null Mon 24 Dec 07:28:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2iiu-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.4-parrot-noncs ############### 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 07:29:00 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/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.4-parrot-noncs/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 534 and 0 Target number of residues in the AU: 534 Target solvent content: 0.6213 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-3.4-parrot-noncs.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-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 5448 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: 132.437 3.400 Wilson plot Bfac: 61.79 10877 reflections ( 99.13 % complete ) and 0 restraints for refining 6091 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3474 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3181 (Rfree = 0.000) for 6091 atoms. Found 35 (45 requested) and removed 85 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 6194 seeds are put forward NCS extension: 0 residues added, 6194 seeds are put forward Round 1: 195 peptides, 40 chains. Longest chain 9 peptides. Score 0.262 Round 2: 277 peptides, 54 chains. Longest chain 12 peptides. Score 0.317 Round 3: 306 peptides, 55 chains. Longest chain 17 peptides. Score 0.372 Round 4: 313 peptides, 56 chains. Longest chain 12 peptides. Score 0.378 Round 5: 326 peptides, 55 chains. Longest chain 15 peptides. Score 0.414 Taking the results from Round 5 Chains 55, Residues 271, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11357 restraints for refining 4954 atoms. 10328 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2728 (Rfree = 0.000) for 4954 atoms. Found 36 (37 requested) and removed 30 (18 requested) atoms. Cycle 2: After refmac, R = 0.2649 (Rfree = 0.000) for 4870 atoms. Found 28 (37 requested) and removed 28 (18 requested) atoms. Cycle 3: After refmac, R = 0.2545 (Rfree = 0.000) for 4838 atoms. Found 29 (36 requested) and removed 28 (18 requested) atoms. Cycle 4: After refmac, R = 0.2478 (Rfree = 0.000) for 4818 atoms. Found 28 (36 requested) and removed 36 (18 requested) atoms. Cycle 5: After refmac, R = 0.2403 (Rfree = 0.000) for 4801 atoms. Found 30 (36 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.07 Search for helices and strands: 0 residues in 0 chains, 5010 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5024 seeds are put forward Round 1: 278 peptides, 58 chains. Longest chain 8 peptides. Score 0.280 Round 2: 344 peptides, 62 chains. Longest chain 14 peptides. Score 0.389 Round 3: 334 peptides, 55 chains. Longest chain 16 peptides. Score 0.431 Round 4: 349 peptides, 55 chains. Longest chain 16 peptides. Score 0.460 Round 5: 337 peptides, 56 chains. Longest chain 21 peptides. Score 0.428 Taking the results from Round 4 Chains 55, Residues 294, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11082 restraints for refining 4886 atoms. 9961 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2384 (Rfree = 0.000) for 4886 atoms. Found 28 (36 requested) and removed 49 (18 requested) atoms. Cycle 7: After refmac, R = 0.2473 (Rfree = 0.000) for 4830 atoms. Found 36 (36 requested) and removed 43 (18 requested) atoms. Cycle 8: After refmac, R = 0.2147 (Rfree = 0.000) for 4798 atoms. Found 20 (36 requested) and removed 26 (18 requested) atoms. Cycle 9: After refmac, R = 0.2147 (Rfree = 0.000) for 4776 atoms. Found 28 (36 requested) and removed 28 (18 requested) atoms. Cycle 10: After refmac, R = 0.2003 (Rfree = 0.000) for 4761 atoms. Found 16 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.07 Search for helices and strands: 0 residues in 0 chains, 5006 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 5016 seeds are put forward Round 1: 315 peptides, 64 chains. Longest chain 14 peptides. Score 0.308 Round 2: 342 peptides, 60 chains. Longest chain 16 peptides. Score 0.403 Round 3: 340 peptides, 58 chains. Longest chain 13 peptides. Score 0.416 Round 4: 348 peptides, 57 chains. Longest chain 17 peptides. Score 0.441 Round 5: 343 peptides, 55 chains. Longest chain 15 peptides. Score 0.449 Taking the results from Round 5 Chains 55, Residues 288, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11322 restraints for refining 4952 atoms. 