null Mon 24 Dec 07:35:56 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.8-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 07:36:01 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.8-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 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-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-3.8-parrot-noncs.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 5999 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3661 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3344 (Rfree = 0.000) for 5999 atoms. Found 22 (32 requested) and removed 72 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 6055 seeds are put forward NCS extension: 0 residues added, 6055 seeds are put forward Round 1: 165 peptides, 34 chains. Longest chain 10 peptides. Score 0.250 Round 2: 212 peptides, 40 chains. Longest chain 10 peptides. Score 0.304 Round 3: 231 peptides, 42 chains. Longest chain 11 peptides. Score 0.329 Round 4: 235 peptides, 40 chains. Longest chain 16 peptides. Score 0.359 Round 5: 253 peptides, 43 chains. Longest chain 17 peptides. Score 0.370 Taking the results from Round 5 Chains 43, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11973 restraints for refining 4925 atoms. 11176 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2823 (Rfree = 0.000) for 4925 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 2: After refmac, R = 0.2543 (Rfree = 0.000) for 4854 atoms. Found 17 (27 requested) and removed 25 (13 requested) atoms. Cycle 3: After refmac, R = 0.2435 (Rfree = 0.000) for 4817 atoms. Found 8 (26 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.2449 (Rfree = 0.000) for 4795 atoms. Found 7 (26 requested) and removed 18 (13 requested) atoms. Cycle 5: After refmac, R = 0.2296 (Rfree = 0.000) for 4775 atoms. Found 3 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 4903 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4922 seeds are put forward Round 1: 211 peptides, 44 chains. Longest chain 9 peptides. Score 0.260 Round 2: 250 peptides, 46 chains. Longest chain 10 peptides. Score 0.333 Round 3: 272 peptides, 45 chains. Longest chain 12 peptides. Score 0.392 Round 4: 246 peptides, 40 chains. Longest chain 13 peptides. Score 0.383 Round 5: 258 peptides, 43 chains. Longest chain 17 peptides. Score 0.381 Taking the results from Round 3 Chains 45, Residues 227, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11021 restraints for refining 4741 atoms. 10138 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2532 (Rfree = 0.000) for 4741 atoms. Found 17 (26 requested) and removed 32 (13 requested) atoms. Cycle 7: After refmac, R = 0.2403 (Rfree = 0.000) for 4710 atoms. Found 4 (25 requested) and removed 21 (12 requested) atoms. Cycle 8: After refmac, R = 0.2374 (Rfree = 0.000) for 4685 atoms. Found 6 (25 requested) and removed 14 (12 requested) atoms. Cycle 9: After refmac, R = 0.2341 (Rfree = 0.000) for 4673 atoms. Found 2 (25 requested) and removed 13 (12 requested) atoms. Cycle 10: After refmac, R = 0.2320 (Rfree = 0.000) for 4659 atoms. Found 6 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 4813 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4828 seeds are put forward Round 1: 239 peptides, 48 chains. Longest chain 11 peptides. Score 0.287 Round 2: 270 peptides, 44 chains. Longest chain 12 peptides. Score 0.397 Round 3: 284 peptides, 47 chains. Longest chain 14 peptides. Score 0.399 Round 4: 288 peptides, 45 chains. Longest chain 15 peptides. Score 0.426 Round 5: 290 peptides, 47 chains. Longest chain 16 peptides. Score 0.412 Taking the results from Round 4 Chains 45, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11428 restraints for refining 4841 atoms. 