null Sun 23 Dec 22:22:46 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nwv-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nwv-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-4.0-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 22:22:56 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-4.0-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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 912 target number of atoms Had to go as low as 0.95 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 4.002 Wilson plot Bfac: 71.83 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1564 reflections ( 99.62 % complete ) and 0 restraints for refining 1004 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3877 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3998 (Rfree = 0.000) for 1004 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.29 3.75 Search for helices and strands: 0 residues in 0 chains, 1024 seeds are put forward Round 1: 35 peptides, 6 chains. Longest chain 10 peptides. Score 0.320 Round 2: 53 peptides, 10 chains. Longest chain 9 peptides. Score 0.327 Round 3: 63 peptides, 9 chains. Longest chain 14 peptides. Score 0.477 Round 4: 64 peptides, 8 chains. Longest chain 14 peptides. Score 0.528 Round 5: 70 peptides, 8 chains. Longest chain 16 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 ------------------------------------------------------ 1564 reflections ( 99.62 % complete ) and 1868 restraints for refining 814 atoms. 1628 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3624 (Rfree = 0.000) for 814 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 2: After refmac, R = 0.3272 (Rfree = 0.000) for 802 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 3: After refmac, R = 0.3184 (Rfree = 0.000) for 793 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. Cycle 4: After refmac, R = 0.3129 (Rfree = 0.000) for 786 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 5: After refmac, R = 0.3008 (Rfree = 0.000) for 784 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.09 Search for helices and strands: 0 residues in 0 chains, 825 seeds are put forward Round 1: 68 peptides, 11 chains. Longest chain 11 peptides. Score 0.440 Round 2: 70 peptides, 9 chains. Longest chain 15 peptides. Score 0.541 Round 3: 76 peptides, 10 chains. Longest chain 17 peptides. Score 0.554 Round 4: 71 peptides, 10 chains. Longest chain 14 peptides. Score 0.510 Round 5: 71 peptides, 9 chains. Longest chain 18 peptides. Score 0.550 Taking the results from Round 3 Chains 10, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.62 % complete ) and 1806 restraints for refining 824 atoms. 1552 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3154 (Rfree = 0.000) for 824 atoms. Found 2 (3 requested) and removed 7 (1 requested) atoms. Cycle 7: After refmac, R = 0.2956 (Rfree = 0.000) for 809 atoms. Found 0 (3 requested) and removed 7 (1 requested) atoms. Cycle 8: After refmac, R = 0.2906 (Rfree = 0.000) for 800 atoms. Found 1 (3 requested) and removed 5 (1 requested) atoms. Cycle 9: After refmac, R = 0.2790 (Rfree = 0.000) for 794 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 10: After refmac, R = 0.2722 (Rfree = 0.000) for 790 atoms. Found 0 (3 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.15 Search for helices and strands: 0 residues in 0 chains, 829 seeds are put forward Round 1: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.399 Round 2: 61 peptides, 9 chains. Longest chain 11 peptides. Score 0.458 Round 3: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.410 Round 4: 63 peptides, 8 chains. Longest chain 16 peptides. Score 0.519 Round 5: 61 peptides, 10 chains. Longest chain 11 peptides. Score 0.413 Taking the results from Round 4 Chains 8, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.62 % complete ) and 1820 restraints for refining 824 atoms. 1608 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3614 (Rfree = 0.000) for 824 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 12: After refmac, R = 0.3037 (Rfree = 0.000) for 817 atoms. Found 3 (3 requested) and removed 10 (1 requested) atoms. Cycle 13: After refmac, R = 0.2930 (Rfree = 0.000) for 807 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. Cycle 14: After refmac, R = 0.2805 (Rfree = 0.000) for 802 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. Cycle 15: After refmac, R = 0.2898 (Rfree = 0.000) for 798 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.15 Search for helices and strands: 0 residues in 0 chains, 831 seeds are put forward Round 1: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.382 Round 2: 56 peptides, 10 chains. Longest chain 12 peptides. Score 0.360 Round 3: 58 peptides, 8 chains. Longest chain 14 peptides. Score 0.472 Round 4: 54 peptides, 9 chains. Longest chain 11 peptides. Score 0.385 Round 5: 53 peptides, 9 chains. Longest chain 13 peptides. Score 0.375 Taking the results from Round 3 Chains 8, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.62 % complete ) and 1854 restraints for refining 824 atoms. 1662 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3318 (Rfree = 0.000) for 824 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 17: After refmac, R = 0.3165 (Rfree = 0.000) for 817 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 18: After refmac, R = 0.2834 (Rfree = 0.000) for 807 atoms. Found 1 (3 requested) and removed 7 (1 requested) atoms. Cycle 19: After refmac, R = 0.3194 (Rfree = 0.000) for 794 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 20: After refmac, R = 0.3040 (Rfree = 0.000) for 791 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.97 3.47 Search for helices and strands: 0 residues in 0 chains, 832 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.263 Round 2: 57 peptides, 10 chains. Longest chain 11 peptides. Score 0.371 Round 3: 51 peptides, 8 chains. Longest chain 11 peptides. Score 0.401 Round 4: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.360 Round 5: 56 peptides, 9 chains. Longest chain 9 peptides. Score 0.407 Taking the results from Round 5 Chains 9, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.62 % complete ) and 1859 restraints for refining 824 atoms. 