Sun 23 Dec 23:45:12 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ajr-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.8-parrot-mrncs ############### 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 23:45:17 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.8-parrot-mrncs/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-mrncs.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-mrncs.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 5881 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3629 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2829 (Rfree = 0.000) for 5881 atoms. Found 18 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.27 Search for helices and strands: 0 residues in 0 chains, 6000 seeds are put forward NCS extension: 0 residues added, 6000 seeds are put forward Round 1: 244 peptides, 47 chains. Longest chain 11 peptides. Score 0.300 Round 2: 310 peptides, 47 chains. Longest chain 17 peptides. Score 0.435 Round 3: 339 peptides, 47 chains. Longest chain 19 peptides. Score 0.488 Round 4: 351 peptides, 53 chains. Longest chain 19 peptides. Score 0.462 Round 5: 360 peptides, 51 chains. Longest chain 16 peptides. Score 0.493 Taking the results from Round 5 Chains 52, Residues 309, Estimated correctness of the model 0.0 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11280 restraints for refining 4789 atoms. 9995 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2984 (Rfree = 0.000) for 4789 atoms. Found 19 (26 requested) and removed 23 (13 requested) atoms. Cycle 2: After refmac, R = 0.2864 (Rfree = 0.000) for 4746 atoms. Found 13 (26 requested) and removed 18 (13 requested) atoms. Cycle 3: After refmac, R = 0.2825 (Rfree = 0.000) for 4734 atoms. Found 9 (26 requested) and removed 15 (13 requested) atoms. Cycle 4: After refmac, R = 0.2786 (Rfree = 0.000) for 4724 atoms. Found 3 (26 requested) and removed 14 (13 requested) atoms. Cycle 5: After refmac, R = 0.2767 (Rfree = 0.000) for 4709 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.26 Search for helices and strands: 0 residues in 0 chains, 4853 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4870 seeds are put forward Round 1: 299 peptides, 50 chains. Longest chain 15 peptides. Score 0.388 Round 2: 330 peptides, 48 chains. Longest chain 19 peptides. Score 0.464 Round 3: 346 peptides, 48 chains. Longest chain 16 peptides. Score 0.492 Round 4: 342 peptides, 43 chains. Longest chain 25 peptides. Score 0.524 Round 5: 341 peptides, 48 chains. Longest chain 24 peptides. Score 0.483 Taking the results from Round 4 Chains 45, Residues 299, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11034 restraints for refining 4790 atoms. 9812 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2896 (Rfree = 0.000) for 4790 atoms. Found 18 (26 requested) and removed 27 (13 requested) atoms. Cycle 7: After refmac, R = 0.2798 (Rfree = 0.000) for 4750 atoms. Found 5 (26 requested) and removed 19 (13 requested) atoms. Cycle 8: After refmac, R = 0.2760 (Rfree = 0.000) for 4730 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2714 (Rfree = 0.000) for 4718 atoms. Found 4 (25 requested) and removed 13 (12 requested) atoms. Cycle 10: After refmac, R = 0.2689 (Rfree = 0.000) for 4703 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.28 Search for helices and strands: 0 residues in 0 chains, 4815 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 4845 seeds are put forward Round 1: 299 peptides, 54 chains. Longest chain 12 peptides. Score 0.353 Round 2: 330 peptides, 49 chains. Longest chain 16 peptides. Score 0.456 Round 3: 332 peptides, 52 chains. Longest chain 13 peptides. Score 0.435 Round 4: 328 peptides, 49 chains. Longest chain 15 peptides. Score 0.452 Round 5: 348 peptides, 50 chains. Longest chain 15 peptides. Score 0.480 Taking the results from Round 5 Chains 51, Residues 298, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11073 restraints for refining 4790 atoms. 