null Sun 23 Dec 22:23:08 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vku-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vku-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-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/1vku-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-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 22:23:17 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-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 59 and 0 Target number of residues in the AU: 59 Target solvent content: 0.6398 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-3.6-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: 154 Cell parameters: 45.440 45.440 74.373 90.000 90.000 120.000 Input sequence file: 1vku-3.6-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 3.603 Wilson plot Bfac: 70.86 1158 reflections ( 99.31 % complete ) and 0 restraints for refining 890 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3355 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2864 (Rfree = 0.000) for 890 atoms. Found 5 (5 requested) and removed 22 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 4.16 Search for helices and strands: 0 residues in 0 chains, 892 seeds are put forward Round 1: 21 peptides, 5 chains. Longest chain 5 peptides. Score 0.191 Round 2: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.290 Round 3: 40 peptides, 7 chains. Longest chain 10 peptides. Score 0.406 Round 4: 45 peptides, 8 chains. Longest chain 9 peptides. Score 0.419 Round 5: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.402 Taking the results from Round 4 Chains 8, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1158 reflections ( 99.31 % complete ) and 1774 restraints for refining 725 atoms. 1634 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2769 (Rfree = 0.000) for 725 atoms. Found 1 (4 requested) and removed 10 (2 requested) atoms. Cycle 2: After refmac, R = 0.2910 (Rfree = 0.000) for 705 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 3: After refmac, R = 0.2717 (Rfree = 0.000) for 703 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 4: After refmac, R = 0.2889 (Rfree = 0.000) for 698 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.2853 (Rfree = 0.000) for 693 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.93 Search for helices and strands: 0 residues in 0 chains, 716 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 6 peptides. Score 0.252 Round 2: 37 peptides, 7 chains. Longest chain 9 peptides. Score 0.351 Round 3: 39 peptides, 7 chains. Longest chain 8 peptides. Score 0.388 Round 4: 35 peptides, 5 chains. Longest chain 11 peptides. Score 0.472 Round 5: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.313 Taking the results from Round 4 Chains 5, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1158 reflections ( 99.31 % complete ) and 1610 restraints for refining 673 atoms. 1495 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2772 (Rfree = 0.000) for 673 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 7: After refmac, R = 0.2701 (Rfree = 0.000) for 666 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 8: After refmac, R = 0.2374 (Rfree = 0.000) for 662 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.2128 (Rfree = 0.000) for 660 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.1976 (Rfree = 0.000) for 661 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 695 seeds are put forward Round 1: 42 peptides, 8 chains. Longest chain 7 peptides. Score 0.366 Round 2: 38 peptides, 6 chains. Longest chain 9 peptides. Score 0.447 Round 3: 43 peptides, 6 chains. Longest chain 14 peptides. Score 0.529 Round 4: 42 peptides, 7 chains. Longest chain 10 peptides. Score 0.441 Round 5: 35 peptides, 5 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 3 Chains 6, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1158 reflections ( 99.31 % complete ) and 1569 restraints for refining 673 atoms. 1427 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2452 (Rfree = 0.000) for 673 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 12: After refmac, R = 0.2185 (Rfree = 0.000) for 675 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.2116 (Rfree = 0.000) for 672 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2100 (Rfree = 0.000) for 671 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.2134 (Rfree = 0.000) for 669 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.97 Search for helices and strands: 0 residues in 0 chains, 696 seeds are put forward Round 1: 35 peptides, 7 chains. Longest chain 10 peptides. Score 0.313 Round 2: 37 peptides, 5 chains. Longest chain 16 peptides. Score 0.505 Round 3: 38 peptides, 4 chains. Longest chain 18 peptides. Score 0.590 Round 4: 39 peptides, 4 chains. Longest chain 20 peptides. Score 0.604 Round 5: 47 peptides, 5 chains. Longest chain 19 peptides. Score 0.647 Taking the results from Round 5 Chains 5, Residues 42, Estimated correctness of the model 31.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1158 reflections ( 99.31 % complete ) and 1565 restraints for refining 687 atoms. 1402 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2701 (Rfree = 0.000) for 687 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 17: After refmac, R = 0.2327 (Rfree = 0.000) for 685 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 18: After refmac, R = 0.2538 (Rfree = 0.000) for 686 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.2231 (Rfree = 0.000) for 684 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2124 (Rfree = 0.000) for 683 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 4.07 Search for helices and strands: 0 residues in 0 chains, 710 seeds are put forward Round 1: 35 peptides, 6 chains. Longest chain 8 peptides. Score 0.394 Round 2: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.366 Round 3: 47 peptides, 7 chains. Longest chain 10 peptides. Score 0.523 Round 4: 42 peptides, 7 chains. Longest chain 10 peptides. Score 0.441 Round 5: 40 peptides, 6 chains. Longest chain 10 peptides. Score 0.481 Taking the results from Round 3 Chains 7, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1158 reflections ( 99.31 % complete ) and 1504 restraints for refining 665 atoms. 