Mon 24 Dec 00:39:39 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 2opl-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-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/2opl-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-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 ============================================================ Mon 24 Dec 00:39:43 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/2opl-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-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 239 and 0 Target number of residues in the AU: 239 Target solvent content: 0.6536 Checking the provided sequence file Detected sequence length: 187 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 374 Adjusted target solvent content: 0.46 Input MTZ file: 2opl-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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2992 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: 62.588 3.801 Wilson plot Bfac: 79.76 3962 reflections ( 99.30 % complete ) and 0 restraints for refining 3315 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3350 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3136 (Rfree = 0.000) for 3315 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.88 Search for helices and strands: 0 residues in 0 chains, 3388 seeds are put forward NCS extension: 0 residues added, 3388 seeds are put forward Round 1: 137 peptides, 28 chains. Longest chain 9 peptides. Score 0.292 Round 2: 185 peptides, 32 chains. Longest chain 13 peptides. Score 0.429 Round 3: 186 peptides, 27 chains. Longest chain 17 peptides. Score 0.518 Round 4: 190 peptides, 29 chains. Longest chain 15 peptides. Score 0.500 Round 5: 200 peptides, 31 chains. Longest chain 15 peptides. Score 0.505 Taking the results from Round 3 Chains 28, Residues 159, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6108 restraints for refining 2705 atoms. 5449 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2393 (Rfree = 0.000) for 2705 atoms. Found 10 (14 requested) and removed 18 (7 requested) atoms. Cycle 2: After refmac, R = 0.2223 (Rfree = 0.000) for 2674 atoms. Found 6 (14 requested) and removed 11 (7 requested) atoms. Cycle 3: After refmac, R = 0.2258 (Rfree = 0.000) for 2662 atoms. Found 6 (14 requested) and removed 25 (7 requested) atoms. Cycle 4: After refmac, R = 0.2364 (Rfree = 0.000) for 2637 atoms. Found 12 (14 requested) and removed 34 (7 requested) atoms. Cycle 5: After refmac, R = 0.1918 (Rfree = 0.000) for 2598 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.82 Search for helices and strands: 0 residues in 0 chains, 2680 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2697 seeds are put forward Round 1: 178 peptides, 30 chains. Longest chain 23 peptides. Score 0.436 Round 2: 194 peptides, 31 chains. Longest chain 17 peptides. Score 0.482 Round 3: 189 peptides, 30 chains. Longest chain 26 peptides. Score 0.479 Round 4: 211 peptides, 30 chains. Longest chain 27 peptides. Score 0.559 Round 5: 201 peptides, 30 chains. Longest chain 22 peptides. Score 0.524 Taking the results from Round 4 Chains 30, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6353 restraints for refining 2703 atoms. 5659 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2937 (Rfree = 0.000) for 2703 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 7: After refmac, R = 0.2437 (Rfree = 0.000) for 2685 atoms. Found 6 (14 requested) and removed 16 (7 requested) atoms. Cycle 8: After refmac, R = 0.2579 (Rfree = 0.000) for 2670 atoms. Found 7 (14 requested) and removed 32 (7 requested) atoms. Cycle 9: After refmac, R = 0.2063 (Rfree = 0.000) for 2641 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.2444 (Rfree = 0.000) for 2632 atoms. Found 6 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.80 Search for helices and strands: 0 residues in 0 chains, 2707 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 2739 seeds are put forward Round 1: 164 peptides, 29 chains. Longest chain 11 peptides. Score 0.395 Round 2: 187 peptides, 28 chains. Longest chain 22 peptides. Score 0.505 Round 3: 196 peptides, 28 chains. Longest chain 18 peptides. Score 0.538 Round 4: 187 peptides, 26 chains. Longest chain 23 peptides. Score 0.537 Round 5: 190 peptides, 27 chains. Longest chain 22 peptides. Score 0.532 Taking the results from Round 3 Chains 28, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6349 restraints for refining 2704 atoms. 5705 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2181 (Rfree = 0.000) for 2704 atoms. Found 7 (14 requested) and removed 15 (7 requested) atoms. Cycle 12: After refmac, R = 0.1937 (Rfree = 0.000) for 2685 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 13: After refmac, R = 0.1834 (Rfree = 0.000) for 2671 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 14: After refmac, R = 0.1903 (Rfree = 0.000) for 2662 atoms. Found 9 (14 requested) and removed 15 (7 requested) atoms. Cycle 15: After refmac, R = 0.1677 (Rfree = 0.000) for 2653 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.82 Search for helices and strands: 0 residues in 0 chains, 2749 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2766 seeds are put forward Round 1: 162 peptides, 30 chains. Longest chain 16 peptides. Score 0.368 Round 2: 183 peptides, 27 chains. Longest chain 19 peptides. Score 0.506 Round 3: 168 peptides, 24 chains. Longest chain 16 peptides. Score 0.500 Round 4: 184 peptides, 28 chains. Longest chain 23 peptides. Score 0.494 Round 5: 184 peptides, 27 chains. Longest chain 16 peptides. Score 0.510 Taking the results from Round 5 Chains 27, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6453 restraints for refining 2706 atoms. 5852 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2196 (Rfree = 0.000) for 2706 atoms. Found 3 (14 requested) and removed 19 (7 requested) atoms. Cycle 17: After refmac, R = 0.2328 (Rfree = 0.000) for 2677 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 18: After refmac, R = 0.2227 (Rfree = 0.000) for 2665 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 19: After refmac, R = 0.2063 (Rfree = 0.000) for 2645 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 20: After refmac, R = 0.2062 (Rfree = 0.000) for 2640 atoms. Found 13 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.82 Search for helices and strands: 0 residues in 0 chains, 2717 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2736 seeds are put forward Round 1: 148 peptides, 31 chains. Longest chain 8 peptides. Score 0.285 Round 2: 171 peptides, 29 chains. Longest chain 12 peptides. Score 0.425 Round 3: 169 peptides, 30 chains. Longest chain 13 peptides. Score 0.398 Round 4: 171 peptides, 25 chains. Longest chain 20 peptides. Score 0.494 Round 5: 150 peptides, 23 chains. Longest chain 11 peptides. Score 0.446 Taking the results from Round 4 Chains 25, Residues 146, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6032 restraints for refining 2706 atoms. 