Mon 24 Dec 00:22:50 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 2o08-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-4.0-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/2o08-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-4.0-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 00:22:54 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/2o08-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-4.0-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 333 and 0 Target number of residues in the AU: 333 Target solvent content: 0.6691 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: 2o08-4.0-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: 2o08-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3008 target number of atoms Had to go as low as 0.95 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 4.000 Wilson plot Bfac: 91.80 4727 reflections ( 97.24 % complete ) and 0 restraints for refining 3357 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3457 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3765 (Rfree = 0.000) for 3357 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.72 3.95 Search for helices and strands: 0 residues in 0 chains, 3460 seeds are put forward NCS extension: 0 residues added, 3460 seeds are put forward Round 1: 126 peptides, 26 chains. Longest chain 11 peptides. Score 0.254 Round 2: 168 peptides, 23 chains. Longest chain 16 peptides. Score 0.436 Round 3: 170 peptides, 21 chains. Longest chain 18 peptides. Score 0.469 Round 4: 184 peptides, 25 chains. Longest chain 13 peptides. Score 0.456 Round 5: 180 peptides, 22 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 5 Chains 22, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6519 restraints for refining 2716 atoms. 5909 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3003 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 2: After refmac, R = 0.2638 (Rfree = 0.000) for 2679 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 3: After refmac, R = 0.2567 (Rfree = 0.000) for 2656 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 4: After refmac, R = 0.2339 (Rfree = 0.000) for 2639 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2231 (Rfree = 0.000) for 2630 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.21 Search for helices and strands: 0 residues in 0 chains, 2759 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2782 seeds are put forward Round 1: 176 peptides, 31 chains. Longest chain 13 peptides. Score 0.351 Round 2: 193 peptides, 27 chains. Longest chain 17 peptides. Score 0.456 Round 3: 201 peptides, 25 chains. Longest chain 16 peptides. Score 0.503 Round 4: 200 peptides, 24 chains. Longest chain 21 peptides. Score 0.512 Round 5: 187 peptides, 20 chains. Longest chain 21 peptides. Score 0.528 Taking the results from Round 5 Chains 20, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6277 restraints for refining 2717 atoms. 5629 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2627 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 7: After refmac, R = 0.2231 (Rfree = 0.000) for 2681 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 8: After refmac, R = 0.2174 (Rfree = 0.000) for 2655 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 9: After refmac, R = 0.2045 (Rfree = 0.000) for 2636 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 10: After refmac, R = 0.2013 (Rfree = 0.000) for 2624 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.17 Search for helices and strands: 0 residues in 0 chains, 2734 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 2751 seeds are put forward Round 1: 167 peptides, 29 chains. Longest chain 15 peptides. Score 0.350 Round 2: 194 peptides, 27 chains. Longest chain 15 peptides. Score 0.458 Round 3: 196 peptides, 25 chains. Longest chain 15 peptides. Score 0.489 Round 4: 193 peptides, 25 chains. Longest chain 23 peptides. Score 0.481 Round 5: 206 peptides, 25 chains. Longest chain 21 peptides. Score 0.516 Taking the results from Round 5 Chains 25, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6288 restraints for refining 2715 atoms. 5589 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2511 (Rfree = 0.000) for 2715 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 12: After refmac, R = 0.2267 (Rfree = 0.000) for 2682 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2200 (Rfree = 0.000) for 2671 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2175 (Rfree = 0.000) for 2668 atoms. Found 3 (12 requested) and removed 16 (6 requested) atoms. Cycle 15: After refmac, R = 0.2080 (Rfree = 0.000) for 2649 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 3.20 Search for helices and strands: 0 residues in 0 chains, 2773 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 2805 seeds are put forward Round 1: 181 peptides, 31 chains. Longest chain 10 peptides. Score 0.367 Round 2: 182 peptides, 22 chains. Longest chain 19 peptides. Score 0.489 Round 3: 209 peptides, 26 chains. Longest chain 18 peptides. Score 0.512 Round 4: 210 peptides, 25 chains. Longest chain 30 peptides. Score 0.526 Round 5: 204 peptides, 24 chains. Longest chain 21 peptides. Score 0.523 Taking the results from Round 4 Chains 27, Residues 185, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6117 restraints for refining 2717 atoms. 5365 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2606 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 17: After refmac, R = 0.2319 (Rfree = 0.000) for 2684 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 18: After refmac, R = 0.2228 (Rfree = 0.000) for 2664 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 19: After refmac, R = 0.2038 (Rfree = 0.000) for 2650 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 20: After refmac, R = 0.1781 (Rfree = 0.000) for 2640 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 3.17 Search for helices and strands: 0 residues in 0 chains, 2765 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2793 seeds are put forward Round 1: 186 peptides, 31 chains. Longest chain 17 peptides. Score 0.382 Round 2: 189 peptides, 26 chains. Longest chain 19 peptides. Score 0.457 Round 3: 195 peptides, 26 chains. Longest chain 21 peptides. Score 0.474 Round 4: 210 peptides, 29 chains. Longest chain 18 peptides. Score 0.478 Round 5: 205 peptides, 25 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 5 Chains 26, Residues 180, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6015 restraints for refining 2716 atoms. 