Mon 24 Dec 00:01:02 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 2pke-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-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/2pke-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-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 00:01:06 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/2pke-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-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 274 and 0 Target number of residues in the AU: 274 Target solvent content: 0.6701 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.50 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: 61.213 4.000 Wilson plot Bfac: 91.86 3613 reflections ( 95.46 % complete ) and 0 restraints for refining 4451 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3100 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3371 (Rfree = 0.000) for 4451 atoms. Found 21 (21 requested) and removed 384 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.76 3.16 Search for helices and strands: 0 residues in 0 chains, 4157 seeds are put forward NCS extension: 0 residues added, 4157 seeds are put forward Round 1: 109 peptides, 26 chains. Longest chain 6 peptides. Score 0.190 Round 2: 156 peptides, 32 chains. Longest chain 9 peptides. Score 0.285 Round 3: 149 peptides, 30 chains. Longest chain 9 peptides. Score 0.291 Round 4: 158 peptides, 32 chains. Longest chain 10 peptides. Score 0.293 Round 5: 149 peptides, 29 chains. Longest chain 9 peptides. Score 0.308 Taking the results from Round 5 Chains 29, Residues 120, Estimated correctness of the model 0.0 % 6 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 8893 restraints for refining 3626 atoms. 8375 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2990 (Rfree = 0.000) for 3626 atoms. Found 17 (17 requested) and removed 89 (8 requested) atoms. Cycle 2: After refmac, R = 0.2974 (Rfree = 0.000) for 3505 atoms. Found 16 (16 requested) and removed 80 (8 requested) atoms. Cycle 3: After refmac, R = 0.2987 (Rfree = 0.000) for 3417 atoms. Found 16 (16 requested) and removed 69 (8 requested) atoms. Cycle 4: After refmac, R = 0.2479 (Rfree = 0.000) for 3342 atoms. Found 15 (15 requested) and removed 35 (7 requested) atoms. Cycle 5: After refmac, R = 0.2941 (Rfree = 0.000) for 3308 atoms. Found 15 (15 requested) and removed 53 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.87 3.28 Search for helices and strands: 0 residues in 0 chains, 3370 seeds are put forward NCS extension: 0 residues added, 3370 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 6 peptides. Score 0.199 Round 2: 136 peptides, 28 chains. Longest chain 12 peptides. Score 0.272 Round 3: 148 peptides, 30 chains. Longest chain 8 peptides. Score 0.287 Round 4: 141 peptides, 28 chains. Longest chain 11 peptides. Score 0.293 Round 5: 148 peptides, 29 chains. Longest chain 9 peptides. Score 0.304 Taking the results from Round 5 Chains 29, Residues 119, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 7021 restraints for refining 3076 atoms. 6519 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3062 (Rfree = 0.000) for 3076 atoms. Found 14 (14 requested) and removed 59 (7 requested) atoms. Cycle 7: After refmac, R = 0.2939 (Rfree = 0.000) for 3007 atoms. Found 14 (14 requested) and removed 41 (7 requested) atoms. Cycle 8: After refmac, R = 0.2971 (Rfree = 0.000) for 2956 atoms. Found 14 (14 requested) and removed 32 (7 requested) atoms. Cycle 9: After refmac, R = 0.2600 (Rfree = 0.000) for 2931 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 10: After refmac, R = 0.2428 (Rfree = 0.000) for 2909 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.99 3.42 Search for helices and strands: 0 residues in 0 chains, 3020 seeds are put forward NCS extension: 0 residues added, 3020 seeds are put forward Round 1: 127 peptides, 30 chains. Longest chain 6 peptides. Score 0.198 Round 2: 142 peptides, 29 chains. Longest chain 8 peptides. Score 0.280 Round 3: 150 peptides, 29 chains. Longest chain 10 peptides. Score 0.312 Round 4: 149 peptides, 30 chains. Longest chain 10 peptides. Score 0.291 Round 5: 177 peptides, 33 chains. Longest chain 11 peptides. Score 0.350 Taking the results from Round 5 Chains 33, Residues 144, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 6311 restraints for refining 2918 atoms. 