Sun 23 Dec 22:22:44 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 2ia7-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-4.0-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/2ia7-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-4.0-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 22:22:52 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/2ia7-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-4.0-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 74 and 0 Target number of residues in the AU: 74 Target solvent content: 0.6449 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 134 Adjusted target solvent content: 0.36 Input MTZ file: 2ia7-4.0-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: 19 Cell parameters: 40.240 43.350 64.660 90.000 90.000 90.000 Input sequence file: 2ia7-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1072 target number of atoms Had to go as low as 0.60 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: 26.833 4.001 Wilson plot Bfac: 72.83 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1044 reflections ( 96.58 % complete ) and 0 restraints for refining 1184 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3624 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3230 (Rfree = 0.000) for 1184 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 4.46 Search for helices and strands: 0 residues in 0 chains, 1191 seeds are put forward Round 1: 16 peptides, 4 chains. Longest chain 4 peptides. Score 0.167 Round 2: 19 peptides, 3 chains. Longest chain 8 peptides. Score 0.316 Round 3: 21 peptides, 4 chains. Longest chain 7 peptides. Score 0.270 Round 4: 29 peptides, 6 chains. Longest chain 7 peptides. Score 0.259 Round 5: 26 peptides, 5 chains. Longest chain 7 peptides. Score 0.281 Taking the results from Round 2 Chains 3, Residues 16, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1044 reflections ( 96.58 % complete ) and 2609 restraints for refining 968 atoms. 2548 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2423 (Rfree = 0.000) for 968 atoms. Found 1 (4 requested) and removed 8 (2 requested) atoms. Cycle 2: After refmac, R = 0.2570 (Rfree = 0.000) for 958 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 3: After refmac, R = 0.2579 (Rfree = 0.000) for 952 atoms. Found 3 (4 requested) and removed 10 (2 requested) atoms. Cycle 4: After refmac, R = 0.2089 (Rfree = 0.000) for 935 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.2194 (Rfree = 0.000) for 927 atoms. Found 1 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 4.42 Search for helices and strands: 0 residues in 0 chains, 932 seeds are put forward Round 1: 21 peptides, 5 chains. Longest chain 5 peptides. Score 0.187 Round 2: 26 peptides, 6 chains. Longest chain 5 peptides. Score 0.205 Round 3: 40 peptides, 9 chains. Longest chain 5 peptides. Score 0.234 Round 4: 45 peptides, 9 chains. Longest chain 7 peptides. Score 0.313 Round 5: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.288 Taking the results from Round 4 Chains 9, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1044 reflections ( 96.58 % complete ) and 1757 restraints for refining 741 atoms. 1622 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2315 (Rfree = 0.000) for 741 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 7: After refmac, R = 0.2184 (Rfree = 0.000) for 732 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. Cycle 8: After refmac, R = 0.2030 (Rfree = 0.000) for 729 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 9: After refmac, R = 0.1901 (Rfree = 0.000) for 725 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 10: After refmac, R = 0.1937 (Rfree = 0.000) for 722 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 4.48 Search for helices and strands: 0 residues in 0 chains, 764 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 5 peptides. Score 0.221 Round 2: 43 peptides, 7 chains. Longest chain 8 peptides. Score 0.410 Round 3: 34 peptides, 6 chains. Longest chain 8 peptides. Score 0.341 Round 4: 46 peptides, 8 chains. Longest chain 7 peptides. Score 0.391 Round 5: 44 peptides, 8 chains. Longest chain 7 peptides. Score 0.362 Taking the results from Round 2 Chains 7, Residues 36, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1044 reflections ( 96.58 % complete ) and 1573 restraints for refining 715 atoms. 1416 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2218 (Rfree = 0.000) for 715 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 12: After refmac, R = 0.2072 (Rfree = 0.000) for 710 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. Cycle 13: After refmac, R = 0.2059 (Rfree = 0.000) for 703 atoms. Found 0 (3 requested) and removed 4 (1 requested) atoms. Cycle 14: After refmac, R = 0.1913 (Rfree = 0.000) for 698 atoms. Found 0 (3 requested) and removed 10 (1 requested) atoms. Cycle 15: After refmac, R = 0.1907 (Rfree = 0.000) for 688 atoms. Found 0 (3 requested) and removed 5 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 4.47 Search for helices and strands: 0 residues in 0 chains, 711 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 6 peptides. Score 0.221 Round 2: 35 peptides, 8 chains. Longest chain 6 peptides. Score 0.219 Round 3: 38 peptides, 7 chains. Longest chain 8 peptides. Score 0.336 Round 4: 33 peptides, 7 chains. Longest chain 6 peptides. Score 0.255 Round 5: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.285 Taking the results from Round 3 Chains 7, Residues 31, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1044 reflections ( 96.58 % complete ) and 1766 restraints for refining 737 atoms. 1649 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2093 (Rfree = 0.000) for 737 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 17: After refmac, R = 0.1922 (Rfree = 0.000) for 729 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 18: After refmac, R = 0.1867 (Rfree = 0.000) for 723 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. Cycle 19: After refmac, R = 0.1794 (Rfree = 0.000) for 720 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 20: After refmac, R = 0.1745 (Rfree = 0.000) for 717 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 4.43 Search for helices and strands: 0 residues in 0 chains, 755 seeds are put forward Round 1: 45 peptides, 9 chains. Longest chain 7 peptides. Score 0.313 Round 2: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.263 Round 3: 43 peptides, 8 chains. Longest chain 10 peptides. Score 0.347 Round 4: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.328 Round 5: 46 peptides, 8 chains. Longest chain 9 peptides. Score 0.391 Taking the results from Round 5 Chains 8, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1044 reflections ( 96.58 % complete ) and 1842 restraints for refining 783 atoms. 