1351 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3079 (Rfree = 0.000) for 665 atoms. Found 4 (4 requested) and removed 13 (2 requested) atoms. Cycle 22: After refmac, R = 0.2858 (Rfree = 0.000) for 655 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 23: After refmac, R = 0.2711 (Rfree = 0.000) for 653 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.2510 (Rfree = 0.000) for 652 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2405 (Rfree = 0.000) for 647 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 4.05 Search for helices and strands: 0 residues in 0 chains, 682 seeds are put forward Round 1: 21 peptides, 5 chains. Longest chain 5 peptides. Score 0.191 Round 2: 30 peptides, 5 chains. Longest chain 10 peptides. Score 0.382 Round 3: 37 peptides, 6 chains. Longest chain 9 peptides. Score 0.430 Round 4: 34 peptides, 5 chains. Longest chain 12 peptides. Score 0.454 Round 5: 33 peptides, 5 chains. Longest chain 8 peptides. Score 0.437 Taking the results from Round 4 Chains 5, Residues 29, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1158 reflections ( 99.31 % complete ) and 1565 restraints for refining 653 atoms. 1454 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2331 (Rfree = 0.000) for 653 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 27: After refmac, R = 0.2534 (Rfree = 0.000) for 652 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.2150 (Rfree = 0.000) for 650 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.2282 (Rfree = 0.000) for 647 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2313 (Rfree = 0.000) for 644 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 4.05 Search for helices and strands: 0 residues in 0 chains, 670 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 6 peptides. Score 0.231 Round 2: 36 peptides, 7 chains. Longest chain 7 peptides. Score 0.332 Round 3: 36 peptides, 6 chains. Longest chain 12 peptides. Score 0.412 Round 4: 39 peptides, 7 chains. Longest chain 9 peptides. Score 0.388 Round 5: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.317 Taking the results from Round 3 Chains 6, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1158 reflections ( 99.31 % complete ) and 1627 restraints for refining 672 atoms. 1513 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2660 (Rfree = 0.000) for 672 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 32: After refmac, R = 0.2677 (Rfree = 0.000) for 671 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2580 (Rfree = 0.000) for 665 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.2424 (Rfree = 0.000) for 663 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2359 (Rfree = 0.000) for 663 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 4.09 Search for helices and strands: 0 residues in 0 chains, 702 seeds are put forward Round 1: 30 peptides, 6 chains. Longest chain 7 peptides. Score 0.297 Round 2: 33 peptides, 7 chains. Longest chain 6 peptides. Score 0.273 Round 3: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.313 Round 4: 27 peptides, 5 chains. Longest chain 8 peptides. Score 0.323 Round 5: 27 peptides, 4 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 5 Chains 4, Residues 23, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1158 reflections ( 99.31 % complete ) and 1665 restraints for refining 678 atoms. 1577 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2381 (Rfree = 0.000) for 678 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 37: After refmac, R = 0.2364 (Rfree = 0.000) for 677 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.2151 (Rfree = 0.000) for 674 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.2000 (Rfree = 0.000) for 673 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.1882 (Rfree = 0.000) for 671 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 4.02 Search for helices and strands: 0 residues in 0 chains, 695 seeds are put forward Round 1: 14 peptides, 3 chains. Longest chain 5 peptides. Score 0.223 Round 2: 18 peptides, 3 chains. Longest chain 8 peptides. Score 0.319 Round 3: 19 peptides, 4 chains. Longest chain 6 peptides. Score 0.242 Round 4: 21 peptides, 4 chains. Longest chain 8 peptides. Score 0.287 Round 5: 22 peptides, 4 chains. Longest chain 7 peptides. Score 0.309 Taking the results from Round 2 Chains 3, Residues 15, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1158 reflections ( 99.31 % complete ) and 1707 restraints for refining 666 atoms. 1650 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1951 (Rfree = 0.000) for 666 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 42: After refmac, R = 0.2094 (Rfree = 0.000) for 664 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.1906 (Rfree = 0.000) for 662 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2024 (Rfree = 0.000) for 660 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.1734 (Rfree = 0.000) for 658 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 686 seeds are put forward Round 1: 20 peptides, 4 chains. Longest chain 8 peptides. Score 0.265 Round 2: 17 peptides, 3 chains. Longest chain 9 peptides. Score 0.297 Round 3: 17 peptides, 4 chains. Longest chain 5 peptides. Score 0.193 Round 4: 19 peptides, 4 chains. Longest chain 7 peptides. Score 0.242 Round 5: 18 peptides, 4 chains. Longest chain 5 peptides. Score 0.218 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 14, 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. 1158 reflections ( 99.31 % complete ) and 1642 restraints for refining 658 atoms. 1589 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1877 (Rfree = 0.000) for 658 atoms. Found 0 (4 requested) and removed 0 (2 requested) atoms. Cycle 47: After refmac, R = 0.1991 (Rfree = 0.000) for 658 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1804 (Rfree = 0.000) for 655 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Cycle 49: After refmac, R = 0.1724 (Rfree = 0.000) for 653 atoms. Found 0 (4 requested) and removed 0 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:43:45 GMT 2018 Job finished. TimeTaking 20.61 Used memory is bytes: 6005944