Mon 24 Dec 08:03:18 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pke-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pke-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pke-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-noncs ############### 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 08:03:28 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/noncs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.55 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 4423 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3221 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3310 (Rfree = 0.000) for 4423 atoms. Found 21 (21 requested) and removed 332 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.56 Search for helices and strands: 0 residues in 0 chains, 4191 seeds are put forward NCS extension: 0 residues added, 4191 seeds are put forward Round 1: 86 peptides, 20 chains. Longest chain 6 peptides. Score 0.197 Round 2: 123 peptides, 26 chains. Longest chain 7 peptides. Score 0.253 Round 3: 147 peptides, 29 chains. Longest chain 8 peptides. Score 0.300 Round 4: 160 peptides, 30 chains. Longest chain 10 peptides. Score 0.334 Round 5: 150 peptides, 25 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 5 Chains 25, Residues 125, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 8798 restraints for refining 3587 atoms. 8264 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3096 (Rfree = 0.000) for 3587 atoms. Found 17 (17 requested) and removed 114 (8 requested) atoms. Cycle 2: After refmac, R = 0.2969 (Rfree = 0.000) for 3438 atoms. Found 16 (16 requested) and removed 72 (8 requested) atoms. Cycle 3: After refmac, R = 0.2692 (Rfree = 0.000) for 3355 atoms. Found 16 (16 requested) and removed 84 (8 requested) atoms. Cycle 4: After refmac, R = 0.3034 (Rfree = 0.000) for 3274 atoms. Found 15 (15 requested) and removed 48 (7 requested) atoms. Cycle 5: After refmac, R = 0.3048 (Rfree = 0.000) for 3224 atoms. Found 15 (15 requested) and removed 49 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 3257 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 3266 seeds are put forward Round 1: 88 peptides, 21 chains. Longest chain 6 peptides. Score 0.187 Round 2: 127 peptides, 26 chains. Longest chain 7 peptides. Score 0.270 Round 3: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.331 Round 4: 139 peptides, 27 chains. Longest chain 8 peptides. Score 0.302 Round 5: 154 peptides, 26 chains. Longest chain 9 peptides. Score 0.377 Taking the results from Round 5 Chains 26, Residues 128, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 6763 restraints for refining 2977 atoms. 6238 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3088 (Rfree = 0.000) for 2977 atoms. Found 14 (14 requested) and removed 86 (7 requested) atoms. Cycle 7: After refmac, R = 0.2946 (Rfree = 0.000) for 2874 atoms. Found 13 (13 requested) and removed 57 (6 requested) atoms. Cycle 8: After refmac, R = 0.2966 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 48 (6 requested) atoms. Cycle 9: After refmac, R = 0.2925 (Rfree = 0.000) for 2770 atoms. Found 13 (13 requested) and removed 32 (6 requested) atoms. Cycle 10: After refmac, R = 0.2691 (Rfree = 0.000) for 2737 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.51 Search for helices and strands: 0 residues in 0 chains, 2826 seeds are put forward NCS extension: 0 residues added, 2826 seeds are put forward Round 1: 136 peptides, 31 chains. Longest chain 6 peptides. Score 0.220 Round 2: 157 peptides, 29 chains. Longest chain 11 peptides. Score 0.339 Round 3: 170 peptides, 31 chains. Longest chain 10 peptides. Score 0.356 Round 4: 165 peptides, 29 chains. Longest chain 11 peptides. Score 0.370 Round 5: 176 peptides, 33 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 4 Chains 30, Residues 136, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5889 restraints for refining 2774 atoms. 