Mon 24 Dec 00:19:07 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 2p1a-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-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/2p1a-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-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 ============================================================ Mon 24 Dec 00:19:11 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/2p1a-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-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 195 and 0 Target number of residues in the AU: 195 Target solvent content: 0.6562 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: 0.46 Input MTZ file: 2p1a-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: 19 Cell parameters: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.60 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: 29.570 3.600 Wilson plot Bfac: 81.53 3840 reflections ( 99.43 % complete ) and 0 restraints for refining 2733 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3517 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3129 (Rfree = 0.000) for 2733 atoms. Found 10 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.83 Search for helices and strands: 0 residues in 0 chains, 2800 seeds are put forward NCS extension: 0 residues added, 2800 seeds are put forward Round 1: 93 peptides, 20 chains. Longest chain 10 peptides. Score 0.250 Round 2: 120 peptides, 22 chains. Longest chain 11 peptides. Score 0.358 Round 3: 124 peptides, 21 chains. Longest chain 11 peptides. Score 0.402 Round 4: 130 peptides, 21 chains. Longest chain 11 peptides. Score 0.433 Round 5: 142 peptides, 25 chains. Longest chain 11 peptides. Score 0.406 Taking the results from Round 4 Chains 21, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 5402 restraints for refining 2231 atoms. 4987 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2551 (Rfree = 0.000) for 2231 atoms. Found 9 (14 requested) and removed 18 (7 requested) atoms. Cycle 2: After refmac, R = 0.2458 (Rfree = 0.000) for 2196 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. Cycle 3: After refmac, R = 0.2027 (Rfree = 0.000) for 2179 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.1907 (Rfree = 0.000) for 2167 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.1914 (Rfree = 0.000) for 2157 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.74 Search for helices and strands: 0 residues in 0 chains, 2284 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2298 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 9 peptides. Score 0.284 Round 2: 137 peptides, 23 chains. Longest chain 11 peptides. Score 0.425 Round 3: 129 peptides, 22 chains. Longest chain 9 peptides. Score 0.406 Round 4: 134 peptides, 20 chains. Longest chain 17 peptides. Score 0.474 Round 5: 133 peptides, 21 chains. Longest chain 13 peptides. Score 0.448 Taking the results from Round 4 Chains 20, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4886 restraints for refining 2100 atoms. 4450 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2186 (Rfree = 0.000) for 2100 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.2079 (Rfree = 0.000) for 2079 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.1955 (Rfree = 0.000) for 2073 atoms. Found 5 (13 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.1863 (Rfree = 0.000) for 2063 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.1606 (Rfree = 0.000) for 2056 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 2167 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2184 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 10 peptides. Score 0.294 Round 2: 129 peptides, 20 chains. Longest chain 12 peptides. Score 0.450 Round 3: 135 peptides, 20 chains. Longest chain 12 peptides. Score 0.479 Round 4: 132 peptides, 20 chains. Longest chain 13 peptides. Score 0.465 Round 5: 130 peptides, 19 chains. Longest chain 11 peptides. Score 0.476 Taking the results from Round 3 Chains 20, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4764 restraints for refining 2093 atoms. 4324 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2084 (Rfree = 0.000) for 2093 atoms. Found 7 (13 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.1987 (Rfree = 0.000) for 2074 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 13: After refmac, R = 0.1953 (Rfree = 0.000) for 2071 atoms. Found 5 (13 requested) and removed 11 (6 requested) atoms. Cycle 14: After refmac, R = 0.1935 (Rfree = 0.000) for 2062 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.1877 (Rfree = 0.000) for 2061 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.73 Search for helices and strands: 0 residues in 0 chains, 2179 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2195 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 8 peptides. Score 0.272 Round 2: 127 peptides, 23 chains. Longest chain 10 peptides. Score 0.373 Round 3: 133 peptides, 23 chains. Longest chain 10 peptides. Score 0.404 Round 4: 137 peptides, 23 chains. Longest chain 12 peptides. Score 0.425 Round 5: 136 peptides, 24 chains. Longest chain 11 peptides. Score 0.397 Taking the results from Round 4 Chains 23, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4801 restraints for refining 2135 atoms. 4368 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2123 (Rfree = 0.000) for 2135 atoms. Found 9 (13 requested) and removed 19 (6 requested) atoms. Cycle 17: After refmac, R = 0.2001 (Rfree = 0.000) for 2116 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 18: After refmac, R = 0.1954 (Rfree = 0.000) for 2113 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.1923 (Rfree = 0.000) for 2104 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1924 (Rfree = 0.000) for 2100 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 2222 seeds are put forward NCS extension: 0 residues added, 2222 seeds are put forward Round 1: 118 peptides, 24 chains. Longest chain 9 peptides. Score 0.299 Round 2: 120 peptides, 21 chains. Longest chain 10 peptides. Score 0.381 Round 3: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.379 Round 4: 134 peptides, 20 chains. Longest chain 20 peptides. Score 0.474 Round 5: 133 peptides, 21 chains. Longest chain 16 peptides. Score 0.448 Taking the results from Round 4 Chains 20, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 5081 restraints for refining 2174 atoms. 