null Sun 23 Dec 22:22:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pke-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pke-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pke-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:03 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/hancs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-4.0-parrot-hancs/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-hancs.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-hancs.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 4443 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3127 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3122 (Rfree = 0.000) for 4443 atoms. Found 21 (21 requested) and removed 419 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 4.19 Search for helices and strands: 0 residues in 0 chains, 4097 seeds are put forward NCS extension: 0 residues added, 4097 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.215 Round 2: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.297 Round 3: 108 peptides, 20 chains. Longest chain 11 peptides. Score 0.299 Round 4: 119 peptides, 19 chains. Longest chain 17 peptides. Score 0.362 Round 5: 128 peptides, 21 chains. Longest chain 15 peptides. Score 0.362 Taking the results from Round 5 Chains 21, Residues 107, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 8931 restraints for refining 3627 atoms. 8501 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3146 (Rfree = 0.000) for 3627 atoms. Found 17 (17 requested) and removed 168 (8 requested) atoms. Cycle 2: After refmac, R = 0.3073 (Rfree = 0.000) for 3441 atoms. Found 16 (16 requested) and removed 79 (8 requested) atoms. Cycle 3: After refmac, R = 0.2716 (Rfree = 0.000) for 3359 atoms. Found 16 (16 requested) and removed 57 (8 requested) atoms. Cycle 4: After refmac, R = 0.2811 (Rfree = 0.000) for 3302 atoms. Found 15 (15 requested) and removed 42 (7 requested) atoms. Cycle 5: After refmac, R = 0.2701 (Rfree = 0.000) for 3260 atoms. Found 15 (15 requested) and removed 44 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.78 3.18 Search for helices and strands: 0 residues in 0 chains, 3286 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3305 seeds are put forward Round 1: 94 peptides, 22 chains. Longest chain 5 peptides. Score 0.196 Round 2: 116 peptides, 24 chains. Longest chain 10 peptides. Score 0.259 Round 3: 130 peptides, 23 chains. Longest chain 11 peptides. Score 0.335 Round 4: 133 peptides, 25 chains. Longest chain 8 peptides. Score 0.312 Round 5: 117 peptides, 23 chains. Longest chain 7 peptides. Score 0.282 Taking the results from Round 3 Chains 23, Residues 107, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 6559 restraints for refining 2883 atoms. 6093 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2950 (Rfree = 0.000) for 2883 atoms. Found 13 (13 requested) and removed 53 (6 requested) atoms. Cycle 7: After refmac, R = 0.3039 (Rfree = 0.000) for 2827 atoms. Found 13 (13 requested) and removed 51 (6 requested) atoms. Cycle 8: After refmac, R = 0.2958 (Rfree = 0.000) for 2785 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 9: After refmac, R = 0.3010 (Rfree = 0.000) for 2762 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 10: After refmac, R = 0.2949 (Rfree = 0.000) for 2741 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.80 3.20 Search for helices and strands: 0 residues in 0 chains, 2834 seeds are put forward NCS extension: 0 residues added, 2834 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 7 peptides. Score 0.232 Round 2: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.327 Round 3: 146 peptides, 26 chains. Longest chain 11 peptides. Score 0.347 Round 4: 148 peptides, 26 chains. Longest chain 15 peptides. Score 0.355 Round 5: 154 peptides, 28 chains. Longest chain 8 peptides. Score 0.344 Taking the results from Round 4 Chains 26, Residues 122, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5350 restraints for refining 2652 atoms. 4840 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3127 (Rfree = 0.000) for 2652 atoms. Found 12 (12 requested) and removed 48 (6 requested) atoms. Cycle 12: After refmac, R = 0.2796 (Rfree = 0.000) for 2603 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 13: After refmac, R = 0.3104 (Rfree = 0.000) for 2582 atoms. Found 12 (12 requested) and removed 31 (6 requested) atoms. Cycle 14: After refmac, R = 0.2549 (Rfree = 0.000) for 2558 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 15: After refmac, R = 0.2634 (Rfree = 0.000) for 2548 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.72 1.97 Search for helices and strands: 0 residues in 0 chains, 2628 seeds are put forward NCS extension: 0 residues added, 2628 seeds are put forward Round 1: 134 peptides, 30 chains. Longest chain 7 peptides. Score 0.229 Round 2: 169 peptides, 33 chains. Longest chain 9 peptides. Score 0.320 Round 3: 161 peptides, 31 chains. Longest chain 9 peptides. Score 0.322 Round 4: 164 peptides, 31 chains. Longest chain 8 peptides. Score 0.333 Round 5: 186 peptides, 33 chains. Longest chain 8 peptides. Score 0.384 Taking the results from Round 5 Chains 33, Residues 153, Estimated correctness of the model 0.0 % 6 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5589 restraints for refining 2779 atoms. 