Sun 23 Dec 23:57:31 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pr7-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-parrot-mrncs ############### 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 23:57:35 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-parrot-mrncs/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-mrncs.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-mrncs.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 2427 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3102 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2724 (Rfree = 0.000) for 2427 atoms. Found 13 (13 requested) and removed 35 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.66 Search for helices and strands: 0 residues in 0 chains, 2450 seeds are put forward NCS extension: 0 residues added, 2450 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.258 Round 2: 107 peptides, 19 chains. Longest chain 8 peptides. Score 0.364 Round 3: 110 peptides, 18 chains. Longest chain 11 peptides. Score 0.406 Round 4: 119 peptides, 20 chains. Longest chain 11 peptides. Score 0.407 Round 5: 131 peptides, 20 chains. Longest chain 11 peptides. Score 0.470 Taking the results from Round 5 Chains 20, Residues 111, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4486 restraints for refining 1981 atoms. 3967 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2071 (Rfree = 0.000) for 1981 atoms. Found 5 (10 requested) and removed 13 (5 requested) atoms. Cycle 2: After refmac, R = 0.2087 (Rfree = 0.000) for 1943 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 3: After refmac, R = 0.1973 (Rfree = 0.000) for 1925 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 4: After refmac, R = 0.1977 (Rfree = 0.000) for 1914 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 5: After refmac, R = 0.1810 (Rfree = 0.000) for 1899 atoms. Found 6 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 1975 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 1987 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 8 peptides. Score 0.263 Round 2: 118 peptides, 21 chains. Longest chain 10 peptides. Score 0.378 Round 3: 111 peptides, 16 chains. Longest chain 13 peptides. Score 0.459 Round 4: 108 peptides, 17 chains. Longest chain 10 peptides. Score 0.419 Round 5: 115 peptides, 18 chains. Longest chain 13 peptides. Score 0.433 Taking the results from Round 3 Chains 16, Residues 95, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4552 restraints for refining 1916 atoms. 4175 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1999 (Rfree = 0.000) for 1916 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 7: After refmac, R = 0.1791 (Rfree = 0.000) for 1883 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 8: After refmac, R = 0.1865 (Rfree = 0.000) for 1865 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.1715 (Rfree = 0.000) for 1856 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.1816 (Rfree = 0.000) for 1848 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 1940 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1957 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 7 peptides. Score 0.258 Round 2: 115 peptides, 21 chains. Longest chain 9 peptides. Score 0.361 Round 3: 112 peptides, 21 chains. Longest chain 8 peptides. Score 0.344 Round 4: 111 peptides, 18 chains. Longest chain 10 peptides. Score 0.411 Round 5: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 4 Chains 18, Residues 93, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4332 restraints for refining 1931 atoms. 3916 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1961 (Rfree = 0.000) for 1931 atoms. Found 10 (10 requested) and removed 42 (5 requested) atoms. Cycle 12: After refmac, R = 0.1682 (Rfree = 0.000) for 1885 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 13: After refmac, R = 0.1742 (Rfree = 0.000) for 1862 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 14: After refmac, R = 0.1588 (Rfree = 0.000) for 1849 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 15: After refmac, R = 0.1583 (Rfree = 0.000) for 1840 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.62 Search for helices and strands: 0 residues in 0 chains, 1933 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1942 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 9 peptides. Score 0.260 Round 2: 124 peptides, 23 chains. Longest chain 9 peptides. Score 0.364 Round 3: 123 peptides, 20 chains. Longest chain 12 peptides. Score 0.429 Round 4: 112 peptides, 19 chains. Longest chain 9 peptides. Score 0.393 Round 5: 95 peptides, 18 chains. Longest chain 7 peptides. Score 0.319 Taking the results from Round 3 Chains 20, Residues 103, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4386 restraints for refining 1900 atoms. 3987 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1686 (Rfree = 0.000) for 1900 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.1897 (Rfree = 0.000) for 1894 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.1766 (Rfree = 0.000) for 1890 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.1669 (Rfree = 0.000) for 1880 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 20: After refmac, R = 0.1455 (Rfree = 0.000) for 1873 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.66 Search for helices and strands: 0 residues in 0 chains, 1958 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1972 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.280 Round 2: 121 peptides, 20 chains. Longest chain 12 peptides. Score 0.418 Round 3: 131 peptides, 22 chains. Longest chain 12 peptides. Score 0.425 Round 4: 110 peptides, 17 chains. Longest chain 12 peptides. Score 0.430 Round 5: 119 peptides, 18 chains. Longest chain 12 peptides. Score 0.454 Taking the results from Round 5 Chains 18, Residues 101, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4604 restraints for refining 1980 atoms. 