Sun 23 Dec 22:23:14 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 2p1a-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-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/2p1a-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-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 22:23:22 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/2p1a-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-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 201 and 0 Target number of residues in the AU: 201 Target solvent content: 0.6456 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-3.4-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: 19 Cell parameters: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 75.28 4531 reflections ( 99.47 % complete ) and 0 restraints for refining 2734 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3398 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3046 (Rfree = 0.000) for 2734 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.64 Search for helices and strands: 0 residues in 0 chains, 2819 seeds are put forward NCS extension: 0 residues added, 2819 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 11 peptides. Score 0.267 Round 2: 132 peptides, 25 chains. Longest chain 8 peptides. Score 0.354 Round 3: 134 peptides, 24 chains. Longest chain 12 peptides. Score 0.387 Round 4: 136 peptides, 23 chains. Longest chain 12 peptides. Score 0.419 Round 5: 139 peptides, 20 chains. Longest chain 12 peptides. Score 0.498 Taking the results from Round 5 Chains 20, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5368 restraints for refining 2241 atoms. 4912 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2424 (Rfree = 0.000) for 2241 atoms. Found 3 (16 requested) and removed 14 (8 requested) atoms. Cycle 2: After refmac, R = 0.2234 (Rfree = 0.000) for 2213 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 3: After refmac, R = 0.2324 (Rfree = 0.000) for 2197 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. Cycle 4: After refmac, R = 0.2325 (Rfree = 0.000) for 2195 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 5: After refmac, R = 0.2271 (Rfree = 0.000) for 2185 atoms. Found 9 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.59 Search for helices and strands: 0 residues in 0 chains, 2319 seeds are put forward NCS extension: 0 residues added, 2319 seeds are put forward Round 1: 120 peptides, 24 chains. Longest chain 9 peptides. Score 0.311 Round 2: 131 peptides, 22 chains. Longest chain 11 peptides. Score 0.416 Round 3: 134 peptides, 22 chains. Longest chain 11 peptides. Score 0.431 Round 4: 131 peptides, 22 chains. Longest chain 13 peptides. Score 0.416 Round 5: 124 peptides, 18 chains. Longest chain 10 peptides. Score 0.469 Taking the results from Round 5 Chains 18, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5220 restraints for refining 2192 atoms. 4814 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2288 (Rfree = 0.000) for 2192 atoms. Found 8 (16 requested) and removed 18 (8 requested) atoms. Cycle 7: After refmac, R = 0.2217 (Rfree = 0.000) for 2176 atoms. Found 5 (16 requested) and removed 14 (8 requested) atoms. Cycle 8: After refmac, R = 0.2243 (Rfree = 0.000) for 2165 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2253 (Rfree = 0.000) for 2160 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2316 (Rfree = 0.000) for 2155 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2261 seeds are put forward NCS extension: 0 residues added, 2261 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 9 peptides. Score 0.267 Round 2: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.411 Round 3: 129 peptides, 21 chains. Longest chain 11 peptides. Score 0.428 Round 4: 122 peptides, 22 chains. Longest chain 13 peptides. Score 0.369 Round 5: 122 peptides, 22 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 3 Chains 21, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5245 restraints for refining 2203 atoms. 4834 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2226 (Rfree = 0.000) for 2203 atoms. Found 9 (16 requested) and removed 14 (8 requested) atoms. Cycle 12: After refmac, R = 0.2239 (Rfree = 0.000) for 2195 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Cycle 13: After refmac, R = 0.2598 (Rfree = 0.000) for 2188 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2053 (Rfree = 0.000) for 2189 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.1994 (Rfree = 0.000) for 2186 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.50 Search for helices and strands: 0 residues in 0 chains, 2279 seeds are put forward NCS extension: 0 residues added, 2279 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 8 peptides. Score 0.256 Round 2: 127 peptides, 24 chains. Longest chain 10 peptides. Score 0.350 Round 3: 122 peptides, 21 chains. Longest chain 10 peptides. Score 0.392 Round 4: 118 peptides, 19 chains. Longest chain 11 peptides. Score 0.416 Round 5: 120 peptides, 19 chains. Longest chain 11 peptides. Score 0.427 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 ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5341 restraints for refining 2241 atoms. 4956 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2190 (Rfree = 0.000) for 2241 atoms. Found 11 (16 requested) and removed 15 (8 requested) atoms. Cycle 17: After refmac, R = 0.2072 (Rfree = 0.000) for 2224 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2214 (Rfree = 0.000) for 2220 atoms. Found 14 (16 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.1775 (Rfree = 0.000) for 2217 atoms. Found 1 (16 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.1885 (Rfree = 0.000) for 2202 atoms. Found 12 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.55 Search for helices and strands: 0 residues in 0 chains, 2317 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2329 seeds are put forward Round 1: 99 peptides, 20 chains. Longest chain 8 peptides. Score 0.287 Round 2: 123 peptides, 23 chains. Longest chain 10 peptides. Score 0.351 Round 3: 128 peptides, 24 chains. Longest chain 11 peptides. Score 0.355 Round 4: 129 peptides, 22 chains. Longest chain 10 peptides. Score 0.406 Round 5: 125 peptides, 22 chains. Longest chain 15 peptides. Score 0.385 Taking the results from Round 4 Chains 22, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5195 restraints for refining 2214 atoms. 