1698 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2119 (Rfree = 0.000) for 783 atoms. Found 2 (3 requested) and removed 6 (1 requested) atoms. Cycle 22: After refmac, R = 0.2030 (Rfree = 0.000) for 773 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 23: After refmac, R = 0.1828 (Rfree = 0.000) for 770 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. Cycle 24: After refmac, R = 0.2271 (Rfree = 0.000) for 768 atoms. Found 0 (3 requested) and removed 4 (1 requested) atoms. Cycle 25: After refmac, R = 0.1775 (Rfree = 0.000) for 764 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 4.45 Search for helices and strands: 0 residues in 0 chains, 787 seeds are put forward Round 1: 36 peptides, 9 chains. Longest chain 4 peptides. Score 0.167 Round 2: 39 peptides, 8 chains. Longest chain 6 peptides. Score 0.285 Round 3: 42 peptides, 8 chains. Longest chain 7 peptides. Score 0.332 Round 4: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.316 Round 5: 39 peptides, 7 chains. Longest chain 8 peptides. Score 0.351 Taking the results from Round 5 Chains 7, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1044 reflections ( 96.58 % complete ) and 1986 restraints for refining 796 atoms. 1865 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2330 (Rfree = 0.000) for 796 atoms. Found 2 (3 requested) and removed 4 (1 requested) atoms. Cycle 27: After refmac, R = 0.2120 (Rfree = 0.000) for 791 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 28: After refmac, R = 0.2625 (Rfree = 0.000) for 788 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 29: After refmac, R = 0.1858 (Rfree = 0.000) for 787 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 30: After refmac, R = 0.1789 (Rfree = 0.000) for 784 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 4.42 Search for helices and strands: 0 residues in 0 chains, 809 seeds are put forward Round 1: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.269 Round 2: 42 peptides, 8 chains. Longest chain 10 peptides. Score 0.332 Round 3: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.249 Round 4: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.264 Round 5: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.298 Taking the results from Round 2 Chains 8, Residues 34, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1044 reflections ( 96.58 % complete ) and 1788 restraints for refining 766 atoms. 1660 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2016 (Rfree = 0.000) for 766 atoms. Found 1 (3 requested) and removed 5 (1 requested) atoms. Cycle 32: After refmac, R = 0.2147 (Rfree = 0.000) for 760 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. Cycle 33: After refmac, R = 0.2393 (Rfree = 0.000) for 760 atoms. Found 2 (3 requested) and removed 5 (1 requested) atoms. Cycle 34: After refmac, R = 0.2420 (Rfree = 0.000) for 757 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. Cycle 35: After refmac, R = 0.2542 (Rfree = 0.000) for 756 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 4.53 Search for helices and strands: 0 residues in 0 chains, 784 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.236 Round 2: 44 peptides, 8 chains. Longest chain 10 peptides. Score 0.362 Round 3: 39 peptides, 8 chains. Longest chain 8 peptides. Score 0.285 Round 4: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.362 Round 5: 43 peptides, 9 chains. Longest chain 7 peptides. Score 0.282 Taking the results from Round 4 Chains 8, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1044 reflections ( 96.58 % complete ) and 1865 restraints for refining 792 atoms. 1729 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2178 (Rfree = 0.000) for 792 atoms. Found 0 (3 requested) and removed 7 (1 requested) atoms. Cycle 37: After refmac, R = 0.2020 (Rfree = 0.000) for 785 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. Cycle 38: After refmac, R = 0.2633 (Rfree = 0.000) for 784 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 39: After refmac, R = 0.1858 (Rfree = 0.000) for 776 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 40: After refmac, R = 0.2680 (Rfree = 0.000) for 777 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 4.47 Search for helices and strands: 0 residues in 0 chains, 813 seeds are put forward Round 1: 25 peptides, 6 chains. Longest chain 5 peptides. Score 0.186 Round 2: 35 peptides, 7 chains. Longest chain 8 peptides. Score 0.288 Round 3: 36 peptides, 7 chains. Longest chain 6 peptides. Score 0.304 Round 4: 39 peptides, 6 chains. Longest chain 11 peptides. Score 0.416 Round 5: 34 peptides, 7 chains. Longest chain 6 peptides. Score 0.272 Taking the results from Round 4 Chains 6, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1044 reflections ( 96.58 % complete ) and 1863 restraints for refining 798 atoms. 1737 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2033 (Rfree = 0.000) for 798 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. Cycle 42: After refmac, R = 0.1916 (Rfree = 0.000) for 793 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. Cycle 43: After refmac, R = 0.1782 (Rfree = 0.000) for 793 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. Cycle 44: After refmac, R = 0.1718 (Rfree = 0.000) for 793 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 45: After refmac, R = 0.2384 (Rfree = 0.000) for 792 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 4.29 Search for helices and strands: 0 residues in 0 chains, 824 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 6 peptides. Score 0.221 Round 2: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.288 Round 3: 31 peptides, 7 chains. Longest chain 6 peptides. Score 0.221 Round 4: 32 peptides, 7 chains. Longest chain 6 peptides. Score 0.238 Round 5: 33 peptides, 7 chains. Longest chain 6 peptides. Score 0.255 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 28, 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 2ia7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1044 reflections ( 96.58 % complete ) and 1872 restraints for refining 790 atoms. 1767 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1891 (Rfree = 0.000) for 790 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.1825 (Rfree = 0.000) for 788 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.2059 (Rfree = 0.000) for 786 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.1962 (Rfree = 0.000) for 783 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Writing output files ... TimeTaking 20.83