5292 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2709 (Rfree = 0.000) for 2774 atoms. Found 13 (13 requested) and removed 41 (6 requested) atoms. Cycle 12: After refmac, R = 0.2737 (Rfree = 0.000) for 2736 atoms. Found 13 (13 requested) and removed 37 (6 requested) atoms. Cycle 13: After refmac, R = 0.2318 (Rfree = 0.000) for 2703 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.2348 (Rfree = 0.000) for 2695 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 15: After refmac, R = 0.2305 (Rfree = 0.000) for 2683 atoms. Found 8 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.54 Search for helices and strands: 0 residues in 0 chains, 2779 seeds are put forward NCS extension: 0 residues added, 2779 seeds are put forward Round 1: 141 peptides, 30 chains. Longest chain 8 peptides. Score 0.258 Round 2: 164 peptides, 32 chains. Longest chain 8 peptides. Score 0.317 Round 3: 176 peptides, 30 chains. Longest chain 12 peptides. Score 0.394 Round 4: 161 peptides, 28 chains. Longest chain 14 peptides. Score 0.371 Round 5: 170 peptides, 29 chains. Longest chain 14 peptides. Score 0.388 Taking the results from Round 3 Chains 30, Residues 146, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5913 restraints for refining 2836 atoms. 5320 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3375 (Rfree = 0.000) for 2836 atoms. Found 13 (13 requested) and removed 131 (6 requested) atoms. Cycle 17: After refmac, R = 0.2778 (Rfree = 0.000) for 2708 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 18: After refmac, R = 0.2902 (Rfree = 0.000) for 2684 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 19: After refmac, R = 0.2972 (Rfree = 0.000) for 2670 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. Cycle 20: After refmac, R = 0.2641 (Rfree = 0.000) for 2642 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.02 3.46 Search for helices and strands: 0 residues in 0 chains, 2725 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2740 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 7 peptides. Score 0.269 Round 2: 180 peptides, 33 chains. Longest chain 12 peptides. Score 0.362 Round 3: 177 peptides, 33 chains. Longest chain 11 peptides. Score 0.350 Round 4: 180 peptides, 34 chains. Longest chain 12 peptides. Score 0.346 Round 5: 183 peptides, 32 chains. Longest chain 9 peptides. Score 0.388 Taking the results from Round 5 Chains 32, Residues 151, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5812 restraints for refining 2867 atoms. 5178 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2987 (Rfree = 0.000) for 2867 atoms. Found 13 (13 requested) and removed 54 (6 requested) atoms. Cycle 22: After refmac, R = 0.3070 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 35 (6 requested) atoms. Cycle 23: After refmac, R = 0.3043 (Rfree = 0.000) for 2785 atoms. Found 13 (13 requested) and removed 46 (6 requested) atoms. Cycle 24: After refmac, R = 0.2596 (Rfree = 0.000) for 2744 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 25: After refmac, R = 0.2708 (Rfree = 0.000) for 2732 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.88 Search for helices and strands: 0 residues in 0 chains, 2819 seeds are put forward NCS extension: 0 residues added, 2819 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 7 peptides. Score 0.233 Round 2: 156 peptides, 28 chains. Longest chain 12 peptides. Score 0.352 Round 3: 164 peptides, 32 chains. Longest chain 9 peptides. Score 0.317 Round 4: 163 peptides, 30 chains. Longest chain 11 peptides. Score 0.346 Round 5: 164 peptides, 28 chains. Longest chain 15 peptides. Score 0.382 Taking the results from Round 5 Chains 28, Residues 136, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5958 restraints for refining 2846 atoms. 5394 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3149 (Rfree = 0.000) for 2846 atoms. Found 13 (13 requested) and removed 60 (6 requested) atoms. Cycle 27: After refmac, R = 0.3088 (Rfree = 0.000) for 2786 atoms. Found 13 (13 requested) and removed 52 (6 requested) atoms. Cycle 28: After refmac, R = 0.2905 (Rfree = 0.000) for 2736 atoms. Found 13 (13 requested) and removed 32 (6 requested) atoms. Cycle 29: After refmac, R = 0.2514 (Rfree = 0.000) for 2705 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 30: After refmac, R = 0.2675 (Rfree = 0.000) for 2688 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.63 Search for helices and strands: 0 residues in 0 chains, 2716 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2731 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 8 peptides. Score 0.260 Round 2: 151 peptides, 27 chains. Longest chain 11 peptides. Score 0.349 Round 3: 153 peptides, 25 chains. Longest chain 11 peptides. Score 0.390 Round 4: 149 peptides, 25 chains. Longest chain 11 peptides. Score 0.375 Round 5: 159 peptides, 28 chains. Longest chain 9 peptides. Score 0.363 Taking the results from Round 3 Chains 25, Residues 128, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5681 restraints for refining 2762 atoms. 