null Sun 23 Dec 22:22:58 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 1vku-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vku-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vku-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-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/1vku-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-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 22:23:07 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/1vku-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-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 60 and 0 Target number of residues in the AU: 60 Target solvent content: 0.6337 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 100 Adjusted target solvent content: 0.39 Input MTZ file: 1vku-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: 154 Cell parameters: 45.440 45.440 74.373 90.000 90.000 120.000 Input sequence file: 1vku-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 800 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 Loops will be built when appropriate and at the last cycle Resolution range: 39.352 3.201 Wilson plot Bfac: 67.89 1629 reflections ( 99.51 % complete ) and 0 restraints for refining 892 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3321 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3053 (Rfree = 0.000) for 892 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.93 Search for helices and strands: 0 residues in 0 chains, 914 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.287 Round 2: 57 peptides, 8 chains. Longest chain 14 peptides. Score 0.602 Round 3: 61 peptides, 9 chains. Longest chain 14 peptides. Score 0.598 Round 4: 63 peptides, 7 chains. Longest chain 14 peptides. Score 0.721 Round 5: 69 peptides, 7 chains. Longest chain 17 peptides. Score 0.773 Taking the results from Round 5 Chains 7, Residues 62, Estimated correctness of the model 79.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1629 reflections ( 99.51 % complete ) and 1567 restraints for refining 707 atoms. 1326 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2821 (Rfree = 0.000) for 707 atoms. Found 3 (6 requested) and removed 9 (3 requested) atoms. Cycle 2: After refmac, R = 0.3129 (Rfree = 0.000) for 693 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2964 (Rfree = 0.000) for 687 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 4: After refmac, R = 0.3083 (Rfree = 0.000) for 681 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.2667 (Rfree = 0.000) for 677 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.69 Search for helices and strands: 0 residues in 0 chains, 705 seeds are put forward Round 1: 55 peptides, 6 chains. Longest chain 14 peptides. Score 0.686 Round 2: 65 peptides, 3 chains. Longest chain 31 peptides. Score 0.876 Round 3: 62 peptides, 8 chains. Longest chain 13 peptides. Score 0.663 Round 4: 62 peptides, 6 chains. Longest chain 19 peptides. Score 0.755 Round 5: 62 peptides, 8 chains. Longest chain 13 peptides. Score 0.663 Taking the results from Round 2 Chains 3, Residues 62, Estimated correctness of the model 93.1 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 1629 reflections ( 99.51 % complete ) and 1243 restraints for refining 719 atoms. 876 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2848 (Rfree = 0.000) for 719 atoms. Found 5 (5 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.2774 (Rfree = 0.000) for 706 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.2813 (Rfree = 0.000) for 696 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2705 (Rfree = 0.000) for 689 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2280 (Rfree = 0.000) for 689 atoms. Found 3 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.69 Search for helices and strands: 0 residues in 0 chains, 712 seeds are put forward Round 1: 61 peptides, 7 chains. Longest chain 15 peptides. Score 0.701 Round 2: 67 peptides, 6 chains. Longest chain 21 peptides. Score 0.794 Round 3: 71 peptides, 5 chains. Longest chain 17 peptides. Score 0.851 Round 4: 67 peptides, 7 chains. Longest chain 16 peptides. Score 0.757 Round 5: 67 peptides, 6 chains. Longest chain 17 peptides. Score 0.794 Taking the results from Round 3 Chains 5, Residues 66, Estimated correctness of the model 90.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1629 reflections ( 99.51 % complete ) and 1473 restraints for refining 700 atoms. 