null Tue 25 Dec 19:27:57 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-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 ============================================================ Tue 25 Dec 19:28:07 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-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 527 and 0 Target number of residues in the AU: 527 Target solvent content: 0.6262 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 64.45 9174 reflections ( 98.96 % complete ) and 0 restraints for refining 6012 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3505 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3490 (Rfree = 0.000) for 6012 atoms. Found 38 (38 requested) and removed 73 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 6088 seeds are put forward NCS extension: 0 residues added, 6088 seeds are put forward Round 1: 195 peptides, 45 chains. Longest chain 7 peptides. Score 0.208 Round 2: 253 peptides, 49 chains. Longest chain 12 peptides. Score 0.310 Round 3: 276 peptides, 51 chains. Longest chain 16 peptides. Score 0.344 Round 4: 294 peptides, 54 chains. Longest chain 16 peptides. Score 0.355 Round 5: 298 peptides, 49 chains. Longest chain 17 peptides. Score 0.410 Taking the results from Round 5 Chains 49, Residues 249, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11610 restraints for refining 4938 atoms. 10663 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3062 (Rfree = 0.000) for 4938 atoms. Found 31 (31 requested) and removed 52 (15 requested) atoms. Cycle 2: After refmac, R = 0.2877 (Rfree = 0.000) for 4831 atoms. Found 30 (31 requested) and removed 31 (15 requested) atoms. Cycle 3: After refmac, R = 0.2826 (Rfree = 0.000) for 4784 atoms. Found 29 (30 requested) and removed 35 (15 requested) atoms. Cycle 4: After refmac, R = 0.2830 (Rfree = 0.000) for 4751 atoms. Found 30 (30 requested) and removed 37 (15 requested) atoms. Cycle 5: After refmac, R = 0.2808 (Rfree = 0.000) for 4723 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 4949 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4963 seeds are put forward Round 1: 263 peptides, 56 chains. Longest chain 12 peptides. Score 0.264 Round 2: 306 peptides, 56 chains. Longest chain 14 peptides. Score 0.363 Round 3: 307 peptides, 53 chains. Longest chain 15 peptides. Score 0.393 Round 4: 299 peptides, 51 chains. Longest chain 18 peptides. Score 0.394 Round 5: 301 peptides, 47 chains. Longest chain 19 peptides. Score 0.435 Taking the results from Round 5 Chains 47, Residues 254, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11280 restraints for refining 4861 atoms. 10311 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2733 (Rfree = 0.000) for 4861 atoms. Found 31 (31 requested) and removed 63 (15 requested) atoms. Cycle 7: After refmac, R = 0.2765 (Rfree = 0.000) for 4781 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 8: After refmac, R = 0.2702 (Rfree = 0.000) for 4745 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. Cycle 9: After refmac, R = 0.2605 (Rfree = 0.000) for 4728 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Cycle 10: After refmac, R = 0.2478 (Rfree = 0.000) for 4710 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 4941 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4963 seeds are put forward Round 1: 241 peptides, 51 chains. Longest chain 11 peptides. Score 0.261 Round 2: 284 peptides, 48 chains. Longest chain 15 peptides. Score 0.390 Round 3: 283 peptides, 53 chains. Longest chain 12 peptides. Score 0.340 Round 4: 304 peptides, 54 chains. Longest chain 11 peptides. Score 0.377 Round 5: 300 peptides, 50 chains. Longest chain 16 peptides. Score 0.405 Taking the results from Round 5 Chains 50, Residues 250, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11525 restraints for refining 4939 atoms. 10575 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2832 (Rfree = 0.000) for 4939 atoms. Found 31 (31 requested) and removed 59 (15 requested) atoms. Cycle 12: After refmac, R = 0.2638 (Rfree = 0.000) for 4876 atoms. Found 31 (31 requested) and removed 47 (15 requested) atoms. Cycle 13: After refmac, R = 0.2605 (Rfree = 0.000) for 4845 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. Cycle 14: After refmac, R = 0.2457 (Rfree = 0.000) for 4822 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 15: After refmac, R = 0.2367 (Rfree = 0.000) for 4811 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 5058 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5082 seeds are put forward Round 1: 255 peptides, 51 chains. Longest chain 10 peptides. Score 0.295 Round 2: 302 peptides, 53 chains. Longest chain 13 peptides. Score 0.382 Round 3: 302 peptides, 48 chains. Longest chain 16 peptides. Score 0.428 Round 4: 305 peptides, 49 chains. Longest chain 20 peptides. Score 0.425 Round 5: 302 peptides, 50 chains. Longest chain 17 peptides. Score 0.409 Taking the results from Round 3 Chains 49, Residues 254, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11151 restraints for refining 4929 atoms. 10143 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2576 (Rfree = 0.000) for 4929 atoms. Found 31 (31 requested) and removed 42 (15 requested) atoms. Cycle 17: After refmac, R = 0.2477 (Rfree = 0.000) for 4881 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 18: After refmac, R = 0.2464 (Rfree = 0.000) for 4864 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 19: After refmac, R = 0.2419 (Rfree = 0.000) for 4846 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 20: After refmac, R = 0.2290 (Rfree = 0.000) for 4832 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 5019 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5036 seeds are put forward Round 1: 267 peptides, 55 chains. Longest chain 10 peptides. Score 0.284 Round 2: 301 peptides, 51 chains. Longest chain 15 peptides. Score 0.398 Round 3: 277 peptides, 48 chains. Longest chain 13 peptides. Score 0.374 Round 4: 291 peptides, 53 chains. Longest chain 17 peptides. Score 0.358 Round 5: 299 peptides, 50 chains. Longest chain 15 peptides. Score 0.403 Taking the results from Round 5 Chains 50, Residues 249, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11399 restraints for refining 4938 atoms. 