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 2a9v-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-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/2a9v-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-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 22:23:11 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/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-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 492 and 0 Target number of residues in the AU: 492 Target solvent content: 0.6375 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 848 Adjusted target solvent content: 0.38 Input MTZ file: 2a9v-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 6784 target number of atoms Had to go as low as 0.55 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: 137.806 4.001 Wilson plot Bfac: 70.41 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 6772 reflections ( 99.99 % complete ) and 0 restraints for refining 7524 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3842 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3642 (Rfree = 0.000) for 7524 atoms. Found 27 (35 requested) and removed 209 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 4.27 Search for helices and strands: 0 residues in 0 chains, 7441 seeds are put forward NCS extension: 0 residues added, 7441 seeds are put forward Round 1: 128 peptides, 28 chains. Longest chain 9 peptides. Score 0.219 Round 2: 156 peptides, 35 chains. Longest chain 6 peptides. Score 0.215 Round 3: 150 peptides, 31 chains. Longest chain 8 peptides. Score 0.246 Round 4: 157 peptides, 30 chains. Longest chain 9 peptides. Score 0.278 Round 5: 162 peptides, 33 chains. Longest chain 9 peptides. Score 0.256 Taking the results from Round 4 Chains 30, Residues 127, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 16122 restraints for refining 6125 atoms. 15626 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2987 (Rfree = 0.000) for 6125 atoms. Found 22 (29 requested) and removed 84 (14 requested) atoms. Cycle 2: After refmac, R = 0.2978 (Rfree = 0.000) for 5983 atoms. Found 28 (28 requested) and removed 67 (14 requested) atoms. Cycle 3: After refmac, R = 0.2742 (Rfree = 0.000) for 5892 atoms. Found 20 (28 requested) and removed 61 (14 requested) atoms. Cycle 4: After refmac, R = 0.2827 (Rfree = 0.000) for 5805 atoms. Found 27 (27 requested) and removed 58 (13 requested) atoms. Cycle 5: After refmac, R = 0.2717 (Rfree = 0.000) for 5735 atoms. Found 27 (27 requested) and removed 52 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 4.21 Search for helices and strands: 0 residues in 0 chains, 5856 seeds are put forward NCS extension: 0 residues added, 5856 seeds are put forward Round 1: 143 peptides, 33 chains. Longest chain 7 peptides. Score 0.201 Round 2: 171 peptides, 36 chains. Longest chain 9 peptides. Score 0.246 Round 3: 191 peptides, 39 chains. Longest chain 10 peptides. Score 0.265 Round 4: 202 peptides, 39 chains. Longest chain 11 peptides. Score 0.294 Round 5: 209 peptides, 39 chains. Longest chain 12 peptides. Score 0.312 Taking the results from Round 5 Chains 39, Residues 170, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 12035 restraints for refining 5079 atoms. 11376 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2493 (Rfree = 0.000) for 5079 atoms. Found 24 (24 requested) and removed 52 (12 requested) atoms. Cycle 7: After refmac, R = 0.2292 (Rfree = 0.000) for 5024 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 8: After refmac, R = 0.2226 (Rfree = 0.000) for 4995 atoms. Found 23 (23 requested) and removed 39 (11 requested) atoms. Cycle 9: After refmac, R = 0.2298 (Rfree = 0.000) for 4963 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. Cycle 10: After refmac, R = 0.2229 (Rfree = 0.000) for 4939 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 4.11 Search for helices and strands: 0 residues in 0 chains, 5076 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5089 seeds are put forward Round 1: 222 peptides, 49 chains. Longest chain 7 peptides. Score 0.237 Round 2: 255 peptides, 49 chains. Longest chain 15 peptides. Score 0.319 Round 3: 239 peptides, 45 chains. Longest chain 10 peptides. Score 0.322 Round 4: 256 peptides, 44 chains. Longest chain 14 peptides. Score 0.372 Round 5: 249 peptides, 42 chains. Longest chain 15 peptides. Score 0.376 Taking the results from Round 5 Chains 42, Residues 207, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 11915 restraints for refining 5192 atoms. 