1214 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2828 (Rfree = 0.000) for 700 atoms. Found 4 (5 requested) and removed 12 (3 requested) atoms. Cycle 12: After refmac, R = 0.3205 (Rfree = 0.000) for 685 atoms. Found 5 (5 requested) and removed 15 (3 requested) atoms. Cycle 13: After refmac, R = 0.2980 (Rfree = 0.000) for 673 atoms. Found 5 (5 requested) and removed 13 (3 requested) atoms. Cycle 14: After refmac, R = 0.2503 (Rfree = 0.000) for 664 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 15: After refmac, R = 0.2432 (Rfree = 0.000) for 661 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.78 Search for helices and strands: 0 residues in 0 chains, 689 seeds are put forward Round 1: 40 peptides, 6 chains. Longest chain 11 peptides. Score 0.481 Round 2: 59 peptides, 8 chains. Longest chain 13 peptides. Score 0.628 Round 3: 62 peptides, 8 chains. Longest chain 14 peptides. Score 0.663 Round 4: 67 peptides, 7 chains. Longest chain 16 peptides. Score 0.757 Round 5: 64 peptides, 7 chains. Longest chain 18 peptides. Score 0.731 Taking the results from Round 4 Chains 7, Residues 60, Estimated correctness of the model 76.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1629 reflections ( 99.51 % complete ) and 1484 restraints for refining 679 atoms. 1251 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2455 (Rfree = 0.000) for 679 atoms. Found 1 (4 requested) and removed 3 (3 requested) atoms. Cycle 17: After refmac, R = 0.2395 (Rfree = 0.000) for 672 atoms. Found 2 (4 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.2464 (Rfree = 0.000) for 669 atoms. Found 4 (4 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2393 (Rfree = 0.000) for 667 atoms. Found 3 (3 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2156 (Rfree = 0.000) for 667 atoms. Found 2 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.75 Search for helices and strands: 0 residues in 0 chains, 696 seeds are put forward Round 1: 52 peptides, 7 chains. Longest chain 15 peptides. Score 0.595 Round 2: 60 peptides, 7 chains. Longest chain 17 peptides. Score 0.691 Round 3: 60 peptides, 7 chains. Longest chain 15 peptides. Score 0.691 Round 4: 61 peptides, 6 chains. Longest chain 20 peptides. Score 0.746 Round 5: 58 peptides, 7 chains. Longest chain 15 peptides. Score 0.669 Taking the results from Round 4 Chains 6, Residues 55, Estimated correctness of the model 74.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1629 reflections ( 99.51 % complete ) and 1455 restraints for refining 676 atoms. 1241 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2519 (Rfree = 0.000) for 676 atoms. Found 3 (4 requested) and removed 4 (3 requested) atoms. Cycle 22: After refmac, R = 0.2438 (Rfree = 0.000) for 674 atoms. Found 4 (4 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2221 (Rfree = 0.000) for 673 atoms. Found 0 (3 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.2276 (Rfree = 0.000) for 666 atoms. Found 3 (3 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2301 (Rfree = 0.000) for 664 atoms. Found 3 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.78 Search for helices and strands: 0 residues in 0 chains, 693 seeds are put forward Round 1: 54 peptides, 7 chains. Longest chain 18 peptides. Score 0.621 Round 2: 60 peptides, 6 chains. Longest chain 19 peptides. Score 0.737 Round 3: 62 peptides, 6 chains. Longest chain 19 peptides. Score 0.755 Round 4: 56 peptides, 6 chains. Longest chain 16 peptides. Score 0.697 Round 5: 60 peptides, 7 chains. Longest chain 16 peptides. Score 0.691 Taking the results from Round 3 Chains 6, Residues 56, Estimated correctness of the model 75.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1629 reflections ( 99.51 % complete ) and 1419 restraints for refining 669 atoms. 1201 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2362 (Rfree = 0.000) for 669 atoms. Found 0 (3 requested) and removed 32 (2 requested) atoms. Cycle 27: After refmac, R = 0.2308 (Rfree = 0.000) for 634 atoms. Found 2 (2 requested) and removed 10 (2 requested) atoms. Cycle 28: After refmac, R = 0.2265 (Rfree = 0.000) for 625 atoms. Found 2 (2 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.2173 (Rfree = 0.000) for 625 atoms. Found 2 (2 requested) and removed 5 (2 requested) atoms. Cycle 30: After refmac, R = 0.2102 (Rfree = 0.000) for 621 atoms. Found 1 (2 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.75 Search for helices and strands: 0 residues in 0 chains, 648 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 9 peptides. Score 0.270 Round 2: 43 peptides, 8 chains. Longest chain 9 peptides. Score 0.384 Round 3: 42 peptides, 6 chains. Longest chain 10 peptides. Score 0.513 Round 4: 41 peptides, 6 chains. Longest chain 11 peptides. Score 0.497 Round 5: 38 peptides, 6 chains. Longest chain 11 peptides. Score 0.447 Taking the results from Round 3 Chains 6, Residues 36, Estimated correctness of the model 15.