Sun 23 Dec 23:55:36 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 2pr7-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.6-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/2pr7-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.6-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 23:56:00 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/2pr7-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.6-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 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-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: 2pr7-3.6-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 3.600 Wilson plot Bfac: 72.71 3180 reflections ( 96.95 % complete ) and 0 restraints for refining 2413 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3076 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2721 (Rfree = 0.000) for 2413 atoms. Found 15 (15 requested) and removed 38 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 2433 seeds are put forward NCS extension: 0 residues added, 2433 seeds are put forward Round 1: 108 peptides, 22 chains. Longest chain 8 peptides. Score 0.295 Round 2: 143 peptides, 25 chains. Longest chain 9 peptides. Score 0.421 Round 3: 144 peptides, 21 chains. Longest chain 15 peptides. Score 0.513 Round 4: 153 peptides, 21 chains. Longest chain 15 peptides. Score 0.554 Round 5: 140 peptides, 20 chains. Longest chain 13 peptides. Score 0.515 Taking the results from Round 4 Chains 21, Residues 132, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4284 restraints for refining 1985 atoms. 3711 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2530 (Rfree = 0.000) for 1985 atoms. Found 10 (12 requested) and removed 19 (6 requested) atoms. Cycle 2: After refmac, R = 0.2276 (Rfree = 0.000) for 1948 atoms. Found 9 (12 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.1864 (Rfree = 0.000) for 1927 atoms. Found 7 (12 requested) and removed 11 (6 requested) atoms. Cycle 4: After refmac, R = 0.1887 (Rfree = 0.000) for 1913 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.1985 (Rfree = 0.000) for 1905 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 1982 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1997 seeds are put forward Round 1: 116 peptides, 24 chains. Longest chain 10 peptides. Score 0.293 Round 2: 133 peptides, 23 chains. Longest chain 16 peptides. Score 0.413 Round 3: 139 peptides, 20 chains. Longest chain 12 peptides. Score 0.510 Round 4: 140 peptides, 20 chains. Longest chain 16 peptides. Score 0.515 Round 5: 144 peptides, 21 chains. Longest chain 15 peptides. Score 0.513 Taking the results from Round 4 Chains 20, Residues 120, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4281 restraints for refining 1937 atoms. 3784 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2216 (Rfree = 0.000) for 1937 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 7: After refmac, R = 0.2070 (Rfree = 0.000) for 1916 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 8: After refmac, R = 0.2195 (Rfree = 0.000) for 1908 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.1863 (Rfree = 0.000) for 1902 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2011 (Rfree = 0.000) for 1897 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 1984 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 2010 seeds are put forward Round 1: 131 peptides, 24 chains. Longest chain 15 peptides. Score 0.379 Round 2: 154 peptides, 21 chains. Longest chain 14 peptides. Score 0.558 Round 3: 152 peptides, 22 chains. Longest chain 14 peptides. Score 0.529 Round 4: 150 peptides, 22 chains. Longest chain 14 peptides. Score 0.520 Round 5: 141 peptides, 22 chains. Longest chain 12 peptides. Score 0.477 Taking the results from Round 2 Chains 23, Residues 133, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4274 restraints for refining 1967 atoms. 3735 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2097 (Rfree = 0.000) for 1967 atoms. Found 5 (12 requested) and removed 14 (6 requested) atoms. Cycle 12: After refmac, R = 0.2004 (Rfree = 0.000) for 1950 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. Cycle 13: After refmac, R = 0.1644 (Rfree = 0.000) for 1934 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.1679 (Rfree = 0.000) for 1928 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1695 (Rfree = 0.000) for 1922 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.43 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: 129 peptides, 25 chains. Longest chain 10 peptides. Score 0.344 Round 2: 145 peptides, 24 chains. Longest chain 12 peptides. Score 0.453 Round 3: 151 peptides, 24 chains. Longest chain 15 peptides. Score 0.483 Round 4: 161 peptides, 21 chains. Longest chain 15 peptides. Score 0.588 Round 5: 160 peptides, 21 chains. Longest chain 14 peptides. Score 0.584 Taking the results from Round 4 Chains 21, Residues 140, Estimated correctness of the model 9.9 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4224 restraints for refining 1987 atoms. 3647 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1938 (Rfree = 0.000) for 1987 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.1812 (Rfree = 0.000) for 1975 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.1753 (Rfree = 0.000) for 1964 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 19: After refmac, R = 0.1668 (Rfree = 0.000) for 1956 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1604 (Rfree = 0.000) for 1948 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 2022 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2039 seeds are put forward Round 1: 131 peptides, 20 chains. Longest chain 14 peptides. Score 0.470 Round 2: 146 peptides, 20 chains. Longest chain 15 peptides. Score 0.542 Round 3: 145 peptides, 20 chains. Longest chain 15 peptides. Score 0.538 Round 4: 153 peptides, 23 chains. Longest chain 14 peptides. Score 0.514 Round 5: 155 peptides, 21 chains. Longest chain 22 peptides. Score 0.563 Taking the results from Round 5 Chains 21, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3180 reflections ( 96.95 % complete ) and 4387 restraints for refining 1987 atoms. 