Mon 24 Dec 00:31:38 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 2o08-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-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/2o08-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-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 ============================================================ Mon 24 Dec 00:31:43 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/2o08-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-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 369 and 0 Target number of residues in the AU: 369 Target solvent content: 0.6334 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-3.6-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3008 target number of atoms Had to go as low as 0.90 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: 83.235 3.600 Wilson plot Bfac: 68.09 6473 reflections ( 97.75 % complete ) and 0 restraints for refining 3346 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3269 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2828 (Rfree = 0.000) for 3346 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 2.93 Search for helices and strands: 0 residues in 0 chains, 3451 seeds are put forward NCS extension: 0 residues added, 3451 seeds are put forward Round 1: 191 peptides, 35 chains. Longest chain 11 peptides. Score 0.343 Round 2: 227 peptides, 31 chains. Longest chain 14 peptides. Score 0.499 Round 3: 229 peptides, 28 chains. Longest chain 25 peptides. Score 0.539 Round 4: 235 peptides, 28 chains. Longest chain 19 peptides. Score 0.554 Round 5: 237 peptides, 29 chains. Longest chain 17 peptides. Score 0.548 Taking the results from Round 4 Chains 28, Residues 207, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5908 restraints for refining 2725 atoms. 5108 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2737 (Rfree = 0.000) for 2725 atoms. Found 14 (17 requested) and removed 16 (8 requested) atoms. Cycle 2: After refmac, R = 0.2452 (Rfree = 0.000) for 2682 atoms. Found 14 (17 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.2419 (Rfree = 0.000) for 2657 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2409 (Rfree = 0.000) for 2651 atoms. Found 13 (17 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.2290 (Rfree = 0.000) for 2630 atoms. Found 15 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 2.91 Search for helices and strands: 0 residues in 0 chains, 2789 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2804 seeds are put forward Round 1: 212 peptides, 34 chains. Longest chain 17 peptides. Score 0.420 Round 2: 224 peptides, 30 chains. Longest chain 14 peptides. Score 0.503 Round 3: 234 peptides, 28 chains. Longest chain 22 peptides. Score 0.552 Round 4: 226 peptides, 27 chains. Longest chain 31 peptides. Score 0.543 Round 5: 234 peptides, 25 chains. Longest chain 37 peptides. Score 0.585 Taking the results from Round 5 Chains 25, Residues 209, Estimated correctness of the model 8.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 6002 restraints for refining 2727 atoms. 5191 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2613 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 7: After refmac, R = 0.2237 (Rfree = 0.000) for 2705 atoms. Found 10 (17 requested) and removed 16 (8 requested) atoms. Cycle 8: After refmac, R = 0.2170 (Rfree = 0.000) for 2687 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 9: After refmac, R = 0.2196 (Rfree = 0.000) for 2675 atoms. Found 8 (17 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.2228 (Rfree = 0.000) for 2664 atoms. Found 11 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 2.90 Search for helices and strands: 0 residues in 0 chains, 2818 seeds are put forward NCS extension: 53 residues added (3 deleted due to clashes), 2871 seeds are put forward Round 1: 224 peptides, 40 chains. Longest chain 14 peptides. Score 0.379 Round 2: 239 peptides, 28 chains. Longest chain 26 peptides. Score 0.564 Round 3: 231 peptides, 27 chains. Longest chain 25 peptides. Score 0.556 Round 4: 236 peptides, 30 chains. Longest chain 22 peptides. Score 0.534 Round 5: 246 peptides, 32 chains. Longest chain 22 peptides. Score 0.536 Taking the results from Round 2 Chains 28, Residues 211, Estimated correctness of the model 0.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5723 restraints for refining 2668 atoms. 4907 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2489 (Rfree = 0.000) for 2668 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 12: After refmac, R = 0.2173 (Rfree = 0.000) for 2653 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. Cycle 13: After refmac, R = 0.2100 (Rfree = 0.000) for 2640 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2087 (Rfree = 0.000) for 2632 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. Cycle 15: After refmac, R = 0.2016 (Rfree = 0.000) for 2627 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 2.87 Search for helices and strands: 0 residues in 0 chains, 2774 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 2793 seeds are put forward Round 1: 213 peptides, 36 chains. Longest chain 11 peptides. Score 0.398 Round 2: 229 peptides, 29 chains. Longest chain 17 peptides. Score 0.528 Round 3: 226 peptides, 28 chains. Longest chain 16 peptides. Score 0.532 Round 4: 228 peptides, 28 chains. Longest chain 15 peptides. Score 0.537 Round 5: 226 peptides, 28 chains. Longest chain 18 peptides. Score 0.532 Taking the results from Round 4 Chains 29, Residues 200, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5981 restraints for refining 2727 atoms. 5185 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2902 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2590 (Rfree = 0.000) for 2721 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 18: After refmac, R = 0.2429 (Rfree = 0.000) for 2720 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.2366 (Rfree = 0.000) for 2718 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.2286 (Rfree = 0.000) for 2711 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 2.91 Search for helices and strands: 0 residues in 0 chains, 2868 seeds are put forward NCS extension: 0 residues added, 2868 seeds are put forward Round 1: 210 peptides, 38 chains. Longest chain 13 peptides. Score 0.363 Round 2: 223 peptides, 34 chains. Longest chain 17 peptides. Score 0.452 Round 3: 233 peptides, 31 chains. Longest chain 19 peptides. Score 0.515 Round 4: 230 peptides, 29 chains. Longest chain 20 peptides. Score 0.530 Round 5: 227 peptides, 27 chains. Longest chain 19 peptides. Score 0.546 Taking the results from Round 5 Chains 27, Residues 200, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5769 restraints for refining 2727 atoms. 