5155 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3294 (Rfree = 0.000) for 2762 atoms. Found 13 (13 requested) and removed 48 (6 requested) atoms. Cycle 32: After refmac, R = 0.3161 (Rfree = 0.000) for 2713 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. Cycle 33: After refmac, R = 0.3055 (Rfree = 0.000) for 2682 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 34: After refmac, R = 0.3171 (Rfree = 0.000) for 2661 atoms. Found 12 (12 requested) and removed 30 (6 requested) atoms. Cycle 35: After refmac, R = 0.2553 (Rfree = 0.000) for 2636 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.62 Search for helices and strands: 0 residues in 0 chains, 2696 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2709 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 6 peptides. Score 0.233 Round 2: 174 peptides, 33 chains. Longest chain 10 peptides. Score 0.339 Round 3: 186 peptides, 34 chains. Longest chain 9 peptides. Score 0.368 Round 4: 176 peptides, 31 chains. Longest chain 12 peptides. Score 0.378 Round 5: 170 peptides, 30 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 4 Chains 31, Residues 145, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5713 restraints for refining 2810 atoms. 5101 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3337 (Rfree = 0.000) for 2810 atoms. Found 13 (13 requested) and removed 50 (6 requested) atoms. Cycle 37: After refmac, R = 0.3093 (Rfree = 0.000) for 2755 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 38: After refmac, R = 0.3194 (Rfree = 0.000) for 2730 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 39: After refmac, R = 0.2682 (Rfree = 0.000) for 2705 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 40: After refmac, R = 0.3192 (Rfree = 0.000) for 2694 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.69 Search for helices and strands: 0 residues in 0 chains, 2735 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2753 seeds are put forward Round 1: 136 peptides, 27 chains. Longest chain 10 peptides. Score 0.290 Round 2: 139 peptides, 25 chains. Longest chain 9 peptides. Score 0.336 Round 3: 151 peptides, 25 chains. Longest chain 14 peptides. Score 0.383 Round 4: 152 peptides, 25 chains. Longest chain 16 peptides. Score 0.386 Round 5: 149 peptides, 27 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 4 Chains 25, Residues 127, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5966 restraints for refining 2837 atoms. 5428 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3273 (Rfree = 0.000) for 2837 atoms. Found 13 (13 requested) and removed 56 (6 requested) atoms. Cycle 42: After refmac, R = 0.3258 (Rfree = 0.000) for 2776 atoms. Found 13 (13 requested) and removed 34 (6 requested) atoms. Cycle 43: After refmac, R = 0.2782 (Rfree = 0.000) for 2744 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 44: After refmac, R = 0.3128 (Rfree = 0.000) for 2731 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 45: After refmac, R = 0.3261 (Rfree = 0.000) for 2708 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.89 Search for helices and strands: 0 residues in 0 chains, 2781 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2799 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 6 peptides. Score 0.229 Round 2: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.320 Round 3: 132 peptides, 23 chains. Longest chain 13 peptides. Score 0.343 Round 4: 139 peptides, 27 chains. Longest chain 10 peptides. Score 0.302 Round 5: 136 peptides, 24 chains. Longest chain 11 peptides. Score 0.342 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 109, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2pke-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3613 reflections ( 95.46 % complete ) and 5597 restraints for refining 2678 atoms. 5162 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3379 (Rfree = 0.000) for 2678 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3256 (Rfree = 0.000) for 2656 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2843 (Rfree = 0.000) for 2640 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2613 (Rfree = 0.000) for 2629 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 37.9