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 2pr7-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-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/2pr7-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-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 22:22:52 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/2pr7-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-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 188 and 0 Target number of residues in the AU: 188 Target solvent content: 0.6519 Checking the provided sequence file Detected sequence length: 137 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 274 Adjusted target solvent content: 0.49 Input MTZ file: 2pr7-3.8-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: 1 Cell parameters: 29.149 45.153 60.777 100.722 103.858 103.308 Input sequence file: 2pr7-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2192 target number of atoms Had to go as low as 0.65 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 57.053 3.801 Wilson plot Bfac: 79.01 2688 reflections ( 96.76 % complete ) and 0 restraints for refining 2413 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3160 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2783 (Rfree = 0.000) for 2413 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 2456 seeds are put forward NCS extension: 0 residues added, 2456 seeds are put forward Round 1: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.312 Round 2: 114 peptides, 20 chains. Longest chain 9 peptides. Score 0.380 Round 3: 110 peptides, 17 chains. Longest chain 11 peptides. Score 0.430 Round 4: 113 peptides, 18 chains. Longest chain 11 peptides. Score 0.422 Round 5: 110 peptides, 18 chains. Longest chain 11 peptides. Score 0.406 Taking the results from Round 3 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4583 restraints for refining 1981 atoms. 4172 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2424 (Rfree = 0.000) for 1981 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. Cycle 2: After refmac, R = 0.2211 (Rfree = 0.000) for 1933 atoms. Found 6 (10 requested) and removed 13 (5 requested) atoms. Cycle 3: After refmac, R = 0.2147 (Rfree = 0.000) for 1899 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 4: After refmac, R = 0.1970 (Rfree = 0.000) for 1888 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2201 (Rfree = 0.000) for 1876 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.62 Search for helices and strands: 0 residues in 0 chains, 1971 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1985 seeds are put forward Round 1: 102 peptides, 20 chains. Longest chain 10 peptides. Score 0.310 Round 2: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.391 Round 3: 120 peptides, 18 chains. Longest chain 11 peptides. Score 0.459 Round 4: 104 peptides, 16 chains. Longest chain 13 peptides. Score 0.421 Round 5: 118 peptides, 19 chains. Longest chain 12 peptides. Score 0.426 Taking the results from Round 3 Chains 19, Residues 102, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 3839 restraints for refining 1784 atoms. 3409 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2024 (Rfree = 0.000) for 1784 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 7: After refmac, R = 0.2021 (Rfree = 0.000) for 1765 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 8: After refmac, R = 0.1918 (Rfree = 0.000) for 1747 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 9: After refmac, R = 0.1854 (Rfree = 0.000) for 1739 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.1792 (Rfree = 0.000) for 1730 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward NCS extension: 0 residues added, 1826 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 7 peptides. Score 0.258 Round 2: 111 peptides, 19 chains. Longest chain 10 peptides. Score 0.387 Round 3: 121 peptides, 18 chains. Longest chain 11 peptides. Score 0.464 Round 4: 128 peptides, 19 chains. Longest chain 13 peptides. Score 0.478 Round 5: 123 peptides, 19 chains. Longest chain 13 peptides. Score 0.452 Taking the results from Round 4 Chains 19, Residues 109, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 3986 restraints for refining 1809 atoms. 3533 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1811 (Rfree = 0.000) for 1809 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 12: After refmac, R = 0.1893 (Rfree = 0.000) for 1797 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.1697 (Rfree = 0.000) for 1787 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.1677 (Rfree = 0.000) for 1780 atoms. Found 7 (9 requested) and removed 12 (4 requested) atoms. Cycle 15: After refmac, R = 0.1586 (Rfree = 0.000) for 1774 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.60 Search for helices and strands: 0 residues in 0 chains, 1879 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1895 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 7 peptides. Score 0.283 Round 2: 141 peptides, 26 chains. Longest chain 13 peptides. Score 0.387 Round 3: 135 peptides, 18 chains. Longest chain 16 peptides. Score 0.533 Round 4: 110 peptides, 16 chains. Longest chain 12 peptides. Score 0.454 Round 5: 120 peptides, 16 chains. Longest chain 14 peptides. Score 0.504 Taking the results from Round 3 Chains 19, Residues 117, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4177 restraints for refining 1922 atoms. 3710 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1963 (Rfree = 0.000) for 1922 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.2009 (Rfree = 0.000) for 1898 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.1843 (Rfree = 0.000) for 1889 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.1947 (Rfree = 0.000) for 1877 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 20: After refmac, R = 0.1764 (Rfree = 0.000) for 1871 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 1966 seeds are put forward NCS extension: 0 residues added, 1966 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.302 Round 2: 103 peptides, 16 chains. Longest chain 14 peptides. Score 0.416 Round 3: 111 peptides, 16 chains. Longest chain 10 peptides. Score 0.459 Round 4: 123 peptides, 17 chains. Longest chain 16 peptides. Score 0.497 Round 5: 128 peptides, 17 chains. Longest chain 16 peptides. Score 0.521 Taking the results from Round 5 Chains 17, Residues 111, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4226 restraints for refining 1917 atoms. 