10225 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2265 (Rfree = 0.000) for 4952 atoms. Found 27 (37 requested) and removed 36 (18 requested) atoms. Cycle 12: After refmac, R = 0.2135 (Rfree = 0.000) for 4925 atoms. Found 30 (37 requested) and removed 32 (18 requested) atoms. Cycle 13: After refmac, R = 0.2053 (Rfree = 0.000) for 4909 atoms. Found 17 (37 requested) and removed 22 (18 requested) atoms. Cycle 14: After refmac, R = 0.1951 (Rfree = 0.000) for 4897 atoms. Found 15 (37 requested) and removed 24 (18 requested) atoms. Cycle 15: After refmac, R = 0.1925 (Rfree = 0.000) for 4884 atoms. Found 10 (36 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.09 Search for helices and strands: 0 residues in 0 chains, 5129 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5149 seeds are put forward Round 1: 310 peptides, 64 chains. Longest chain 16 peptides. Score 0.296 Round 2: 313 peptides, 57 chains. Longest chain 11 peptides. Score 0.369 Round 3: 329 peptides, 56 chains. Longest chain 11 peptides. Score 0.411 Round 4: 321 peptides, 52 chains. Longest chain 15 peptides. Score 0.431 Round 5: 315 peptides, 51 chains. Longest chain 13 peptides. Score 0.427 Taking the results from Round 4 Chains 52, Residues 269, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11352 restraints for refining 4952 atoms. 10328 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2168 (Rfree = 0.000) for 4952 atoms. Found 26 (37 requested) and removed 32 (18 requested) atoms. Cycle 17: After refmac, R = 0.2078 (Rfree = 0.000) for 4927 atoms. Found 26 (37 requested) and removed 25 (18 requested) atoms. Cycle 18: After refmac, R = 0.2031 (Rfree = 0.000) for 4913 atoms. Found 26 (37 requested) and removed 22 (18 requested) atoms. Cycle 19: After refmac, R = 0.2019 (Rfree = 0.000) for 4904 atoms. Found 23 (37 requested) and removed 25 (18 requested) atoms. Cycle 20: After refmac, R = 0.1948 (Rfree = 0.000) for 4890 atoms. Found 24 (36 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.08 Search for helices and strands: 0 residues in 0 chains, 5117 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5133 seeds are put forward Round 1: 302 peptides, 63 chains. Longest chain 11 peptides. Score 0.288 Round 2: 349 peptides, 63 chains. Longest chain 13 peptides. Score 0.391 Round 3: 356 peptides, 63 chains. Longest chain 13 peptides. Score 0.405 Round 4: 374 peptides, 64 chains. Longest chain 21 peptides. Score 0.433 Round 5: 360 peptides, 59 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 5 Chains 61, Residues 301, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11109 restraints for refining 4954 atoms. 9926 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2201 (Rfree = 0.000) for 4954 atoms. Found 33 (37 requested) and removed 30 (18 requested) atoms. Cycle 22: After refmac, R = 0.2043 (Rfree = 0.000) for 4937 atoms. Found 29 (37 requested) and removed 30 (18 requested) atoms. Cycle 23: After refmac, R = 0.2117 (Rfree = 0.000) for 4929 atoms. Found 30 (37 requested) and removed 26 (18 requested) atoms. Cycle 24: After refmac, R = 0.2015 (Rfree = 0.000) for 4928 atoms. Found 25 (37 requested) and removed 29 (18 requested) atoms. Cycle 25: After refmac, R = 0.1715 (Rfree = 0.000) for 4913 atoms. Found 15 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.07 Search for helices and strands: 0 residues in 0 chains, 5116 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5130 seeds are put forward Round 1: 286 peptides, 58 chains. Longest chain 10 peptides. Score 0.299 Round 2: 352 peptides, 66 chains. Longest chain 14 peptides. Score 0.370 Round 3: 329 peptides, 57 chains. Longest chain 16 peptides. Score 0.403 Round 4: 335 peptides, 58 chains. Longest chain 15 peptides. Score 0.406 Round 5: 344 peptides, 61 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 4 Chains 58, Residues 277, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11356 restraints for refining 4954 atoms. 10306 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2137 (Rfree = 0.000) for 4954 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. Cycle 27: After refmac, R = 0.1961 (Rfree = 0.000) for 4950 atoms. Found 30 (37 requested) and removed 28 (18 requested) atoms. Cycle 28: After refmac, R = 0.2566 (Rfree = 0.000) for 4943 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 29: After refmac, R = 0.1747 (Rfree = 0.000) for 4934 atoms. Found 18 (37 requested) and removed 30 (18 requested) atoms. Cycle 30: After refmac, R = 0.2657 (Rfree = 0.000) for 4915 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.07 Search for helices and strands: 0 residues in 0 chains, 5120 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5138 seeds are put forward Round 1: 263 peptides, 58 chains. Longest chain 9 peptides. Score 0.244 Round 2: 301 peptides, 52 chains. Longest chain 21 peptides. Score 0.389 Round 3: 306 peptides, 54 chains. Longest chain 17 peptides. Score 0.381 Round 4: 288 peptides, 47 chains. Longest chain 15 peptides. Score 0.408 Round 5: 291 peptides, 50 chains. Longest chain 12 peptides. Score 0.386 Taking the results from Round 4 Chains 47, Residues 241, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11457 restraints for refining 4954 atoms. 