9855 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3031 (Rfree = 0.000) for 4790 atoms. Found 26 (26 requested) and removed 57 (13 requested) atoms. Cycle 12: After refmac, R = 0.2550 (Rfree = 0.000) for 4706 atoms. Found 12 (26 requested) and removed 38 (13 requested) atoms. Cycle 13: After refmac, R = 0.2466 (Rfree = 0.000) for 4657 atoms. Found 5 (25 requested) and removed 25 (12 requested) atoms. Cycle 14: After refmac, R = 0.2450 (Rfree = 0.000) for 4620 atoms. Found 7 (25 requested) and removed 24 (12 requested) atoms. Cycle 15: After refmac, R = 0.2438 (Rfree = 0.000) for 4596 atoms. Found 5 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.26 Search for helices and strands: 0 residues in 0 chains, 4748 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4769 seeds are put forward Round 1: 298 peptides, 59 chains. Longest chain 13 peptides. Score 0.307 Round 2: 329 peptides, 54 chains. Longest chain 18 peptides. Score 0.412 Round 3: 340 peptides, 51 chains. Longest chain 22 peptides. Score 0.458 Round 4: 313 peptides, 48 chains. Longest chain 14 peptides. Score 0.432 Round 5: 327 peptides, 49 chains. Longest chain 17 peptides. Score 0.450 Taking the results from Round 3 Chains 51, Residues 289, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 10827 restraints for refining 4788 atoms. 9658 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2618 (Rfree = 0.000) for 4788 atoms. Found 21 (26 requested) and removed 27 (13 requested) atoms. Cycle 17: After refmac, R = 0.2507 (Rfree = 0.000) for 4763 atoms. Found 11 (26 requested) and removed 17 (13 requested) atoms. Cycle 18: After refmac, R = 0.2464 (Rfree = 0.000) for 4749 atoms. Found 4 (26 requested) and removed 14 (13 requested) atoms. Cycle 19: After refmac, R = 0.2445 (Rfree = 0.000) for 4735 atoms. Found 4 (26 requested) and removed 14 (13 requested) atoms. Cycle 20: After refmac, R = 0.2440 (Rfree = 0.000) for 4725 atoms. Found 1 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.28 Search for helices and strands: 0 residues in 0 chains, 4850 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 4876 seeds are put forward Round 1: 274 peptides, 49 chains. Longest chain 11 peptides. Score 0.346 Round 2: 296 peptides, 47 chains. Longest chain 15 peptides. Score 0.408 Round 3: 310 peptides, 46 chains. Longest chain 17 peptides. Score 0.443 Round 4: 317 peptides, 48 chains. Longest chain 15 peptides. Score 0.440 Round 5: 292 peptides, 44 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 3 Chains 46, Residues 264, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11108 restraints for refining 4790 atoms. 10080 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2675 (Rfree = 0.000) for 4790 atoms. Found 23 (26 requested) and removed 23 (13 requested) atoms. Cycle 22: After refmac, R = 0.2548 (Rfree = 0.000) for 4765 atoms. Found 7 (26 requested) and removed 22 (13 requested) atoms. Cycle 23: After refmac, R = 0.2534 (Rfree = 0.000) for 4746 atoms. Found 3 (26 requested) and removed 16 (13 requested) atoms. Cycle 24: After refmac, R = 0.2514 (Rfree = 0.000) for 4725 atoms. Found 7 (26 requested) and removed 17 (13 requested) atoms. Cycle 25: After refmac, R = 0.2470 (Rfree = 0.000) for 4711 atoms. Found 4 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 4813 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4831 seeds are put forward Round 1: 269 peptides, 50 chains. Longest chain 11 peptides. Score 0.327 Round 2: 314 peptides, 54 chains. Longest chain 12 peptides. Score 0.383 Round 3: 305 peptides, 50 chains. Longest chain 18 peptides. Score 0.400 Round 4: 319 peptides, 48 chains. Longest chain 18 peptides. Score 0.444 Round 5: 316 peptides, 47 chains. Longest chain 18 peptides. Score 0.446 Taking the results from Round 5 Chains 50, Residues 269, Estimated correctness of the model 0.0 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11049 restraints for refining 4790 atoms. 9921 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2721 (Rfree = 0.000) for 4790 atoms. Found 18 (26 requested) and removed 24 (13 requested) atoms. Cycle 27: After refmac, R = 0.2611 (Rfree = 0.000) for 4759 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. Cycle 28: After refmac, R = 0.2603 (Rfree = 0.000) for 4742 atoms. Found 4 (26 requested) and removed 19 (13 requested) atoms. Cycle 29: After refmac, R = 0.2552 (Rfree = 0.000) for 4716 atoms. Found 7 (25 requested) and removed 17 (12 requested) atoms. Cycle 30: After refmac, R = 0.2527 (Rfree = 0.000) for 4702 atoms. Found 6 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 4804 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4817 seeds are put forward Round 1: 277 peptides, 50 chains. Longest chain 11 peptides. Score 0.343 Round 2: 288 peptides, 45 chains. Longest chain 14 peptides. Score 0.410 Round 3: 299 peptides, 46 chains. Longest chain 14 peptides. Score 0.423 Round 4: 301 peptides, 47 chains. Longest chain 16 peptides. Score 0.418 Round 5: 296 peptides, 42 chains. Longest chain 16 peptides. Score 0.451 Taking the results from Round 5 Chains 45, Residues 254, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11049 restraints for refining 4790 atoms. 