1680 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3370 (Rfree = 0.000) for 824 atoms. Found 2 (3 requested) and removed 8 (1 requested) atoms. Cycle 22: After refmac, R = 0.3130 (Rfree = 0.000) for 809 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 23: After refmac, R = 0.3234 (Rfree = 0.000) for 804 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 24: After refmac, R = 0.2848 (Rfree = 0.000) for 794 atoms. Found 2 (3 requested) and removed 5 (1 requested) atoms. Cycle 25: After refmac, R = 0.2643 (Rfree = 0.000) for 790 atoms. Found 2 (3 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 3.36 Search for helices and strands: 0 residues in 0 chains, 835 seeds are put forward Round 1: 45 peptides, 9 chains. Longest chain 11 peptides. Score 0.283 Round 2: 51 peptides, 7 chains. Longest chain 14 peptides. Score 0.448 Round 3: 49 peptides, 7 chains. Longest chain 14 peptides. Score 0.427 Round 4: 55 peptides, 7 chains. Longest chain 20 peptides. Score 0.487 Round 5: 49 peptides, 7 chains. Longest chain 13 peptides. Score 0.427 Taking the results from Round 4 Chains 7, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.62 % complete ) and 1864 restraints for refining 824 atoms. 1679 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2994 (Rfree = 0.000) for 824 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 27: After refmac, R = 0.2873 (Rfree = 0.000) for 817 atoms. Found 2 (3 requested) and removed 5 (1 requested) atoms. Cycle 28: After refmac, R = 0.2822 (Rfree = 0.000) for 812 atoms. Found 2 (3 requested) and removed 4 (1 requested) atoms. Cycle 29: After refmac, R = 0.2686 (Rfree = 0.000) for 806 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 30: After refmac, R = 0.2703 (Rfree = 0.000) for 805 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.35 Search for helices and strands: 0 residues in 0 chains, 843 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 5 peptides. Score 0.211 Round 2: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.330 Round 3: 43 peptides, 7 chains. Longest chain 9 peptides. Score 0.362 Round 4: 49 peptides, 8 chains. Longest chain 11 peptides. Score 0.379 Round 5: 41 peptides, 7 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 4 Chains 8, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.62 % complete ) and 1838 restraints for refining 815 atoms. 1682 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3329 (Rfree = 0.000) for 815 atoms. Found 3 (3 requested) and removed 8 (1 requested) atoms. Cycle 32: After refmac, R = 0.2963 (Rfree = 0.000) for 805 atoms. Found 1 (3 requested) and removed 7 (1 requested) atoms. Cycle 33: After refmac, R = 0.2697 (Rfree = 0.000) for 798 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. Cycle 34: After refmac, R = 0.2630 (Rfree = 0.000) for 793 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. Cycle 35: After refmac, R = 0.2583 (Rfree = 0.000) for 791 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.92 3.42 Search for helices and strands: 0 residues in 0 chains, 829 seeds are put forward Round 1: 43 peptides, 9 chains. Longest chain 6 peptides. Score 0.258 Round 2: 49 peptides, 8 chains. Longest chain 10 peptides. Score 0.379 Round 3: 43 peptides, 7 chains. Longest chain 11 peptides. Score 0.362 Round 4: 49 peptides, 8 chains. Longest chain 10 peptides. Score 0.379 Round 5: 52 peptides, 8 chains. Longest chain 12 peptides. Score 0.411 Taking the results from Round 5 Chains 8, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.62 % complete ) and 1863 restraints for refining 824 atoms. 1695 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2923 (Rfree = 0.000) for 824 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 37: After refmac, R = 0.2653 (Rfree = 0.000) for 819 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 38: After refmac, R = 0.2588 (Rfree = 0.000) for 812 atoms. Found 0 (3 requested) and removed 4 (1 requested) atoms. Cycle 39: After refmac, R = 0.2531 (Rfree = 0.000) for 806 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. Cycle 40: After refmac, R = 0.2531 (Rfree = 0.000) for 803 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.93 3.43 Search for helices and strands: 0 residues in 0 chains, 850 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.244 Round 2: 47 peptides, 8 chains. Longest chain 11 peptides. Score 0.357 Round 3: 43 peptides, 8 chains. Longest chain 7 peptides. Score 0.310 Round 4: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.364 Round 5: 49 peptides, 8 chains. Longest chain 10 peptides. Score 0.379 Taking the results from Round 5 Chains 8, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.62 % complete ) and 1951 restraints for refining 824 atoms. 1795 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3288 (Rfree = 0.000) for 824 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 42: After refmac, R = 0.3138 (Rfree = 0.000) for 819 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. Cycle 43: After refmac, R = 0.2831 (Rfree = 0.000) for 813 atoms. Found 0 (3 requested) and removed 4 (1 requested) atoms. Cycle 44: After refmac, R = 0.2764 (Rfree = 0.000) for 806 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 45: After refmac, R = 0.2749 (Rfree = 0.000) for 804 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.07 3.56 Search for helices and strands: 0 residues in 0 chains, 826 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 9 peptides. Score 0.233 Round 2: 43 peptides, 9 chains. Longest chain 9 peptides. Score 0.258 Round 3: 37 peptides, 7 chains. Longest chain 7 peptides. Score 0.290 Round 4: 33 peptides, 6 chains. Longest chain 7 peptides. Score 0.295 Round 5: 40 peptides, 8 chains. Longest chain 8 peptides. Score 0.274 Taking the results from Round 4 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 2nwv-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1564 reflections ( 99.62 % complete ) and 1977 restraints for refining 824 atoms. 1875 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3166 (Rfree = 0.000) for 824 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.3416 (Rfree = 0.000) for 822 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.2873 (Rfree = 0.000) for 818 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.2905 (Rfree = 0.000) for 816 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:44 GMT 2018 Job finished. TimeTaking 22.97 Used memory is bytes: 2981264