null Sun 23 Dec 22:23:08 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 2prv-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prv-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prv-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-3.2-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/2prv-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-3.2-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 22:23:18 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/2prv-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-3.2-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 210 and 0 Target number of residues in the AU: 210 Target solvent content: 0.6309 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-3.2-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: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.75 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: 44.420 3.200 Wilson plot Bfac: 66.67 4810 reflections ( 97.72 % complete ) and 0 restraints for refining 2694 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3838 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3395 (Rfree = 0.000) for 2694 atoms. Found 12 (24 requested) and removed 54 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.35 Search for helices and strands: 0 residues in 0 chains, 2671 seeds are put forward NCS extension: 0 residues added, 2671 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.245 Round 2: 103 peptides, 21 chains. Longest chain 9 peptides. Score 0.285 Round 3: 108 peptides, 20 chains. Longest chain 10 peptides. Score 0.339 Round 4: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.267 Round 5: 112 peptides, 20 chains. Longest chain 9 peptides. Score 0.361 Taking the results from Round 5 Chains 20, Residues 92, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 5126 restraints for refining 2235 atoms. 4771 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2631 (Rfree = 0.000) for 2235 atoms. Found 16 (20 requested) and removed 12 (10 requested) atoms. Cycle 2: After refmac, R = 0.2493 (Rfree = 0.000) for 2231 atoms. Found 7 (20 requested) and removed 14 (10 requested) atoms. Cycle 3: After refmac, R = 0.2412 (Rfree = 0.000) for 2213 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 4: After refmac, R = 0.2312 (Rfree = 0.000) for 2199 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.2299 (Rfree = 0.000) for 2192 atoms. Found 1 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.32 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 0 residues added, 2215 seeds are put forward Round 1: 115 peptides, 26 chains. Longest chain 12 peptides. Score 0.234 Round 2: 123 peptides, 23 chains. Longest chain 12 peptides. Score 0.351 Round 3: 119 peptides, 22 chains. Longest chain 15 peptides. Score 0.352 Round 4: 115 peptides, 21 chains. Longest chain 12 peptides. Score 0.354 Round 5: 122 peptides, 20 chains. Longest chain 15 peptides. Score 0.414 Taking the results from Round 5 Chains 20, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 5115 restraints for refining 2234 atoms. 4727 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2579 (Rfree = 0.000) for 2234 atoms. Found 8 (20 requested) and removed 16 (10 requested) atoms. Cycle 7: After refmac, R = 0.2290 (Rfree = 0.000) for 2219 atoms. Found 6 (19 requested) and removed 12 (9 requested) atoms. Cycle 8: After refmac, R = 0.2641 (Rfree = 0.000) for 2210 atoms. Found 16 (19 requested) and removed 14 (9 requested) atoms. Cycle 9: After refmac, R = 0.2129 (Rfree = 0.000) for 2207 atoms. Found 1 (19 requested) and removed 11 (9 requested) atoms. Cycle 10: After refmac, R = 0.2474 (Rfree = 0.000) for 2195 atoms. Found 15 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.35 Search for helices and strands: 0 residues in 0 chains, 2241 seeds are put forward NCS extension: 0 residues added, 2241 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 9 peptides. Score 0.266 Round 2: 105 peptides, 19 chains. Longest chain 12 peptides. Score 0.346 Round 3: 106 peptides, 17 chains. Longest chain 13 peptides. Score 0.400 Round 4: 108 peptides, 18 chains. Longest chain 11 peptides. Score 0.387 Round 5: 114 peptides, 19 chains. Longest chain 14 peptides. Score 0.395 Taking the results from Round 3 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 5006 restraints for refining 2235 atoms. 4667 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2169 (Rfree = 0.000) for 2235 atoms. Found 10 (20 requested) and removed 14 (10 requested) atoms. Cycle 12: After refmac, R = 0.2117 (Rfree = 0.000) for 2226 atoms. Found 2 (20 requested) and removed 12 (10 requested) atoms. Cycle 13: After refmac, R = 0.2069 (Rfree = 0.000) for 2216 atoms. Found 1 (19 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2599 (Rfree = 0.000) for 2206 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 15: After refmac, R = 0.2194 (Rfree = 0.000) for 2211 atoms. Found 3 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.33 Search for helices and strands: 0 residues in 0 chains, 2247 seeds are put forward NCS extension: 0 residues added, 2247 seeds are put forward Round 1: 103 peptides, 18 chains. Longest chain 15 peptides. Score 0.359 Round 2: 99 peptides, 16 chains. Longest chain 10 peptides. Score 0.386 Round 3: 102 peptides, 16 chains. Longest chain 11 peptides. Score 0.402 Round 4: 116 peptides, 18 chains. Longest chain 11 peptides. Score 0.429 Round 5: 120 peptides, 19 chains. Longest chain 11 peptides. Score 0.427 Taking the results from Round 4 Chains 18, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4887 restraints for refining 2235 atoms. 4513 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2331 (Rfree = 0.000) for 2235 atoms. Found 11 (20 requested) and removed 12 (10 requested) atoms. Cycle 17: After refmac, R = 0.2370 (Rfree = 0.000) for 2229 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 18: After refmac, R = 0.2332 (Rfree = 0.000) for 2223 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 19: After refmac, R = 0.2019 (Rfree = 0.000) for 2210 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.2254 (Rfree = 0.000) for 2201 atoms. Found 11 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.32 Search for helices and strands: 0 residues in 0 chains, 2237 seeds are put forward NCS extension: 0 residues added, 2237 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 6 peptides. Score 0.234 Round 2: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Round 3: 98 peptides, 19 chains. Longest chain 9 peptides. Score 0.306 Round 4: 112 peptides, 19 chains. Longest chain 10 peptides. Score 0.385 Round 5: 108 peptides, 18 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 5 Chains 18, Residues 90, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4708 restraints for refining 2177 atoms. 