null Sun 23 Dec 22:23:05 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nwv-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nwv-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-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/2nwv-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-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 22:23:13 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-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 102 and 0 Target number of residues in the AU: 102 Target solvent content: 0.6431 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-3.8-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: 179 Cell parameters: 62.452 62.452 137.365 90.000 90.000 120.000 Input sequence file: 2nwv-3.8-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 3.800 Wilson plot Bfac: 71.86 1815 reflections ( 99.67 % complete ) and 0 restraints for refining 1005 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3744 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3947 (Rfree = 0.000) for 1005 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 1020 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 6 peptides. Score 0.268 Round 2: 58 peptides, 9 chains. Longest chain 10 peptides. Score 0.427 Round 3: 67 peptides, 10 chains. Longest chain 14 peptides. Score 0.473 Round 4: 74 peptides, 11 chains. Longest chain 16 peptides. Score 0.497 Round 5: 73 peptides, 10 chains. Longest chain 13 peptides. Score 0.528 Taking the results from Round 5 Chains 10, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1815 reflections ( 99.67 % complete ) and 1789 restraints for refining 810 atoms. 1547 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3484 (Rfree = 0.000) for 810 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 2: After refmac, R = 0.3090 (Rfree = 0.000) for 789 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 3: After refmac, R = 0.3016 (Rfree = 0.000) for 779 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 4: After refmac, R = 0.2615 (Rfree = 0.000) for 769 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 5: After refmac, R = 0.2661 (Rfree = 0.000) for 767 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 799 seeds are put forward Round 1: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.360 Round 2: 75 peptides, 10 chains. Longest chain 14 peptides. Score 0.545 Round 3: 71 peptides, 11 chains. Longest chain 9 peptides. Score 0.469 Round 4: 70 peptides, 9 chains. Longest chain 15 peptides. Score 0.541 Round 5: 70 peptides, 8 chains. Longest chain 15 peptides. Score 0.580 Taking the results from Round 5 Chains 8, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1815 reflections ( 99.67 % complete ) and 1825 restraints for refining 825 atoms. 1585 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3074 (Rfree = 0.000) for 825 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 7: After refmac, R = 0.3247 (Rfree = 0.000) for 804 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 8: After refmac, R = 0.2748 (Rfree = 0.000) for 780 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 9: After refmac, R = 0.2997 (Rfree = 0.000) for 774 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 10: After refmac, R = 0.2953 (Rfree = 0.000) for 767 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 2.88 Search for helices and strands: 0 residues in 0 chains, 800 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.290 Round 2: 57 peptides, 8 chains. Longest chain 13 peptides. Score 0.462 Round 3: 58 peptides, 9 chains. Longest chain 14 peptides. Score 0.427 Round 4: 65 peptides, 8 chains. Longest chain 16 peptides. Score 0.537 Round 5: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.505 Taking the results from Round 4 Chains 8, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1815 reflections ( 99.67 % complete ) and 1754 restraints for refining 807 atoms. 1534 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2935 (Rfree = 0.000) for 807 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 12: After refmac, R = 0.2898 (Rfree = 0.000) for 794 atoms. Found 0 (4 requested) and removed 7 (2 requested) atoms. Cycle 13: After refmac, R = 0.2697 (Rfree = 0.000) for 785 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 14: After refmac, R = 0.2930 (Rfree = 0.000) for 776 atoms. Found 3 (4 requested) and removed 11 (2 requested) atoms. Cycle 15: After refmac, R = 0.2867 (Rfree = 0.000) for 766 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.92 Search for helices and strands: 0 residues in 0 chains, 812 seeds are put forward Round 1: 51 peptides, 9 chains. Longest chain 9 peptides. Score 0.353 Round 2: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.423 Round 3: 66 peptides, 10 chains. Longest chain 15 peptides. Score 0.463 Round 4: 65 peptides, 9 chains. Longest chain 17 peptides. Score 0.496 Round 5: 69 peptides, 10 chains. Longest chain 19 peptides. Score 0.492 Taking the results from Round 4 Chains 9, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1815 reflections ( 99.67 % complete ) and 1784 restraints for refining 820 atoms. 1569 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2880 (Rfree = 0.000) for 820 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 17: After refmac, R = 0.2812 (Rfree = 0.000) for 812 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.2601 (Rfree = 0.000) for 807 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.2768 (Rfree = 0.000) for 800 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.2775 (Rfree = 0.000) for 796 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 2.95 Search for helices and strands: 0 residues in 0 chains, 832 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.321 Round 2: 63 peptides, 10 chains. Longest chain 16 peptides. Score 0.433 Round 3: 66 peptides, 9 chains. Longest chain 21 peptides. Score 0.505 Round 4: 69 peptides, 9 chains. Longest chain 18 peptides. Score 0.532 Round 5: 77 peptides, 12 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 4 Chains 9, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1815 reflections ( 99.67 % complete ) and 1753 restraints for refining 824 atoms. 