Sun 23 Dec 22:22:49 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 2iiu-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-3.4-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/2iiu-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-3.4-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 22:22:59 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/2iiu-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-3.4-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 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-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: 155 Cell parameters: 99.900 99.900 397.311 90.000 90.000 120.000 Input sequence file: 2iiu-3.4-parrot-hancs.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 6011 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3416 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3209 (Rfree = 0.000) for 6011 atoms. Found 37 (45 requested) and removed 73 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.08 Search for helices and strands: 0 residues in 0 chains, 6106 seeds are put forward NCS extension: 0 residues added, 6106 seeds are put forward Round 1: 218 peptides, 46 chains. Longest chain 9 peptides. Score 0.256 Round 2: 296 peptides, 58 chains. Longest chain 12 peptides. Score 0.322 Round 3: 336 peptides, 61 chains. Longest chain 12 peptides. Score 0.381 Round 4: 346 peptides, 66 chains. Longest chain 12 peptides. Score 0.357 Round 5: 345 peptides, 62 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 5 Chains 62, Residues 283, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11468 restraints for refining 4954 atoms. 10398 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2591 (Rfree = 0.000) for 4954 atoms. Found 37 (37 requested) and removed 42 (18 requested) atoms. Cycle 2: After refmac, R = 0.2408 (Rfree = 0.000) for 4886 atoms. Found 21 (37 requested) and removed 25 (18 requested) atoms. Cycle 3: After refmac, R = 0.2143 (Rfree = 0.000) for 4859 atoms. Found 12 (36 requested) and removed 25 (18 requested) atoms. Cycle 4: After refmac, R = 0.2137 (Rfree = 0.000) for 4829 atoms. Found 6 (36 requested) and removed 23 (18 requested) atoms. Cycle 5: After refmac, R = 0.1998 (Rfree = 0.000) for 4807 atoms. Found 5 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.06 Search for helices and strands: 0 residues in 0 chains, 4975 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4988 seeds are put forward Round 1: 309 peptides, 62 chains. Longest chain 10 peptides. Score 0.313 Round 2: 345 peptides, 62 chains. Longest chain 12 peptides. Score 0.391 Round 3: 348 peptides, 57 chains. Longest chain 13 peptides. Score 0.441 Round 4: 355 peptides, 59 chains. Longest chain 14 peptides. Score 0.438 Round 5: 373 peptides, 60 chains. Longest chain 15 peptides. Score 0.465 Taking the results from Round 5 Chains 60, Residues 313, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11301 restraints for refining 4953 atoms. 10109 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2342 (Rfree = 0.000) for 4953 atoms. Found 33 (37 requested) and removed 34 (18 requested) atoms. Cycle 7: After refmac, R = 0.2155 (Rfree = 0.000) for 4936 atoms. Found 11 (37 requested) and removed 23 (18 requested) atoms. Cycle 8: After refmac, R = 0.2078 (Rfree = 0.000) for 4918 atoms. Found 6 (37 requested) and removed 24 (18 requested) atoms. Cycle 9: After refmac, R = 0.2066 (Rfree = 0.000) for 4892 atoms. Found 4 (36 requested) and removed 23 (18 requested) atoms. Cycle 10: After refmac, R = 0.2067 (Rfree = 0.000) for 4870 atoms. Found 6 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.06 Search for helices and strands: 0 residues in 0 chains, 5097 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5113 seeds are put forward Round 1: 321 peptides, 63 chains. Longest chain 11 peptides. Score 0.331 Round 2: 348 peptides, 60 chains. Longest chain 13 peptides. Score 0.415 Round 3: 348 peptides, 57 chains. Longest chain 13 peptides. Score 0.441 Round 4: 350 peptides, 57 chains. Longest chain 18 peptides. Score 0.445 Round 5: 355 peptides, 60 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 4 Chains 57, Residues 293, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10877 reflections ( 99.13 % complete ) and 11322 restraints for refining 4954 atoms. 