4350 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2645 (Rfree = 0.000) for 2177 atoms. Found 16 (19 requested) and removed 70 (9 requested) atoms. Cycle 22: After refmac, R = 0.2427 (Rfree = 0.000) for 2116 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 23: After refmac, R = 0.2524 (Rfree = 0.000) for 2109 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 24: After refmac, R = 0.2169 (Rfree = 0.000) for 2109 atoms. Found 15 (18 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.2009 (Rfree = 0.000) for 2109 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.33 Search for helices and strands: 0 residues in 0 chains, 2150 seeds are put forward NCS extension: 0 residues added, 2150 seeds are put forward Round 1: 108 peptides, 21 chains. Longest chain 10 peptides. Score 0.315 Round 2: 121 peptides, 24 chains. Longest chain 9 peptides. Score 0.317 Round 3: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.411 Round 4: 120 peptides, 23 chains. Longest chain 9 peptides. Score 0.334 Round 5: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 3 Chains 19, Residues 98, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4405 restraints for refining 2130 atoms. 4007 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2271 (Rfree = 0.000) for 2130 atoms. Found 16 (19 requested) and removed 17 (9 requested) atoms. Cycle 27: After refmac, R = 0.2542 (Rfree = 0.000) for 2126 atoms. Found 17 (19 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.2060 (Rfree = 0.000) for 2127 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. Cycle 29: After refmac, R = 0.2026 (Rfree = 0.000) for 2118 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.2053 (Rfree = 0.000) for 2114 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.35 Search for helices and strands: 0 residues in 0 chains, 2133 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2148 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 7 peptides. Score 0.281 Round 2: 130 peptides, 21 chains. Longest chain 10 peptides. Score 0.433 Round 3: 137 peptides, 23 chains. Longest chain 10 peptides. Score 0.425 Round 4: 133 peptides, 21 chains. Longest chain 10 peptides. Score 0.448 Round 5: 123 peptides, 20 chains. Longest chain 11 peptides. Score 0.420 Taking the results from Round 4 Chains 21, Residues 112, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4570 restraints for refining 2199 atoms. 4115 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2089 (Rfree = 0.000) for 2199 atoms. Found 14 (19 requested) and removed 12 (9 requested) atoms. Cycle 32: After refmac, R = 0.2088 (Rfree = 0.000) for 2201 atoms. Found 13 (19 requested) and removed 13 (9 requested) atoms. Cycle 33: After refmac, R = 0.1956 (Rfree = 0.000) for 2198 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.1977 (Rfree = 0.000) for 2186 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.1987 (Rfree = 0.000) for 2180 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.34 Search for helices and strands: 0 residues in 0 chains, 2196 seeds are put forward NCS extension: 0 residues added, 2196 seeds are put forward Round 1: 80 peptides, 19 chains. Longest chain 6 peptides. Score 0.194 Round 2: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 3: 86 peptides, 13 chains. Longest chain 14 peptides. Score 0.388 Round 4: 90 peptides, 16 chains. Longest chain 13 peptides. Score 0.335 Round 5: 93 peptides, 15 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 3 Chains 13, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4853 restraints for refining 2170 atoms. 4574 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2071 (Rfree = 0.000) for 2170 atoms. Found 13 (19 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.2555 (Rfree = 0.000) for 2171 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 38: After refmac, R = 0.2006 (Rfree = 0.000) for 2172 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.2024 (Rfree = 0.000) for 2165 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Cycle 40: After refmac, R = 0.2125 (Rfree = 0.000) for 2159 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.36 Search for helices and strands: 0 residues in 0 chains, 2176 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2197 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 9 peptides. Score 0.254 Round 2: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.270 Round 3: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.291 Round 4: 91 peptides, 17 chains. Longest chain 10 peptides. Score 0.315 Round 5: 84 peptides, 16 chains. Longest chain 10 peptides. Score 0.299 Taking the results from Round 4 Chains 17, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4810 reflections ( 97.72 % complete ) and 4525 restraints for refining 2104 atoms. 4246 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2266 (Rfree = 0.000) for 2104 atoms. Found 12 (18 requested) and removed 12 (9 requested) atoms. Cycle 42: After refmac, R = 0.2078 (Rfree = 0.000) for 2099 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Cycle 43: After refmac, R = 0.2523 (Rfree = 0.000) for 2091 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 44: After refmac, R = 0.2225 (Rfree = 0.000) for 2096 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 45: After refmac, R = 0.2651 (Rfree = 0.000) for 2102 atoms. Found 18 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 2144 seeds are put forward NCS extension: 0 residues added, 2144 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 7 peptides. Score 0.241 Round 2: 93 peptides, 17 chains. Longest chain 10 peptides. Score 0.327 Round 3: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.331 Round 4: 84 peptides, 14 chains. Longest chain 10 peptides. Score 0.351 Round 5: 76 peptides, 12 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 5 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 2prv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4810 reflections ( 97.72 % complete ) and 4612 restraints for refining 2098 atoms. 4368 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2047 (Rfree = 0.000) for 2098 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2501 (Rfree = 0.000) for 2087 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2216 (Rfree = 0.000) for 2074 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2561 (Rfree = 0.000) for 2061 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:53 GMT 2018 Job finished. TimeTaking 33.76 Used memory is bytes: 10998936