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1629 reflections ( 99.51 % complete ) and 1408 restraints for refining 644 atoms. 1270 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2378 (Rfree = 0.000) for 644 atoms. Found 2 (2 requested) and removed 4 (2 requested) atoms. Cycle 32: After refmac, R = 0.2266 (Rfree = 0.000) for 639 atoms. Found 2 (2 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.2793 (Rfree = 0.000) for 637 atoms. Found 2 (2 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.2243 (Rfree = 0.000) for 634 atoms. Found 1 (2 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2781 (Rfree = 0.000) for 632 atoms. Found 2 (2 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.78 Search for helices and strands: 0 residues in 0 chains, 660 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.248 Round 2: 46 peptides, 8 chains. Longest chain 12 peptides. Score 0.437 Round 3: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.366 Round 4: 40 peptides, 7 chains. Longest chain 11 peptides. Score 0.406 Round 5: 45 peptides, 7 chains. Longest chain 12 peptides. Score 0.491 Taking the results from Round 5 Chains 7, Residues 38, Estimated correctness of the model 8.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1629 reflections ( 99.51 % complete ) and 1477 restraints for refining 669 atoms. 1332 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2463 (Rfree = 0.000) for 669 atoms. Found 2 (2 requested) and removed 2 (2 requested) atoms. Cycle 37: After refmac, R = 0.2403 (Rfree = 0.000) for 668 atoms. Found 2 (2 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.2534 (Rfree = 0.000) for 667 atoms. Found 2 (2 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.2353 (Rfree = 0.000) for 664 atoms. Found 2 (2 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2164 (Rfree = 0.000) for 664 atoms. Found 2 (2 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.96 Search for helices and strands: 0 residues in 0 chains, 696 seeds are put forward Round 1: 39 peptides, 6 chains. Longest chain 12 peptides. Score 0.464 Round 2: 38 peptides, 6 chains. Longest chain 12 peptides. Score 0.447 Round 3: 40 peptides, 6 chains. Longest chain 12 peptides. Score 0.481 Round 4: 39 peptides, 7 chains. Longest chain 8 peptides. Score 0.388 Round 5: 35 peptides, 6 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 3 Chains 6, Residues 34, Estimated correctness of the model 5.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1629 reflections ( 99.51 % complete ) and 1505 restraints for refining 666 atoms. 1375 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2311 (Rfree = 0.000) for 666 atoms. Found 2 (2 requested) and removed 3 (2 requested) atoms. Cycle 42: After refmac, R = 0.2117 (Rfree = 0.000) for 664 atoms. Found 1 (2 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.2064 (Rfree = 0.000) for 663 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2019 (Rfree = 0.000) for 661 atoms. Found 1 (2 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.1972 (Rfree = 0.000) for 660 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 685 seeds are put forward Round 1: 27 peptides, 4 chains. Longest chain 12 peptides. Score 0.409 Round 2: 31 peptides, 5 chains. Longest chain 12 peptides. Score 0.400 Round 3: 32 peptides, 5 chains. Longest chain 12 peptides. Score 0.419 Round 4: 33 peptides, 5 chains. Longest chain 12 peptides. Score 0.437 Round 5: 27 peptides, 4 chains. Longest chain 12 peptides. Score 0.409 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 28, 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 1vku-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1629 reflections ( 99.51 % complete ) and 1500 restraints for refining 657 atoms. 1393 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2145 (Rfree = 0.000) for 657 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2943 (Rfree = 0.000) for 654 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2203 (Rfree = 0.000) for 652 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2057 (Rfree = 0.000) for 650 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:44:34 GMT 2018 Job finished. TimeTaking 21.6 Used memory is bytes: 10910320