null Mon 24 Dec 00:52:09 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 2iiu-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2iiu-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2iiu-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.8-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/2iiu-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.8-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 00:52:14 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/2iiu-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.8-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 497 and 0 Target number of residues in the AU: 497 Target solvent content: 0.6475 Checking the provided sequence file Detected sequence length: 227 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 681 Adjusted target solvent content: 0.52 Input MTZ file: 2iiu-3.8-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: 155 Cell parameters: 99.900 99.900 397.311 90.000 90.000 120.000 Input sequence file: 2iiu-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5448 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: 132.437 3.801 Wilson plot Bfac: 76.41 7831 reflections ( 98.91 % complete ) and 0 restraints for refining 6059 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3661 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3374 (Rfree = 0.000) for 6059 atoms. Found 27 (33 requested) and removed 63 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 6124 seeds are put forward NCS extension: 0 residues added, 6124 seeds are put forward Round 1: 163 peptides, 36 chains. Longest chain 8 peptides. Score 0.222 Round 2: 226 peptides, 44 chains. Longest chain 12 peptides. Score 0.297 Round 3: 230 peptides, 42 chains. Longest chain 11 peptides. Score 0.327 Round 4: 270 peptides, 49 chains. Longest chain 15 peptides. Score 0.349 Round 5: 248 peptides, 42 chains. Longest chain 14 peptides. Score 0.368 Taking the results from Round 5 Chains 42, Residues 206, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 12087 restraints for refining 4927 atoms. 11305 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2831 (Rfree = 0.000) for 4927 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 2: After refmac, R = 0.2664 (Rfree = 0.000) for 4891 atoms. Found 14 (27 requested) and removed 14 (13 requested) atoms. Cycle 3: After refmac, R = 0.2628 (Rfree = 0.000) for 4878 atoms. Found 5 (26 requested) and removed 15 (13 requested) atoms. Cycle 4: After refmac, R = 0.2582 (Rfree = 0.000) for 4859 atoms. Found 7 (26 requested) and removed 14 (13 requested) atoms. Cycle 5: After refmac, R = 0.2529 (Rfree = 0.000) for 4846 atoms. Found 3 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 5012 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5028 seeds are put forward Round 1: 221 peptides, 46 chains. Longest chain 10 peptides. Score 0.264 Round 2: 272 peptides, 48 chains. Longest chain 18 peptides. Score 0.363 Round 3: 261 peptides, 47 chains. Longest chain 11 peptides. Score 0.348 Round 4: 273 peptides, 41 chains. Longest chain 19 peptides. Score 0.432 Round 5: 265 peptides, 42 chains. Longest chain 21 peptides. Score 0.405 Taking the results from Round 4 Chains 41, Residues 232, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11860 restraints for refining 4896 atoms. 10973 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2732 (Rfree = 0.000) for 4896 atoms. Found 24 (26 requested) and removed 33 (13 requested) atoms. Cycle 7: After refmac, R = 0.2561 (Rfree = 0.000) for 4868 atoms. Found 9 (26 requested) and removed 20 (13 requested) atoms. Cycle 8: After refmac, R = 0.2490 (Rfree = 0.000) for 4849 atoms. Found 4 (26 requested) and removed 17 (13 requested) atoms. Cycle 9: After refmac, R = 0.2410 (Rfree = 0.000) for 4829 atoms. Found 6 (26 requested) and removed 16 (13 requested) atoms. Cycle 10: After refmac, R = 0.2352 (Rfree = 0.000) for 4812 atoms. Found 5 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.40 Search for helices and strands: 0 residues in 0 chains, 4977 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 4992 seeds are put forward Round 1: 234 peptides, 46 chains. Longest chain 11 peptides. Score 0.296 Round 2: 268 peptides, 47 chains. Longest chain 13 peptides. Score 0.364 Round 3: 260 peptides, 44 chains. Longest chain 13 peptides. Score 0.375 Round 4: 272 peptides, 46 chains. Longest chain 15 peptides. Score 0.383 Round 5: 258 peptides, 43 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 4 Chains 46, Residues 226, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11595 restraints for refining 4927 atoms. 