10416 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2694 (Rfree = 0.000) for 4938 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 22: After refmac, R = 0.2520 (Rfree = 0.000) for 4913 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 23: After refmac, R = 0.2543 (Rfree = 0.000) for 4887 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 24: After refmac, R = 0.2395 (Rfree = 0.000) for 4873 atoms. Found 31 (31 requested) and removed 20 (15 requested) atoms. Cycle 25: After refmac, R = 0.2420 (Rfree = 0.000) for 4859 atoms. Found 31 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 5047 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5063 seeds are put forward Round 1: 247 peptides, 51 chains. Longest chain 9 peptides. Score 0.276 Round 2: 284 peptides, 47 chains. Longest chain 15 peptides. Score 0.399 Round 3: 280 peptides, 47 chains. Longest chain 16 peptides. Score 0.390 Round 4: 271 peptides, 46 chains. Longest chain 11 peptides. Score 0.380 Round 5: 280 peptides, 47 chains. Longest chain 16 peptides. Score 0.390 Taking the results from Round 2 Chains 47, Residues 237, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11134 restraints for refining 4922 atoms. 10193 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2574 (Rfree = 0.000) for 4922 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 27: After refmac, R = 0.2580 (Rfree = 0.000) for 4894 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 28: After refmac, R = 0.2386 (Rfree = 0.000) for 4875 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 29: After refmac, R = 0.2559 (Rfree = 0.000) for 4872 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 30: After refmac, R = 0.2292 (Rfree = 0.000) for 4874 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 5083 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5109 seeds are put forward Round 1: 222 peptides, 46 chains. Longest chain 10 peptides. Score 0.266 Round 2: 254 peptides, 44 chains. Longest chain 13 peptides. Score 0.362 Round 3: 246 peptides, 42 chains. Longest chain 14 peptides. Score 0.364 Round 4: 260 peptides, 46 chains. Longest chain 12 peptides. Score 0.356 Round 5: 266 peptides, 43 chains. Longest chain 14 peptides. Score 0.398 Taking the results from Round 5 Chains 43, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11490 restraints for refining 4938 atoms. 10641 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2612 (Rfree = 0.000) for 4938 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. Cycle 32: After refmac, R = 0.2386 (Rfree = 0.000) for 4917 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 33: After refmac, R = 0.2439 (Rfree = 0.000) for 4908 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 34: After refmac, R = 0.2363 (Rfree = 0.000) for 4901 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 35: After refmac, R = 0.2395 (Rfree = 0.000) for 4889 atoms. Found 31 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 5069 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5092 seeds are put forward Round 1: 219 peptides, 45 chains. Longest chain 7 peptides. Score 0.269 Round 2: 256 peptides, 46 chains. Longest chain 13 peptides. Score 0.347 Round 3: 266 peptides, 45 chains. Longest chain 13 peptides. Score 0.379 Round 4: 257 peptides, 45 chains. Longest chain 18 peptides. Score 0.359 Round 5: 236 peptides, 38 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 5 Chains 38, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11503 restraints for refining 4939 atoms. 10749 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2576 (Rfree = 0.000) for 4939 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 37: After refmac, R = 0.2417 (Rfree = 0.000) for 4924 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 38: After refmac, R = 0.2495 (Rfree = 0.000) for 4907 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 39: After refmac, R = 0.2276 (Rfree = 0.000) for 4902 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 40: After refmac, R = 0.2356 (Rfree = 0.000) for 4897 atoms. Found 31 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 5069 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 5078 seeds are put forward Round 1: 211 peptides, 44 chains. Longest chain 10 peptides. Score 0.260 Round 2: 251 peptides, 44 chains. Longest chain 13 peptides. Score 0.355 Round 3: 258 peptides, 45 chains. Longest chain 16 peptides. Score 0.361 Round 4: 252 peptides, 45 chains. Longest chain 18 peptides. Score 0.348 Round 5: 248 peptides, 43 chains. Longest chain 14 peptides. Score 0.358 Taking the results from Round 3 Chains 45, Residues 213, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11601 restraints for refining 4939 atoms. 10794 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2552 (Rfree = 0.000) for 4939 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 42: After refmac, R = 0.2525 (Rfree = 0.000) for 4926 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 43: After refmac, R = 0.2562 (Rfree = 0.000) for 4916 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 44: After refmac, R = 0.2425 (Rfree = 0.000) for 4919 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 45: After refmac, R = 0.2504 (Rfree = 0.000) for 4920 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 5104 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5125 seeds are put forward Round 1: 224 peptides, 49 chains. Longest chain 9 peptides. Score 0.240 Round 2: 233 peptides, 43 chains. Longest chain 14 peptides. Score 0.324 Round 3: 216 peptides, 38 chains. Longest chain 11 peptides. Score 0.335 Round 4: 242 peptides, 42 chains. Longest chain 11 peptides. Score 0.355 Round 5: 228 peptides, 36 chains. Longest chain 14 peptides. Score 0.383 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 192, 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. 9174 reflections ( 98.96 % complete ) and 11585 restraints for refining 4938 atoms. 10853 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2497 (Rfree = 0.000) for 4938 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2513 (Rfree = 0.000) for 4898 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2409 (Rfree = 0.000) for 4868 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2332 (Rfree = 0.000) for 4843 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:56:08 GMT 2018 Job finished. TimeTaking 88.17 Used memory is bytes: 23344384