Sun 23 Dec 22:22:49 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 2huj-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2huj-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2huj-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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/2huj-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 22:22:59 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/2huj-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 122 and 0 Target number of residues in the AU: 122 Target solvent content: 0.6572 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.61 Input MTZ file: 2huj-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: 182 Cell parameters: 100.110 100.110 66.570 90.000 90.000 120.000 Input sequence file: 2huj-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 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: 86.698 4.000 Wilson plot Bfac: 81.76 1864 reflections ( 99.52 % complete ) and 0 restraints for refining 1243 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3636 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3925 (Rfree = 0.000) for 1243 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.30 Search for helices and strands: 0 residues in 0 chains, 1284 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 12 peptides. Score 0.323 Round 2: 58 peptides, 8 chains. Longest chain 13 peptides. Score 0.430 Round 3: 60 peptides, 8 chains. Longest chain 13 peptides. Score 0.446 Round 4: 61 peptides, 6 chains. Longest chain 21 peptides. Score 0.529 Round 5: 64 peptides, 7 chains. Longest chain 14 peptides. Score 0.515 Taking the results from Round 4 Chains 6, Residues 55, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 1864 reflections ( 99.52 % complete ) and 2224 restraints for refining 1010 atoms. 1926 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2746 (Rfree = 0.000) for 1010 atoms. Found 4 (4 requested) and removed 25 (2 requested) atoms. Cycle 2: After refmac, R = 0.2837 (Rfree = 0.000) for 951 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 3: After refmac, R = 0.2861 (Rfree = 0.000) for 926 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.3116 (Rfree = 0.000) for 892 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.2840 (Rfree = 0.000) for 870 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.18 Search for helices and strands: 0 residues in 0 chains, 935 seeds are put forward Round 1: 56 peptides, 8 chains. Longest chain 14 peptides. Score 0.413 Round 2: 61 peptides, 6 chains. Longest chain 22 peptides. Score 0.529 Round 3: 67 peptides, 7 chains. Longest chain 18 peptides. Score 0.537 Round 4: 65 peptides, 8 chains. Longest chain 21 peptides. Score 0.487 Round 5: 63 peptides, 7 chains. Longest chain 14 peptides. Score 0.507 Taking the results from Round 3 Chains 7, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1864 reflections ( 99.52 % complete ) and 1803 restraints for refining 858 atoms. 1570 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2513 (Rfree = 0.000) for 858 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 7: After refmac, R = 0.2543 (Rfree = 0.000) for 846 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2543 (Rfree = 0.000) for 843 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.2507 (Rfree = 0.000) for 832 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2579 (Rfree = 0.000) for 819 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.20 Search for helices and strands: 0 residues in 0 chains, 894 seeds are put forward Round 1: 51 peptides, 9 chains. Longest chain 8 peptides. Score 0.326 Round 2: 61 peptides, 9 chains. Longest chain 12 peptides. Score 0.416 Round 3: 59 peptides, 5 chains. Longest chain 18 peptides. Score 0.550 Round 4: 55 peptides, 7 chains. Longest chain 12 peptides. Score 0.444 Round 5: 62 peptides, 6 chains. Longest chain 19 peptides. Score 0.536 Taking the results from Round 3 Chains 5, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1864 reflections ( 99.52 % complete ) and 1850 restraints for refining 886 atoms. 1639 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2987 (Rfree = 0.000) for 886 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 12: After refmac, R = 0.2631 (Rfree = 0.000) for 862 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.2542 (Rfree = 0.000) for 858 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2761 (Rfree = 0.000) for 854 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 15: After refmac, R = 0.2467 (Rfree = 0.000) for 848 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.18 Search for helices and strands: 0 residues in 0 chains, 899 seeds are put forward Round 1: 59 peptides, 9 chains. Longest chain 14 peptides. Score 0.399 Round 2: 57 peptides, 7 chains. Longest chain 13 peptides. Score 0.460 Round 3: 62 peptides, 8 chains. Longest chain 14 peptides. Score 0.463 Round 4: 64 peptides, 7 chains. Longest chain 18 peptides. Score 0.515 Round 5: 67 peptides, 7 chains. Longest chain 15 peptides. Score 0.537 Taking the results from Round 5 Chains 7, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1864 reflections ( 99.52 % complete ) and 1897 restraints for refining 891 atoms. 1664 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2862 (Rfree = 0.000) for 891 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 17: After refmac, R = 0.2653 (Rfree = 0.000) for 887 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 18: After refmac, R = 0.2593 (Rfree = 0.000) for 878 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 19: After refmac, R = 0.2491 (Rfree = 0.000) for 874 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.2481 (Rfree = 0.000) for 870 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.21 Search for helices and strands: 0 residues in 0 chains, 924 seeds are put forward Round 1: 54 peptides, 7 chains. Longest chain 12 peptides. Score 0.435 Round 2: 54 peptides, 9 chains. Longest chain 10 peptides. Score 0.354 Round 3: 55 peptides, 9 chains. Longest chain 10 peptides. Score 0.364 Round 4: 61 peptides, 8 chains. Longest chain 12 peptides. Score 0.455 Round 5: 52 peptides, 7 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 4 Chains 8, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1864 reflections ( 99.52 % complete ) and 2001 restraints for refining 913 atoms. 