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 2nwv-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nwv-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nwv-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-3.4-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/2nwv-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-3.4-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 22:23:18 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/2nwv-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-3.4-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 106 and 0 Target number of residues in the AU: 106 Target solvent content: 0.6291 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 114 Adjusted target solvent content: 0.60 Input MTZ file: 2nwv-3.4-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: 179 Cell parameters: 62.452 62.452 137.365 90.000 90.000 120.000 Input sequence file: 2nwv-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 912 target number of atoms Had to go as low as 0.90 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: 28.991 3.400 Wilson plot Bfac: 64.60 2489 reflections ( 99.76 % complete ) and 0 restraints for refining 1010 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3798 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3472 (Rfree = 0.000) for 1010 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 2.81 Search for helices and strands: 0 residues in 0 chains, 1030 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 8 peptides. Score 0.287 Round 2: 70 peptides, 8 chains. Longest chain 18 peptides. Score 0.580 Round 3: 87 peptides, 11 chains. Longest chain 14 peptides. Score 0.606 Round 4: 90 peptides, 10 chains. Longest chain 18 peptides. Score 0.660 Round 5: 92 peptides, 11 chains. Longest chain 14 peptides. Score 0.642 Taking the results from Round 4 Chains 10, Residues 80, Estimated correctness of the model 47.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2489 reflections ( 99.76 % complete ) and 1751 restraints for refining 828 atoms. 1441 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2843 (Rfree = 0.000) for 828 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.2709 (Rfree = 0.000) for 818 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2623 (Rfree = 0.000) for 811 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.2702 (Rfree = 0.000) for 807 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2570 (Rfree = 0.000) for 803 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 2.83 Search for helices and strands: 0 residues in 0 chains, 841 seeds are put forward Round 1: 76 peptides, 8 chains. Longest chain 17 peptides. Score 0.626 Round 2: 91 peptides, 8 chains. Longest chain 19 peptides. Score 0.725 Round 3: 87 peptides, 8 chains. Longest chain 31 peptides. Score 0.701 Round 4: 88 peptides, 10 chains. Longest chain 16 peptides. Score 0.646 Round 5: 83 peptides, 8 chains. Longest chain 16 peptides. Score 0.675 Taking the results from Round 2 Chains 8, Residues 83, Estimated correctness of the model 64.1 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2489 reflections ( 99.76 % complete ) and 1561 restraints for refining 829 atoms. 1147 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2792 (Rfree = 0.000) for 829 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 7: After refmac, R = 0.3070 (Rfree = 0.000) for 825 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 8: After refmac, R = 0.2610 (Rfree = 0.000) for 816 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 9: After refmac, R = 0.2490 (Rfree = 0.000) for 813 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 10: After refmac, R = 0.2956 (Rfree = 0.000) for 809 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 2.81 Search for helices and strands: 0 residues in 0 chains, 843 seeds are put forward Round 1: 80 peptides, 13 chains. Longest chain 14 peptides. Score 0.472 Round 2: 83 peptides, 8 chains. Longest chain 32 peptides. Score 0.675 Round 3: 85 peptides, 10 chains. Longest chain 17 peptides. Score 0.625 Round 4: 87 peptides, 10 chains. Longest chain 16 peptides. Score 0.639 Round 5: 83 peptides, 8 chains. Longest chain 20 peptides. Score 0.675 Taking the results from Round 5 Chains 8, Residues 75, Estimated correctness of the model 51.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2489 reflections ( 99.76 % complete ) and 1800 restraints for refining 829 atoms. 