Mon 24 Dec 07:34:08 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-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 07:34:12 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-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 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-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-3.6-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 3.600 Wilson plot Bfac: 64.45 9174 reflections ( 98.96 % complete ) and 0 restraints for refining 6054 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3559 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3548 (Rfree = 0.000) for 6054 atoms. Found 37 (38 requested) and removed 93 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 6104 seeds are put forward NCS extension: 0 residues added, 6104 seeds are put forward Round 1: 179 peptides, 37 chains. Longest chain 10 peptides. Score 0.254 Round 2: 224 peptides, 43 chains. Longest chain 10 peptides. Score 0.302 Round 3: 258 peptides, 49 chains. Longest chain 11 peptides. Score 0.322 Round 4: 285 peptides, 52 chains. Longest chain 16 peptides. Score 0.354 Round 5: 280 peptides, 49 chains. Longest chain 16 peptides. Score 0.372 Taking the results from Round 5 Chains 49, Residues 231, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11624 restraints for refining 4939 atoms. 10700 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3171 (Rfree = 0.000) for 4939 atoms. Found 31 (31 requested) and removed 44 (15 requested) atoms. Cycle 2: After refmac, R = 0.2959 (Rfree = 0.000) for 4839 atoms. Found 28 (31 requested) and removed 31 (15 requested) atoms. Cycle 3: After refmac, R = 0.2505 (Rfree = 0.000) for 4779 atoms. Found 21 (31 requested) and removed 29 (15 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2816 (Rfree = 0.000) for 4738 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. Cycle 5: After refmac, R = 0.2364 (Rfree = 0.000) for 4714 atoms. Found 14 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 4872 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4891 seeds are put forward Round 1: 224 peptides, 47 chains. Longest chain 10 peptides. Score 0.261 Round 2: 279 peptides, 51 chains. Longest chain 15 peptides. Score 0.350 Round 3: 294 peptides, 51 chains. Longest chain 14 peptides. Score 0.383 Round 4: 294 peptides, 53 chains. Longest chain 15 peptides. Score 0.364 Round 5: 281 peptides, 49 chains. Longest chain 15 peptides. Score 0.374 Taking the results from Round 3 Chains 51, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 10650 restraints for refining 4692 atoms. 9729 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2825 (Rfree = 0.000) for 4692 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 7: After refmac, R = 0.2697 (Rfree = 0.000) for 4648 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 8: After refmac, R = 0.2798 (Rfree = 0.000) for 4616 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. Cycle 9: After refmac, R = 0.2597 (Rfree = 0.000) for 4597 atoms. Found 28 (29 requested) and removed 21 (14 requested) atoms. Cycle 10: After refmac, R = 0.2773 (Rfree = 0.000) for 4592 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 4858 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4872 seeds are put forward Round 1: 248 peptides, 51 chains. Longest chain 9 peptides. Score 0.278 Round 2: 296 peptides, 54 chains. Longest chain 15 peptides. Score 0.359 Round 3: 314 peptides, 57 chains. Longest chain 16 peptides. Score 0.371 Round 4: 329 peptides, 58 chains. Longest chain 14 peptides. Score 0.394 Round 5: 313 peptides, 52 chains. Longest chain 17 peptides. Score 0.414 Taking the results from Round 5 Chains 52, Residues 261, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11099 restraints for refining 4872 atoms. 10107 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2751 (Rfree = 0.000) for 4872 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 12: After refmac, R = 0.2710 (Rfree = 0.000) for 4827 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 13: After refmac, R = 0.2618 (Rfree = 0.000) for 4810 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 14: After refmac, R = 0.2581 (Rfree = 0.000) for 4788 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 15: After refmac, R = 0.2520 (Rfree = 0.000) for 4773 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.21 Search for helices and strands: 0 residues in 0 chains, 4987 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5004 seeds are put forward Round 1: 255 peptides, 56 chains. Longest chain 8 peptides. Score 0.245 Round 2: 280 peptides, 52 chains. Longest chain 10 peptides. Score 0.343 Round 3: 292 peptides, 51 chains. Longest chain 11 peptides. Score 0.379 Round 4: 306 peptides, 54 chains. Longest chain 15 peptides. Score 0.381 Round 5: 290 peptides, 52 chains. Longest chain 13 peptides. Score 0.365 Taking the results from Round 4 Chains 54, Residues 252, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11333 restraints for refining 4936 atoms. 10379 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2693 (Rfree = 0.000) for 4936 atoms. Found 31 (31 requested) and removed 38 (15 requested) atoms. Cycle 17: After refmac, R = 0.2611 (Rfree = 0.000) for 4899 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. Cycle 18: After refmac, R = 0.2610 (Rfree = 0.000) for 4876 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 19: After refmac, R = 0.2452 (Rfree = 0.000) for 4855 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 20: After refmac, R = 0.2516 (Rfree = 0.000) for 4846 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 5068 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5088 seeds are put forward Round 1: 226 peptides, 49 chains. Longest chain 9 peptides. Score 0.245 Round 2: 285 peptides, 53 chains. Longest chain 11 peptides. Score 0.345 Round 3: 288 peptides, 51 chains. Longest chain 20 peptides. Score 0.370 Round 4: 280 peptides, 49 chains. Longest chain 22 peptides. Score 0.372 Round 5: 283 peptides, 52 chains. Longest chain 12 peptides. Score 0.350 Taking the results from Round 4 Chains 49, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11335 restraints for refining 4937 atoms. 