5698 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3004 (Rfree = 0.000) for 2918 atoms. Found 13 (13 requested) and removed 55 (6 requested) atoms. Cycle 12: After refmac, R = 0.3004 (Rfree = 0.000) for 2856 atoms. Found 13 (13 requested) and removed 37 (6 requested) atoms. Cycle 13: After refmac, R = 0.2884 (Rfree = 0.000) for 2815 atoms. Found 13 (13 requested) and removed 38 (6 requested) atoms. Cycle 14: After refmac, R = 0.2677 (Rfree = 0.000) for 2785 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 15: After refmac, R = 0.3091 (Rfree = 0.000) for 2770 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.58 2.95 Search for helices and strands: 0 residues in 0 chains, 2854 seeds are put forward NCS extension: 0 residues added, 2854 seeds are put forward Round 1: 147 peptides, 33 chains. Longest chain 7 peptides. Score 0.231 Round 2: 184 peptides, 36 chains. Longest chain 9 peptides. Score 0.329 Round 3: 190 peptides, 37 chains. Longest chain 10 peptides. Score 0.336 Round 4: 165 peptides, 32 chains. Longest chain 11 peptides. Score 0.321 Round 5: 171 peptides, 33 chains. Longest chain 9 peptides. Score 0.328 Taking the results from Round 3 Chains 37, Residues 153, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 6089 restraints for refining 2919 atoms. 5436 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2974 (Rfree = 0.000) for 2919 atoms. Found 13 (13 requested) and removed 56 (6 requested) atoms. Cycle 17: After refmac, R = 0.2964 (Rfree = 0.000) for 2855 atoms. Found 13 (13 requested) and removed 46 (6 requested) atoms. Cycle 18: After refmac, R = 0.2895 (Rfree = 0.000) for 2806 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 19: After refmac, R = 0.2896 (Rfree = 0.000) for 2783 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 20: After refmac, R = 0.2875 (Rfree = 0.000) for 2765 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.85 3.26 Search for helices and strands: 0 residues in 0 chains, 2823 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 2828 seeds are put forward Round 1: 130 peptides, 27 chains. Longest chain 8 peptides. Score 0.265 Round 2: 155 peptides, 33 chains. Longest chain 7 peptides. Score 0.264 Round 3: 166 peptides, 33 chains. Longest chain 7 peptides. Score 0.308 Round 4: 156 peptides, 29 chains. Longest chain 7 peptides. Score 0.335 Round 5: 173 peptides, 30 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 5 Chains 30, Residues 143, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 6107 restraints for refining 2921 atoms. 5547 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2993 (Rfree = 0.000) for 2921 atoms. Found 13 (13 requested) and removed 59 (6 requested) atoms. Cycle 22: After refmac, R = 0.3041 (Rfree = 0.000) for 2852 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 23: After refmac, R = 0.2601 (Rfree = 0.000) for 2812 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 24: After refmac, R = 0.2491 (Rfree = 0.000) for 2795 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 25: After refmac, R = 0.2525 (Rfree = 0.000) for 2790 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 3.49 Search for helices and strands: 0 residues in 0 chains, 2864 seeds are put forward NCS extension: 0 residues added, 2864 seeds are put forward Round 1: 150 peptides, 33 chains. Longest chain 7 peptides. Score 0.244 Round 2: 183 peptides, 36 chains. Longest chain 8 peptides. Score 0.325 Round 3: 178 peptides, 32 chains. Longest chain 10 peptides. Score 0.370 Round 4: 189 peptides, 36 chains. Longest chain 8 peptides. Score 0.348 Round 5: 188 peptides, 35 chains. Longest chain 8 peptides. Score 0.360 Taking the results from Round 3 Chains 32, Residues 146, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3613 reflections ( 95.46 % complete ) and 5890 restraints for refining 2868 atoms. 5270 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2974 (Rfree = 0.000) for 2868 atoms. Found 13 (13 requested) and removed 47 (6 requested) atoms. Cycle 27: After refmac, R = 0.3094 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 28: After refmac, R = 0.2955 (Rfree = 0.000) for 2787 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 29: After refmac, R = 0.2959 (Rfree = 0.000) for 2765 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 30: After refmac, R = 0.2978 (Rfree = 0.000) for 2748 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 2796 seeds are put forward NCS extension: 0 residues added, 2796 seeds are put forward Round 1: 123 peptides, 27 chains. Longest chain 6 peptides. Score 0.235 Round 2: 132 peptides, 25 chains. Longest chain 9 peptides. Score 0.308 Round 3: 138 peptides, 25 chains. Longest chain 10 peptides. Score 0.332 Round 4: 146 peptides, 25 chains. Longest chain 11 peptides. Score 0.364 Round 5: 132 peptides, 23 chains. Longest chain 9 peptides. Score 0.343 Taking the results from Round 4 Chains 25, Residues 121, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 6160 restraints for refining 2856 atoms. 