10658 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2527 (Rfree = 0.000) for 4927 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 12: After refmac, R = 0.2351 (Rfree = 0.000) for 4899 atoms. Found 8 (27 requested) and removed 24 (13 requested) atoms. Cycle 13: After refmac, R = 0.2228 (Rfree = 0.000) for 4877 atoms. Found 3 (26 requested) and removed 21 (13 requested) atoms. Cycle 14: After refmac, R = 0.2193 (Rfree = 0.000) for 4852 atoms. Found 4 (26 requested) and removed 14 (13 requested) atoms. Cycle 15: After refmac, R = 0.2175 (Rfree = 0.000) for 4836 atoms. Found 2 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 4998 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 5017 seeds are put forward Round 1: 255 peptides, 50 chains. Longest chain 11 peptides. Score 0.305 Round 2: 269 peptides, 45 chains. Longest chain 13 peptides. Score 0.386 Round 3: 283 peptides, 48 chains. Longest chain 19 peptides. Score 0.388 Round 4: 269 peptides, 47 chains. Longest chain 11 peptides. Score 0.366 Round 5: 279 peptides, 46 chains. Longest chain 16 peptides. Score 0.398 Taking the results from Round 5 Chains 46, Residues 233, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11723 restraints for refining 4928 atoms. 10814 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2563 (Rfree = 0.000) for 4928 atoms. Found 21 (27 requested) and removed 23 (13 requested) atoms. Cycle 17: After refmac, R = 0.2424 (Rfree = 0.000) for 4917 atoms. Found 7 (27 requested) and removed 16 (13 requested) atoms. Cycle 18: After refmac, R = 0.2378 (Rfree = 0.000) for 4906 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.2366 (Rfree = 0.000) for 4896 atoms. Found 5 (26 requested) and removed 15 (13 requested) atoms. Cycle 20: After refmac, R = 0.2342 (Rfree = 0.000) for 4886 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 5077 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5095 seeds are put forward Round 1: 234 peptides, 46 chains. Longest chain 11 peptides. Score 0.296 Round 2: 270 peptides, 44 chains. Longest chain 13 peptides. Score 0.397 Round 3: 287 peptides, 46 chains. Longest chain 23 peptides. Score 0.415 Round 4: 289 peptides, 46 chains. Longest chain 14 peptides. Score 0.419 Round 5: 282 peptides, 44 chains. Longest chain 16 peptides. Score 0.423 Taking the results from Round 5 Chains 44, Residues 238, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11861 restraints for refining 4927 atoms. 10953 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2642 (Rfree = 0.000) for 4927 atoms. Found 17 (27 requested) and removed 16 (13 requested) atoms. Cycle 22: After refmac, R = 0.2542 (Rfree = 0.000) for 4919 atoms. Found 10 (27 requested) and removed 14 (13 requested) atoms. Cycle 23: After refmac, R = 0.2487 (Rfree = 0.000) for 4907 atoms. Found 4 (26 requested) and removed 15 (13 requested) atoms. Cycle 24: After refmac, R = 0.2462 (Rfree = 0.000) for 4893 atoms. Found 0 (26 requested) and removed 14 (13 requested) atoms. Cycle 25: After refmac, R = 0.2446 (Rfree = 0.000) for 4877 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 5022 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 5043 seeds are put forward Round 1: 237 peptides, 45 chains. Longest chain 12 peptides. Score 0.313 Round 2: 275 peptides, 46 chains. Longest chain 19 peptides. Score 0.389 Round 3: 283 peptides, 49 chains. Longest chain 15 peptides. Score 0.378 Round 4: 283 peptides, 45 chains. Longest chain 19 peptides. Score 0.416 Round 5: 255 peptides, 44 chains. Longest chain 10 peptides. Score 0.364 Taking the results from Round 4 Chains 45, Residues 238, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11868 restraints for refining 4928 atoms. 10961 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2504 (Rfree = 0.000) for 4928 atoms. Found 18 (27 requested) and removed 16 (13 requested) atoms. Cycle 27: After refmac, R = 0.2408 (Rfree = 0.000) for 4919 atoms. Found 8 (27 requested) and removed 13 (13 requested) atoms. Cycle 28: After refmac, R = 0.2398 (Rfree = 0.000) for 4912 atoms. Found 5 (26 requested) and removed 15 (13 requested) atoms. Cycle 29: After refmac, R = 0.2351 (Rfree = 0.000) for 4899 atoms. Found 3 (26 requested) and removed 15 (13 requested) atoms. Cycle 30: After refmac, R = 0.2348 (Rfree = 0.000) for 4884 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 5050 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 5080 seeds are put forward Round 1: 214 peptides, 44 chains. Longest chain 8 peptides. Score 0.267 Round 2: 254 peptides, 42 chains. Longest chain 13 peptides. Score 0.382 Round 3: 263 peptides, 43 chains. Longest chain 16 peptides. Score 0.392 Round 4: 275 peptides, 46 chains. Longest chain 19 peptides. Score 0.389 Round 5: 282 peptides, 49 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 3 Chains 43, Residues 220, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11901 restraints for refining 4928 atoms. 