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 2ajr-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.8-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/2ajr-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.8-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/2ajr-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.8-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 540 and 0 Target number of residues in the AU: 540 Target solvent content: 0.6503 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 662 Adjusted target solvent content: 0.57 Input MTZ file: 2ajr-3.8-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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5296 target number of atoms Had to go as low as 0.70 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: 29.168 3.800 Wilson plot Bfac: 78.05 8765 reflections ( 99.47 % complete ) and 0 restraints for refining 5874 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3625 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2788 (Rfree = 0.000) for 5874 atoms. Found 17 (32 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.26 Search for helices and strands: 0 residues in 0 chains, 5953 seeds are put forward NCS extension: 0 residues added, 5953 seeds are put forward Round 1: 257 peptides, 49 chains. Longest chain 13 peptides. Score 0.310 Round 2: 306 peptides, 49 chains. Longest chain 20 peptides. Score 0.410 Round 3: 323 peptides, 47 chains. Longest chain 18 peptides. Score 0.459 Round 4: 325 peptides, 49 chains. Longest chain 16 peptides. Score 0.446 Round 5: 336 peptides, 47 chains. Longest chain 14 peptides. Score 0.482 Taking the results from Round 5 Chains 47, Residues 289, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11377 restraints for refining 4785 atoms. 10220 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3055 (Rfree = 0.000) for 4785 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 2: After refmac, R = 0.2886 (Rfree = 0.000) for 4766 atoms. Found 10 (26 requested) and removed 18 (13 requested) atoms. Cycle 3: After refmac, R = 0.2841 (Rfree = 0.000) for 4747 atoms. Found 7 (26 requested) and removed 17 (13 requested) atoms. Cycle 4: After refmac, R = 0.2807 (Rfree = 0.000) for 4733 atoms. Found 4 (26 requested) and removed 14 (13 requested) atoms. Cycle 5: After refmac, R = 0.2793 (Rfree = 0.000) for 4717 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 4867 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 4878 seeds are put forward Round 1: 317 peptides, 57 chains. Longest chain 16 peptides. Score 0.364 Round 2: 333 peptides, 51 chains. Longest chain 14 peptides. Score 0.445 Round 3: 347 peptides, 51 chains. Longest chain 16 peptides. Score 0.470 Round 4: 341 peptides, 47 chains. Longest chain 19 peptides. Score 0.491 Round 5: 355 peptides, 47 chains. Longest chain 20 peptides. Score 0.515 Taking the results from Round 5 Chains 49, Residues 308, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11133 restraints for refining 4789 atoms. 9889 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2799 (Rfree = 0.000) for 4789 atoms. Found 14 (26 requested) and removed 42 (13 requested) atoms. Cycle 7: After refmac, R = 0.2565 (Rfree = 0.000) for 4720 atoms. Found 12 (26 requested) and removed 38 (13 requested) atoms. Cycle 8: After refmac, R = 0.2675 (Rfree = 0.000) for 4680 atoms. Found 14 (25 requested) and removed 28 (12 requested) atoms. Cycle 9: After refmac, R = 0.2578 (Rfree = 0.000) for 4658 atoms. Found 6 (25 requested) and removed 19 (12 requested) atoms. Cycle 10: After refmac, R = 0.2518 (Rfree = 0.000) for 4644 atoms. Found 4 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 4800 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 4825 seeds are put forward Round 1: 312 peptides, 52 chains. Longest chain 12 peptides. Score 0.397 Round 2: 349 peptides, 47 chains. Longest chain 21 peptides. Score 0.505 Round 3: 351 peptides, 48 chains. Longest chain 21 peptides. Score 0.501 Round 4: 331 peptides, 45 chains. Longest chain 19 peptides. Score 0.489 Round 5: 334 peptides, 45 chains. Longest chain 17 peptides. Score 0.495 Taking the results from Round 2 Chains 48, Residues 302, Estimated correctness of the model 0.0 % 4 chains (54 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 10626 restraints for refining 4789 atoms. 