10460 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2685 (Rfree = 0.000) for 4937 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 22: After refmac, R = 0.2666 (Rfree = 0.000) for 4900 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 23: After refmac, R = 0.2641 (Rfree = 0.000) for 4878 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 24: After refmac, R = 0.2529 (Rfree = 0.000) for 4861 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 25: After refmac, R = 0.2567 (Rfree = 0.000) for 4850 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 5024 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5047 seeds are put forward Round 1: 240 peptides, 51 chains. Longest chain 8 peptides. Score 0.259 Round 2: 249 peptides, 45 chains. Longest chain 17 peptides. Score 0.341 Round 3: 242 peptides, 44 chains. Longest chain 9 peptides. Score 0.335 Round 4: 264 peptides, 47 chains. Longest chain 10 peptides. Score 0.355 Round 5: 270 peptides, 47 chains. Longest chain 13 peptides. Score 0.369 Taking the results from Round 5 Chains 47, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11479 restraints for refining 4935 atoms. 10634 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2673 (Rfree = 0.000) for 4935 atoms. Found 31 (31 requested) and removed 47 (15 requested) atoms. Cycle 27: After refmac, R = 0.2585 (Rfree = 0.000) for 4892 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 28: After refmac, R = 0.2356 (Rfree = 0.000) for 4869 atoms. Found 24 (31 requested) and removed 26 (15 requested) atoms. Cycle 29: After refmac, R = 0.2564 (Rfree = 0.000) for 4859 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 30: After refmac, R = 0.2562 (Rfree = 0.000) for 4854 atoms. Found 31 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 5026 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5041 seeds are put forward Round 1: 234 peptides, 51 chains. Longest chain 7 peptides. Score 0.244 Round 2: 261 peptides, 48 chains. Longest chain 14 peptides. Score 0.339 Round 3: 264 peptides, 47 chains. Longest chain 11 peptides. Score 0.355 Round 4: 265 peptides, 49 chains. Longest chain 13 peptides. Score 0.338 Round 5: 261 peptides, 45 chains. Longest chain 14 peptides. Score 0.368 Taking the results from Round 5 Chains 45, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11467 restraints for refining 4939 atoms. 10648 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2694 (Rfree = 0.000) for 4939 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 32: After refmac, R = 0.2587 (Rfree = 0.000) for 4905 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. Cycle 33: After refmac, R = 0.2546 (Rfree = 0.000) for 4898 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 34: After refmac, R = 0.2581 (Rfree = 0.000) for 4883 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 35: After refmac, R = 0.2524 (Rfree = 0.000) for 4878 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.25 Search for helices and strands: 0 residues in 0 chains, 5063 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 5073 seeds are put forward Round 1: 220 peptides, 48 chains. Longest chain 8 peptides. Score 0.240 Round 2: 254 peptides, 47 chains. Longest chain 16 peptides. Score 0.333 Round 3: 253 peptides, 47 chains. Longest chain 11 peptides. Score 0.330 Round 4: 236 peptides, 44 chains. Longest chain 11 peptides. Score 0.321 Round 5: 245 peptides, 44 chains. Longest chain 13 peptides. Score 0.342 Taking the results from Round 5 Chains 44, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11249 restraints for refining 4930 atoms. 10489 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2568 (Rfree = 0.000) for 4930 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 37: After refmac, R = 0.2473 (Rfree = 0.000) for 4891 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 38: After refmac, R = 0.2502 (Rfree = 0.000) for 4880 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 39: After refmac, R = 0.2564 (Rfree = 0.000) for 4866 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 40: After refmac, R = 0.2612 (Rfree = 0.000) for 4851 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 5025 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5045 seeds are put forward Round 1: 182 peptides, 41 chains. Longest chain 7 peptides. Score 0.217 Round 2: 212 peptides, 46 chains. Longest chain 7 peptides. Score 0.241 Round 3: 218 peptides, 44 chains. Longest chain 10 peptides. Score 0.277 Round 4: 221 peptides, 43 chains. Longest chain 8 peptides. Score 0.295 Round 5: 205 peptides, 38 chains. Longest chain 8 peptides. Score 0.309 Taking the results from Round 5 Chains 38, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11025 restraints for refining 4817 atoms. 10395 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2640 (Rfree = 0.000) for 4817 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 42: After refmac, R = 0.2570 (Rfree = 0.000) for 4782 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 43: After refmac, R = 0.2352 (Rfree = 0.000) for 4769 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Cycle 44: After refmac, R = 0.2355 (Rfree = 0.000) for 4766 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Cycle 45: After refmac, R = 0.2304 (Rfree = 0.000) for 4768 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 4925 seeds are put forward NCS extension: 0 residues added, 4925 seeds are put forward Round 1: 179 peptides, 40 chains. Longest chain 7 peptides. Score 0.220 Round 2: 214 peptides, 42 chains. Longest chain 9 peptides. Score 0.288 Round 3: 231 peptides, 44 chains. Longest chain 10 peptides. Score 0.309 Round 4: 226 peptides, 42 chains. Longest chain 10 peptides. Score 0.317 Round 5: 213 peptides, 39 chains. Longest chain 9 peptides. Score 0.317 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 174, 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 10978 restraints for refining 4815 atoms. 10321 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2709 (Rfree = 0.000) for 4815 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2455 (Rfree = 0.000) for 4783 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2437 (Rfree = 0.000) for 4750 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2400 (Rfree = 0.000) for 4727 atoms. TimeTaking 57.77