10501 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2463 (Rfree = 0.000) for 4841 atoms. Found 13 (26 requested) and removed 30 (13 requested) atoms. Cycle 12: After refmac, R = 0.2319 (Rfree = 0.000) for 4808 atoms. Found 11 (26 requested) and removed 19 (13 requested) atoms. Cycle 13: After refmac, R = 0.2269 (Rfree = 0.000) for 4793 atoms. Found 9 (26 requested) and removed 21 (13 requested) atoms. Cycle 14: After refmac, R = 0.2184 (Rfree = 0.000) for 4768 atoms. Found 2 (26 requested) and removed 24 (13 requested) atoms. Cycle 15: After refmac, R = 0.2189 (Rfree = 0.000) for 4744 atoms. Found 7 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 4928 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4941 seeds are put forward Round 1: 263 peptides, 54 chains. Longest chain 8 peptides. Score 0.284 Round 2: 289 peptides, 51 chains. Longest chain 12 peptides. Score 0.372 Round 3: 290 peptides, 49 chains. Longest chain 13 peptides. Score 0.393 Round 4: 288 peptides, 50 chains. Longest chain 22 peptides. Score 0.380 Round 5: 289 peptides, 47 chains. Longest chain 22 peptides. Score 0.410 Taking the results from Round 5 Chains 49, Residues 242, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11532 restraints for refining 4927 atoms. 10559 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2453 (Rfree = 0.000) for 4927 atoms. Found 18 (27 requested) and removed 23 (13 requested) atoms. Cycle 17: After refmac, R = 0.2330 (Rfree = 0.000) for 4896 atoms. Found 7 (27 requested) and removed 17 (13 requested) atoms. Cycle 18: After refmac, R = 0.2276 (Rfree = 0.000) for 4882 atoms. Found 2 (26 requested) and removed 14 (13 requested) atoms. Cycle 19: After refmac, R = 0.2255 (Rfree = 0.000) for 4870 atoms. Found 4 (26 requested) and removed 14 (13 requested) atoms. Cycle 20: After refmac, R = 0.2236 (Rfree = 0.000) for 4859 atoms. Found 2 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 5022 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 5039 seeds are put forward Round 1: 236 peptides, 43 chains. Longest chain 14 peptides. Score 0.331 Round 2: 271 peptides, 45 chains. Longest chain 15 peptides. Score 0.390 Round 3: 281 peptides, 45 chains. Longest chain 17 peptides. Score 0.411 Round 4: 274 peptides, 44 chains. Longest chain 17 peptides. Score 0.406 Round 5: 281 peptides, 47 chains. Longest chain 19 peptides. Score 0.393 Taking the results from Round 3 Chains 45, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11855 restraints for refining 4926 atoms. 10956 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2417 (Rfree = 0.000) for 4926 atoms. Found 18 (27 requested) and removed 26 (13 requested) atoms. Cycle 22: After refmac, R = 0.2249 (Rfree = 0.000) for 4909 atoms. Found 8 (27 requested) and removed 16 (13 requested) atoms. Cycle 23: After refmac, R = 0.2213 (Rfree = 0.000) for 4892 atoms. Found 3 (26 requested) and removed 16 (13 requested) atoms. Cycle 24: After refmac, R = 0.2197 (Rfree = 0.000) for 4878 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.2190 (Rfree = 0.000) for 4865 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 5018 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5032 seeds are put forward Round 1: 236 peptides, 49 chains. Longest chain 9 peptides. Score 0.270 Round 2: 255 peptides, 49 chains. Longest chain 10 peptides. Score 0.315 Round 3: 286 peptides, 49 chains. Longest chain 14 peptides. Score 0.385 Round 4: 291 peptides, 46 chains. Longest chain 16 peptides. Score 0.423 Round 5: 279 peptides, 48 chains. Longest chain 17 peptides. Score 0.379 Taking the results from Round 4 Chains 46, Residues 245, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11717 restraints for refining 4928 atoms. 10783 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2266 (Rfree = 0.000) for 4928 atoms. Found 18 (27 requested) and removed 22 (13 requested) atoms. Cycle 27: After refmac, R = 0.2162 (Rfree = 0.000) for 4903 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. Cycle 28: After refmac, R = 0.2134 (Rfree = 0.000) for 4883 atoms. Found 8 (26 requested) and removed 15 (13 requested) atoms. Cycle 29: After refmac, R = 0.2098 (Rfree = 0.000) for 4876 atoms. Found 0 (26 requested) and removed 14 (13 requested) atoms. Cycle 30: After refmac, R = 0.2093 (Rfree = 0.000) for 4859 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 4996 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5014 seeds are put forward Round 1: 237 peptides, 51 chains. Longest chain 10 peptides. Score 0.252 Round 2: 257 peptides, 45 chains. Longest chain 13 peptides. Score 0.359 Round 3: 258 peptides, 46 chains. Longest chain 14 peptides. Score 0.351 Round 4: 271 peptides, 46 chains. Longest chain 15 peptides. Score 0.380 Round 5: 260 peptides, 39 chains. Longest chain 20 peptides. Score 0.423 Taking the results from Round 5 Chains 39, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11895 restraints for refining 4928 atoms. 