Sun 23 Dec 22:22:40 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 2pr7-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.6-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/2pr7-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.6-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 22:22:49 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/2pr7-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.6-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 193 and 0 Target number of residues in the AU: 193 Target solvent content: 0.6427 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: 2pr7-3.6-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: 1 Cell parameters: 29.149 45.153 60.777 100.722 103.858 103.308 Input sequence file: 2pr7-3.6-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 3.600 Wilson plot Bfac: 72.71 3180 reflections ( 96.95 % complete ) and 0 restraints for refining 2439 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3074 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2757 (Rfree = 0.000) for 2439 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 2480 seeds are put forward NCS extension: 0 residues added, 2480 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 9 peptides. Score 0.260 Round 2: 125 peptides, 22 chains. Longest chain 9 peptides. Score 0.393 Round 3: 124 peptides, 19 chains. Longest chain 13 peptides. Score 0.457 Round 4: 140 peptides, 23 chains. Longest chain 11 peptides. Score 0.450 Round 5: 140 peptides, 21 chains. Longest chain 13 peptides. Score 0.493 Taking the results from Round 5 Chains 21, Residues 119, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4541 restraints for refining 1987 atoms. 4052 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2254 (Rfree = 0.000) for 1987 atoms. Found 9 (12 requested) and removed 13 (6 requested) atoms. Cycle 2: After refmac, R = 0.2295 (Rfree = 0.000) for 1947 atoms. Found 9 (12 requested) and removed 13 (6 requested) atoms. Cycle 3: After refmac, R = 0.1876 (Rfree = 0.000) for 1923 atoms. Found 8 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.1889 (Rfree = 0.000) for 1912 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.1818 (Rfree = 0.000) for 1908 atoms. Found 8 (12 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 1985 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2003 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 8 peptides. Score 0.289 Round 2: 144 peptides, 23 chains. Longest chain 12 peptides. Score 0.470 Round 3: 132 peptides, 21 chains. Longest chain 13 peptides. Score 0.453 Round 4: 125 peptides, 20 chains. Longest chain 12 peptides. Score 0.440 Round 5: 130 peptides, 20 chains. Longest chain 12 peptides. Score 0.465 Taking the results from Round 2 Chains 23, Residues 121, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4180 restraints for refining 1906 atoms. 3690 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1929 (Rfree = 0.000) for 1906 atoms. Found 10 (12 requested) and removed 15 (6 requested) atoms. Cycle 7: After refmac, R = 0.1818 (Rfree = 0.000) for 1887 atoms. Found 10 (12 requested) and removed 15 (6 requested) atoms. Cycle 8: After refmac, R = 0.1760 (Rfree = 0.000) for 1877 atoms. Found 7 (12 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.1594 (Rfree = 0.000) for 1867 atoms. Found 8 (12 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.1610 (Rfree = 0.000) for 1861 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 1963 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 1980 seeds are put forward Round 1: 118 peptides, 23 chains. Longest chain 8 peptides. Score 0.329 Round 2: 127 peptides, 21 chains. Longest chain 12 peptides. Score 0.427 Round 3: 134 peptides, 20 chains. Longest chain 11 peptides. Score 0.485 Round 4: 147 peptides, 21 chains. Longest chain 14 peptides. Score 0.527 Round 5: 146 peptides, 25 chains. Longest chain 10 peptides. Score 0.436 Taking the results from Round 4 Chains 21, Residues 126, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4326 restraints for refining 1938 atoms. 3835 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1822 (Rfree = 0.000) for 1938 atoms. Found 10 (12 requested) and removed 17 (6 requested) atoms. Cycle 12: After refmac, R = 0.1697 (Rfree = 0.000) for 1921 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.1542 (Rfree = 0.000) for 1913 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1505 (Rfree = 0.000) for 1909 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.1432 (Rfree = 0.000) for 1910 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 1993 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2013 seeds are put forward Round 1: 109 peptides, 22 chains. Longest chain 8 peptides. Score 0.301 Round 2: 133 peptides, 24 chains. Longest chain 12 peptides. Score 0.390 Round 3: 152 peptides, 22 chains. Longest chain 12 peptides. Score 0.529 Round 4: 156 peptides, 23 chains. Longest chain 15 peptides. Score 0.527 Round 5: 149 peptides, 21 chains. Longest chain 12 peptides. Score 0.536 Taking the results from Round 5 Chains 21, Residues 128, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4443 restraints for refining 1986 atoms. 3945 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2214 (Rfree = 0.000) for 1986 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 17: After refmac, R = 0.2016 (Rfree = 0.000) for 1971 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. Cycle 18: After refmac, R = 0.2001 (Rfree = 0.000) for 1962 atoms. Found 9 (12 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.2004 (Rfree = 0.000) for 1956 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1741 (Rfree = 0.000) for 1952 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 2026 seeds are put forward NCS extension: 0 residues added, 2026 seeds are put forward Round 1: 126 peptides, 23 chains. Longest chain 12 peptides. Score 0.375 Round 2: 135 peptides, 21 chains. Longest chain 11 peptides. Score 0.469 Round 3: 130 peptides, 17 chains. Longest chain 13 peptides. Score 0.531 Round 4: 145 peptides, 21 chains. Longest chain 12 peptides. Score 0.517 Round 5: 129 peptides, 19 chains. Longest chain 13 peptides. Score 0.483 Taking the results from Round 3 Chains 17, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4545 restraints for refining 1987 atoms. 