10207 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2210 (Rfree = 0.000) for 4954 atoms. Found 32 (37 requested) and removed 31 (18 requested) atoms. Cycle 12: After refmac, R = 0.2048 (Rfree = 0.000) for 4946 atoms. Found 15 (37 requested) and removed 25 (18 requested) atoms. Cycle 13: After refmac, R = 0.2006 (Rfree = 0.000) for 4932 atoms. Found 7 (37 requested) and removed 19 (18 requested) atoms. Cycle 14: After refmac, R = 0.2000 (Rfree = 0.000) for 4918 atoms. Found 6 (37 requested) and removed 20 (18 requested) atoms. Cycle 15: After refmac, R = 0.1995 (Rfree = 0.000) for 4901 atoms. Found 1 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.09 Search for helices and strands: 0 residues in 0 chains, 5121 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 5156 seeds are put forward Round 1: 303 peptides, 63 chains. Longest chain 9 peptides. Score 0.290 Round 2: 351 peptides, 61 chains. Longest chain 11 peptides. Score 0.413 Round 3: 363 peptides, 59 chains. Longest chain 15 peptides. Score 0.454 Round 4: 343 peptides, 55 chains. Longest chain 12 peptides. Score 0.449 Round 5: 339 peptides, 57 chains. Longest chain 17 peptides. Score 0.423 Taking the results from Round 3 Chains 59, Residues 304, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11299 restraints for refining 4952 atoms. 10128 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2266 (Rfree = 0.000) for 4952 atoms. Found 30 (37 requested) and removed 23 (18 requested) atoms. Cycle 17: After refmac, R = 0.2182 (Rfree = 0.000) for 4941 atoms. Found 20 (37 requested) and removed 25 (18 requested) atoms. Cycle 18: After refmac, R = 0.2172 (Rfree = 0.000) for 4927 atoms. Found 21 (37 requested) and removed 21 (18 requested) atoms. Cycle 19: After refmac, R = 0.2162 (Rfree = 0.000) for 4919 atoms. Found 16 (37 requested) and removed 21 (18 requested) atoms. Cycle 20: After refmac, R = 0.2109 (Rfree = 0.000) for 4907 atoms. Found 18 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 5148 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5163 seeds are put forward Round 1: 286 peptides, 58 chains. Longest chain 12 peptides. Score 0.299 Round 2: 352 peptides, 62 chains. Longest chain 13 peptides. Score 0.406 Round 3: 356 peptides, 62 chains. Longest chain 14 peptides. Score 0.414 Round 4: 338 peptides, 63 chains. Longest chain 12 peptides. Score 0.367 Round 5: 337 peptides, 58 chains. Longest chain 15 peptides. Score 0.410 Taking the results from Round 3 Chains 62, Residues 294, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11307 restraints for refining 4953 atoms. 10193 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2305 (Rfree = 0.000) for 4953 atoms. Found 30 (37 requested) and removed 30 (18 requested) atoms. Cycle 22: After refmac, R = 0.2176 (Rfree = 0.000) for 4934 atoms. Found 15 (37 requested) and removed 23 (18 requested) atoms. Cycle 23: After refmac, R = 0.2112 (Rfree = 0.000) for 4920 atoms. Found 11 (37 requested) and removed 22 (18 requested) atoms. Cycle 24: After refmac, R = 0.2104 (Rfree = 0.000) for 4906 atoms. Found 7 (37 requested) and removed 20 (18 requested) atoms. Cycle 25: After refmac, R = 0.1971 (Rfree = 0.000) for 4887 atoms. Found 8 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.10 Search for helices and strands: 0 residues in 0 chains, 5118 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5130 seeds are put forward Round 1: 285 peptides, 58 chains. Longest chain 11 peptides. Score 0.296 Round 2: 325 peptides, 56 chains. Longest chain 18 peptides. Score 0.403 Round 3: 337 peptides, 55 chains. Longest chain 15 peptides. Score 0.437 Round 4: 337 peptides, 53 chains. Longest chain 16 peptides. Score 0.454 Round 5: 336 peptides, 56 chains. Longest chain 19 peptides. Score 0.426 Taking the results from Round 4 Chains 53, Residues 284, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11195 restraints for refining 4953 atoms. 10085 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2340 (Rfree = 0.000) for 4953 atoms. Found 33 (37 requested) and removed 22 (18 requested) atoms. Cycle 27: After refmac, R = 0.2191 (Rfree = 0.000) for 4954 atoms. Found 15 (37 requested) and removed 20 (18 requested) atoms. Cycle 28: After refmac, R = 0.2123 (Rfree = 0.000) for 4946 atoms. Found 5 (37 requested) and removed 20 (18 requested) atoms. Cycle 29: After refmac, R = 0.2090 (Rfree = 0.000) for 4925 atoms. Found 5 (37 requested) and removed 20 (18 requested) atoms. Cycle 30: After refmac, R = 0.2065 (Rfree = 0.000) for 4907 atoms. Found 7 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.07 Search for helices and strands: 0 residues in 0 chains, 5100 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 5113 seeds are put forward Round 1: 290 peptides, 62 chains. Longest chain 10 peptides. Score 0.269 Round 2: 320 peptides, 56 chains. Longest chain 13 peptides. Score 0.393 Round 3: 333 peptides, 58 chains. Longest chain 12 peptides. Score 0.402 Round 4: 326 peptides, 54 chains. Longest chain 18 peptides. Score 0.423 Round 5: 328 peptides, 55 chains. Longest chain 16 peptides. Score 0.418 Taking the results from Round 4 Chains 54, Residues 272, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11569 restraints for refining 4953 atoms. 