10540 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2115 (Rfree = 0.000) for 4954 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 32: After refmac, R = 0.1995 (Rfree = 0.000) for 4946 atoms. Found 37 (37 requested) and removed 19 (18 requested) atoms. Cycle 33: After refmac, R = 0.1893 (Rfree = 0.000) for 4954 atoms. Found 32 (37 requested) and removed 23 (18 requested) atoms. Cycle 34: After refmac, R = 0.1841 (Rfree = 0.000) for 4959 atoms. Found 27 (37 requested) and removed 21 (18 requested) atoms. Cycle 35: After refmac, R = 0.1853 (Rfree = 0.000) for 4957 atoms. Found 34 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.11 Search for helices and strands: 0 residues in 0 chains, 5175 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5201 seeds are put forward Round 1: 236 peptides, 51 chains. Longest chain 8 peptides. Score 0.249 Round 2: 262 peptides, 49 chains. Longest chain 12 peptides. Score 0.331 Round 3: 271 peptides, 50 chains. Longest chain 11 peptides. Score 0.342 Round 4: 274 peptides, 46 chains. Longest chain 11 peptides. Score 0.387 Round 5: 255 peptides, 45 chains. Longest chain 11 peptides. Score 0.354 Taking the results from Round 4 Chains 46, Residues 228, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11376 restraints for refining 4954 atoms. 10457 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2023 (Rfree = 0.000) for 4954 atoms. Found 37 (37 requested) and removed 20 (18 requested) atoms. Cycle 37: After refmac, R = 0.1902 (Rfree = 0.000) for 4956 atoms. Found 37 (37 requested) and removed 20 (18 requested) atoms. Cycle 38: After refmac, R = 0.1896 (Rfree = 0.000) for 4967 atoms. Found 28 (37 requested) and removed 26 (18 requested) atoms. Cycle 39: After refmac, R = 0.1826 (Rfree = 0.000) for 4955 atoms. Found 30 (37 requested) and removed 23 (18 requested) atoms. Cycle 40: After refmac, R = 0.1807 (Rfree = 0.000) for 4955 atoms. Found 30 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.04 Search for helices and strands: 0 residues in 0 chains, 5138 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5150 seeds are put forward Round 1: 204 peptides, 42 chains. Longest chain 9 peptides. Score 0.263 Round 2: 247 peptides, 49 chains. Longest chain 10 peptides. Score 0.296 Round 3: 248 peptides, 45 chains. Longest chain 10 peptides. Score 0.339 Round 4: 252 peptides, 47 chains. Longest chain 13 peptides. Score 0.328 Round 5: 286 peptides, 49 chains. Longest chain 14 peptides. Score 0.385 Taking the results from Round 5 Chains 49, Residues 237, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11341 restraints for refining 4954 atoms. 10407 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2007 (Rfree = 0.000) for 4954 atoms. Found 37 (37 requested) and removed 21 (18 requested) atoms. Cycle 42: After refmac, R = 0.1803 (Rfree = 0.000) for 4961 atoms. Found 19 (37 requested) and removed 19 (18 requested) atoms. Cycle 43: After refmac, R = 0.1867 (Rfree = 0.000) for 4950 atoms. Found 25 (37 requested) and removed 22 (18 requested) atoms. Cycle 44: After refmac, R = 0.1882 (Rfree = 0.000) for 4947 atoms. Found 37 (37 requested) and removed 21 (18 requested) atoms. Cycle 45: After refmac, R = 0.1801 (Rfree = 0.000) for 4956 atoms. Found 27 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.07 Search for helices and strands: 0 residues in 0 chains, 5135 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5150 seeds are put forward Round 1: 210 peptides, 46 chains. Longest chain 9 peptides. Score 0.236 Round 2: 262 peptides, 51 chains. Longest chain 10 peptides. Score 0.311 Round 3: 267 peptides, 50 chains. Longest chain 11 peptides. Score 0.333 Round 4: 284 peptides, 53 chains. Longest chain 12 peptides. Score 0.342 Round 5: 272 peptides, 52 chains. Longest chain 10 peptides. Score 0.325 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 231, 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. 10877 reflections ( 99.13 % complete ) and 11422 restraints for refining 4954 atoms. 10551 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2008 (Rfree = 0.000) for 4954 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2055 (Rfree = 0.000) for 4923 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.1980 (Rfree = 0.000) for 4899 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2166 (Rfree = 0.000) for 4873 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:34:57 GMT 2018 Job finished. TimeTaking 66.05 Used memory is bytes: 2992200