3778 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2431 (Rfree = 0.000) for 1917 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 22: After refmac, R = 0.2122 (Rfree = 0.000) for 1896 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.1909 (Rfree = 0.000) for 1893 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.1920 (Rfree = 0.000) for 1890 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 25: After refmac, R = 0.1729 (Rfree = 0.000) for 1890 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 1956 seeds are put forward NCS extension: 0 residues added, 1956 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.302 Round 2: 104 peptides, 16 chains. Longest chain 12 peptides. Score 0.421 Round 3: 114 peptides, 17 chains. Longest chain 12 peptides. Score 0.451 Round 4: 102 peptides, 14 chains. Longest chain 12 peptides. Score 0.459 Round 5: 98 peptides, 15 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 4 Chains 14, Residues 88, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4558 restraints for refining 1960 atoms. 4204 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2087 (Rfree = 0.000) for 1960 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 27: After refmac, R = 0.2004 (Rfree = 0.000) for 1934 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 28: After refmac, R = 0.1971 (Rfree = 0.000) for 1925 atoms. Found 9 (10 requested) and removed 19 (5 requested) atoms. Cycle 29: After refmac, R = 0.2016 (Rfree = 0.000) for 1906 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 30: After refmac, R = 0.1931 (Rfree = 0.000) for 1900 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 1965 seeds are put forward NCS extension: 0 residues added, 1965 seeds are put forward Round 1: 86 peptides, 15 chains. Longest chain 12 peptides. Score 0.343 Round 2: 93 peptides, 15 chains. Longest chain 13 peptides. Score 0.384 Round 3: 100 peptides, 15 chains. Longest chain 10 peptides. Score 0.424 Round 4: 101 peptides, 14 chains. Longest chain 15 peptides. Score 0.454 Round 5: 100 peptides, 15 chains. Longest chain 13 peptides. Score 0.424 Taking the results from Round 4 Chains 15, Residues 87, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4356 restraints for refining 1964 atoms. 3935 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2184 (Rfree = 0.000) for 1964 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 32: After refmac, R = 0.1917 (Rfree = 0.000) for 1941 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 33: After refmac, R = 0.1695 (Rfree = 0.000) for 1922 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.1844 (Rfree = 0.000) for 1916 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.1376 (Rfree = 0.000) for 1915 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 1965 seeds are put forward NCS extension: 0 residues added, 1965 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 9 peptides. Score 0.278 Round 2: 97 peptides, 16 chains. Longest chain 10 peptides. Score 0.382 Round 3: 99 peptides, 16 chains. Longest chain 9 peptides. Score 0.393 Round 4: 96 peptides, 16 chains. Longest chain 13 peptides. Score 0.376 Round 5: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.351 Taking the results from Round 3 Chains 16, Residues 83, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4370 restraints for refining 1942 atoms. 3996 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1707 (Rfree = 0.000) for 1942 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 37: After refmac, R = 0.1781 (Rfree = 0.000) for 1935 atoms. Found 9 (10 requested) and removed 11 (5 requested) atoms. Cycle 38: After refmac, R = 0.1767 (Rfree = 0.000) for 1930 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 39: After refmac, R = 0.1697 (Rfree = 0.000) for 1922 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.1917 (Rfree = 0.000) for 1918 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 1981 seeds are put forward NCS extension: 0 residues added, 1981 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.300 Round 2: 110 peptides, 21 chains. Longest chain 9 peptides. Score 0.332 Round 3: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.349 Round 4: 116 peptides, 20 chains. Longest chain 14 peptides. Score 0.391 Round 5: 108 peptides, 18 chains. Longest chain 10 peptides. Score 0.395 Taking the results from Round 5 Chains 18, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4650 restraints for refining 1981 atoms. 4308 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1889 (Rfree = 0.000) for 1981 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 42: After refmac, R = 0.2011 (Rfree = 0.000) for 1976 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 43: After refmac, R = 0.1417 (Rfree = 0.000) for 1966 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1235 (Rfree = 0.000) for 1961 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1321 (Rfree = 0.000) for 1955 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 2010 seeds are put forward NCS extension: 0 residues added, 2010 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 10 peptides. Score 0.257 Round 2: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.305 Round 3: 83 peptides, 18 chains. Longest chain 6 peptides. Score 0.243 Round 4: 87 peptides, 16 chains. Longest chain 11 peptides. Score 0.322 Round 5: 86 peptides, 16 chains. Longest chain 8 peptides. Score 0.316 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 71, 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 2pr7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2688 reflections ( 96.76 % complete ) and 4760 restraints for refining 1982 atoms. 4492 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1747 (Rfree = 0.000) for 1982 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1804 (Rfree = 0.000) for 1972 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1756 (Rfree = 0.000) for 1958 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1640 (Rfree = 0.000) for 1947 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:27 GMT 2018 Job finished. TimeTaking 31.75 Used memory is bytes: 6793640