11064 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2541 (Rfree = 0.000) for 4928 atoms. Found 23 (27 requested) and removed 15 (13 requested) atoms. Cycle 32: After refmac, R = 0.2426 (Rfree = 0.000) for 4927 atoms. Found 10 (27 requested) and removed 13 (13 requested) atoms. Cycle 33: After refmac, R = 0.2388 (Rfree = 0.000) for 4921 atoms. Found 1 (27 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.2387 (Rfree = 0.000) for 4906 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.2361 (Rfree = 0.000) for 4893 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 5042 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5063 seeds are put forward Round 1: 197 peptides, 42 chains. Longest chain 12 peptides. Score 0.246 Round 2: 241 peptides, 43 chains. Longest chain 16 peptides. Score 0.342 Round 3: 251 peptides, 47 chains. Longest chain 11 peptides. Score 0.326 Round 4: 263 peptides, 48 chains. Longest chain 13 peptides. Score 0.343 Round 5: 233 peptides, 42 chains. Longest chain 13 peptides. Score 0.334 Taking the results from Round 4 Chains 48, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11935 restraints for refining 4928 atoms. 11123 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2476 (Rfree = 0.000) for 4928 atoms. Found 15 (27 requested) and removed 13 (13 requested) atoms. Cycle 37: After refmac, R = 0.2397 (Rfree = 0.000) for 4923 atoms. Found 3 (27 requested) and removed 15 (13 requested) atoms. Cycle 38: After refmac, R = 0.2368 (Rfree = 0.000) for 4909 atoms. Found 1 (26 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.2353 (Rfree = 0.000) for 4894 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2366 (Rfree = 0.000) for 4881 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 5033 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5049 seeds are put forward Round 1: 187 peptides, 40 chains. Longest chain 7 peptides. Score 0.241 Round 2: 219 peptides, 42 chains. Longest chain 12 peptides. Score 0.301 Round 3: 235 peptides, 46 chains. Longest chain 12 peptides. Score 0.298 Round 4: 216 peptides, 41 chains. Longest chain 10 peptides. Score 0.304 Round 5: 229 peptides, 42 chains. Longest chain 12 peptides. Score 0.325 Taking the results from Round 5 Chains 42, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 12030 restraints for refining 4928 atoms. 11324 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2473 (Rfree = 0.000) for 4928 atoms. Found 16 (27 requested) and removed 15 (13 requested) atoms. Cycle 42: After refmac, R = 0.2400 (Rfree = 0.000) for 4920 atoms. Found 6 (27 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.2380 (Rfree = 0.000) for 4910 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.2360 (Rfree = 0.000) for 4902 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.2346 (Rfree = 0.000) for 4889 atoms. Found 7 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 5042 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5056 seeds are put forward Round 1: 182 peptides, 41 chains. Longest chain 8 peptides. Score 0.217 Round 2: 210 peptides, 42 chains. Longest chain 10 peptides. Score 0.279 Round 3: 216 peptides, 40 chains. Longest chain 17 peptides. Score 0.314 Round 4: 230 peptides, 41 chains. Longest chain 12 peptides. Score 0.337 Round 5: 227 peptides, 39 chains. Longest chain 14 peptides. Score 0.350 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 188, 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 2iiu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7831 reflections ( 98.91 % complete ) and 11999 restraints for refining 4928 atoms. 11286 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2485 (Rfree = 0.000) for 4928 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2418 (Rfree = 0.000) for 4907 atoms. Found 0 (27 requested) and removed 10 (13 requested) atoms. Cycle 48: After refmac, R = 0.2406 (Rfree = 0.000) for 4897 atoms. Found 0 (26 requested) and removed 0 (13 requested) atoms. Cycle 49: After refmac, R = 0.2397 (Rfree = 0.000) for 4897 atoms. Found 0 (26 requested) and removed 1 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:48:40 GMT 2018 Job finished. TimeTaking 56.52 Used memory is bytes: 7516360