Mon 24 Dec 01:00:47 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 2afb-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-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/2afb-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-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 01:00:52 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/2afb-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-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 497 and 0 Target number of residues in the AU: 497 Target solvent content: 0.6332 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.75 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: 97.203 3.600 Wilson plot Bfac: 68.03 8743 reflections ( 99.44 % complete ) and 0 restraints for refining 6199 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3205 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3069 (Rfree = 0.000) for 6199 atoms. Found 39 (39 requested) and removed 41 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 6335 seeds are put forward NCS extension: 0 residues added, 6335 seeds are put forward Round 1: 273 peptides, 52 chains. Longest chain 10 peptides. Score 0.332 Round 2: 361 peptides, 56 chains. Longest chain 17 peptides. Score 0.484 Round 3: 367 peptides, 57 chains. Longest chain 14 peptides. Score 0.487 Round 4: 404 peptides, 59 chains. Longest chain 18 peptides. Score 0.540 Round 5: 426 peptides, 54 chains. Longest chain 23 peptides. Score 0.614 Taking the results from Round 5 Chains 54, Residues 372, Estimated correctness of the model 20.0 % 8 chains (58 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 10782 restraints for refining 5090 atoms. 9161 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2763 (Rfree = 0.000) for 5090 atoms. Found 25 (32 requested) and removed 37 (16 requested) atoms. Cycle 2: After refmac, R = 0.2523 (Rfree = 0.000) for 4948 atoms. Found 28 (32 requested) and removed 27 (16 requested) atoms. Cycle 3: After refmac, R = 0.2360 (Rfree = 0.000) for 4903 atoms. Found 21 (31 requested) and removed 26 (15 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2282 (Rfree = 0.000) for 4858 atoms. Found 17 (31 requested) and removed 29 (15 requested) atoms. Cycle 5: After refmac, R = 0.2126 (Rfree = 0.000) for 4827 atoms. Found 11 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5007 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5023 seeds are put forward Round 1: 364 peptides, 61 chains. Longest chain 17 peptides. Score 0.447 Round 2: 426 peptides, 61 chains. Longest chain 27 peptides. Score 0.563 Round 3: 410 peptides, 56 chains. Longest chain 21 peptides. Score 0.574 Round 4: 426 peptides, 55 chains. Longest chain 28 peptides. Score 0.607 Round 5: 427 peptides, 53 chains. Longest chain 21 peptides. Score 0.623 Taking the results from Round 5 Chains 57, Residues 374, Estimated correctness of the model 23.4 % 7 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 10843 restraints for refining 5091 atoms. 9224 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2447 (Rfree = 0.000) for 5091 atoms. Found 22 (32 requested) and removed 49 (16 requested) atoms. Cycle 7: After refmac, R = 0.2318 (Rfree = 0.000) for 5023 atoms. Found 14 (32 requested) and removed 28 (16 requested) atoms. Cycle 8: After refmac, R = 0.2253 (Rfree = 0.000) for 4988 atoms. Found 14 (32 requested) and removed 29 (16 requested) atoms. Cycle 9: After refmac, R = 0.2247 (Rfree = 0.000) for 4953 atoms. Found 11 (31 requested) and removed 20 (15 requested) atoms. Cycle 10: After refmac, R = 0.2160 (Rfree = 0.000) for 4935 atoms. Found 18 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5125 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5140 seeds are put forward Round 1: 356 peptides, 62 chains. Longest chain 15 peptides. Score 0.422 Round 2: 393 peptides, 57 chains. Longest chain 21 peptides. Score 0.536 Round 3: 386 peptides, 54 chains. Longest chain 20 peptides. Score 0.547 Round 4: 385 peptides, 54 chains. Longest chain 27 peptides. Score 0.546 Round 5: 416 peptides, 54 chains. Longest chain 27 peptides. Score 0.598 Taking the results from Round 5 Chains 56, Residues 362, Estimated correctness of the model 13.9 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11453 restraints for refining 5091 atoms. 