9306 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2816 (Rfree = 0.000) for 4789 atoms. Found 23 (26 requested) and removed 29 (13 requested) atoms. Cycle 12: After refmac, R = 0.2658 (Rfree = 0.000) for 4769 atoms. Found 9 (26 requested) and removed 21 (13 requested) atoms. Cycle 13: After refmac, R = 0.2608 (Rfree = 0.000) for 4747 atoms. Found 6 (26 requested) and removed 19 (13 requested) atoms. Cycle 14: After refmac, R = 0.2558 (Rfree = 0.000) for 4732 atoms. Found 7 (26 requested) and removed 18 (13 requested) atoms. Cycle 15: After refmac, R = 0.2527 (Rfree = 0.000) for 4717 atoms. Found 8 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 4838 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 4873 seeds are put forward Round 1: 298 peptides, 53 chains. Longest chain 13 peptides. Score 0.360 Round 2: 331 peptides, 47 chains. Longest chain 16 peptides. Score 0.474 Round 3: 329 peptides, 47 chains. Longest chain 15 peptides. Score 0.470 Round 4: 332 peptides, 48 chains. Longest chain 17 peptides. Score 0.467 Round 5: 334 peptides, 42 chains. Longest chain 21 peptides. Score 0.518 Taking the results from Round 5 Chains 43, Residues 292, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 10963 restraints for refining 4787 atoms. 9744 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3028 (Rfree = 0.000) for 4787 atoms. Found 26 (26 requested) and removed 26 (13 requested) atoms. Cycle 17: After refmac, R = 0.2861 (Rfree = 0.000) for 4779 atoms. Found 3 (26 requested) and removed 16 (13 requested) atoms. Cycle 18: After refmac, R = 0.2798 (Rfree = 0.000) for 4763 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.2753 (Rfree = 0.000) for 4747 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.2733 (Rfree = 0.000) for 4733 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.28 Search for helices and strands: 0 residues in 0 chains, 4851 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4874 seeds are put forward Round 1: 287 peptides, 50 chains. Longest chain 14 peptides. Score 0.364 Round 2: 326 peptides, 50 chains. Longest chain 14 peptides. Score 0.440 Round 3: 321 peptides, 51 chains. Longest chain 14 peptides. Score 0.422 Round 4: 343 peptides, 54 chains. Longest chain 14 peptides. Score 0.439 Round 5: 334 peptides, 49 chains. Longest chain 13 peptides. Score 0.463 Taking the results from Round 5 Chains 49, Residues 285, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11325 restraints for refining 4790 atoms. 10225 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2965 (Rfree = 0.000) for 4790 atoms. Found 20 (26 requested) and removed 22 (13 requested) atoms. Cycle 22: After refmac, R = 0.2697 (Rfree = 0.000) for 4776 atoms. Found 9 (26 requested) and removed 17 (13 requested) atoms. Cycle 23: After refmac, R = 0.2636 (Rfree = 0.000) for 4758 atoms. Found 3 (26 requested) and removed 15 (13 requested) atoms. Cycle 24: After refmac, R = 0.2589 (Rfree = 0.000) for 4744 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.2555 (Rfree = 0.000) for 4730 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.28 Search for helices and strands: 0 residues in 0 chains, 4846 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 4857 seeds are put forward Round 1: 280 peptides, 53 chains. Longest chain 10 peptides. Score 0.323 Round 2: 311 peptides, 51 chains. Longest chain 15 peptides. Score 0.403 Round 3: 313 peptides, 48 chains. Longest chain 14 peptides. Score 0.432 Round 4: 320 peptides, 46 chains. Longest chain 17 peptides. Score 0.462 Round 5: 332 peptides, 45 chains. Longest chain 14 peptides. Score 0.491 Taking the results from Round 5 Chains 45, Residues 287, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11090 restraints for refining 4787 atoms. 9924 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3008 (Rfree = 0.000) for 4787 atoms. Found 26 (26 requested) and removed 17 (13 requested) atoms. Cycle 27: After refmac, R = 0.2866 (Rfree = 0.000) for 4790 atoms. Found 4 (26 requested) and removed 17 (13 requested) atoms. Cycle 28: After refmac, R = 0.2798 (Rfree = 0.000) for 4772 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.2746 (Rfree = 0.000) for 4759 atoms. Found 2 (26 requested) and removed 15 (13 requested) atoms. Cycle 30: After refmac, R = 0.2700 (Rfree = 0.000) for 4746 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 4871 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4888 seeds are put forward Round 1: 265 peptides, 50 chains. Longest chain 13 peptides. Score 0.318 Round 2: 305 peptides, 51 chains. Longest chain 16 peptides. Score 0.391 Round 3: 285 peptides, 43 chains. Longest chain 16 peptides. Score 0.421 Round 4: 307 peptides, 50 chains. Longest chain 14 peptides. Score 0.404 Round 5: 329 peptides, 48 chains. Longest chain 18 peptides. Score 0.462 Taking the results from Round 5 Chains 48, Residues 281, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11318 restraints for refining 4789 atoms. 