3872 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2012 (Rfree = 0.000) for 1987 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.1831 (Rfree = 0.000) for 1983 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.1757 (Rfree = 0.000) for 1976 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1742 (Rfree = 0.000) for 1972 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1709 (Rfree = 0.000) for 1968 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2057 seeds are put forward Round 1: 135 peptides, 22 chains. Longest chain 19 peptides. Score 0.446 Round 2: 133 peptides, 19 chains. Longest chain 16 peptides. Score 0.502 Round 3: 123 peptides, 17 chains. Longest chain 13 peptides. Score 0.497 Round 4: 139 peptides, 19 chains. Longest chain 18 peptides. Score 0.531 Round 5: 131 peptides, 17 chains. Longest chain 17 peptides. Score 0.535 Taking the results from Round 5 Chains 17, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4523 restraints for refining 1987 atoms. 4084 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2021 (Rfree = 0.000) for 1987 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.1736 (Rfree = 0.000) for 1981 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.1625 (Rfree = 0.000) for 1975 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.1544 (Rfree = 0.000) for 1966 atoms. Found 0 (12 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1555 (Rfree = 0.000) for 1956 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 2012 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2033 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 8 peptides. Score 0.271 Round 2: 120 peptides, 21 chains. Longest chain 12 peptides. Score 0.389 Round 3: 125 peptides, 23 chains. Longest chain 16 peptides. Score 0.369 Round 4: 126 peptides, 20 chains. Longest chain 11 peptides. Score 0.445 Round 5: 121 peptides, 21 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 4 Chains 20, Residues 106, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4624 restraints for refining 1987 atoms. 4199 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1845 (Rfree = 0.000) for 1987 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 32: After refmac, R = 0.1766 (Rfree = 0.000) for 1979 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.1680 (Rfree = 0.000) for 1974 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1702 (Rfree = 0.000) for 1967 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1672 (Rfree = 0.000) for 1962 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 2022 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 2034 seeds are put forward Round 1: 93 peptides, 18 chains. Longest chain 10 peptides. Score 0.306 Round 2: 89 peptides, 13 chains. Longest chain 12 peptides. Score 0.413 Round 3: 93 peptides, 14 chains. Longest chain 12 peptides. Score 0.410 Round 4: 100 peptides, 15 chains. Longest chain 12 peptides. Score 0.424 Round 5: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 4 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4771 restraints for refining 1986 atoms. 4446 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1816 (Rfree = 0.000) for 1986 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.1739 (Rfree = 0.000) for 1982 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.1668 (Rfree = 0.000) for 1978 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1658 (Rfree = 0.000) for 1975 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1636 (Rfree = 0.000) for 1968 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 2040 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 2044 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.304 Round 2: 97 peptides, 18 chains. Longest chain 8 peptides. Score 0.331 Round 3: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.370 Round 4: 114 peptides, 17 chains. Longest chain 14 peptides. Score 0.451 Round 5: 122 peptides, 19 chains. Longest chain 15 peptides. Score 0.447 Taking the results from Round 4 Chains 17, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4673 restraints for refining 1987 atoms. 4302 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2028 (Rfree = 0.000) for 1987 atoms. Found 10 (12 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.1832 (Rfree = 0.000) for 1983 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.1794 (Rfree = 0.000) for 1978 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1742 (Rfree = 0.000) for 1973 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1719 (Rfree = 0.000) for 1969 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2048 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.241 Round 2: 110 peptides, 17 chains. Longest chain 14 peptides. Score 0.430 Round 3: 119 peptides, 17 chains. Longest chain 20 peptides. Score 0.477 Round 4: 107 peptides, 16 chains. Longest chain 13 peptides. Score 0.438 Round 5: 112 peptides, 19 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 102, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2pr7-3_warpNtrace.pdb as input Building loops using Loopy2018 17 chains (102 residues) following loop building 2 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3180 reflections ( 96.95 % complete ) and 4441 restraints for refining 1986 atoms. 4003 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2007 (Rfree = 0.000) for 1986 atoms. Found 0 (12 requested) and removed 5 (6 requested) atoms. Cycle 47: After refmac, R = 0.1926 (Rfree = 0.000) for 1977 atoms. Found 0 (12 requested) and removed 2 (6 requested) atoms. Cycle 48: After refmac, R = 0.1894 (Rfree = 0.000) for 1974 atoms. Found 0 (12 requested) and removed 2 (6 requested) atoms. Cycle 49: After refmac, R = 0.1859 (Rfree = 0.000) for 1969 atoms. TimeTaking 58.8