9962 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2536 (Rfree = 0.000) for 5091 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 12: After refmac, R = 0.2283 (Rfree = 0.000) for 5049 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 13: After refmac, R = 0.2253 (Rfree = 0.000) for 5034 atoms. Found 30 (32 requested) and removed 26 (16 requested) atoms. Cycle 14: After refmac, R = 0.2207 (Rfree = 0.000) for 5028 atoms. Found 26 (32 requested) and removed 20 (16 requested) atoms. Cycle 15: After refmac, R = 0.2135 (Rfree = 0.000) for 5019 atoms. Found 24 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 5228 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5243 seeds are put forward Round 1: 347 peptides, 56 chains. Longest chain 18 peptides. Score 0.456 Round 2: 415 peptides, 55 chains. Longest chain 22 peptides. Score 0.589 Round 3: 406 peptides, 56 chains. Longest chain 23 peptides. Score 0.567 Round 4: 381 peptides, 53 chains. Longest chain 20 peptides. Score 0.546 Round 5: 397 peptides, 51 chains. Longest chain 21 peptides. Score 0.589 Taking the results from Round 5 Chains 54, Residues 346, Estimated correctness of the model 10.3 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11316 restraints for refining 5090 atoms. 9858 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2475 (Rfree = 0.000) for 5090 atoms. Found 28 (32 requested) and removed 31 (16 requested) atoms. Cycle 17: After refmac, R = 0.2205 (Rfree = 0.000) for 5035 atoms. Found 18 (32 requested) and removed 25 (16 requested) atoms. Cycle 18: After refmac, R = 0.2102 (Rfree = 0.000) for 5006 atoms. Found 16 (32 requested) and removed 22 (16 requested) atoms. Cycle 19: After refmac, R = 0.2018 (Rfree = 0.000) for 4985 atoms. Found 13 (32 requested) and removed 22 (16 requested) atoms. Cycle 20: After refmac, R = 0.1984 (Rfree = 0.000) for 4967 atoms. Found 12 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5174 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 5215 seeds are put forward Round 1: 320 peptides, 60 chains. Longest chain 15 peptides. Score 0.362 Round 2: 382 peptides, 57 chains. Longest chain 24 peptides. Score 0.516 Round 3: 381 peptides, 60 chains. Longest chain 15 peptides. Score 0.489 Round 4: 370 peptides, 56 chains. Longest chain 16 peptides. Score 0.502 Round 5: 370 peptides, 53 chains. Longest chain 22 peptides. Score 0.526 Taking the results from Round 5 Chains 55, Residues 317, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11432 restraints for refining 5088 atoms. 10103 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2209 (Rfree = 0.000) for 5088 atoms. Found 25 (32 requested) and removed 26 (16 requested) atoms. Cycle 22: After refmac, R = 0.2039 (Rfree = 0.000) for 5060 atoms. Found 15 (32 requested) and removed 24 (16 requested) atoms. Cycle 23: After refmac, R = 0.2032 (Rfree = 0.000) for 5037 atoms. Found 20 (32 requested) and removed 22 (16 requested) atoms. Cycle 24: After refmac, R = 0.1956 (Rfree = 0.000) for 5028 atoms. Found 17 (32 requested) and removed 21 (16 requested) atoms. Cycle 25: After refmac, R = 0.1925 (Rfree = 0.000) for 5015 atoms. Found 14 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5175 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 5205 seeds are put forward Round 1: 290 peptides, 53 chains. Longest chain 17 peptides. Score 0.361 Round 2: 327 peptides, 51 chains. Longest chain 12 peptides. Score 0.460 Round 3: 335 peptides, 54 chains. Longest chain 13 peptides. Score 0.450 Round 4: 332 peptides, 53 chains. Longest chain 13 peptides. Score 0.452 Round 5: 321 peptides, 49 chains. Longest chain 15 peptides. Score 0.466 Taking the results from Round 5 Chains 50, Residues 272, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11959 restraints for refining 5091 atoms. 10883 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2144 (Rfree = 0.000) for 5091 atoms. Found 28 (32 requested) and removed 21 (16 requested) atoms. Cycle 27: After refmac, R = 0.2058 (Rfree = 0.000) for 5068 atoms. Found 20 (32 requested) and removed 22 (16 requested) atoms. Cycle 28: After refmac, R = 0.1994 (Rfree = 0.000) for 5061 atoms. Found 29 (32 requested) and removed 21 (16 requested) atoms. Cycle 29: After refmac, R = 0.1911 (Rfree = 0.000) for 5061 atoms. Found 30 (32 requested) and removed 22 (16 requested) atoms. Cycle 30: After refmac, R = 0.1792 (Rfree = 0.000) for 5065 atoms. Found 17 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 5268 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5282 seeds are put forward Round 1: 284 peptides, 57 chains. Longest chain 10 peptides. Score 0.308 Round 2: 325 peptides, 55 chains. Longest chain 13 peptides. Score 0.419 Round 3: 323 peptides, 54 chains. Longest chain 13 peptides. Score 0.424 Round 4: 331 peptides, 53 chains. Longest chain 16 peptides. Score 0.450 Round 5: 332 peptides, 53 chains. Longest chain 14 peptides. Score 0.452 Taking the results from Round 5 Chains 55, Residues 279, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11858 restraints for refining 5089 atoms. 