Mon 24 Dec 00:40:01 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 2hq7-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hq7-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hq7-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-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/2hq7-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-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 ============================================================ Mon 24 Dec 00:40:06 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/2hq7-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-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 183 and 0 Target number of residues in the AU: 183 Target solvent content: 0.6503 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-4.0-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2336 target number of atoms Had to go as low as 0.80 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: 89.671 4.000 Wilson plot Bfac: 77.90 2485 reflections ( 99.04 % complete ) and 0 restraints for refining 2579 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3441 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3300 (Rfree = 0.000) for 2579 atoms. Found 12 (12 requested) and removed 44 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.86 Search for helices and strands: 0 residues in 0 chains, 2583 seeds are put forward NCS extension: 0 residues added, 2583 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 9 peptides. Score 0.291 Round 2: 127 peptides, 23 chains. Longest chain 13 peptides. Score 0.386 Round 3: 123 peptides, 19 chains. Longest chain 13 peptides. Score 0.459 Round 4: 130 peptides, 22 chains. Longest chain 13 peptides. Score 0.427 Round 5: 131 peptides, 18 chains. Longest chain 16 peptides. Score 0.522 Taking the results from Round 5 Chains 18, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4879 restraints for refining 2109 atoms. 4445 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2693 (Rfree = 0.000) for 2109 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 2: After refmac, R = 0.2796 (Rfree = 0.000) for 2062 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 3: After refmac, R = 0.2563 (Rfree = 0.000) for 2039 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 4: After refmac, R = 0.1948 (Rfree = 0.000) for 2012 atoms. Found 2 (9 requested) and removed 11 (4 requested) atoms. Cycle 5: After refmac, R = 0.1858 (Rfree = 0.000) for 1988 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2067 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 7 peptides. Score 0.271 Round 2: 103 peptides, 20 chains. Longest chain 10 peptides. Score 0.319 Round 3: 108 peptides, 18 chains. Longest chain 12 peptides. Score 0.400 Round 4: 118 peptides, 21 chains. Longest chain 10 peptides. Score 0.383 Round 5: 120 peptides, 21 chains. Longest chain 10 peptides. Score 0.395 Taking the results from Round 3 Chains 18, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4608 restraints for refining 1944 atoms. 4266 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2423 (Rfree = 0.000) for 1944 atoms. Found 9 (9 requested) and removed 28 (4 requested) atoms. Cycle 7: After refmac, R = 0.2217 (Rfree = 0.000) for 1910 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 8: After refmac, R = 0.2575 (Rfree = 0.000) for 1894 atoms. Found 9 (9 requested) and removed 28 (4 requested) atoms. Cycle 9: After refmac, R = 0.2260 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.2299 (Rfree = 0.000) for 1857 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.90 Search for helices and strands: 0 residues in 0 chains, 1936 seeds are put forward NCS extension: 0 residues added, 1936 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 11 peptides. Score 0.313 Round 2: 109 peptides, 21 chains. Longest chain 10 peptides. Score 0.330 Round 3: 112 peptides, 18 chains. Longest chain 13 peptides. Score 0.423 Round 4: 111 peptides, 17 chains. Longest chain 13 peptides. Score 0.442 Round 5: 119 peptides, 18 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 5 Chains 18, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4247 restraints for refining 1874 atoms. 3861 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2252 (Rfree = 0.000) for 1874 atoms. Found 8 (8 requested) and removed 26 (4 requested) atoms. Cycle 12: After refmac, R = 0.2556 (Rfree = 0.000) for 1843 atoms. Found 8 (8 requested) and removed 29 (4 requested) atoms. Cycle 13: After refmac, R = 0.2227 (Rfree = 0.000) for 1814 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 14: After refmac, R = 0.2208 (Rfree = 0.000) for 1803 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 15: After refmac, R = 0.2051 (Rfree = 0.000) for 1790 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.94 Search for helices and strands: 0 residues in 0 chains, 1845 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1859 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.242 Round 2: 115 peptides, 22 chains. Longest chain 11 peptides. Score 0.341 Round 3: 119 peptides, 21 chains. Longest chain 14 peptides. Score 0.389 Round 4: 114 peptides, 21 chains. Longest chain 8 peptides. Score 0.360 Round 5: 119 peptides, 20 chains. Longest chain 10 peptides. Score 0.413 Taking the results from Round 5 Chains 20, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4327 restraints for refining 1908 atoms. 3951 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2372 (Rfree = 0.000) for 1908 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 17: After refmac, R = 0.2031 (Rfree = 0.000) for 1884 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 18: After refmac, R = 0.1934 (Rfree = 0.000) for 1866 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1886 (Rfree = 0.000) for 1855 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 20: After refmac, R = 0.2097 (Rfree = 0.000) for 1843 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 1919 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 1927 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 8 peptides. Score 0.278 Round 2: 118 peptides, 23 chains. Longest chain 9 peptides. Score 0.334 Round 3: 115 peptides, 20 chains. Longest chain 12 peptides. Score 0.391 Round 4: 118 peptides, 22 chains. Longest chain 8 peptides. Score 0.359 Round 5: 118 peptides, 22 chains. Longest chain 8 peptides. Score 0.359 Taking the results from Round 3 Chains 20, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4395 restraints for refining 1931 atoms. 