4893 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2747 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 22: After refmac, R = 0.2517 (Rfree = 0.000) for 2709 atoms. Found 12 (17 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.2455 (Rfree = 0.000) for 2687 atoms. Found 9 (17 requested) and removed 15 (8 requested) atoms. Cycle 24: After refmac, R = 0.2441 (Rfree = 0.000) for 2667 atoms. Found 12 (17 requested) and removed 15 (8 requested) atoms. Cycle 25: After refmac, R = 0.2370 (Rfree = 0.000) for 2653 atoms. Found 8 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 2.89 Search for helices and strands: 0 residues in 0 chains, 2786 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2811 seeds are put forward Round 1: 190 peptides, 36 chains. Longest chain 8 peptides. Score 0.327 Round 2: 202 peptides, 32 chains. Longest chain 13 peptides. Score 0.417 Round 3: 223 peptides, 35 chains. Longest chain 15 peptides. Score 0.440 Round 4: 203 peptides, 31 chains. Longest chain 14 peptides. Score 0.433 Round 5: 212 peptides, 30 chains. Longest chain 19 peptides. Score 0.471 Taking the results from Round 5 Chains 31, Residues 182, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5908 restraints for refining 2727 atoms. 5158 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2719 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 27: After refmac, R = 0.2501 (Rfree = 0.000) for 2701 atoms. Found 14 (17 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2538 (Rfree = 0.000) for 2699 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.2527 (Rfree = 0.000) for 2696 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.2423 (Rfree = 0.000) for 2686 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 2.90 Search for helices and strands: 0 residues in 0 chains, 2846 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2871 seeds are put forward Round 1: 170 peptides, 32 chains. Longest chain 11 peptides. Score 0.317 Round 2: 203 peptides, 31 chains. Longest chain 14 peptides. Score 0.433 Round 3: 204 peptides, 32 chains. Longest chain 17 peptides. Score 0.423 Round 4: 215 peptides, 31 chains. Longest chain 17 peptides. Score 0.467 Round 5: 197 peptides, 28 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 4 Chains 32, Residues 184, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 6058 restraints for refining 2727 atoms. 5323 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2808 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 32: After refmac, R = 0.2586 (Rfree = 0.000) for 2706 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.2512 (Rfree = 0.000) for 2698 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 34: After refmac, R = 0.2409 (Rfree = 0.000) for 2695 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.2497 (Rfree = 0.000) for 2691 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 2.87 Search for helices and strands: 0 residues in 0 chains, 2850 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2872 seeds are put forward Round 1: 190 peptides, 36 chains. Longest chain 12 peptides. Score 0.327 Round 2: 192 peptides, 30 chains. Longest chain 16 peptides. Score 0.414 Round 3: 192 peptides, 28 chains. Longest chain 15 peptides. Score 0.440 Round 4: 211 peptides, 28 chains. Longest chain 20 peptides. Score 0.493 Round 5: 201 peptides, 27 chains. Longest chain 22 peptides. Score 0.478 Taking the results from Round 4 Chains 28, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5974 restraints for refining 2727 atoms. 5270 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2862 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 37: After refmac, R = 0.2712 (Rfree = 0.000) for 2713 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 38: After refmac, R = 0.2718 (Rfree = 0.000) for 2696 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 39: After refmac, R = 0.2703 (Rfree = 0.000) for 2678 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 40: After refmac, R = 0.2550 (Rfree = 0.000) for 2663 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.97 3.33 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward NCS extension: 0 residues added, 2793 seeds are put forward Round 1: 168 peptides, 33 chains. Longest chain 13 peptides. Score 0.296 Round 2: 186 peptides, 29 chains. Longest chain 14 peptides. Score 0.409 Round 3: 179 peptides, 24 chains. Longest chain 16 peptides. Score 0.455 Round 4: 163 peptides, 25 chains. Longest chain 12 peptides. Score 0.393 Round 5: 174 peptides, 25 chains. Longest chain 17 peptides. Score 0.427 Taking the results from Round 3 Chains 24, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 6056 restraints for refining 2726 atoms. 5460 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2798 (Rfree = 0.000) for 2726 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 42: After refmac, R = 0.2557 (Rfree = 0.000) for 2712 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2670 (Rfree = 0.000) for 2704 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.2440 (Rfree = 0.000) for 2689 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.2402 (Rfree = 0.000) for 2685 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 2.90 Search for helices and strands: 0 residues in 0 chains, 2831 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2847 seeds are put forward Round 1: 155 peptides, 30 chains. Longest chain 9 peptides. Score 0.296 Round 2: 166 peptides, 25 chains. Longest chain 17 peptides. Score 0.403 Round 3: 180 peptides, 30 chains. Longest chain 15 peptides. Score 0.377 Round 4: 174 peptides, 25 chains. Longest chain 21 peptides. Score 0.427 Round 5: 163 peptides, 25 chains. Longest chain 15 peptides. Score 0.393 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 149, 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 2o08-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6473 reflections ( 97.75 % complete ) and 6249 restraints for refining 2726 atoms. 5678 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2679 (Rfree = 0.000) for 2726 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2693 (Rfree = 0.000) for 2702 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2500 (Rfree = 0.000) for 2684 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2424 (Rfree = 0.000) for 2672 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 41.23