null Sun 23 Dec 22:22:43 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 2hsb-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hsb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hsb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-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/2hsb-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-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 22:22:53 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/2hsb-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-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 97 and 0 Target number of residues in the AU: 97 Target solvent content: 0.6449 Checking the provided sequence file Detected sequence length: 126 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 126 Adjusted target solvent content: 0.54 Input MTZ file: 2hsb-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: 96 Cell parameters: 60.666 60.666 80.341 90.000 90.000 90.000 Input sequence file: 2hsb-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1008 target number of atoms Had to go as low as 0.80 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: 48.414 3.600 Wilson plot Bfac: 73.08 1950 reflections ( 99.74 % complete ) and 0 restraints for refining 1115 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3611 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3684 (Rfree = 0.000) for 1115 atoms. Found 7 (7 requested) and removed 25 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 1137 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 9 peptides. Score 0.246 Round 2: 58 peptides, 8 chains. Longest chain 13 peptides. Score 0.481 Round 3: 59 peptides, 8 chains. Longest chain 13 peptides. Score 0.491 Round 4: 58 peptides, 8 chains. Longest chain 11 peptides. Score 0.481 Round 5: 58 peptides, 8 chains. Longest chain 12 peptides. Score 0.481 Taking the results from Round 3 Chains 8, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1950 reflections ( 99.74 % complete ) and 2065 restraints for refining 912 atoms. 1869 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3228 (Rfree = 0.000) for 912 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 2: After refmac, R = 0.2909 (Rfree = 0.000) for 887 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 3: After refmac, R = 0.2850 (Rfree = 0.000) for 875 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 4: After refmac, R = 0.2791 (Rfree = 0.000) for 867 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.2961 (Rfree = 0.000) for 862 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 934 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.246 Round 2: 60 peptides, 9 chains. Longest chain 10 peptides. Score 0.456 Round 3: 58 peptides, 9 chains. Longest chain 9 peptides. Score 0.436 Round 4: 65 peptides, 8 chains. Longest chain 11 peptides. Score 0.548 Round 5: 64 peptides, 9 chains. Longest chain 10 peptides. Score 0.496 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 ------------------------------------------------------ 1950 reflections ( 99.74 % complete ) and 1748 restraints for refining 816 atoms. 1528 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3211 (Rfree = 0.000) for 816 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 7: After refmac, R = 0.2995 (Rfree = 0.000) for 794 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2917 (Rfree = 0.000) for 794 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.2938 (Rfree = 0.000) for 790 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.3006 (Rfree = 0.000) for 788 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 857 seeds are put forward Round 1: 48 peptides, 8 chains. Longest chain 10 peptides. Score 0.374 Round 2: 60 peptides, 9 chains. Longest chain 13 peptides. Score 0.456 Round 3: 63 peptides, 10 chains. Longest chain 10 peptides. Score 0.442 Round 4: 57 peptides, 8 chains. Longest chain 11 peptides. Score 0.471 Round 5: 67 peptides, 8 chains. Longest chain 12 peptides. Score 0.566 Taking the results from Round 5 Chains 8, Residues 59, Estimated correctness of the model 0.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1950 reflections ( 99.74 % complete ) and 1771 restraints for refining 825 atoms. 1543 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2946 (Rfree = 0.000) for 825 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 12: After refmac, R = 0.2640 (Rfree = 0.000) for 812 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 13: After refmac, R = 0.2403 (Rfree = 0.000) for 807 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.2485 (Rfree = 0.000) for 802 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 15: After refmac, R = 0.2334 (Rfree = 0.000) for 796 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 848 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.352 Round 2: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.417 Round 3: 64 peptides, 9 chains. Longest chain 14 peptides. Score 0.496 Round 4: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.407 Round 5: 67 peptides, 10 chains. Longest chain 13 peptides. Score 0.482 Taking the results from Round 3 Chains 10, Residues 55, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1950 reflections ( 99.74 % complete ) and 1853 restraints for refining 874 atoms. 1602 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2727 (Rfree = 0.000) for 874 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 17: After refmac, R = 0.2580 (Rfree = 0.000) for 857 atoms. Found 3 (5 requested) and removed 29 (2 requested) atoms. Cycle 18: After refmac, R = 0.2595 (Rfree = 0.000) for 830 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 19: After refmac, R = 0.2552 (Rfree = 0.000) for 820 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.2530 (Rfree = 0.000) for 816 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 869 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.293 Round 2: 58 peptides, 9 chains. Longest chain 15 peptides. Score 0.436 Round 3: 60 peptides, 8 chains. Longest chain 16 peptides. Score 0.501 Round 4: 64 peptides, 10 chains. Longest chain 11 peptides. Score 0.452 Round 5: 65 peptides, 9 chains. Longest chain 16 peptides. Score 0.506 Taking the results from Round 5 Chains 9, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1950 reflections ( 99.74 % complete ) and 1935 restraints for refining 868 atoms. 