1797 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2992 (Rfree = 0.000) for 913 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 22: After refmac, R = 0.2995 (Rfree = 0.000) for 904 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.2917 (Rfree = 0.000) for 901 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.2926 (Rfree = 0.000) for 889 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 25: After refmac, R = 0.2968 (Rfree = 0.000) for 885 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.18 Search for helices and strands: 0 residues in 0 chains, 953 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.272 Round 2: 61 peptides, 9 chains. Longest chain 11 peptides. Score 0.416 Round 3: 55 peptides, 6 chains. Longest chain 14 peptides. Score 0.483 Round 4: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.364 Round 5: 62 peptides, 7 chains. Longest chain 20 peptides. Score 0.500 Taking the results from Round 5 Chains 7, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1864 reflections ( 99.52 % complete ) and 2127 restraints for refining 948 atoms. 1914 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3223 (Rfree = 0.000) for 948 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 27: After refmac, R = 0.3162 (Rfree = 0.000) for 935 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 28: After refmac, R = 0.2716 (Rfree = 0.000) for 919 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 29: After refmac, R = 0.3058 (Rfree = 0.000) for 910 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2704 (Rfree = 0.000) for 902 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 950 seeds are put forward Round 1: 45 peptides, 9 chains. Longest chain 8 peptides. Score 0.267 Round 2: 56 peptides, 12 chains. Longest chain 6 peptides. Score 0.250 Round 3: 60 peptides, 10 chains. Longest chain 12 peptides. Score 0.369 Round 4: 53 peptides, 7 chains. Longest chain 12 peptides. Score 0.427 Round 5: 49 peptides, 6 chains. Longest chain 14 peptides. Score 0.433 Taking the results from Round 5 Chains 6, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1864 reflections ( 99.52 % complete ) and 2129 restraints for refining 927 atoms. 1963 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2976 (Rfree = 0.000) for 927 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 32: After refmac, R = 0.2579 (Rfree = 0.000) for 914 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 33: After refmac, R = 0.2591 (Rfree = 0.000) for 902 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.2650 (Rfree = 0.000) for 897 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.2529 (Rfree = 0.000) for 893 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 3.25 Search for helices and strands: 0 residues in 0 chains, 938 seeds are put forward Round 1: 43 peptides, 9 chains. Longest chain 6 peptides. Score 0.246 Round 2: 59 peptides, 11 chains. Longest chain 7 peptides. Score 0.320 Round 3: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.291 Round 4: 48 peptides, 8 chains. Longest chain 12 peptides. Score 0.340 Round 5: 51 peptides, 7 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 5 Chains 7, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1864 reflections ( 99.52 % complete ) and 2071 restraints for refining 915 atoms. 1902 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2638 (Rfree = 0.000) for 915 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 37: After refmac, R = 0.2411 (Rfree = 0.000) for 907 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 38: After refmac, R = 0.2377 (Rfree = 0.000) for 901 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 39: After refmac, R = 0.2395 (Rfree = 0.000) for 894 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2288 (Rfree = 0.000) for 892 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.16 Search for helices and strands: 0 residues in 0 chains, 953 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 6 peptides. Score 0.189 Round 2: 52 peptides, 8 chains. Longest chain 15 peptides. Score 0.377 Round 3: 54 peptides, 9 chains. Longest chain 8 peptides. Score 0.354 Round 4: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.320 Round 5: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.323 Taking the results from Round 2 Chains 8, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1864 reflections ( 99.52 % complete ) and 2066 restraints for refining 909 atoms. 1898 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2619 (Rfree = 0.000) for 909 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 42: After refmac, R = 0.2503 (Rfree = 0.000) for 902 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.2362 (Rfree = 0.000) for 900 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 44: After refmac, R = 0.2246 (Rfree = 0.000) for 893 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.2219 (Rfree = 0.000) for 885 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.09 Search for helices and strands: 0 residues in 0 chains, 929 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.213 Round 2: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.256 Round 3: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.306 Round 4: 44 peptides, 8 chains. Longest chain 7 peptides. Score 0.301 Round 5: 47 peptides, 8 chains. Longest chain 8 peptides. Score 0.331 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 39, 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 2huj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1864 reflections ( 99.52 % complete ) and 1976 restraints for refining 879 atoms. 1828 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2639 (Rfree = 0.000) for 879 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2780 (Rfree = 0.000) for 874 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2761 (Rfree = 0.000) for 867 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2535 (Rfree = 0.000) for 862 atoms. TimeTaking 26.68