null Sun 23 Dec 22:23:02 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.6-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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.6-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 513 and 0 Target number of residues in the AU: 513 Target solvent content: 0.6220 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-3.6-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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 6784 target number of atoms Had to go as low as 0.50 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 3.600 Wilson plot Bfac: 62.41 9184 reflections ( 99.99 % complete ) and 0 restraints for refining 7469 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3743 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3682 (Rfree = 0.000) for 7469 atoms. Found 47 (47 requested) and removed 250 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.92 Search for helices and strands: 0 residues in 0 chains, 7380 seeds are put forward NCS extension: 0 residues added, 7380 seeds are put forward Round 1: 186 peptides, 42 chains. Longest chain 6 peptides. Score 0.218 Round 2: 237 peptides, 49 chains. Longest chain 13 peptides. Score 0.275 Round 3: 245 peptides, 48 chains. Longest chain 8 peptides. Score 0.305 Round 4: 244 peptides, 47 chains. Longest chain 11 peptides. Score 0.313 Round 5: 267 peptides, 52 chains. Longest chain 9 peptides. Score 0.318 Taking the results from Round 5 Chains 52, Residues 215, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 15543 restraints for refining 6147 atoms. 14722 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2919 (Rfree = 0.000) for 6147 atoms. Found 20 (39 requested) and removed 117 (19 requested) atoms. Cycle 2: After refmac, R = 0.2734 (Rfree = 0.000) for 5981 atoms. Found 33 (38 requested) and removed 58 (19 requested) atoms. Cycle 3: After refmac, R = 0.2539 (Rfree = 0.000) for 5916 atoms. Found 21 (38 requested) and removed 68 (19 requested) atoms. Cycle 4: After refmac, R = 0.2136 (Rfree = 0.000) for 5845 atoms. Found 10 (37 requested) and removed 36 (18 requested) atoms. Cycle 5: After refmac, R = 0.1991 (Rfree = 0.000) for 5805 atoms. Found 6 (37 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.90 Search for helices and strands: 0 residues in 0 chains, 5961 seeds are put forward NCS extension: 0 residues added, 5961 seeds are put forward Round 1: 249 peptides, 51 chains. Longest chain 8 peptides. Score 0.284 Round 2: 305 peptides, 56 chains. Longest chain 12 peptides. Score 0.366 Round 3: 318 peptides, 59 chains. Longest chain 10 peptides. Score 0.367 Round 4: 312 peptides, 56 chains. Longest chain 12 peptides. Score 0.382 Round 5: 301 peptides, 50 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 50, Residues 251, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14062 restraints for refining 5908 atoms. 13047 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2537 (Rfree = 0.000) for 5908 atoms. Found 12 (37 requested) and removed 110 (18 requested) atoms. Cycle 7: After refmac, R = 0.2371 (Rfree = 0.000) for 5769 atoms. Found 33 (37 requested) and removed 52 (18 requested) atoms. Cycle 8: After refmac, R = 0.2305 (Rfree = 0.000) for 5725 atoms. Found 23 (36 requested) and removed 46 (18 requested) atoms. Cycle 9: After refmac, R = 0.2264 (Rfree = 0.000) for 5689 atoms. Found 23 (36 requested) and removed 42 (18 requested) atoms. Cycle 10: After refmac, R = 0.1954 (Rfree = 0.000) for 5660 atoms. Found 13 (36 requested) and removed 35 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.90 Search for helices and strands: 0 residues in 0 chains, 5790 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5804 seeds are put forward Round 1: 260 peptides, 57 chains. Longest chain 7 peptides. Score 0.249 Round 2: 296 peptides, 55 chains. Longest chain 12 peptides. Score 0.355 Round 3: 328 peptides, 58 chains. Longest chain 14 peptides. Score 0.398 Round 4: 306 peptides, 52 chains. Longest chain 20 peptides. Score 0.406 Round 5: 307 peptides, 49 chains. Longest chain 20 peptides. Score 0.436 Taking the results from Round 5 Chains 49, Residues 258, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14170 restraints for refining 5929 atoms. 