10535 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2342 (Rfree = 0.000) for 4953 atoms. Found 30 (37 requested) and removed 23 (18 requested) atoms. Cycle 32: After refmac, R = 0.2171 (Rfree = 0.000) for 4949 atoms. Found 23 (37 requested) and removed 23 (18 requested) atoms. Cycle 33: After refmac, R = 0.2190 (Rfree = 0.000) for 4933 atoms. Found 25 (37 requested) and removed 25 (18 requested) atoms. Cycle 34: After refmac, R = 0.2066 (Rfree = 0.000) for 4917 atoms. Found 21 (37 requested) and removed 27 (18 requested) atoms. Cycle 35: After refmac, R = 0.1967 (Rfree = 0.000) for 4894 atoms. Found 26 (37 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.10 Search for helices and strands: 0 residues in 0 chains, 5111 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5130 seeds are put forward Round 1: 232 peptides, 48 chains. Longest chain 8 peptides. Score 0.270 Round 2: 271 peptides, 48 chains. Longest chain 11 peptides. Score 0.361 Round 3: 281 peptides, 51 chains. Longest chain 10 peptides. Score 0.355 Round 4: 285 peptides, 49 chains. Longest chain 14 peptides. Score 0.382 Round 5: 281 peptides, 50 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 4 Chains 49, Residues 236, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11334 restraints for refining 4954 atoms. 10425 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2167 (Rfree = 0.000) for 4954 atoms. Found 31 (37 requested) and removed 29 (18 requested) atoms. Cycle 37: After refmac, R = 0.2105 (Rfree = 0.000) for 4948 atoms. Found 22 (37 requested) and removed 28 (18 requested) atoms. Cycle 38: After refmac, R = 0.2011 (Rfree = 0.000) for 4935 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. Cycle 39: After refmac, R = 0.1974 (Rfree = 0.000) for 4939 atoms. Found 16 (37 requested) and removed 28 (18 requested) atoms. Cycle 40: After refmac, R = 0.1935 (Rfree = 0.000) for 4920 atoms. Found 22 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.04 Search for helices and strands: 0 residues in 0 chains, 5129 seeds are put forward NCS extension: 0 residues added, 5129 seeds are put forward Round 1: 243 peptides, 51 chains. Longest chain 9 peptides. Score 0.266 Round 2: 274 peptides, 52 chains. Longest chain 11 peptides. Score 0.329 Round 3: 274 peptides, 51 chains. Longest chain 9 peptides. Score 0.339 Round 4: 268 peptides, 47 chains. Longest chain 10 peptides. Score 0.364 Round 5: 274 peptides, 47 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 5 Chains 47, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10877 reflections ( 99.13 % complete ) and 11490 restraints for refining 4954 atoms. 10629 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2158 (Rfree = 0.000) for 4954 atoms. Found 25 (37 requested) and removed 24 (18 requested) atoms. Cycle 42: After refmac, R = 0.2805 (Rfree = 0.000) for 4946 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 43: After refmac, R = 0.2758 (Rfree = 0.000) for 4942 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. Cycle 44: After refmac, R = 0.2010 (Rfree = 0.000) for 4933 atoms. Found 23 (37 requested) and removed 24 (18 requested) atoms. Cycle 45: After refmac, R = 0.1993 (Rfree = 0.000) for 4923 atoms. Found 19 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.08 Search for helices and strands: 0 residues in 0 chains, 5148 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5161 seeds are put forward Round 1: 217 peptides, 46 chains. Longest chain 10 peptides. Score 0.254 Round 2: 281 peptides, 53 chains. Longest chain 12 peptides. Score 0.336 Round 3: 279 peptides, 49 chains. Longest chain 13 peptides. Score 0.369 Round 4: 269 peptides, 47 chains. Longest chain 12 peptides. Score 0.366 Round 5: 267 peptides, 43 chains. Longest chain 13 peptides. Score 0.400 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 224, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 4 % 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 11424 restraints for refining 4953 atoms. 10535 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2154 (Rfree = 0.000) for 4953 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2095 (Rfree = 0.000) for 4922 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2029 (Rfree = 0.000) for 4897 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1985 (Rfree = 0.000) for 4877 atoms. TimeTaking 80.3