9973 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2624 (Rfree = 0.000) for 4790 atoms. Found 15 (26 requested) and removed 26 (13 requested) atoms. Cycle 32: After refmac, R = 0.2499 (Rfree = 0.000) for 4759 atoms. Found 6 (26 requested) and removed 16 (13 requested) atoms. Cycle 33: After refmac, R = 0.2442 (Rfree = 0.000) for 4732 atoms. Found 1 (26 requested) and removed 16 (13 requested) atoms. Cycle 34: After refmac, R = 0.2398 (Rfree = 0.000) for 4713 atoms. Found 6 (25 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2384 (Rfree = 0.000) for 4703 atoms. Found 1 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.28 Search for helices and strands: 0 residues in 0 chains, 4827 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4848 seeds are put forward Round 1: 274 peptides, 51 chains. Longest chain 12 peptides. Score 0.328 Round 2: 305 peptides, 48 chains. Longest chain 23 peptides. Score 0.417 Round 3: 299 peptides, 47 chains. Longest chain 15 peptides. Score 0.414 Round 4: 299 peptides, 45 chains. Longest chain 17 peptides. Score 0.431 Round 5: 306 peptides, 48 chains. Longest chain 15 peptides. Score 0.419 Taking the results from Round 4 Chains 47, Residues 254, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11125 restraints for refining 4790 atoms. 10098 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2623 (Rfree = 0.000) for 4790 atoms. Found 16 (26 requested) and removed 25 (13 requested) atoms. Cycle 37: After refmac, R = 0.2529 (Rfree = 0.000) for 4774 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. Cycle 38: After refmac, R = 0.2487 (Rfree = 0.000) for 4758 atoms. Found 3 (26 requested) and removed 18 (13 requested) atoms. Cycle 39: After refmac, R = 0.2461 (Rfree = 0.000) for 4741 atoms. Found 6 (26 requested) and removed 18 (13 requested) atoms. Cycle 40: After refmac, R = 0.2460 (Rfree = 0.000) for 4727 atoms. Found 3 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 4816 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4839 seeds are put forward Round 1: 250 peptides, 47 chains. Longest chain 11 peptides. Score 0.313 Round 2: 265 peptides, 43 chains. Longest chain 15 peptides. Score 0.382 Round 3: 274 peptides, 44 chains. Longest chain 13 peptides. Score 0.391 Round 4: 289 peptides, 46 chains. Longest chain 16 peptides. Score 0.403 Round 5: 291 peptides, 46 chains. Longest chain 16 peptides. Score 0.407 Taking the results from Round 5 Chains 47, Residues 245, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8765 reflections ( 99.47 % complete ) and 11326 restraints for refining 4790 atoms. 10370 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2638 (Rfree = 0.000) for 4790 atoms. Found 18 (26 requested) and removed 21 (13 requested) atoms. Cycle 42: After refmac, R = 0.2537 (Rfree = 0.000) for 4780 atoms. Found 10 (26 requested) and removed 17 (13 requested) atoms. Cycle 43: After refmac, R = 0.2475 (Rfree = 0.000) for 4769 atoms. Found 4 (26 requested) and removed 16 (13 requested) atoms. Cycle 44: After refmac, R = 0.2447 (Rfree = 0.000) for 4756 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.2433 (Rfree = 0.000) for 4744 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 4857 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4876 seeds are put forward Round 1: 231 peptides, 46 chains. Longest chain 16 peptides. Score 0.281 Round 2: 251 peptides, 43 chains. Longest chain 19 peptides. Score 0.353 Round 3: 257 peptides, 40 chains. Longest chain 13 peptides. Score 0.393 Round 4: 255 peptides, 39 chains. Longest chain 14 peptides. Score 0.398 Round 5: 259 peptides, 38 chains. Longest chain 17 peptides. Score 0.415 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 221, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2ajr-3_warpNtrace.pdb as input Building loops using Loopy2018 38 chains (221 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8765 reflections ( 99.47 % complete ) and 11425 restraints for refining 4788 atoms. 10566 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2590 (Rfree = 0.000) for 4788 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2530 (Rfree = 0.000) for 4769 atoms. Found 0 (26 requested) and removed 7 (13 requested) atoms. Cycle 48: After refmac, R = 0.2506 (Rfree = 0.000) for 4761 atoms. Found 0 (26 requested) and removed 3 (13 requested) atoms. Cycle 49: After refmac, R = 0.2478 (Rfree = 0.000) for 4756 atoms. TimeTaking 57.65