13187 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2276 (Rfree = 0.000) for 5929 atoms. Found 14 (38 requested) and removed 64 (19 requested) atoms. Cycle 12: After refmac, R = 0.2196 (Rfree = 0.000) for 5842 atoms. Found 26 (37 requested) and removed 52 (18 requested) atoms. Cycle 13: After refmac, R = 0.2102 (Rfree = 0.000) for 5798 atoms. Found 19 (37 requested) and removed 42 (18 requested) atoms. Cycle 14: After refmac, R = 0.2038 (Rfree = 0.000) for 5770 atoms. Found 25 (37 requested) and removed 35 (18 requested) atoms. Cycle 15: After refmac, R = 0.2063 (Rfree = 0.000) for 5756 atoms. Found 22 (36 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.90 Search for helices and strands: 0 residues in 0 chains, 5925 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 5944 seeds are put forward Round 1: 263 peptides, 57 chains. Longest chain 9 peptides. Score 0.257 Round 2: 312 peptides, 57 chains. Longest chain 13 peptides. Score 0.372 Round 3: 296 peptides, 53 chains. Longest chain 10 peptides. Score 0.375 Round 4: 296 peptides, 48 chains. Longest chain 17 peptides. Score 0.422 Round 5: 309 peptides, 56 chains. Longest chain 11 peptides. Score 0.375 Taking the results from Round 4 Chains 49, Residues 248, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14303 restraints for refining 6005 atoms. 13308 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2211 (Rfree = 0.000) for 6005 atoms. Found 21 (38 requested) and removed 76 (19 requested) atoms. Cycle 17: After refmac, R = 0.2127 (Rfree = 0.000) for 5931 atoms. Found 24 (38 requested) and removed 47 (19 requested) atoms. Cycle 18: After refmac, R = 0.2020 (Rfree = 0.000) for 5897 atoms. Found 32 (37 requested) and removed 36 (18 requested) atoms. Cycle 19: After refmac, R = 0.2041 (Rfree = 0.000) for 5886 atoms. Found 35 (37 requested) and removed 34 (18 requested) atoms. Cycle 20: After refmac, R = 0.2002 (Rfree = 0.000) for 5882 atoms. Found 23 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.85 Search for helices and strands: 0 residues in 0 chains, 6040 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6065 seeds are put forward Round 1: 252 peptides, 55 chains. Longest chain 8 peptides. Score 0.250 Round 2: 268 peptides, 49 chains. Longest chain 12 peptides. Score 0.350 Round 3: 267 peptides, 49 chains. Longest chain 11 peptides. Score 0.348 Round 4: 267 peptides, 47 chains. Longest chain 10 peptides. Score 0.367 Round 5: 271 peptides, 47 chains. Longest chain 13 peptides. Score 0.377 Taking the results from Round 5 Chains 47, Residues 224, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 15095 restraints for refining 6130 atoms. 14216 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2257 (Rfree = 0.000) for 6130 atoms. Found 29 (39 requested) and removed 79 (19 requested) atoms. Cycle 22: After refmac, R = 0.2112 (Rfree = 0.000) for 6058 atoms. Found 35 (39 requested) and removed 45 (19 requested) atoms. Cycle 23: After refmac, R = 0.2048 (Rfree = 0.000) for 6041 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 24: After refmac, R = 0.1661 (Rfree = 0.000) for 6034 atoms. Found 8 (38 requested) and removed 27 (19 requested) atoms. Cycle 25: After refmac, R = 0.1605 (Rfree = 0.000) for 6010 atoms. Found 1 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.88 Search for helices and strands: 0 residues in 0 chains, 6109 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6122 seeds are put forward Round 1: 231 peptides, 49 chains. Longest chain 11 peptides. Score 0.260 Round 2: 247 peptides, 41 chains. Longest chain 13 peptides. Score 0.382 Round 3: 256 peptides, 43 chains. Longest chain 16 peptides. Score 0.382 Round 4: 255 peptides, 40 chains. Longest chain 16 peptides. Score 0.410 Round 5: 256 peptides, 41 chains. Longest chain 24 peptides. Score 0.402 Taking the results from Round 4 Chains 40, Residues 215, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 15073 restraints for refining 6132 atoms. 14233 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2170 (Rfree = 0.000) for 6132 atoms. Found 20 (39 requested) and removed 58 (19 requested) atoms. Cycle 27: After refmac, R = 0.2034 (Rfree = 0.000) for 6075 atoms. Found 30 (39 requested) and removed 40 (19 requested) atoms. Cycle 28: After refmac, R = 0.2006 (Rfree = 0.000) for 6057 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 29: After refmac, R = 0.1938 (Rfree = 0.000) for 6052 atoms. Found 25 (38 requested) and removed 35 (19 requested) atoms. Cycle 30: After refmac, R = 0.1644 (Rfree = 0.000) for 6034 atoms. Found 7 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.87 Search for helices and strands: 0 residues in 0 chains, 6199 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 6217 seeds are put forward Round 1: 218 peptides, 46 chains. Longest chain 10 peptides. Score 0.259 Round 2: 267 peptides, 46 chains. Longest chain 18 peptides. Score 0.377 Round 3: 261 peptides, 43 chains. Longest chain 13 peptides. Score 0.393 Round 4: 266 peptides, 40 chains. Longest chain 24 peptides. Score 0.434 Round 5: 263 peptides, 45 chains. Longest chain 15 peptides. Score 0.378 Taking the results from Round 4 Chains 42, Residues 226, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14790 restraints for refining 6124 atoms. 