4110 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1859 (Rfree = 0.000) for 1987 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.1714 (Rfree = 0.000) for 1976 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.1664 (Rfree = 0.000) for 1973 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.1769 (Rfree = 0.000) for 1960 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.1671 (Rfree = 0.000) for 1954 atoms. Found 9 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.38 Search for helices and strands: 0 residues in 0 chains, 2010 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 2025 seeds are put forward Round 1: 110 peptides, 21 chains. Longest chain 9 peptides. Score 0.332 Round 2: 129 peptides, 21 chains. Longest chain 10 peptides. Score 0.438 Round 3: 117 peptides, 16 chains. Longest chain 15 peptides. Score 0.490 Round 4: 127 peptides, 17 chains. Longest chain 21 peptides. Score 0.516 Round 5: 106 peptides, 18 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 4 Chains 18, Residues 110, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4261 restraints for refining 1987 atoms. 3764 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1932 (Rfree = 0.000) for 1987 atoms. Found 9 (12 requested) and removed 17 (6 requested) atoms. Cycle 27: After refmac, R = 0.1794 (Rfree = 0.000) for 1970 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.1601 (Rfree = 0.000) for 1966 atoms. Found 9 (12 requested) and removed 10 (6 requested) atoms. Cycle 29: After refmac, R = 0.1808 (Rfree = 0.000) for 1963 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.1509 (Rfree = 0.000) for 1963 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 2015 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2034 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.323 Round 2: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.413 Round 3: 126 peptides, 23 chains. Longest chain 12 peptides. Score 0.375 Round 4: 120 peptides, 19 chains. Longest chain 12 peptides. Score 0.436 Round 5: 118 peptides, 20 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 4 Chains 19, Residues 101, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4535 restraints for refining 1985 atoms. 4122 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1867 (Rfree = 0.000) for 1985 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 32: After refmac, R = 0.1860 (Rfree = 0.000) for 1983 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.1620 (Rfree = 0.000) for 1981 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 34: After refmac, R = 0.1814 (Rfree = 0.000) for 1980 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.1597 (Rfree = 0.000) for 1979 atoms. Found 8 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 2033 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2044 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 9 peptides. Score 0.281 Round 2: 125 peptides, 21 chains. Longest chain 10 peptides. Score 0.416 Round 3: 129 peptides, 20 chains. Longest chain 15 peptides. Score 0.460 Round 4: 117 peptides, 18 chains. Longest chain 14 peptides. Score 0.444 Round 5: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.409 Taking the results from Round 3 Chains 20, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4541 restraints for refining 1987 atoms. 4125 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1724 (Rfree = 0.000) for 1987 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.1583 (Rfree = 0.000) for 1981 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.1571 (Rfree = 0.000) for 1974 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.1540 (Rfree = 0.000) for 1971 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1477 (Rfree = 0.000) for 1969 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2053 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 9 peptides. Score 0.299 Round 2: 121 peptides, 21 chains. Longest chain 11 peptides. Score 0.395 Round 3: 126 peptides, 22 chains. Longest chain 11 peptides. Score 0.399 Round 4: 120 peptides, 19 chains. Longest chain 11 peptides. Score 0.436 Round 5: 121 peptides, 21 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 4 Chains 19, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4580 restraints for refining 1987 atoms. 4195 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2149 (Rfree = 0.000) for 1987 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.1760 (Rfree = 0.000) for 1988 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.1859 (Rfree = 0.000) for 1988 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1245 (Rfree = 0.000) for 1990 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1683 (Rfree = 0.000) for 1986 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 2041 seeds are put forward NCS extension: 0 residues added, 2041 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 8 peptides. Score 0.250 Round 2: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.331 Round 3: 90 peptides, 17 chains. Longest chain 10 peptides. Score 0.314 Round 4: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.339 Round 5: 84 peptides, 18 chains. Longest chain 7 peptides. Score 0.249 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 67, 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. 3180 reflections ( 96.95 % complete ) and 4784 restraints for refining 1987 atoms. 4530 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1898 (Rfree = 0.000) for 1987 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1803 (Rfree = 0.000) for 1978 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1946 (Rfree = 0.000) for 1970 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1736 (Rfree = 0.000) for 1962 atoms. TimeTaking 32.53