4035 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2236 (Rfree = 0.000) for 1931 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 22: After refmac, R = 0.2185 (Rfree = 0.000) for 1898 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 23: After refmac, R = 0.2134 (Rfree = 0.000) for 1887 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.1951 (Rfree = 0.000) for 1881 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2347 (Rfree = 0.000) for 1875 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.96 Search for helices and strands: 0 residues in 0 chains, 1945 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 1956 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 8 peptides. Score 0.242 Round 2: 111 peptides, 21 chains. Longest chain 10 peptides. Score 0.342 Round 3: 125 peptides, 24 chains. Longest chain 14 peptides. Score 0.350 Round 4: 125 peptides, 25 chains. Longest chain 9 peptides. Score 0.325 Round 5: 120 peptides, 23 chains. Longest chain 9 peptides. Score 0.345 Taking the results from Round 3 Chains 24, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4241 restraints for refining 1928 atoms. 3861 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2129 (Rfree = 0.000) for 1928 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 27: After refmac, R = 0.2256 (Rfree = 0.000) for 1909 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.1815 (Rfree = 0.000) for 1899 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 29: After refmac, R = 0.1897 (Rfree = 0.000) for 1889 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 30: After refmac, R = 0.1875 (Rfree = 0.000) for 1885 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.90 Search for helices and strands: 0 residues in 0 chains, 1960 seeds are put forward NCS extension: 0 residues added, 1960 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 7 peptides. Score 0.241 Round 2: 100 peptides, 20 chains. Longest chain 10 peptides. Score 0.301 Round 3: 116 peptides, 20 chains. Longest chain 9 peptides. Score 0.396 Round 4: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.344 Round 5: 103 peptides, 19 chains. Longest chain 8 peptides. Score 0.345 Taking the results from Round 3 Chains 20, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4473 restraints for refining 1955 atoms. 4109 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2264 (Rfree = 0.000) for 1955 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 32: After refmac, R = 0.2194 (Rfree = 0.000) for 1930 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 33: After refmac, R = 0.2018 (Rfree = 0.000) for 1919 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.1934 (Rfree = 0.000) for 1906 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.1915 (Rfree = 0.000) for 1905 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.93 Search for helices and strands: 0 residues in 0 chains, 1974 seeds are put forward NCS extension: 0 residues added, 1974 seeds are put forward Round 1: 96 peptides, 22 chains. Longest chain 6 peptides. Score 0.221 Round 2: 113 peptides, 22 chains. Longest chain 10 peptides. Score 0.329 Round 3: 116 peptides, 21 chains. Longest chain 11 peptides. Score 0.372 Round 4: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.360 Round 5: 120 peptides, 21 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 5 Chains 21, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4614 restraints for refining 2032 atoms. 4239 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2196 (Rfree = 0.000) for 2032 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 37: After refmac, R = 0.1938 (Rfree = 0.000) for 2010 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.1893 (Rfree = 0.000) for 2008 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.1813 (Rfree = 0.000) for 2007 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.1305 (Rfree = 0.000) for 2006 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 2058 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2074 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 6 peptides. Score 0.229 Round 2: 104 peptides, 21 chains. Longest chain 11 peptides. Score 0.299 Round 3: 104 peptides, 20 chains. Longest chain 8 peptides. Score 0.325 Round 4: 106 peptides, 20 chains. Longest chain 9 peptides. Score 0.338 Round 5: 104 peptides, 18 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 5 Chains 18, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4785 restraints for refining 2075 atoms. 4459 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2288 (Rfree = 0.000) for 2075 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 42: After refmac, R = 0.1969 (Rfree = 0.000) for 2053 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 43: After refmac, R = 0.1373 (Rfree = 0.000) for 2035 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.1222 (Rfree = 0.000) for 2029 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1170 (Rfree = 0.000) for 2021 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.93 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2066 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 6 peptides. Score 0.224 Round 2: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.322 Round 3: 102 peptides, 21 chains. Longest chain 8 peptides. Score 0.287 Round 4: 97 peptides, 18 chains. Longest chain 10 peptides. Score 0.335 Round 5: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.361 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 80, 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 2hq7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2485 reflections ( 99.04 % complete ) and 4752 restraints for refining 2052 atoms. 4449 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2007 (Rfree = 0.000) for 2052 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1937 (Rfree = 0.000) for 2039 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1884 (Rfree = 0.000) for 2025 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2060 (Rfree = 0.000) for 2016 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 30.2