Sun 23 Dec 22:23:01 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 2eth-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2eth-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2eth-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-4.0-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/2eth-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-4.0-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 22:23:10 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/2eth-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-4.0-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 227 and 0 Target number of residues in the AU: 227 Target solvent content: 0.6735 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.56 Input MTZ file: 2eth-4.0-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: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2464 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: 65.143 4.000 Wilson plot Bfac: 94.99 3175 reflections ( 98.08 % complete ) and 0 restraints for refining 2719 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3479 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3459 (Rfree = 0.000) for 2719 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.98 3.67 Search for helices and strands: 0 residues in 0 chains, 2786 seeds are put forward NCS extension: 0 residues added, 2786 seeds are put forward Round 1: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.310 Round 2: 111 peptides, 17 chains. Longest chain 18 peptides. Score 0.392 Round 3: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.372 Round 4: 128 peptides, 18 chains. Longest chain 14 peptides. Score 0.446 Round 5: 127 peptides, 19 chains. Longest chain 14 peptides. Score 0.423 Taking the results from Round 4 Chains 18, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 5486 restraints for refining 2174 atoms. 5064 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2611 (Rfree = 0.000) for 2174 atoms. Found 8 (10 requested) and removed 19 (5 requested) atoms. Cycle 2: After refmac, R = 0.2681 (Rfree = 0.000) for 2116 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 3: After refmac, R = 0.2450 (Rfree = 0.000) for 2073 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 4: After refmac, R = 0.2448 (Rfree = 0.000) for 2047 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 5: After refmac, R = 0.2447 (Rfree = 0.000) for 2024 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.87 3.57 Search for helices and strands: 0 residues in 0 chains, 2129 seeds are put forward NCS extension: 0 residues added, 2129 seeds are put forward Round 1: 119 peptides, 22 chains. Longest chain 10 peptides. Score 0.327 Round 2: 132 peptides, 20 chains. Longest chain 11 peptides. Score 0.425 Round 3: 136 peptides, 16 chains. Longest chain 20 peptides. Score 0.515 Round 4: 133 peptides, 19 chains. Longest chain 12 peptides. Score 0.448 Round 5: 137 peptides, 17 chains. Longest chain 19 peptides. Score 0.501 Taking the results from Round 3 Chains 19, Residues 120, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4480 restraints for refining 2077 atoms. 3921 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2284 (Rfree = 0.000) for 2077 atoms. Found 8 (9 requested) and removed 25 (4 requested) atoms. Cycle 7: After refmac, R = 0.2403 (Rfree = 0.000) for 2036 atoms. Found 7 (9 requested) and removed 15 (4 requested) atoms. Cycle 8: After refmac, R = 0.2333 (Rfree = 0.000) for 2005 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 9: After refmac, R = 0.2983 (Rfree = 0.000) for 1985 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 10: After refmac, R = 0.2125 (Rfree = 0.000) for 1950 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.01 3.70 Search for helices and strands: 0 residues in 0 chains, 2057 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2071 seeds are put forward Round 1: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.347 Round 2: 129 peptides, 18 chains. Longest chain 17 peptides. Score 0.450 Round 3: 127 peptides, 15 chains. Longest chain 15 peptides. Score 0.498 Round 4: 121 peptides, 16 chains. Longest chain 15 peptides. Score 0.455 Round 5: 131 peptides, 17 chains. Longest chain 13 peptides. Score 0.477 Taking the results from Round 3 Chains 16, Residues 112, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4798 restraints for refining 2141 atoms. 4323 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2286 (Rfree = 0.000) for 2141 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 12: After refmac, R = 0.2255 (Rfree = 0.000) for 2112 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 13: After refmac, R = 0.1847 (Rfree = 0.000) for 2097 atoms. Found 0 (10 requested) and removed 10 (5 requested) atoms. Cycle 14: After refmac, R = 0.1678 (Rfree = 0.000) for 2076 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.1710 (Rfree = 0.000) for 2067 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.97 3.66 Search for helices and strands: 0 residues in 0 chains, 2148 seeds are put forward NCS extension: 0 residues added, 2148 seeds are put forward Round 1: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.366 Round 2: 135 peptides, 21 chains. Longest chain 12 peptides. Score 0.419 Round 3: 131 peptides, 21 chains. Longest chain 10 peptides. Score 0.401 Round 4: 137 peptides, 19 chains. Longest chain 14 peptides. Score 0.464 Round 5: 134 peptides, 21 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 4 Chains 19, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4816 restraints for refining 2136 atoms. 4363 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2173 (Rfree = 0.000) for 2136 atoms. Found 8 (10 requested) and removed 21 (5 requested) atoms. Cycle 17: After refmac, R = 0.2296 (Rfree = 0.000) for 2104 atoms. Found 7 (10 requested) and removed 15 (5 requested) atoms. Cycle 18: After refmac, R = 0.2211 (Rfree = 0.000) for 2089 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.2112 (Rfree = 0.000) for 2078 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 20: After refmac, R = 0.2317 (Rfree = 0.000) for 2071 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.99 3.68 Search for helices and strands: 0 residues in 0 chains, 2185 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2198 seeds are put forward Round 1: 99 peptides, 19 chains. Longest chain 12 peptides. Score 0.293 Round 2: 108 peptides, 20 chains. Longest chain 11 peptides. Score 0.316 Round 3: 115 peptides, 17 chains. Longest chain 13 peptides. Score 0.410 Round 4: 123 peptides, 18 chains. Longest chain 15 peptides. Score 0.425 Round 5: 127 peptides, 17 chains. Longest chain 16 peptides. Score 0.461 Taking the results from Round 5 Chains 17, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4971 restraints for refining 2145 atoms. 