13902 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2096 (Rfree = 0.000) for 6124 atoms. Found 32 (39 requested) and removed 60 (19 requested) atoms. Cycle 32: After refmac, R = 0.1995 (Rfree = 0.000) for 6074 atoms. Found 39 (39 requested) and removed 38 (19 requested) atoms. Cycle 33: After refmac, R = 0.1902 (Rfree = 0.000) for 6057 atoms. Found 36 (38 requested) and removed 32 (19 requested) atoms. Cycle 34: After refmac, R = 0.1895 (Rfree = 0.000) for 6050 atoms. Found 28 (38 requested) and removed 29 (19 requested) atoms. Cycle 35: After refmac, R = 0.1927 (Rfree = 0.000) for 6042 atoms. Found 38 (38 requested) and removed 40 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.85 Search for helices and strands: 0 residues in 0 chains, 6216 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 6243 seeds are put forward Round 1: 210 peptides, 43 chains. Longest chain 17 peptides. Score 0.271 Round 2: 247 peptides, 42 chains. Longest chain 21 peptides. Score 0.371 Round 3: 221 peptides, 42 chains. Longest chain 11 peptides. Score 0.309 Round 4: 236 peptides, 38 chains. Longest chain 21 peptides. Score 0.387 Round 5: 215 peptides, 38 chains. Longest chain 11 peptides. Score 0.337 Taking the results from Round 4 Chains 38, Residues 198, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 15002 restraints for refining 6150 atoms. 14226 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2045 (Rfree = 0.000) for 6150 atoms. Found 34 (39 requested) and removed 56 (19 requested) atoms. Cycle 37: After refmac, R = 0.2099 (Rfree = 0.000) for 6107 atoms. Found 39 (39 requested) and removed 47 (19 requested) atoms. Cycle 38: After refmac, R = 0.2015 (Rfree = 0.000) for 6088 atoms. Found 32 (39 requested) and removed 37 (19 requested) atoms. Cycle 39: After refmac, R = 0.1978 (Rfree = 0.000) for 6075 atoms. Found 39 (39 requested) and removed 33 (19 requested) atoms. Cycle 40: After refmac, R = 0.1993 (Rfree = 0.000) for 6075 atoms. Found 39 (39 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.88 Search for helices and strands: 0 residues in 0 chains, 6243 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 6277 seeds are put forward Round 1: 196 peptides, 44 chains. Longest chain 7 peptides. Score 0.223 Round 2: 217 peptides, 42 chains. Longest chain 8 peptides. Score 0.299 Round 3: 208 peptides, 38 chains. Longest chain 11 peptides. Score 0.320 Round 4: 226 peptides, 42 chains. Longest chain 9 peptides. Score 0.322 Round 5: 225 peptides, 38 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 5 Chains 38, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 15030 restraints for refining 6122 atoms. 14320 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2016 (Rfree = 0.000) for 6122 atoms. Found 37 (39 requested) and removed 52 (19 requested) atoms. Cycle 42: After refmac, R = 0.1965 (Rfree = 0.000) for 6097 atoms. Found 39 (39 requested) and removed 44 (19 requested) atoms. Cycle 43: After refmac, R = 0.1890 (Rfree = 0.000) for 6083 atoms. Found 25 (39 requested) and removed 37 (19 requested) atoms. Cycle 44: After refmac, R = 0.1843 (Rfree = 0.000) for 6064 atoms. Found 35 (38 requested) and removed 25 (19 requested) atoms. Cycle 45: After refmac, R = 0.1502 (Rfree = 0.000) for 6069 atoms. Found 5 (38 requested) and removed 29 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.86 Search for helices and strands: 0 residues in 0 chains, 6192 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6212 seeds are put forward Round 1: 182 peptides, 41 chains. Longest chain 7 peptides. Score 0.218 Round 2: 216 peptides, 40 chains. Longest chain 12 peptides. Score 0.318 Round 3: 216 peptides, 38 chains. Longest chain 12 peptides. Score 0.339 Round 4: 197 peptides, 33 chains. Longest chain 11 peptides. Score 0.347 Round 5: 198 peptides, 34 chains. Longest chain 16 peptides. Score 0.339 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 164, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9184 reflections ( 99.99 % complete ) and 14931 restraints for refining 6059 atoms. 14308 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1898 (Rfree = 0.000) for 6059 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1977 (Rfree = 0.000) for 6023 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1960 (Rfree = 0.000) for 5999 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1933 (Rfree = 0.000) for 5974 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:46:24 GMT 2018 Job finished. TimeTaking 83.38 Used memory is bytes: 11926088