4789 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1937 (Rfree = 0.000) for 2214 atoms. Found 11 (16 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.2583 (Rfree = 0.000) for 2200 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.1912 (Rfree = 0.000) for 2199 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.1826 (Rfree = 0.000) for 2192 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2132 (Rfree = 0.000) for 2192 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2301 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2304 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 7 peptides. Score 0.255 Round 2: 113 peptides, 23 chains. Longest chain 8 peptides. Score 0.295 Round 3: 112 peptides, 21 chains. Longest chain 12 peptides. Score 0.337 Round 4: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.411 Round 5: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.326 Taking the results from Round 4 Chains 19, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5248 restraints for refining 2220 atoms. 4875 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1989 (Rfree = 0.000) for 2220 atoms. Found 8 (16 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2479 (Rfree = 0.000) for 2205 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 28: After refmac, R = 0.2023 (Rfree = 0.000) for 2199 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1737 (Rfree = 0.000) for 2187 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.1838 (Rfree = 0.000) for 2180 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.53 Search for helices and strands: 0 residues in 0 chains, 2256 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2270 seeds are put forward Round 1: 84 peptides, 19 chains. Longest chain 7 peptides. Score 0.220 Round 2: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.306 Round 3: 103 peptides, 19 chains. Longest chain 8 peptides. Score 0.335 Round 4: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.374 Round 5: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.350 Taking the results from Round 4 Chains 19, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5165 restraints for refining 2194 atoms. 4820 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2069 (Rfree = 0.000) for 2194 atoms. Found 13 (16 requested) and removed 13 (8 requested) atoms. Cycle 32: After refmac, R = 0.2138 (Rfree = 0.000) for 2189 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 33: After refmac, R = 0.2412 (Rfree = 0.000) for 2187 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 34: After refmac, R = 0.2148 (Rfree = 0.000) for 2191 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.1812 (Rfree = 0.000) for 2195 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2299 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2308 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 8 peptides. Score 0.238 Round 2: 121 peptides, 24 chains. Longest chain 10 peptides. Score 0.317 Round 3: 111 peptides, 21 chains. Longest chain 10 peptides. Score 0.332 Round 4: 109 peptides, 20 chains. Longest chain 10 peptides. Score 0.344 Round 5: 111 peptides, 20 chains. Longest chain 8 peptides. Score 0.355 Taking the results from Round 5 Chains 20, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5367 restraints for refining 2240 atoms. 5023 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2161 (Rfree = 0.000) for 2240 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 37: After refmac, R = 0.2055 (Rfree = 0.000) for 2237 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.1900 (Rfree = 0.000) for 2237 atoms. Found 12 (16 requested) and removed 11 (8 requested) atoms. Cycle 39: After refmac, R = 0.2286 (Rfree = 0.000) for 2234 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 40: After refmac, R = 0.1866 (Rfree = 0.000) for 2229 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 2308 seeds are put forward NCS extension: 0 residues added, 2308 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.253 Round 2: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 3: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.285 Round 4: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.341 Round 5: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.335 Taking the results from Round 4 Chains 16, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5400 restraints for refining 2240 atoms. 5116 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1967 (Rfree = 0.000) for 2240 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 42: After refmac, R = 0.1956 (Rfree = 0.000) for 2238 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2558 (Rfree = 0.000) for 2243 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.2515 (Rfree = 0.000) for 2235 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.1862 (Rfree = 0.000) for 2235 atoms. Found 13 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.50 Search for helices and strands: 0 residues in 0 chains, 2313 seeds are put forward NCS extension: 0 residues added, 2313 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 6 peptides. Score 0.237 Round 2: 89 peptides, 17 chains. Longest chain 8 peptides. Score 0.303 Round 3: 86 peptides, 17 chains. Longest chain 7 peptides. Score 0.285 Round 4: 93 peptides, 18 chains. Longest chain 7 peptides. Score 0.302 Round 5: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.311 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 70, 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. 4531 reflections ( 99.47 % complete ) and 5402 restraints for refining 2227 atoms. 5138 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1780 (Rfree = 0.000) for 2227 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2075 (Rfree = 0.000) for 2214 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1766 (Rfree = 0.000) for 2204 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1651 (Rfree = 0.000) for 2193 atoms. TimeTaking 42.67