4645 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2172 (Rfree = 0.000) for 2174 atoms. Found 5 (13 requested) and removed 15 (6 requested) atoms. Cycle 22: After refmac, R = 0.2125 (Rfree = 0.000) for 2159 atoms. Found 8 (13 requested) and removed 16 (6 requested) atoms. Cycle 23: After refmac, R = 0.2100 (Rfree = 0.000) for 2142 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 24: After refmac, R = 0.1984 (Rfree = 0.000) for 2139 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.1644 (Rfree = 0.000) for 2131 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 2225 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2250 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 6 peptides. Score 0.213 Round 2: 111 peptides, 23 chains. Longest chain 7 peptides. Score 0.283 Round 3: 125 peptides, 25 chains. Longest chain 11 peptides. Score 0.315 Round 4: 122 peptides, 23 chains. Longest chain 11 peptides. Score 0.346 Round 5: 125 peptides, 24 chains. Longest chain 8 peptides. Score 0.339 Taking the results from Round 4 Chains 23, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 5156 restraints for refining 2229 atoms. 4783 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2111 (Rfree = 0.000) for 2229 atoms. Found 10 (14 requested) and removed 20 (7 requested) atoms. Cycle 27: After refmac, R = 0.1966 (Rfree = 0.000) for 2208 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 28: After refmac, R = 0.2048 (Rfree = 0.000) for 2198 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 29: After refmac, R = 0.1995 (Rfree = 0.000) for 2193 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 30: After refmac, R = 0.1682 (Rfree = 0.000) for 2191 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 2274 seeds are put forward NCS extension: 0 residues added, 2274 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.267 Round 2: 121 peptides, 22 chains. Longest chain 9 peptides. Score 0.363 Round 3: 113 peptides, 20 chains. Longest chain 12 peptides. Score 0.367 Round 4: 116 peptides, 21 chains. Longest chain 12 peptides. Score 0.359 Round 5: 111 peptides, 18 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 5 Chains 18, Residues 93, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 5190 restraints for refining 2233 atoms. 4782 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2516 (Rfree = 0.000) for 2233 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2323 (Rfree = 0.000) for 2218 atoms. Found 13 (14 requested) and removed 14 (7 requested) atoms. Cycle 33: After refmac, R = 0.1875 (Rfree = 0.000) for 2209 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.1831 (Rfree = 0.000) for 2200 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.1884 (Rfree = 0.000) for 2190 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2263 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2279 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 9 peptides. Score 0.266 Round 2: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.323 Round 3: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.348 Round 4: 109 peptides, 20 chains. Longest chain 9 peptides. Score 0.344 Round 5: 116 peptides, 20 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 5 Chains 20, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 5240 restraints for refining 2196 atoms. 4876 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2313 (Rfree = 0.000) for 2196 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 37: After refmac, R = 0.2322 (Rfree = 0.000) for 2194 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 38: After refmac, R = 0.2083 (Rfree = 0.000) for 2188 atoms. Found 9 (14 requested) and removed 12 (7 requested) atoms. Cycle 39: After refmac, R = 0.2251 (Rfree = 0.000) for 2181 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2101 (Rfree = 0.000) for 2179 atoms. Found 8 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.74 Search for helices and strands: 0 residues in 0 chains, 2258 seeds are put forward NCS extension: 0 residues added, 2258 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 8 peptides. Score 0.255 Round 2: 108 peptides, 20 chains. Longest chain 13 peptides. Score 0.339 Round 3: 94 peptides, 17 chains. Longest chain 8 peptides. Score 0.333 Round 4: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.342 Round 5: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 5 Chains 17, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 5077 restraints for refining 2157 atoms. 4742 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2185 (Rfree = 0.000) for 2157 atoms. Found 11 (13 requested) and removed 17 (6 requested) atoms. Cycle 42: After refmac, R = 0.2314 (Rfree = 0.000) for 2143 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.2127 (Rfree = 0.000) for 2142 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1749 (Rfree = 0.000) for 2140 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. Cycle 45: After refmac, R = 0.1635 (Rfree = 0.000) for 2130 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 2189 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2205 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 7 peptides. Score 0.237 Round 2: 110 peptides, 22 chains. Longest chain 9 peptides. Score 0.302 Round 3: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.318 Round 4: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.299 Round 5: 107 peptides, 19 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 88, 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 2p1a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3840 reflections ( 99.43 % complete ) and 4953 restraints for refining 2119 atoms. 4620 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2274 (Rfree = 0.000) for 2119 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2155 (Rfree = 0.000) for 2107 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1955 (Rfree = 0.000) for 2099 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2024 (Rfree = 0.000) for 2092 atoms. TimeTaking 25.72