11050 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2237 (Rfree = 0.000) for 4928 atoms. Found 16 (27 requested) and removed 27 (13 requested) atoms. Cycle 32: After refmac, R = 0.2119 (Rfree = 0.000) for 4902 atoms. Found 5 (27 requested) and removed 17 (13 requested) atoms. Cycle 33: After refmac, R = 0.2302 (Rfree = 0.000) for 4882 atoms. Found 18 (26 requested) and removed 17 (13 requested) atoms. Cycle 34: After refmac, R = 0.2104 (Rfree = 0.000) for 4878 atoms. Found 10 (26 requested) and removed 21 (13 requested) atoms. Cycle 35: After refmac, R = 0.2111 (Rfree = 0.000) for 4862 atoms. Found 12 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 5035 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5047 seeds are put forward Round 1: 194 peptides, 43 chains. Longest chain 7 peptides. Score 0.227 Round 2: 255 peptides, 50 chains. Longest chain 11 peptides. Score 0.305 Round 3: 249 peptides, 46 chains. Longest chain 12 peptides. Score 0.331 Round 4: 223 peptides, 41 chains. Longest chain 9 peptides. Score 0.321 Round 5: 242 peptides, 44 chains. Longest chain 12 peptides. Score 0.335 Taking the results from Round 5 Chains 44, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11756 restraints for refining 4924 atoms. 11008 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2093 (Rfree = 0.000) for 4924 atoms. Found 22 (27 requested) and removed 20 (13 requested) atoms. Cycle 37: After refmac, R = 0.1945 (Rfree = 0.000) for 4918 atoms. Found 12 (27 requested) and removed 17 (13 requested) atoms. Cycle 38: After refmac, R = 0.1931 (Rfree = 0.000) for 4911 atoms. Found 9 (26 requested) and removed 17 (13 requested) atoms. Cycle 39: After refmac, R = 0.1929 (Rfree = 0.000) for 4902 atoms. Found 7 (26 requested) and removed 14 (13 requested) atoms. Cycle 40: After refmac, R = 0.1927 (Rfree = 0.000) for 4894 atoms. Found 2 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 5066 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5082 seeds are put forward Round 1: 175 peptides, 39 chains. Longest chain 7 peptides. Score 0.220 Round 2: 240 peptides, 46 chains. Longest chain 10 peptides. Score 0.310 Round 3: 234 peptides, 42 chains. Longest chain 14 peptides. Score 0.336 Round 4: 227 peptides, 40 chains. Longest chain 13 peptides. Score 0.340 Round 5: 238 peptides, 38 chains. Longest chain 16 peptides. Score 0.385 Taking the results from Round 5 Chains 38, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11759 restraints for refining 4928 atoms. 10997 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2209 (Rfree = 0.000) for 4928 atoms. Found 16 (27 requested) and removed 21 (13 requested) atoms. Cycle 42: After refmac, R = 0.2490 (Rfree = 0.000) for 4904 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 43: After refmac, R = 0.2060 (Rfree = 0.000) for 4876 atoms. Found 21 (26 requested) and removed 21 (13 requested) atoms. Cycle 44: After refmac, R = 0.1873 (Rfree = 0.000) for 4866 atoms. Found 13 (26 requested) and removed 16 (13 requested) atoms. Cycle 45: After refmac, R = 0.1686 (Rfree = 0.000) for 4857 atoms. Found 7 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 5057 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5079 seeds are put forward Round 1: 178 peptides, 39 chains. Longest chain 10 peptides. Score 0.229 Round 2: 217 peptides, 45 chains. Longest chain 9 peptides. Score 0.264 Round 3: 195 peptides, 37 chains. Longest chain 10 peptides. Score 0.295 Round 4: 199 peptides, 37 chains. Longest chain 10 peptides. Score 0.304 Round 5: 192 peptides, 35 chains. Longest chain 10 peptides. Score 0.309 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 157, 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 12003 restraints for refining 4894 atoms. 11410 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1975 (Rfree = 0.000) for 4894 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1828 (Rfree = 0.000) for 4873 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1811 (Rfree = 0.000) for 4857 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1808 (Rfree = 0.000) for 4843 atoms. Found 0 (26 requested) and removed 12 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:40:08 GMT 2018 Job finished. TimeTaking 64.21 Used memory is bytes: 14711752