null Sun 23 Dec 22:22:59 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vku-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vku-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-3.8-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 22:23:08 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-3.8-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 58 and 0 Target number of residues in the AU: 58 Target solvent content: 0.6460 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-3.8-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-3.8-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 3.803 Wilson plot Bfac: 74.95 990 reflections ( 99.20 % complete ) and 0 restraints for refining 886 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3503 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3581 (Rfree = 0.000) for 886 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 4.33 Search for helices and strands: 0 residues in 0 chains, 899 seeds are put forward Round 1: 27 peptides, 6 chains. Longest chain 5 peptides. Score 0.234 Round 2: 34 peptides, 6 chains. Longest chain 8 peptides. Score 0.375 Round 3: 39 peptides, 7 chains. Longest chain 8 peptides. Score 0.388 Round 4: 39 peptides, 6 chains. Longest chain 8 peptides. Score 0.464 Round 5: 36 peptides, 6 chains. Longest chain 7 peptides. Score 0.412 Taking the results from Round 4 Chains 6, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 990 reflections ( 99.20 % complete ) and 1799 restraints for refining 722 atoms. 1673 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2964 (Rfree = 0.000) for 722 atoms. Found 1 (3 requested) and removed 10 (1 requested) atoms. Cycle 2: After refmac, R = 0.2439 (Rfree = 0.000) for 693 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. Cycle 3: After refmac, R = 0.2268 (Rfree = 0.000) for 688 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. Cycle 4: After refmac, R = 0.2712 (Rfree = 0.000) for 683 atoms. Found 1 (3 requested) and removed 7 (1 requested) atoms. Cycle 5: After refmac, R = 0.1990 (Rfree = 0.000) for 677 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 4.09 Search for helices and strands: 0 residues in 0 chains, 720 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 6 peptides. Score 0.230 Round 2: 45 peptides, 7 chains. Longest chain 11 peptides. Score 0.491 Round 3: 46 peptides, 9 chains. Longest chain 7 peptides. Score 0.362 Round 4: 47 peptides, 6 chains. Longest chain 14 peptides. Score 0.587 Round 5: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.380 Taking the results from Round 4 Chains 6, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 990 reflections ( 99.20 % complete ) and 1598 restraints for refining 672 atoms. 1440 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3055 (Rfree = 0.000) for 672 atoms. Found 2 (3 requested) and removed 5 (1 requested) atoms. Cycle 7: After refmac, R = 0.2943 (Rfree = 0.000) for 661 atoms. Found 1 (3 requested) and removed 5 (1 requested) atoms. Cycle 8: After refmac, R = 0.2262 (Rfree = 0.000) for 654 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 9: After refmac, R = 0.2240 (Rfree = 0.000) for 653 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 10: After refmac, R = 0.2094 (Rfree = 0.000) for 652 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 4.13 Search for helices and strands: 0 residues in 0 chains, 687 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 6 peptides. Score 0.252 Round 2: 37 peptides, 6 chains. Longest chain 12 peptides. Score 0.430 Round 3: 44 peptides, 7 chains. Longest chain 13 peptides. Score 0.475 Round 4: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.406 Round 5: 40 peptides, 7 chains. Longest chain 10 peptides. Score 0.406 Taking the results from Round 3 Chains 7, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 990 reflections ( 99.20 % complete ) and 1540 restraints for refining 647 atoms. 1399 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2766 (Rfree = 0.000) for 647 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 12: After refmac, R = 0.2384 (Rfree = 0.000) for 644 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 13: After refmac, R = 0.2216 (Rfree = 0.000) for 643 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 14: After refmac, R = 0.2293 (Rfree = 0.000) for 641 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. Cycle 15: After refmac, R = 0.2102 (Rfree = 0.000) for 641 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 4.20 Search for helices and strands: 0 residues in 0 chains, 663 seeds are put forward Round 1: 36 peptides, 6 chains. Longest chain 8 peptides. Score 0.412 Round 2: 39 peptides, 5 chains. Longest chain 13 peptides. Score 0.536 Round 3: 41 peptides, 5 chains. Longest chain 14 peptides. Score 0.567 Round 4: 37 peptides, 5 chains. Longest chain 14 peptides. Score 0.505 Round 5: 43 peptides, 5 chains. Longest chain 14 peptides. Score 0.595 Taking the results from Round 5 Chains 5, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 990 reflections ( 99.20 % complete ) and 1484 restraints for refining 635 atoms. 1337 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3222 (Rfree = 0.000) for 635 atoms. Found 3 (3 requested) and removed 9 (1 requested) atoms. Cycle 17: After refmac, R = 0.2155 (Rfree = 0.000) for 629 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 18: After refmac, R = 0.2232 (Rfree = 0.000) for 623 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. Cycle 19: After refmac, R = 0.2272 (Rfree = 0.000) for 622 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 20: After refmac, R = 0.2947 (Rfree = 0.000) for 623 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 4.11 Search for helices and strands: 0 residues in 0 chains, 637 seeds are put forward Round 1: 33 peptides, 6 chains. Longest chain 9 peptides. Score 0.356 Round 2: 40 peptides, 7 chains. Longest chain 11 peptides. Score 0.406 Round 3: 39 peptides, 6 chains. Longest chain 12 peptides. Score 0.464 Round 4: 37 peptides, 5 chains. Longest chain 13 peptides. Score 0.505 Round 5: 34 peptides, 5 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 4 Chains 5, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 990 reflections ( 99.20 % complete ) and 1476 restraints for refining 633 atoms. 