Sun 23 Dec 22:22:49 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 2hq7-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.8-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/2hq7-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.8-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 22:22:58 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/2hq7-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.8-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 184 and 0 Target number of residues in the AU: 184 Target solvent content: 0.6484 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: 2hq7-3.8-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-3.8-parrot-hancs.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 3.800 Wilson plot Bfac: 76.26 2895 reflections ( 99.18 % complete ) and 0 restraints for refining 2592 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3316 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3285 (Rfree = 0.000) for 2592 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 2639 seeds are put forward NCS extension: 0 residues added, 2639 seeds are put forward Round 1: 108 peptides, 19 chains. Longest chain 13 peptides. Score 0.375 Round 2: 145 peptides, 25 chains. Longest chain 11 peptides. Score 0.438 Round 3: 155 peptides, 22 chains. Longest chain 17 peptides. Score 0.552 Round 4: 170 peptides, 24 chains. Longest chain 19 peptides. Score 0.579 Round 5: 163 peptides, 22 chains. Longest chain 20 peptides. Score 0.587 Taking the results from Round 5 Chains 22, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 2895 reflections ( 99.18 % complete ) and 4888 restraints for refining 2113 atoms. 4346 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2665 (Rfree = 0.000) for 2113 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 2: After refmac, R = 0.2348 (Rfree = 0.000) for 2067 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 3: After refmac, R = 0.2410 (Rfree = 0.000) for 2039 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 4: After refmac, R = 0.2145 (Rfree = 0.000) for 2009 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.2352 (Rfree = 0.000) for 1999 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.81 Search for helices and strands: 0 residues in 0 chains, 2109 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 2143 seeds are put forward Round 1: 119 peptides, 23 chains. Longest chain 15 peptides. Score 0.339 Round 2: 135 peptides, 22 chains. Longest chain 15 peptides. Score 0.453 Round 3: 132 peptides, 20 chains. Longest chain 12 peptides. Score 0.483 Round 4: 139 peptides, 19 chains. Longest chain 32 peptides. Score 0.539 Round 5: 134 peptides, 19 chains. Longest chain 21 peptides. Score 0.515 Taking the results from Round 4 Chains 21, Residues 120, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4617 restraints for refining 2113 atoms. 4044 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2338 (Rfree = 0.000) for 2113 atoms. Found 11 (11 requested) and removed 42 (5 requested) atoms. Cycle 7: After refmac, R = 0.2382 (Rfree = 0.000) for 2062 atoms. Found 11 (11 requested) and removed 31 (5 requested) atoms. Cycle 8: After refmac, R = 0.2132 (Rfree = 0.000) for 2025 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 9: After refmac, R = 0.2172 (Rfree = 0.000) for 2003 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 10: After refmac, R = 0.2103 (Rfree = 0.000) for 1986 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.81 Search for helices and strands: 0 residues in 0 chains, 2040 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 2075 seeds are put forward Round 1: 121 peptides, 24 chains. Longest chain 8 peptides. Score 0.326 Round 2: 139 peptides, 21 chains. Longest chain 13 peptides. Score 0.496 Round 3: 133 peptides, 22 chains. Longest chain 12 peptides. Score 0.443 Round 4: 146 peptides, 20 chains. Longest chain 18 peptides. Score 0.551 Round 5: 147 peptides, 22 chains. Longest chain 11 peptides. Score 0.514 Taking the results from Round 4 Chains 20, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4693 restraints for refining 2079 atoms. 4209 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2214 (Rfree = 0.000) for 2079 atoms. Found 11 (11 requested) and removed 21 (5 requested) atoms. Cycle 12: After refmac, R = 0.2299 (Rfree = 0.000) for 2057 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 13: After refmac, R = 0.2147 (Rfree = 0.000) for 2043 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 14: After refmac, R = 0.2136 (Rfree = 0.000) for 2031 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 15: After refmac, R = 0.2091 (Rfree = 0.000) for 2008 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 2095 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2118 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 7 peptides. Score 0.288 Round 2: 125 peptides, 23 chains. Longest chain 10 peptides. Score 0.375 Round 3: 128 peptides, 22 chains. Longest chain 12 peptides. Score 0.415 Round 4: 136 peptides, 23 chains. Longest chain 13 peptides. Score 0.436 Round 5: 136 peptides, 23 chains. Longest chain 12 peptides. Score 0.436 Taking the results from Round 5 Chains 23, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4709 restraints for refining 2037 atoms. 4280 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2194 (Rfree = 0.000) for 2037 atoms. Found 8 (11 requested) and removed 54 (5 requested) atoms. Cycle 17: After refmac, R = 0.2190 (Rfree = 0.000) for 1975 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 18: After refmac, R = 0.2283 (Rfree = 0.000) for 1960 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 19: After refmac, R = 0.1993 (Rfree = 0.000) for 1942 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 20: After refmac, R = 0.2100 (Rfree = 0.000) for 1930 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 2015 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2033 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 9 peptides. Score 0.292 Round 2: 105 peptides, 20 chains. Longest chain 15 peptides. Score 0.332 Round 3: 108 peptides, 22 chains. Longest chain 8 peptides. Score 0.298 Round 4: 112 peptides, 22 chains. Longest chain 8 peptides. Score 0.323 Round 5: 113 peptides, 21 chains. Longest chain 13 peptides. Score 0.354 Taking the results from Round 5 Chains 21, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4705 restraints for refining 2001 atoms. 