10742 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2298 (Rfree = 0.000) for 5089 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 32: After refmac, R = 0.2019 (Rfree = 0.000) for 5061 atoms. Found 32 (32 requested) and removed 17 (16 requested) atoms. Cycle 33: After refmac, R = 0.1975 (Rfree = 0.000) for 5061 atoms. Found 24 (32 requested) and removed 20 (16 requested) atoms. Cycle 34: After refmac, R = 0.1837 (Rfree = 0.000) for 5055 atoms. Found 31 (32 requested) and removed 21 (16 requested) atoms. Cycle 35: After refmac, R = 0.1856 (Rfree = 0.000) for 5054 atoms. Found 30 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5243 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5256 seeds are put forward Round 1: 240 peptides, 48 chains. Longest chain 11 peptides. Score 0.293 Round 2: 300 peptides, 53 chains. Longest chain 13 peptides. Score 0.384 Round 3: 313 peptides, 49 chains. Longest chain 15 peptides. Score 0.449 Round 4: 295 peptides, 47 chains. Longest chain 16 peptides. Score 0.430 Round 5: 304 peptides, 51 chains. Longest chain 21 peptides. Score 0.412 Taking the results from Round 3 Chains 50, Residues 264, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11847 restraints for refining 5090 atoms. 10767 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2010 (Rfree = 0.000) for 5090 atoms. Found 32 (32 requested) and removed 21 (16 requested) atoms. Cycle 37: After refmac, R = 0.1907 (Rfree = 0.000) for 5072 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 38: After refmac, R = 0.1826 (Rfree = 0.000) for 5070 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 39: After refmac, R = 0.1810 (Rfree = 0.000) for 5076 atoms. Found 26 (32 requested) and removed 20 (16 requested) atoms. Cycle 40: After refmac, R = 0.1806 (Rfree = 0.000) for 5073 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5307 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5326 seeds are put forward Round 1: 232 peptides, 50 chains. Longest chain 8 peptides. Score 0.252 Round 2: 290 peptides, 48 chains. Longest chain 19 peptides. Score 0.409 Round 3: 279 peptides, 48 chains. Longest chain 13 peptides. Score 0.385 Round 4: 285 peptides, 47 chains. Longest chain 19 peptides. Score 0.408 Round 5: 292 peptides, 48 chains. Longest chain 17 peptides. Score 0.414 Taking the results from Round 5 Chains 48, Residues 244, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 12020 restraints for refining 5091 atoms. 11014 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2028 (Rfree = 0.000) for 5091 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 42: After refmac, R = 0.1924 (Rfree = 0.000) for 5079 atoms. Found 29 (32 requested) and removed 26 (16 requested) atoms. Cycle 43: After refmac, R = 0.1885 (Rfree = 0.000) for 5069 atoms. Found 31 (32 requested) and removed 23 (16 requested) atoms. Cycle 44: After refmac, R = 0.1828 (Rfree = 0.000) for 5063 atoms. Found 24 (32 requested) and removed 21 (16 requested) atoms. Cycle 45: After refmac, R = 0.1876 (Rfree = 0.000) for 5055 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 5259 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5281 seeds are put forward Round 1: 224 peptides, 44 chains. Longest chain 10 peptides. Score 0.296 Round 2: 262 peptides, 45 chains. Longest chain 14 peptides. Score 0.376 Round 3: 255 peptides, 41 chains. Longest chain 12 peptides. Score 0.400 Round 4: 281 peptides, 45 chains. Longest chain 15 peptides. Score 0.418 Round 5: 275 peptides, 46 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 236, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input Building loops using Loopy2018 45 chains (236 residues) following loop building 3 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8743 reflections ( 99.44 % complete ) and 12183 restraints for refining 5090 atoms. 11251 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1999 (Rfree = 0.000) for 5090 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1867 (Rfree = 0.000) for 5060 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1882 (Rfree = 0.000) for 5041 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1889 (Rfree = 0.000) for 5016 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 71.72