11100 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2250 (Rfree = 0.000) for 5192 atoms. Found 24 (24 requested) and removed 65 (12 requested) atoms. Cycle 12: After refmac, R = 0.2224 (Rfree = 0.000) for 5118 atoms. Found 24 (24 requested) and removed 50 (12 requested) atoms. Cycle 13: After refmac, R = 0.2220 (Rfree = 0.000) for 5078 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 14: After refmac, R = 0.2025 (Rfree = 0.000) for 5054 atoms. Found 24 (24 requested) and removed 41 (12 requested) atoms. Cycle 15: After refmac, R = 0.1993 (Rfree = 0.000) for 5026 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 4.12 Search for helices and strands: 0 residues in 0 chains, 5179 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5196 seeds are put forward Round 1: 241 peptides, 50 chains. Longest chain 10 peptides. Score 0.275 Round 2: 263 peptides, 48 chains. Longest chain 16 peptides. Score 0.348 Round 3: 267 peptides, 47 chains. Longest chain 15 peptides. Score 0.367 Round 4: 271 peptides, 47 chains. Longest chain 14 peptides. Score 0.377 Round 5: 281 peptides, 42 chains. Longest chain 18 peptides. Score 0.447 Taking the results from Round 5 Chains 42, Residues 239, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 11924 restraints for refining 5337 atoms. 10921 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2160 (Rfree = 0.000) for 5337 atoms. Found 25 (25 requested) and removed 86 (12 requested) atoms. Cycle 17: After refmac, R = 0.1987 (Rfree = 0.000) for 5254 atoms. Found 25 (25 requested) and removed 56 (12 requested) atoms. Cycle 18: After refmac, R = 0.1893 (Rfree = 0.000) for 5213 atoms. Found 24 (24 requested) and removed 36 (12 requested) atoms. Cycle 19: After refmac, R = 0.1925 (Rfree = 0.000) for 5195 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 20: After refmac, R = 0.1830 (Rfree = 0.000) for 5175 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 5302 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 5335 seeds are put forward Round 1: 218 peptides, 46 chains. Longest chain 10 peptides. Score 0.259 Round 2: 244 peptides, 45 chains. Longest chain 13 peptides. Score 0.334 Round 3: 257 peptides, 48 chains. Longest chain 12 peptides. Score 0.334 Round 4: 258 peptides, 42 chains. Longest chain 13 peptides. Score 0.397 Round 5: 241 peptides, 39 chains. Longest chain 18 peptides. Score 0.388 Taking the results from Round 4 Chains 42, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 12525 restraints for refining 5408 atoms. 11703 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2070 (Rfree = 0.000) for 5408 atoms. Found 18 (25 requested) and removed 72 (12 requested) atoms. Cycle 22: After refmac, R = 0.2155 (Rfree = 0.000) for 5332 atoms. Found 25 (25 requested) and removed 40 (12 requested) atoms. Cycle 23: After refmac, R = 0.2054 (Rfree = 0.000) for 5300 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 24: After refmac, R = 0.2095 (Rfree = 0.000) for 5279 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 25: After refmac, R = 0.1482 (Rfree = 0.000) for 5262 atoms. Found 7 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 4.13 Search for helices and strands: 0 residues in 0 chains, 5407 seeds are put forward NCS extension: 0 residues added, 5407 seeds are put forward Round 1: 222 peptides, 49 chains. Longest chain 8 peptides. Score 0.237 Round 2: 256 peptides, 51 chains. Longest chain 10 peptides. Score 0.301 Round 3: 253 peptides, 48 chains. Longest chain 11 peptides. Score 0.325 Round 4: 253 peptides, 46 chains. Longest chain 13 peptides. Score 0.345 Round 5: 258 peptides, 47 chains. Longest chain 13 peptides. Score 0.347 Taking the results from Round 5 Chains 47, Residues 211, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 12765 restraints for refining 5518 atoms. 11946 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2083 (Rfree = 0.000) for 5518 atoms. Found 26 (26 requested) and removed 78 (13 requested) atoms. Cycle 27: After refmac, R = 0.2024 (Rfree = 0.000) for 5435 atoms. Found 25 (25 requested) and removed 40 (12 requested) atoms. Cycle 28: After refmac, R = 0.2063 (Rfree = 0.000) for 5406 atoms. Found 25 (25 requested) and removed 37 (12 requested) atoms. Cycle 29: After refmac, R = 0.1918 (Rfree = 0.000) for 5380 atoms. Found 25 (25 requested) and removed 40 (12 requested) atoms. Cycle 30: After refmac, R = 0.2026 (Rfree = 0.000) for 5352 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 4.10 Search for helices and strands: 0 residues in 0 chains, 5520 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5534 seeds are put forward Round 1: 206 peptides, 46 chains. Longest chain 7 peptides. Score 0.227 Round 2: 228 peptides, 45 chains. Longest chain 10 peptides. Score 0.295 Round 3: 247 peptides, 46 chains. Longest chain 13 peptides. Score 0.331 Round 4: 234 peptides, 43 chains. Longest chain 12 peptides. Score 0.331 Round 5: 224 peptides, 40 chains. Longest chain 13 peptides. Score 0.338 Taking the results from Round 5 Chains 40, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 12769 restraints for refining 5495 atoms. 