5290 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2873 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 22: After refmac, R = 0.2483 (Rfree = 0.000) for 2663 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 23: After refmac, R = 0.2358 (Rfree = 0.000) for 2635 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.2249 (Rfree = 0.000) for 2623 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2240 (Rfree = 0.000) for 2614 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 3.18 Search for helices and strands: 0 residues in 0 chains, 2727 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2746 seeds are put forward Round 1: 159 peptides, 29 chains. Longest chain 10 peptides. Score 0.324 Round 2: 189 peptides, 29 chains. Longest chain 10 peptides. Score 0.418 Round 3: 180 peptides, 25 chains. Longest chain 14 peptides. Score 0.444 Round 4: 187 peptides, 25 chains. Longest chain 19 peptides. Score 0.464 Round 5: 187 peptides, 23 chains. Longest chain 26 peptides. Score 0.490 Taking the results from Round 5 Chains 23, Residues 164, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 5906 restraints for refining 2716 atoms. 5150 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2648 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 32 (6 requested) atoms. Cycle 27: After refmac, R = 0.2315 (Rfree = 0.000) for 2669 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.2116 (Rfree = 0.000) for 2659 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.2174 (Rfree = 0.000) for 2651 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.2088 (Rfree = 0.000) for 2645 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.17 Search for helices and strands: 0 residues in 0 chains, 2724 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 2759 seeds are put forward Round 1: 160 peptides, 31 chains. Longest chain 15 peptides. Score 0.298 Round 2: 180 peptides, 29 chains. Longest chain 14 peptides. Score 0.391 Round 3: 180 peptides, 28 chains. Longest chain 11 peptides. Score 0.404 Round 4: 185 peptides, 28 chains. Longest chain 11 peptides. Score 0.419 Round 5: 188 peptides, 29 chains. Longest chain 12 peptides. Score 0.415 Taking the results from Round 4 Chains 28, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6152 restraints for refining 2715 atoms. 5552 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2339 (Rfree = 0.000) for 2715 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.2488 (Rfree = 0.000) for 2681 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 33: After refmac, R = 0.2201 (Rfree = 0.000) for 2660 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.2204 (Rfree = 0.000) for 2643 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.2323 (Rfree = 0.000) for 2631 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.18 Search for helices and strands: 0 residues in 0 chains, 2733 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2744 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 8 peptides. Score 0.264 Round 2: 165 peptides, 27 chains. Longest chain 13 peptides. Score 0.372 Round 3: 166 peptides, 29 chains. Longest chain 13 peptides. Score 0.347 Round 4: 165 peptides, 26 chains. Longest chain 14 peptides. Score 0.386 Round 5: 162 peptides, 25 chains. Longest chain 15 peptides. Score 0.390 Taking the results from Round 5 Chains 25, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6288 restraints for refining 2716 atoms. 5765 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2574 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. Cycle 37: After refmac, R = 0.2508 (Rfree = 0.000) for 2671 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 38: After refmac, R = 0.2409 (Rfree = 0.000) for 2655 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 39: After refmac, R = 0.2368 (Rfree = 0.000) for 2642 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.2216 (Rfree = 0.000) for 2635 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 3.22 Search for helices and strands: 0 residues in 0 chains, 2747 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2767 seeds are put forward Round 1: 149 peptides, 31 chains. Longest chain 10 peptides. Score 0.260 Round 2: 155 peptides, 26 chains. Longest chain 14 peptides. Score 0.354 Round 3: 151 peptides, 25 chains. Longest chain 10 peptides. Score 0.355 Round 4: 164 peptides, 29 chains. Longest chain 10 peptides. Score 0.340 Round 5: 149 peptides, 23 chains. Longest chain 11 peptides. Score 0.378 Taking the results from Round 5 Chains 23, Residues 126, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6208 restraints for refining 2717 atoms. 5698 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2633 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 42: After refmac, R = 0.2397 (Rfree = 0.000) for 2685 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.2303 (Rfree = 0.000) for 2673 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 44: After refmac, R = 0.2296 (Rfree = 0.000) for 2662 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 45: After refmac, R = 0.2205 (Rfree = 0.000) for 2648 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.15 Search for helices and strands: 0 residues in 0 chains, 2712 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 2722 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 7 peptides. Score 0.236 Round 2: 146 peptides, 25 chains. Longest chain 12 peptides. Score 0.339 Round 3: 139 peptides, 22 chains. Longest chain 11 peptides. Score 0.360 Round 4: 141 peptides, 22 chains. Longest chain 12 peptides. Score 0.367 Round 5: 149 peptides, 24 chains. Longest chain 14 peptides. Score 0.363 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 119, 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 2o08-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4727 reflections ( 97.24 % complete ) and 6014 restraints for refining 2653 atoms. 5560 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2363 (Rfree = 0.000) for 2653 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2390 (Rfree = 0.000) for 2637 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2384 (Rfree = 0.000) for 2625 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2119 (Rfree = 0.000) for 2613 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 32.38