4161 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1884 (Rfree = 0.000) for 1980 atoms. Found 7 (10 requested) and removed 15 (5 requested) atoms. Cycle 22: After refmac, R = 0.1865 (Rfree = 0.000) for 1953 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 23: After refmac, R = 0.1815 (Rfree = 0.000) for 1946 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.1783 (Rfree = 0.000) for 1943 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1672 (Rfree = 0.000) for 1933 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.60 Search for helices and strands: 0 residues in 0 chains, 2001 seeds are put forward NCS extension: 0 residues added, 2001 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.288 Round 2: 114 peptides, 20 chains. Longest chain 11 peptides. Score 0.380 Round 3: 109 peptides, 18 chains. Longest chain 12 peptides. Score 0.400 Round 4: 108 peptides, 15 chains. Longest chain 12 peptides. Score 0.467 Round 5: 113 peptides, 15 chains. Longest chain 16 peptides. Score 0.492 Taking the results from Round 5 Chains 15, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4691 restraints for refining 1981 atoms. 4314 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2301 (Rfree = 0.000) for 1981 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 27: After refmac, R = 0.2039 (Rfree = 0.000) for 1973 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 28: After refmac, R = 0.1865 (Rfree = 0.000) for 1962 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.1555 (Rfree = 0.000) for 1959 atoms. Found 4 (10 requested) and removed 11 (5 requested) atoms. Cycle 30: After refmac, R = 0.1408 (Rfree = 0.000) for 1951 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 2008 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2033 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.241 Round 2: 105 peptides, 18 chains. Longest chain 9 peptides. Score 0.378 Round 3: 111 peptides, 18 chains. Longest chain 12 peptides. Score 0.411 Round 4: 111 peptides, 17 chains. Longest chain 13 peptides. Score 0.435 Round 5: 107 peptides, 19 chains. Longest chain 9 peptides. Score 0.364 Taking the results from Round 4 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4683 restraints for refining 1982 atoms. 4315 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2007 (Rfree = 0.000) for 1982 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 32: After refmac, R = 0.1773 (Rfree = 0.000) for 1970 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.1844 (Rfree = 0.000) for 1966 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.1677 (Rfree = 0.000) for 1963 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 35: After refmac, R = 0.1626 (Rfree = 0.000) for 1960 atoms. Found 6 (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, 2021 seeds are put forward NCS extension: 8 residues added (2 deleted due to clashes), 2029 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 7 peptides. Score 0.235 Round 2: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.319 Round 3: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.303 Round 4: 109 peptides, 18 chains. Longest chain 9 peptides. Score 0.400 Round 5: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.366 Taking the results from Round 4 Chains 18, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4644 restraints for refining 1981 atoms. 4298 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1838 (Rfree = 0.000) for 1981 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.1836 (Rfree = 0.000) for 1972 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 38: After refmac, R = 0.1965 (Rfree = 0.000) for 1966 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 39: After refmac, R = 0.1784 (Rfree = 0.000) for 1962 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.1816 (Rfree = 0.000) for 1960 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.61 Search for helices and strands: 0 residues in 0 chains, 2043 seeds are put forward NCS extension: 0 residues added, 2043 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.252 Round 2: 108 peptides, 23 chains. Longest chain 7 peptides. Score 0.269 Round 3: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.384 Round 4: 103 peptides, 17 chains. Longest chain 11 peptides. Score 0.391 Round 5: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 4 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4667 restraints for refining 1970 atoms. 4340 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1696 (Rfree = 0.000) for 1970 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 42: After refmac, R = 0.1869 (Rfree = 0.000) for 1953 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 43: After refmac, R = 0.1781 (Rfree = 0.000) for 1946 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1708 (Rfree = 0.000) for 1943 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.1191 (Rfree = 0.000) for 1943 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward NCS extension: 0 residues added, 2006 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.235 Round 2: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.273 Round 3: 75 peptides, 13 chains. Longest chain 8 peptides. Score 0.329 Round 4: 76 peptides, 12 chains. Longest chain 15 peptides. Score 0.363 Round 5: 77 peptides, 13 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 64, 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 4603 restraints for refining 1946 atoms. 4359 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1699 (Rfree = 0.000) for 1946 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1951 (Rfree = 0.000) for 1935 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2004 (Rfree = 0.000) for 1929 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1309 (Rfree = 0.000) for 1923 atoms. TimeTaking 24.2