10230 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3075 (Rfree = 0.000) for 4789 atoms. Found 21 (26 requested) and removed 16 (13 requested) atoms. Cycle 32: After refmac, R = 0.2930 (Rfree = 0.000) for 4793 atoms. Found 3 (26 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.2866 (Rfree = 0.000) for 4781 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.2820 (Rfree = 0.000) for 4768 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.2800 (Rfree = 0.000) for 4759 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 4858 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4880 seeds are put forward Round 1: 274 peptides, 54 chains. Longest chain 9 peptides. Score 0.301 Round 2: 285 peptides, 46 chains. Longest chain 15 peptides. Score 0.395 Round 3: 288 peptides, 47 chains. Longest chain 18 peptides. Score 0.392 Round 4: 304 peptides, 46 chains. Longest chain 18 peptides. Score 0.432 Round 5: 300 peptides, 44 chains. Longest chain 19 peptides. Score 0.441 Taking the results from Round 5 Chains 46, Residues 256, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11315 restraints for refining 4790 atoms. 10267 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2990 (Rfree = 0.000) for 4790 atoms. Found 23 (26 requested) and removed 19 (13 requested) atoms. Cycle 37: After refmac, R = 0.2851 (Rfree = 0.000) for 4790 atoms. Found 9 (26 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.2817 (Rfree = 0.000) for 4783 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.2775 (Rfree = 0.000) for 4773 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2744 (Rfree = 0.000) for 4761 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.30 Search for helices and strands: 0 residues in 0 chains, 4859 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4879 seeds are put forward Round 1: 241 peptides, 48 chains. Longest chain 9 peptides. Score 0.284 Round 2: 278 peptides, 49 chains. Longest chain 14 peptides. Score 0.354 Round 3: 278 peptides, 45 chains. Longest chain 16 peptides. Score 0.390 Round 4: 302 peptides, 50 chains. Longest chain 14 peptides. Score 0.394 Round 5: 310 peptides, 48 chains. Longest chain 16 peptides. Score 0.427 Taking the results from Round 5 Chains 49, Residues 262, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11442 restraints for refining 4790 atoms. 10399 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2931 (Rfree = 0.000) for 4790 atoms. Found 16 (26 requested) and removed 19 (13 requested) atoms. Cycle 42: After refmac, R = 0.2777 (Rfree = 0.000) for 4783 atoms. Found 7 (26 requested) and removed 18 (13 requested) atoms. Cycle 43: After refmac, R = 0.2722 (Rfree = 0.000) for 4770 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.2685 (Rfree = 0.000) for 4755 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.2689 (Rfree = 0.000) for 4743 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 4857 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 4883 seeds are put forward Round 1: 229 peptides, 47 chains. Longest chain 9 peptides. Score 0.267 Round 2: 267 peptides, 46 chains. Longest chain 14 peptides. Score 0.359 Round 3: 280 peptides, 45 chains. Longest chain 14 peptides. Score 0.394 Round 4: 283 peptides, 44 chains. Longest chain 20 peptides. Score 0.409 Round 5: 272 peptides, 45 chains. Longest chain 15 peptides. Score 0.378 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 239, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2ajr-3_warpNtrace.pdb as input Building loops using Loopy2018 45 chains (239 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8765 reflections ( 99.47 % complete ) and 11756 restraints for refining 4790 atoms. 10806 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2836 (Rfree = 0.000) for 4790 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2735 (Rfree = 0.000) for 4768 atoms. Found 0 (26 requested) and removed 6 (13 requested) atoms. Cycle 48: After refmac, R = 0.2691 (Rfree = 0.000) for 4760 atoms. Found 0 (26 requested) and removed 2 (13 requested) atoms. Cycle 49: After refmac, R = 0.2651 (Rfree = 0.000) for 4756 atoms. Found 0 (26 requested) and removed 3 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:43:41 GMT 2018 Job finished. TimeTaking 75.74 Used memory is bytes: 7494096