1353 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2414 (Rfree = 0.000) for 633 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 22: After refmac, R = 0.2058 (Rfree = 0.000) for 635 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. Cycle 23: After refmac, R = 0.2099 (Rfree = 0.000) for 635 atoms. Found 3 (3 requested) and removed 10 (1 requested) atoms. Cycle 24: After refmac, R = 0.2227 (Rfree = 0.000) for 626 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. Cycle 25: After refmac, R = 0.2009 (Rfree = 0.000) for 621 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 4.18 Search for helices and strands: 0 residues in 0 chains, 644 seeds are put forward Round 1: 33 peptides, 8 chains. Longest chain 5 peptides. Score 0.188 Round 2: 40 peptides, 7 chains. Longest chain 8 peptides. Score 0.406 Round 3: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.366 Round 4: 35 peptides, 5 chains. Longest chain 14 peptides. Score 0.472 Round 5: 35 peptides, 6 chains. Longest chain 9 peptides. Score 0.394 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 ------------------------------------------------------ 990 reflections ( 99.20 % complete ) and 1597 restraints for refining 667 atoms. 1482 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2496 (Rfree = 0.000) for 667 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. Cycle 27: After refmac, R = 0.2413 (Rfree = 0.000) for 664 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 28: After refmac, R = 0.2181 (Rfree = 0.000) for 661 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 29: After refmac, R = 0.2166 (Rfree = 0.000) for 660 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 30: After refmac, R = 0.2309 (Rfree = 0.000) for 656 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 4.22 Search for helices and strands: 0 residues in 0 chains, 684 seeds are put forward Round 1: 28 peptides, 6 chains. Longest chain 8 peptides. Score 0.255 Round 2: 45 peptides, 8 chains. Longest chain 10 peptides. Score 0.419 Round 3: 36 peptides, 7 chains. Longest chain 9 peptides. Score 0.332 Round 4: 38 peptides, 7 chains. Longest chain 8 peptides. Score 0.370 Round 5: 37 peptides, 7 chains. Longest chain 9 peptides. Score 0.351 Taking the results from Round 2 Chains 8, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 990 reflections ( 99.20 % complete ) and 1477 restraints for refining 660 atoms. 1337 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3038 (Rfree = 0.000) for 660 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 32: After refmac, R = 0.3136 (Rfree = 0.000) for 654 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 33: After refmac, R = 0.2329 (Rfree = 0.000) for 651 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 34: After refmac, R = 0.2204 (Rfree = 0.000) for 649 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 35: After refmac, R = 0.2454 (Rfree = 0.000) for 650 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 4.12 Search for helices and strands: 0 residues in 0 chains, 677 seeds are put forward Round 1: 24 peptides, 5 chains. Longest chain 7 peptides. Score 0.259 Round 2: 36 peptides, 7 chains. Longest chain 9 peptides. Score 0.332 Round 3: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.370 Round 4: 37 peptides, 6 chains. Longest chain 8 peptides. Score 0.430 Round 5: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.406 Taking the results from Round 4 Chains 6, Residues 31, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 990 reflections ( 99.20 % complete ) and 1686 restraints for refining 682 atoms. 1568 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2553 (Rfree = 0.000) for 682 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 37: After refmac, R = 0.2661 (Rfree = 0.000) for 681 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 38: After refmac, R = 0.2196 (Rfree = 0.000) for 680 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. Cycle 39: After refmac, R = 0.2124 (Rfree = 0.000) for 680 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 40: After refmac, R = 0.1838 (Rfree = 0.000) for 681 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 4.20 Search for helices and strands: 0 residues in 0 chains, 709 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 7 peptides. Score 0.270 Round 2: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.270 Round 3: 26 peptides, 5 chains. Longest chain 6 peptides. Score 0.302 Round 4: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.313 Round 5: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.313 Taking the results from Round 5 Chains 7, Residues 28, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 990 reflections ( 99.20 % complete ) and 1826 restraints for refining 723 atoms. 1721 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3083 (Rfree = 0.000) for 723 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. Cycle 42: After refmac, R = 0.2214 (Rfree = 0.000) for 717 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 43: After refmac, R = 0.2222 (Rfree = 0.000) for 716 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 44: After refmac, R = 0.2755 (Rfree = 0.000) for 718 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. Cycle 45: After refmac, R = 0.1736 (Rfree = 0.000) for 718 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 4.19 Search for helices and strands: 0 residues in 0 chains, 751 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 7 peptides. Score 0.231 Round 2: 33 peptides, 6 chains. Longest chain 9 peptides. Score 0.356 Round 3: 35 peptides, 7 chains. Longest chain 9 peptides. Score 0.313 Round 4: 36 peptides, 7 chains. Longest chain 10 peptides. Score 0.332 Round 5: 32 peptides, 6 chains. Longest chain 9 peptides. Score 0.337 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 27, 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. 990 reflections ( 99.20 % complete ) and 1808 restraints for refining 720 atoms. 1706 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2640 (Rfree = 0.000) for 720 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.3001 (Rfree = 0.000) for 718 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.2853 (Rfree = 0.000) for 716 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.2428 (Rfree = 0.000) for 713 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:43:50 GMT 2018 Job finished. TimeTaking 20.85 Used memory is bytes: 17354448