12073 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2228 (Rfree = 0.000) for 5495 atoms. Found 26 (26 requested) and removed 66 (13 requested) atoms. Cycle 32: After refmac, R = 0.2112 (Rfree = 0.000) for 5434 atoms. Found 25 (25 requested) and removed 41 (12 requested) atoms. Cycle 33: After refmac, R = 0.2189 (Rfree = 0.000) for 5391 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 34: After refmac, R = 0.2083 (Rfree = 0.000) for 5366 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 35: After refmac, R = 0.2110 (Rfree = 0.000) for 5349 atoms. Found 25 (25 requested) and removed 41 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 4.19 Search for helices and strands: 0 residues in 0 chains, 5484 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5497 seeds are put forward Round 1: 182 peptides, 41 chains. Longest chain 8 peptides. Score 0.218 Round 2: 233 peptides, 44 chains. Longest chain 12 peptides. Score 0.318 Round 3: 230 peptides, 43 chains. Longest chain 11 peptides. Score 0.321 Round 4: 230 peptides, 44 chains. Longest chain 12 peptides. Score 0.310 Round 5: 214 peptides, 42 chains. Longest chain 12 peptides. Score 0.292 Taking the results from Round 3 Chains 43, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 12069 restraints for refining 5267 atoms. 11364 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1998 (Rfree = 0.000) for 5267 atoms. Found 25 (25 requested) and removed 44 (12 requested) atoms. Cycle 37: After refmac, R = 0.2076 (Rfree = 0.000) for 5224 atoms. Found 24 (24 requested) and removed 41 (12 requested) atoms. Cycle 38: After refmac, R = 0.2072 (Rfree = 0.000) for 5193 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 39: After refmac, R = 0.1979 (Rfree = 0.000) for 5172 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 40: After refmac, R = 0.2033 (Rfree = 0.000) for 5155 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 4.19 Search for helices and strands: 0 residues in 0 chains, 5308 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 5316 seeds are put forward Round 1: 174 peptides, 40 chains. Longest chain 9 peptides. Score 0.207 Round 2: 194 peptides, 37 chains. Longest chain 12 peptides. Score 0.295 Round 3: 181 peptides, 36 chains. Longest chain 12 peptides. Score 0.273 Round 4: 197 peptides, 35 chains. Longest chain 13 peptides. Score 0.325 Round 5: 182 peptides, 33 chains. Longest chain 13 peptides. Score 0.309 Taking the results from Round 4 Chains 35, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 11774 restraints for refining 5131 atoms. 11161 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2023 (Rfree = 0.000) for 5131 atoms. Found 24 (24 requested) and removed 45 (12 requested) atoms. Cycle 42: After refmac, R = 0.1934 (Rfree = 0.000) for 5094 atoms. Found 24 (24 requested) and removed 37 (12 requested) atoms. Cycle 43: After refmac, R = 0.1379 (Rfree = 0.000) for 5072 atoms. Found 7 (24 requested) and removed 19 (12 requested) atoms. Cycle 44: After refmac, R = 0.1223 (Rfree = 0.000) for 5055 atoms. Found 6 (24 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.1195 (Rfree = 0.000) for 5045 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 5173 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5187 seeds are put forward Round 1: 185 peptides, 43 chains. Longest chain 6 peptides. Score 0.204 Round 2: 191 peptides, 38 chains. Longest chain 9 peptides. Score 0.276 Round 3: 211 peptides, 40 chains. Longest chain 9 peptides. Score 0.306 Round 4: 205 peptides, 39 chains. Longest chain 9 peptides. Score 0.302 Round 5: 206 peptides, 38 chains. Longest chain 9 peptides. Score 0.315 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 168, 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 2a9v-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6772 reflections ( 99.99 % complete ) and 12066 restraints for refining 5264 atoms. 11432 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1784 (Rfree = 0.000) for 5264 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1872 (Rfree = 0.000) for 5243 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1815 (Rfree = 0.000) for 5222 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1743 (Rfree = 0.000) for 5205 atoms. TimeTaking 77.07