5663 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2931 (Rfree = 0.000) for 2856 atoms. Found 13 (13 requested) and removed 60 (6 requested) atoms. Cycle 32: After refmac, R = 0.3038 (Rfree = 0.000) for 2796 atoms. Found 13 (13 requested) and removed 41 (6 requested) atoms. Cycle 33: After refmac, R = 0.2497 (Rfree = 0.000) for 2761 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 34: After refmac, R = 0.2580 (Rfree = 0.000) for 2751 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 35: After refmac, R = 0.2543 (Rfree = 0.000) for 2744 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.80 Search for helices and strands: 0 residues in 0 chains, 2824 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2836 seeds are put forward Round 1: 146 peptides, 32 chains. Longest chain 7 peptides. Score 0.244 Round 2: 162 peptides, 31 chains. Longest chain 11 peptides. Score 0.326 Round 3: 165 peptides, 30 chains. Longest chain 11 peptides. Score 0.353 Round 4: 170 peptides, 29 chains. Longest chain 13 peptides. Score 0.388 Round 5: 162 peptides, 28 chains. Longest chain 9 peptides. Score 0.375 Taking the results from Round 4 Chains 29, Residues 141, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5690 restraints for refining 2771 atoms. 5139 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3129 (Rfree = 0.000) for 2771 atoms. Found 13 (13 requested) and removed 57 (6 requested) atoms. Cycle 37: After refmac, R = 0.3177 (Rfree = 0.000) for 2712 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 38: After refmac, R = 0.3039 (Rfree = 0.000) for 2685 atoms. Found 12 (12 requested) and removed 30 (6 requested) atoms. Cycle 39: After refmac, R = 0.2648 (Rfree = 0.000) for 2659 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. Cycle 40: After refmac, R = 0.2925 (Rfree = 0.000) for 2654 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.59 Search for helices and strands: 0 residues in 0 chains, 2718 seeds are put forward NCS extension: 0 residues added, 2718 seeds are put forward Round 1: 133 peptides, 30 chains. Longest chain 6 peptides. Score 0.224 Round 2: 148 peptides, 28 chains. Longest chain 11 peptides. Score 0.321 Round 3: 163 peptides, 29 chains. Longest chain 11 peptides. Score 0.362 Round 4: 145 peptides, 27 chains. Longest chain 12 peptides. Score 0.326 Round 5: 163 peptides, 29 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 5 Chains 29, Residues 134, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5550 restraints for refining 2728 atoms. 4987 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3071 (Rfree = 0.000) for 2728 atoms. Found 12 (12 requested) and removed 61 (6 requested) atoms. Cycle 42: After refmac, R = 0.2828 (Rfree = 0.000) for 2667 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 43: After refmac, R = 0.2968 (Rfree = 0.000) for 2651 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 44: After refmac, R = 0.2782 (Rfree = 0.000) for 2632 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 45: After refmac, R = 0.3037 (Rfree = 0.000) for 2616 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.58 Search for helices and strands: 0 residues in 0 chains, 2660 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2673 seeds are put forward Round 1: 130 peptides, 30 chains. Longest chain 8 peptides. Score 0.211 Round 2: 136 peptides, 28 chains. Longest chain 8 peptides. Score 0.272 Round 3: 158 peptides, 31 chains. Longest chain 8 peptides. Score 0.310 Round 4: 149 peptides, 28 chains. Longest chain 10 peptides. Score 0.325 Round 5: 149 peptides, 27 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 122, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2pke-4_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (122 residues) following loop building 2 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3613 reflections ( 95.46 % complete ) and 6102 restraints for refining 2828 atoms. 5603 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3378 (Rfree = 0.000) for 2828 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3178 (Rfree = 0.000) for 2801 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2888 (Rfree = 0.000) for 2780 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2841 (Rfree = 0.000) for 2767 atoms. TimeTaking 30.2