4358 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2148 (Rfree = 0.000) for 2001 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 22: After refmac, R = 0.2139 (Rfree = 0.000) for 1986 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 23: After refmac, R = 0.2332 (Rfree = 0.000) for 1965 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 24: After refmac, R = 0.2053 (Rfree = 0.000) for 1957 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 25: After refmac, R = 0.2127 (Rfree = 0.000) for 1952 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.84 Search for helices and strands: 0 residues in 0 chains, 2023 seeds are put forward NCS extension: 0 residues added, 2023 seeds are put forward Round 1: 94 peptides, 21 chains. Longest chain 6 peptides. Score 0.235 Round 2: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.391 Round 3: 111 peptides, 19 chains. Longest chain 10 peptides. Score 0.393 Round 4: 118 peptides, 20 chains. Longest chain 10 peptides. Score 0.408 Round 5: 112 peptides, 19 chains. Longest chain 15 peptides. Score 0.398 Taking the results from Round 4 Chains 20, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4843 restraints for refining 2052 atoms. 4471 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2151 (Rfree = 0.000) for 2052 atoms. Found 9 (11 requested) and removed 36 (5 requested) atoms. Cycle 27: After refmac, R = 0.2258 (Rfree = 0.000) for 2010 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 28: After refmac, R = 0.2134 (Rfree = 0.000) for 1997 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 29: After refmac, R = 0.1980 (Rfree = 0.000) for 1988 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 30: After refmac, R = 0.2074 (Rfree = 0.000) for 1987 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 2043 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2055 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.254 Round 2: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.343 Round 3: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.313 Round 4: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.355 Round 5: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 5 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4770 restraints for refining 2038 atoms. 4482 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2360 (Rfree = 0.000) for 2038 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 32: After refmac, R = 0.2331 (Rfree = 0.000) for 2017 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 33: After refmac, R = 0.2187 (Rfree = 0.000) for 1999 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.2078 (Rfree = 0.000) for 1988 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 35: After refmac, R = 0.2079 (Rfree = 0.000) for 1976 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.88 Search for helices and strands: 0 residues in 0 chains, 2033 seeds are put forward NCS extension: 0 residues added, 2033 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 6 peptides. Score 0.225 Round 2: 83 peptides, 17 chains. Longest chain 11 peptides. Score 0.273 Round 3: 86 peptides, 17 chains. Longest chain 7 peptides. Score 0.292 Round 4: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.309 Round 5: 86 peptides, 17 chains. Longest chain 9 peptides. Score 0.292 Taking the results from Round 4 Chains 15, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4590 restraints for refining 1974 atoms. 4345 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2316 (Rfree = 0.000) for 1974 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 37: After refmac, R = 0.2237 (Rfree = 0.000) for 1967 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 38: After refmac, R = 0.2388 (Rfree = 0.000) for 1955 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 39: After refmac, R = 0.2139 (Rfree = 0.000) for 1946 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2050 (Rfree = 0.000) for 1944 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.90 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: 67 peptides, 16 chains. Longest chain 6 peptides. Score 0.189 Round 2: 74 peptides, 13 chains. Longest chain 11 peptides. Score 0.327 Round 3: 72 peptides, 13 chains. Longest chain 11 peptides. Score 0.314 Round 4: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.316 Round 5: 68 peptides, 12 chains. Longest chain 8 peptides. Score 0.316 Taking the results from Round 2 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4281 restraints for refining 1902 atoms. 4050 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2112 (Rfree = 0.000) for 1902 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 42: After refmac, R = 0.2131 (Rfree = 0.000) for 1889 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.1957 (Rfree = 0.000) for 1884 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.2261 (Rfree = 0.000) for 1882 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.2032 (Rfree = 0.000) for 1880 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.86 Search for helices and strands: 0 residues in 0 chains, 1955 seeds are put forward NCS extension: 0 residues added, 1955 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 6 peptides. Score 0.219 Round 2: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.282 Round 3: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.278 Round 4: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.267 Round 5: 81 peptides, 15 chains. Longest chain 10 peptides. Score 0.315 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 66, 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 2hq7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2895 reflections ( 99.18 % complete ) and 4233 restraints for refining 1874 atoms. 3984 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2087 (Rfree = 0.000) for 1874 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1976 (Rfree = 0.000) for 1859 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1946 (Rfree = 0.000) for 1852 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1912 (Rfree = 0.000) for 1844 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 33.63