1522 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3224 (Rfree = 0.000) for 824 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 22: After refmac, R = 0.3044 (Rfree = 0.000) for 810 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 23: After refmac, R = 0.2779 (Rfree = 0.000) for 795 atoms. Found 3 (4 requested) and removed 9 (2 requested) atoms. Cycle 24: After refmac, R = 0.2738 (Rfree = 0.000) for 787 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. Cycle 25: After refmac, R = 0.2799 (Rfree = 0.000) for 782 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.00 Search for helices and strands: 0 residues in 0 chains, 813 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 6 peptides. Score 0.299 Round 2: 73 peptides, 13 chains. Longest chain 14 peptides. Score 0.404 Round 3: 68 peptides, 12 chains. Longest chain 16 peptides. Score 0.396 Round 4: 72 peptides, 12 chains. Longest chain 15 peptides. Score 0.437 Round 5: 78 peptides, 12 chains. Longest chain 17 peptides. Score 0.494 Taking the results from Round 5 Chains 12, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1815 reflections ( 99.67 % complete ) and 1748 restraints for refining 825 atoms. 1496 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3234 (Rfree = 0.000) for 825 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 27: After refmac, R = 0.2920 (Rfree = 0.000) for 809 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.2621 (Rfree = 0.000) for 801 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 29: After refmac, R = 0.2673 (Rfree = 0.000) for 789 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 30: After refmac, R = 0.2696 (Rfree = 0.000) for 784 atoms. Found 3 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 2.92 Search for helices and strands: 0 residues in 0 chains, 824 seeds are put forward Round 1: 60 peptides, 11 chains. Longest chain 15 peptides. Score 0.357 Round 2: 68 peptides, 11 chains. Longest chain 16 peptides. Score 0.440 Round 3: 75 peptides, 11 chains. Longest chain 17 peptides. Score 0.506 Round 4: 72 peptides, 10 chains. Longest chain 18 peptides. Score 0.519 Round 5: 67 peptides, 10 chains. Longest chain 11 peptides. Score 0.473 Taking the results from Round 4 Chains 10, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1815 reflections ( 99.67 % complete ) and 1831 restraints for refining 825 atoms. 1593 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2928 (Rfree = 0.000) for 825 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 32: After refmac, R = 0.2913 (Rfree = 0.000) for 813 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2809 (Rfree = 0.000) for 809 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.2715 (Rfree = 0.000) for 807 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 35: After refmac, R = 0.2629 (Rfree = 0.000) for 806 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.05 Search for helices and strands: 0 residues in 0 chains, 848 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 9 peptides. Score 0.335 Round 2: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.368 Round 3: 65 peptides, 10 chains. Longest chain 15 peptides. Score 0.453 Round 4: 68 peptides, 9 chains. Longest chain 25 peptides. Score 0.523 Round 5: 60 peptides, 10 chains. Longest chain 11 peptides. Score 0.403 Taking the results from Round 4 Chains 9, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1815 reflections ( 99.67 % complete ) and 1816 restraints for refining 825 atoms. 1589 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3596 (Rfree = 0.000) for 825 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 37: After refmac, R = 0.3138 (Rfree = 0.000) for 807 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 38: After refmac, R = 0.3193 (Rfree = 0.000) for 799 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 39: After refmac, R = 0.2672 (Rfree = 0.000) for 790 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2924 (Rfree = 0.000) for 790 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 2.93 Search for helices and strands: 0 residues in 0 chains, 820 seeds are put forward Round 1: 48 peptides, 11 chains. Longest chain 7 peptides. Score 0.218 Round 2: 66 peptides, 12 chains. Longest chain 9 peptides. Score 0.375 Round 3: 65 peptides, 11 chains. Longest chain 12 peptides. Score 0.410 Round 4: 57 peptides, 10 chains. Longest chain 11 peptides. Score 0.371 Round 5: 58 peptides, 9 chains. Longest chain 17 peptides. Score 0.427 Taking the results from Round 5 Chains 9, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1815 reflections ( 99.67 % complete ) and 1879 restraints for refining 814 atoms. 1692 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2908 (Rfree = 0.000) for 814 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 42: After refmac, R = 0.2800 (Rfree = 0.000) for 801 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.2767 (Rfree = 0.000) for 796 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.3112 (Rfree = 0.000) for 792 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2952 (Rfree = 0.000) for 790 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 2.98 Search for helices and strands: 0 residues in 0 chains, 828 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.216 Round 2: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.389 Round 3: 66 peptides, 9 chains. Longest chain 14 peptides. Score 0.505 Round 4: 61 peptides, 8 chains. Longest chain 16 peptides. Score 0.501 Round 5: 58 peptides, 7 chains. Longest chain 15 peptides. Score 0.516 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 51, 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 2nwv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1815 reflections ( 99.67 % complete ) and 1662 restraints for refining 780 atoms. 1465 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3125 (Rfree = 0.000) for 780 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2764 (Rfree = 0.000) for 771 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2634 (Rfree = 0.000) for 764 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2733 (Rfree = 0.000) for 756 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:46:18 GMT 2018 Job finished. TimeTaking 23.22 Used memory is bytes: 15894200