1508 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2917 (Rfree = 0.000) for 829 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 12: After refmac, R = 0.2717 (Rfree = 0.000) for 827 atoms. Found 5 (5 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.2529 (Rfree = 0.000) for 822 atoms. Found 2 (5 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2473 (Rfree = 0.000) for 818 atoms. Found 4 (5 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2407 (Rfree = 0.000) for 818 atoms. Found 4 (5 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.87 Search for helices and strands: 0 residues in 0 chains, 847 seeds are put forward Round 1: 75 peptides, 11 chains. Longest chain 14 peptides. Score 0.506 Round 2: 76 peptides, 9 chains. Longest chain 15 peptides. Score 0.591 Round 3: 82 peptides, 8 chains. Longest chain 36 peptides. Score 0.669 Round 4: 78 peptides, 11 chains. Longest chain 20 peptides. Score 0.533 Round 5: 85 peptides, 8 chains. Longest chain 29 peptides. Score 0.688 Taking the results from Round 5 Chains 8, Residues 77, Estimated correctness of the model 54.7 % 2 chains (53 residues) have been docked in sequence ------------------------------------------------------ 2489 reflections ( 99.76 % complete ) and 1348 restraints for refining 891 atoms. 789 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3480 (Rfree = 0.000) for 891 atoms. Found 5 (5 requested) and removed 21 (3 requested) atoms. Cycle 17: After refmac, R = 0.3236 (Rfree = 0.000) for 868 atoms. Found 5 (5 requested) and removed 11 (3 requested) atoms. Cycle 18: After refmac, R = 0.3006 (Rfree = 0.000) for 856 atoms. Found 3 (5 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2909 (Rfree = 0.000) for 853 atoms. Found 4 (5 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2865 (Rfree = 0.000) for 851 atoms. Found 1 (5 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.90 Search for helices and strands: 0 residues in 0 chains, 879 seeds are put forward Round 1: 86 peptides, 10 chains. Longest chain 17 peptides. Score 0.632 Round 2: 91 peptides, 7 chains. Longest chain 22 peptides. Score 0.751 Round 3: 92 peptides, 7 chains. Longest chain 24 peptides. Score 0.756 Round 4: 90 peptides, 7 chains. Longest chain 32 peptides. Score 0.746 Round 5: 100 peptides, 9 chains. Longest chain 22 peptides. Score 0.747 Taking the results from Round 3 Chains 7, Residues 85, Estimated correctness of the model 71.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2489 reflections ( 99.76 % complete ) and 1735 restraints for refining 829 atoms. 1402 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3049 (Rfree = 0.000) for 829 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 22: After refmac, R = 0.2771 (Rfree = 0.000) for 825 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2623 (Rfree = 0.000) for 825 atoms. Found 5 (5 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.2512 (Rfree = 0.000) for 826 atoms. Found 3 (5 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2544 (Rfree = 0.000) for 823 atoms. Found 1 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 2.86 Search for helices and strands: 0 residues in 0 chains, 849 seeds are put forward Round 1: 70 peptides, 9 chains. Longest chain 13 peptides. Score 0.541 Round 2: 75 peptides, 8 chains. Longest chain 17 peptides. Score 0.619 Round 3: 76 peptides, 9 chains. Longest chain 18 peptides. Score 0.591 Round 4: 82 peptides, 9 chains. Longest chain 22 peptides. Score 0.636 Round 5: 76 peptides, 7 chains. Longest chain 18 peptides. Score 0.660 Taking the results from Round 5 Chains 7, Residues 69, Estimated correctness of the model 47.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2489 reflections ( 99.76 % complete ) and 1827 restraints for refining 828 atoms. 1558 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2878 (Rfree = 0.000) for 828 atoms. Found 3 (5 requested) and removed 3 (3 requested) atoms. Cycle 27: After refmac, R = 0.2619 (Rfree = 0.000) for 827 atoms. Found 5 (5 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.2466 (Rfree = 0.000) for 828 atoms. Found 3 (5 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.2260 (Rfree = 0.000) for 824 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.2229 (Rfree = 0.000) for 820 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 2.86 Search for helices and strands: 0 residues in 0 chains, 851 seeds are put forward Round 1: 68 peptides, 11 chains. Longest chain 14 peptides. Score 0.440 Round 2: 78 peptides, 9 chains. Longest chain 23 peptides. Score 0.606 Round 3: 81 peptides, 8 chains. Longest chain 32 peptides. Score 0.662 Round 4: 78 peptides, 7 chains. Longest chain 23 peptides. Score 0.674 Round 5: 86 peptides, 11 chains. Longest chain 23 peptides. Score 0.598 Taking the results from Round 4 Chains 7, Residues 71, Estimated correctness of the model 50.