1720 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2858 (Rfree = 0.000) for 868 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 22: After refmac, R = 0.2717 (Rfree = 0.000) for 858 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 23: After refmac, R = 0.2608 (Rfree = 0.000) for 856 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.2303 (Rfree = 0.000) for 854 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 25: After refmac, R = 0.2391 (Rfree = 0.000) for 850 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 891 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.326 Round 2: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.338 Round 3: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.385 Round 4: 57 peptides, 9 chains. Longest chain 11 peptides. Score 0.425 Round 5: 60 peptides, 9 chains. Longest chain 13 peptides. Score 0.456 Taking the results from Round 5 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1950 reflections ( 99.74 % complete ) and 2080 restraints for refining 913 atoms. 1885 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2718 (Rfree = 0.000) for 913 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 27: After refmac, R = 0.2910 (Rfree = 0.000) for 910 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 28: After refmac, R = 0.2760 (Rfree = 0.000) for 900 atoms. Found 5 (5 requested) and removed 22 (2 requested) atoms. Cycle 29: After refmac, R = 0.3005 (Rfree = 0.000) for 875 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2975 (Rfree = 0.000) for 875 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 904 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 7 peptides. Score 0.279 Round 2: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.329 Round 3: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.366 Round 4: 60 peptides, 10 chains. Longest chain 11 peptides. Score 0.410 Round 5: 52 peptides, 9 chains. Longest chain 8 peptides. Score 0.370 Taking the results from Round 4 Chains 10, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1950 reflections ( 99.74 % complete ) and 2036 restraints for refining 890 atoms. 1846 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2775 (Rfree = 0.000) for 890 atoms. Found 5 (5 requested) and removed 16 (2 requested) atoms. Cycle 32: After refmac, R = 0.2754 (Rfree = 0.000) for 873 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 33: After refmac, R = 0.2580 (Rfree = 0.000) for 872 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 34: After refmac, R = 0.2635 (Rfree = 0.000) for 870 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.2594 (Rfree = 0.000) for 868 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 918 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.243 Round 2: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.317 Round 3: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.324 Round 4: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.366 Round 5: 57 peptides, 11 chains. Longest chain 7 peptides. Score 0.329 Taking the results from Round 4 Chains 10, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1950 reflections ( 99.74 % complete ) and 2101 restraints for refining 914 atoms. 1927 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2740 (Rfree = 0.000) for 914 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 37: After refmac, R = 0.2607 (Rfree = 0.000) for 898 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 38: After refmac, R = 0.2461 (Rfree = 0.000) for 891 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 39: After refmac, R = 0.2388 (Rfree = 0.000) for 889 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.2367 (Rfree = 0.000) for 887 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 925 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 6 peptides. Score 0.259 Round 2: 51 peptides, 10 chains. Longest chain 6 peptides. Score 0.308 Round 3: 49 peptides, 9 chains. Longest chain 8 peptides. Score 0.335 Round 4: 49 peptides, 10 chains. Longest chain 6 peptides. Score 0.284 Round 5: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.311 Taking the results from Round 3 Chains 9, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1950 reflections ( 99.74 % complete ) and 2148 restraints for refining 914 atoms. 1997 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2820 (Rfree = 0.000) for 914 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 42: After refmac, R = 0.2965 (Rfree = 0.000) for 907 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 43: After refmac, R = 0.2651 (Rfree = 0.000) for 906 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 44: After refmac, R = 0.2876 (Rfree = 0.000) for 903 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2858 (Rfree = 0.000) for 905 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 922 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 8 peptides. Score 0.259 Round 2: 40 peptides, 7 chains. Longest chain 7 peptides. Score 0.331 Round 3: 46 peptides, 8 chains. Longest chain 8 peptides. Score 0.351 Round 4: 45 peptides, 8 chains. Longest chain 8 peptides. Score 0.339 Round 5: 47 peptides, 7 chains. Longest chain 9 peptides. Score 0.413 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 40, 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 2hsb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1950 reflections ( 99.74 % complete ) and 2139 restraints for refining 914 atoms. 1986 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2731 (Rfree = 0.000) for 914 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3041 (Rfree = 0.000) for 910 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2565 (Rfree = 0.000) for 907 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2522 (Rfree = 0.000) for 901 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:00 GMT 2018 Job finished. TimeTaking 22.29 Used memory is bytes: 3432648