5346 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2248 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 22: After refmac, R = 0.1873 (Rfree = 0.000) for 2690 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.1767 (Rfree = 0.000) for 2682 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.1743 (Rfree = 0.000) for 2683 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.1886 (Rfree = 0.000) for 2680 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 2763 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 2792 seeds are put forward Round 1: 140 peptides, 31 chains. Longest chain 7 peptides. Score 0.247 Round 2: 176 peptides, 29 chains. Longest chain 11 peptides. Score 0.445 Round 3: 161 peptides, 29 chains. Longest chain 10 peptides. Score 0.382 Round 4: 164 peptides, 30 chains. Longest chain 11 peptides. Score 0.377 Round 5: 167 peptides, 26 chains. Longest chain 18 peptides. Score 0.462 Taking the results from Round 5 Chains 26, Residues 141, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6401 restraints for refining 2705 atoms. 5824 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2112 (Rfree = 0.000) for 2705 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 27: After refmac, R = 0.1993 (Rfree = 0.000) for 2686 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.1832 (Rfree = 0.000) for 2674 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.1443 (Rfree = 0.000) for 2666 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 30: After refmac, R = 0.1635 (Rfree = 0.000) for 2657 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.83 Search for helices and strands: 0 residues in 0 chains, 2724 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2744 seeds are put forward Round 1: 130 peptides, 27 chains. Longest chain 8 peptides. Score 0.279 Round 2: 145 peptides, 26 chains. Longest chain 11 peptides. Score 0.368 Round 3: 159 peptides, 24 chains. Longest chain 13 peptides. Score 0.465 Round 4: 180 peptides, 29 chains. Longest chain 13 peptides. Score 0.461 Round 5: 190 peptides, 30 chains. Longest chain 13 peptides. Score 0.483 Taking the results from Round 5 Chains 30, Residues 160, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6369 restraints for refining 2706 atoms. 5734 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2187 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 32: After refmac, R = 0.1904 (Rfree = 0.000) for 2678 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 33: After refmac, R = 0.1915 (Rfree = 0.000) for 2666 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 34: After refmac, R = 0.1777 (Rfree = 0.000) for 2663 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.1702 (Rfree = 0.000) for 2657 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.79 Search for helices and strands: 0 residues in 0 chains, 2746 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2764 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 9 peptides. Score 0.270 Round 2: 156 peptides, 29 chains. Longest chain 10 peptides. Score 0.360 Round 3: 161 peptides, 27 chains. Longest chain 17 peptides. Score 0.419 Round 4: 161 peptides, 26 chains. Longest chain 10 peptides. Score 0.437 Round 5: 169 peptides, 27 chains. Longest chain 12 peptides. Score 0.452 Taking the results from Round 5 Chains 27, Residues 142, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6413 restraints for refining 2706 atoms. 5849 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2238 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 37: After refmac, R = 0.1865 (Rfree = 0.000) for 2678 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 38: After refmac, R = 0.1843 (Rfree = 0.000) for 2665 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.1835 (Rfree = 0.000) for 2661 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 40: After refmac, R = 0.1730 (Rfree = 0.000) for 2653 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.84 Search for helices and strands: 0 residues in 0 chains, 2733 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2747 seeds are put forward Round 1: 106 peptides, 23 chains. Longest chain 7 peptides. Score 0.242 Round 2: 135 peptides, 25 chains. Longest chain 9 peptides. Score 0.343 Round 3: 143 peptides, 25 chains. Longest chain 9 peptides. Score 0.379 Round 4: 136 peptides, 25 chains. Longest chain 9 peptides. Score 0.347 Round 5: 147 peptides, 26 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 3 Chains 25, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6463 restraints for refining 2677 atoms. 6016 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2157 (Rfree = 0.000) for 2677 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 42: After refmac, R = 0.1983 (Rfree = 0.000) for 2665 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.1788 (Rfree = 0.000) for 2658 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 44: After refmac, R = 0.1915 (Rfree = 0.000) for 2654 atoms. Found 13 (14 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.1804 (Rfree = 0.000) for 2651 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.80 Search for helices and strands: 0 residues in 0 chains, 2745 seeds are put forward NCS extension: 0 residues added, 2745 seeds are put forward Round 1: 82 peptides, 20 chains. Longest chain 5 peptides. Score 0.178 Round 2: 89 peptides, 18 chains. Longest chain 7 peptides. Score 0.264 Round 3: 98 peptides, 18 chains. Longest chain 9 peptides. Score 0.310 Round 4: 107 peptides, 20 chains. Longest chain 9 peptides. Score 0.312 Round 5: 113 peptides, 21 chains. Longest chain 10 peptides. Score 0.320 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 92, 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 2opl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3962 reflections ( 99.30 % complete ) and 6638 restraints for refining 2688 atoms. 6291 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2308 (Rfree = 0.000) for 2688 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2101 (Rfree = 0.000) for 2670 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2025 (Rfree = 0.000) for 2659 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2059 (Rfree = 0.000) for 2648 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 33.57