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2489 reflections ( 99.76 % complete ) and 1761 restraints for refining 828 atoms. 1484 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2855 (Rfree = 0.000) for 828 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.2715 (Rfree = 0.000) for 826 atoms. Found 4 (5 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2447 (Rfree = 0.000) for 826 atoms. Found 3 (5 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.2379 (Rfree = 0.000) for 824 atoms. Found 2 (5 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2310 (Rfree = 0.000) for 822 atoms. Found 2 (5 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 2.87 Search for helices and strands: 0 residues in 0 chains, 846 seeds are put forward Round 1: 79 peptides, 10 chains. Longest chain 28 peptides. Score 0.578 Round 2: 84 peptides, 10 chains. Longest chain 23 peptides. Score 0.617 Round 3: 93 peptides, 9 chains. Longest chain 33 peptides. Score 0.708 Round 4: 91 peptides, 9 chains. Longest chain 33 peptides. Score 0.696 Round 5: 86 peptides, 10 chains. Longest chain 18 peptides. Score 0.632 Taking the results from Round 3 Chains 9, Residues 84, Estimated correctness of the model 59.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2489 reflections ( 99.76 % complete ) and 1688 restraints for refining 829 atoms. 1361 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2713 (Rfree = 0.000) for 829 atoms. Found 5 (5 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.2603 (Rfree = 0.000) for 830 atoms. Found 5 (5 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.2460 (Rfree = 0.000) for 830 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2299 (Rfree = 0.000) for 831 atoms. Found 3 (4 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.2264 (Rfree = 0.000) for 830 atoms. Found 3 (4 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 2.85 Search for helices and strands: 0 residues in 0 chains, 856 seeds are put forward Round 1: 90 peptides, 10 chains. Longest chain 22 peptides. Score 0.660 Round 2: 94 peptides, 10 chains. Longest chain 26 peptides. Score 0.686 Round 3: 88 peptides, 9 chains. Longest chain 32 peptides. Score 0.677 Round 4: 85 peptides, 10 chains. Longest chain 15 peptides. Score 0.625 Round 5: 91 peptides, 8 chains. Longest chain 30 peptides. Score 0.725 Taking the results from Round 5 Chains 8, Residues 83, Estimated correctness of the model 64.1 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2489 reflections ( 99.76 % complete ) and 1421 restraints for refining 829 atoms. 968 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3037 (Rfree = 0.000) for 829 atoms. Found 4 (4 requested) and removed 7 (3 requested) atoms. Cycle 42: After refmac, R = 0.2802 (Rfree = 0.000) for 820 atoms. Found 4 (4 requested) and removed 9 (3 requested) atoms. Cycle 43: After refmac, R = 0.2565 (Rfree = 0.000) for 812 atoms. Found 4 (4 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2429 (Rfree = 0.000) for 810 atoms. Found 2 (4 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.2297 (Rfree = 0.000) for 809 atoms. Found 3 (4 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 2.88 Search for helices and strands: 0 residues in 0 chains, 836 seeds are put forward Round 1: 72 peptides, 9 chains. Longest chain 21 peptides. Score 0.558 Round 2: 85 peptides, 8 chains. Longest chain 26 peptides. Score 0.688 Round 3: 83 peptides, 8 chains. Longest chain 21 peptides. Score 0.675 Round 4: 82 peptides, 8 chains. Longest chain 22 peptides. Score 0.669 Round 5: 78 peptides, 7 chains. Longest chain 27 peptides. Score 0.674 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 77, Estimated correctness of the model 54.7 % 1 chains (25 residues) have been docked in sequence Sequence coverage is 32 % Consider running further cycles of model building using 2nwv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2489 reflections ( 99.76 % complete ) and 1437 restraints for refining 829 atoms. 1003 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2608 (Rfree = 0.000) for 829 atoms. Found 0 (4 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2459 (Rfree = 0.000) for 825 atoms. Found 0 (4 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2448 (Rfree = 0.000) for 820 atoms. Found 0 (4 requested) and removed 0 (3 requested) atoms. Cycle 49: After refmac, R = 0.2518 (Rfree = 0.000) for 820 atoms. Found 0 (4 requested) and removed 1 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:37 GMT 2018 Job finished. TimeTaking 24.48 Used memory is bytes: 12307568