4548 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2339 (Rfree = 0.000) for 2145 atoms. Found 5 (10 requested) and removed 20 (5 requested) atoms. Cycle 22: After refmac, R = 0.2350 (Rfree = 0.000) for 2100 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.2248 (Rfree = 0.000) for 2088 atoms. Found 7 (9 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.2303 (Rfree = 0.000) for 2068 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 25: After refmac, R = 0.2191 (Rfree = 0.000) for 2059 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.96 3.65 Search for helices and strands: 0 residues in 0 chains, 2172 seeds are put forward NCS extension: 0 residues added, 2172 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 10 peptides. Score 0.282 Round 2: 123 peptides, 22 chains. Longest chain 11 peptides. Score 0.346 Round 3: 127 peptides, 21 chains. Longest chain 12 peptides. Score 0.384 Round 4: 134 peptides, 23 chains. Longest chain 18 peptides. Score 0.376 Round 5: 120 peptides, 19 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 5 Chains 19, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4963 restraints for refining 2160 atoms. 4578 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2215 (Rfree = 0.000) for 2160 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.2224 (Rfree = 0.000) for 2140 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 28: After refmac, R = 0.2027 (Rfree = 0.000) for 2123 atoms. Found 9 (10 requested) and removed 15 (5 requested) atoms. Cycle 29: After refmac, R = 0.2176 (Rfree = 0.000) for 2107 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.2200 (Rfree = 0.000) for 2094 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.97 3.66 Search for helices and strands: 0 residues in 0 chains, 2194 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2205 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 9 peptides. Score 0.238 Round 2: 111 peptides, 22 chains. Longest chain 11 peptides. Score 0.288 Round 3: 124 peptides, 22 chains. Longest chain 12 peptides. Score 0.350 Round 4: 111 peptides, 21 chains. Longest chain 10 peptides. Score 0.309 Round 5: 117 peptides, 20 chains. Longest chain 16 peptides. Score 0.358 Taking the results from Round 5 Chains 20, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4914 restraints for refining 2153 atoms. 4546 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2487 (Rfree = 0.000) for 2153 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 32: After refmac, R = 0.2168 (Rfree = 0.000) for 2123 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 33: After refmac, R = 0.2128 (Rfree = 0.000) for 2107 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.2147 (Rfree = 0.000) for 2102 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.2153 (Rfree = 0.000) for 2096 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.00 3.69 Search for helices and strands: 0 residues in 0 chains, 2184 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2205 seeds are put forward Round 1: 90 peptides, 21 chains. Longest chain 6 peptides. Score 0.201 Round 2: 93 peptides, 16 chains. Longest chain 8 peptides. Score 0.328 Round 3: 105 peptides, 17 chains. Longest chain 11 peptides. Score 0.364 Round 4: 109 peptides, 18 chains. Longest chain 9 peptides. Score 0.362 Round 5: 112 peptides, 17 chains. Longest chain 16 peptides. Score 0.396 Taking the results from Round 5 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4989 restraints for refining 2157 atoms. 4626 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2904 (Rfree = 0.000) for 2157 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 37: After refmac, R = 0.2467 (Rfree = 0.000) for 2132 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 38: After refmac, R = 0.2249 (Rfree = 0.000) for 2110 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.2464 (Rfree = 0.000) for 2101 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.2342 (Rfree = 0.000) for 2093 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.95 3.65 Search for helices and strands: 0 residues in 0 chains, 2210 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2235 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.205 Round 2: 91 peptides, 17 chains. Longest chain 11 peptides. Score 0.296 Round 3: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.298 Round 4: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.279 Round 5: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.319 Taking the results from Round 5 Chains 18, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4780 restraints for refining 2075 atoms. 4470 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2437 (Rfree = 0.000) for 2075 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 42: After refmac, R = 0.2744 (Rfree = 0.000) for 2056 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.2271 (Rfree = 0.000) for 2042 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.2453 (Rfree = 0.000) for 2040 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.2724 (Rfree = 0.000) for 2034 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.03 3.72 Search for helices and strands: 0 residues in 0 chains, 2129 seeds are put forward NCS extension: 0 residues added, 2129 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 5 peptides. Score 0.215 Round 2: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.287 Round 3: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.298 Round 4: 94 peptides, 16 chains. Longest chain 10 peptides. Score 0.333 Round 5: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.298 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 78, 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 2eth-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3175 reflections ( 98.08 % complete ) and 4326 restraints for refining 1991 atoms. 4030 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2424 (Rfree = 0.000) for 1991 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2623 (Rfree = 0.000) for 1967 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2496 (Rfree = 0.000) for 1956 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2489 (Rfree = 0.000) for 1942 atoms. TimeTaking 44.67