score 0.452 Round 2: 84 peptides, 10 chains. Longest chain 20 peptides. Score 0.595 Round 3: 91 peptides, 13 chains. Longest chain 13 peptides. Score 0.546 Round 4: 84 peptides, 11 chains. Longest chain 21 peptides. Score 0.561 Round 5: 92 peptides, 11 chains. Longest chain 22 peptides. Score 0.619 Taking the results from Round 5 Chains 12, Residues 81, Estimated correctness of the model 21.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2197 reflections ( 99.23 % complete ) and 2144 restraints for refining 1023 atoms. 1798 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2845 (Rfree = 0.000) for 1023 atoms. Found 4 (4 requested) and removed 16 (3 requested) atoms. Cycle 37: After refmac, R = 0.2718 (Rfree = 0.000) for 995 atoms. Found 4 (4 requested) and removed 10 (3 requested) atoms. Cycle 38: After refmac, R = 0.2437 (Rfree = 0.000) for 984 atoms. Found 4 (4 requested) and removed 9 (3 requested) atoms. Cycle 39: After refmac, R = 0.2353 (Rfree = 0.000) for 977 atoms. Found 4 (4 requested) and removed 6 (3 requested) atoms. Cycle 40: After refmac, R = 0.2097 (Rfree = 0.000) for 970 atoms. Found 2 (4 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 1009 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.289 Round 2: 82 peptides, 14 chains. Longest chain 11 peptides. Score 0.434 Round 3: 74 peptides, 10 chains. Longest chain 17 peptides. Score 0.517 Round 4: 74 peptides, 11 chains. Longest chain 19 peptides. Score 0.479 Round 5: 74 peptides, 10 chains. Longest chain 20 peptides. Score 0.517 Taking the results from Round 5 Chains 10, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2197 reflections ( 99.23 % complete ) and 2264 restraints for refining 1023 atoms. 2018 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2376 (Rfree = 0.000) for 1023 atoms. Found 4 (4 requested) and removed 13 (3 requested) atoms. Cycle 42: After refmac, R = 0.1904 (Rfree = 0.000) for 1005 atoms. Found 2 (4 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2463 (Rfree = 0.000) for 1000 atoms. Found 2 (4 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.2104 (Rfree = 0.000) for 992 atoms. Found 4 (4 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.2408 (Rfree = 0.000) for 991 atoms. Found 4 (4 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 1028 seeds are put forward Round 1: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.356 Round 2: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.328 Round 3: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.434 Round 4: 65 peptides, 10 chains. Longest chain 14 peptides. Score 0.437 Round 5: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.370 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pim-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2197 reflections ( 99.23 % complete ) and 2328 restraints for refining 1022 atoms. 2118 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2226 (Rfree = 0.000) for 1022 atoms. Found 0 (4 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2407 (Rfree = 0.000) for 1018 atoms. Found 0 (4 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2070 (Rfree = 0.000) for 1013 atoms. Found 0 (4 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2089 (Rfree = 0.000) for 1008 atoms. Found 0 (4 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:35 GMT 2018 Job finished. TimeTaking 29.41 Used memory is bytes: 5218568