4946 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3167 (Rfree = 0.000) for 2779 atoms. Found 13 (13 requested) and removed 61 (6 requested) atoms. Cycle 17: After refmac, R = 0.3176 (Rfree = 0.000) for 2712 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 18: After refmac, R = 0.2957 (Rfree = 0.000) for 2677 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 19: After refmac, R = 0.2493 (Rfree = 0.000) for 2649 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 20: After refmac, R = 0.2416 (Rfree = 0.000) for 2645 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.89 Search for helices and strands: 0 residues in 0 chains, 2737 seeds are put forward NCS extension: 0 residues added, 2737 seeds are put forward Round 1: 155 peptides, 35 chains. Longest chain 8 peptides. Score 0.231 Round 2: 180 peptides, 36 chains. Longest chain 8 peptides. Score 0.314 Round 3: 175 peptides, 31 chains. Longest chain 14 peptides. Score 0.375 Round 4: 167 peptides, 31 chains. Longest chain 10 peptides. Score 0.345 Round 5: 178 peptides, 32 chains. Longest chain 12 peptides. Score 0.370 Taking the results from Round 3 Chains 32, Residues 144, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5552 restraints for refining 2812 atoms. 4877 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3185 (Rfree = 0.000) for 2812 atoms. Found 13 (13 requested) and removed 46 (6 requested) atoms. Cycle 22: After refmac, R = 0.3199 (Rfree = 0.000) for 2752 atoms. Found 13 (13 requested) and removed 60 (6 requested) atoms. Cycle 23: After refmac, R = 0.3015 (Rfree = 0.000) for 2680 atoms. Found 12 (12 requested) and removed 42 (6 requested) atoms. Cycle 24: After refmac, R = 0.2758 (Rfree = 0.000) for 2633 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 25: After refmac, R = 0.2657 (Rfree = 0.000) for 2620 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 2704 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2724 seeds are put forward Round 1: 149 peptides, 32 chains. Longest chain 7 peptides. Score 0.257 Round 2: 182 peptides, 32 chains. Longest chain 15 peptides. Score 0.385 Round 3: 190 peptides, 32 chains. Longest chain 16 peptides. Score 0.413 Round 4: 178 peptides, 29 chains. Longest chain 13 peptides. Score 0.417 Round 5: 168 peptides, 31 chains. Longest chain 10 peptides. Score 0.349 Taking the results from Round 4 Chains 29, Residues 149, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5836 restraints for refining 2780 atoms. 5232 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2937 (Rfree = 0.000) for 2780 atoms. Found 13 (13 requested) and removed 41 (6 requested) atoms. Cycle 27: After refmac, R = 0.3118 (Rfree = 0.000) for 2732 atoms. Found 13 (13 requested) and removed 33 (6 requested) atoms. Cycle 28: After refmac, R = 0.3021 (Rfree = 0.000) for 2695 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 29: After refmac, R = 0.3004 (Rfree = 0.000) for 2672 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 30: After refmac, R = 0.3056 (Rfree = 0.000) for 2660 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 3.49 Search for helices and strands: 0 residues in 0 chains, 2727 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2741 seeds are put forward Round 1: 121 peptides, 27 chains. Longest chain 7 peptides. Score 0.226 Round 2: 155 peptides, 31 chains. Longest chain 9 peptides. Score 0.298 Round 3: 165 peptides, 31 chains. Longest chain 10 peptides. Score 0.337 Round 4: 177 peptides, 30 chains. Longest chain 10 peptides. Score 0.398 Round 5: 179 peptides, 30 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 5 Chains 30, Residues 149, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 5667 restraints for refining 2826 atoms. 5018 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3151 (Rfree = 0.000) for 2826 atoms. Found 13 (13 requested) and removed 45 (6 requested) atoms. Cycle 32: After refmac, R = 0.3243 (Rfree = 0.000) for 2773 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 33: After refmac, R = 0.3064 (Rfree = 0.000) for 2739 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 34: After refmac, R = 0.3133 (Rfree = 0.000) for 2723 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 35: After refmac, R = 0.3129 (Rfree = 0.000) for 2712 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.61 Search for helices and strands: 0 residues in 0 chains, 2761 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 2777 seeds are put forward Round 1: 109 peptides, 25 chains. Longest chain 6 peptides. Score 0.209 Round 2: 137 peptides, 27 chains. Longest chain 7 peptides. Score 0.294 Round 3: 136 peptides, 26 chains. Longest chain 7 peptides. Score 0.307 Round 4: 151 peptides, 29 chains. Longest chain 9 peptides. Score 0.316 Round 5: 159 peptides, 28 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 5 Chains 28, Residues 131, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 6064 restraints for refining 2850 atoms. 5529 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3191 (Rfree = 0.000) for 2850 atoms. Found 13 (13 requested) and removed 46 (6 requested) atoms. Cycle 37: After refmac, R = 0.2642 (Rfree = 0.000) for 2795 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 38: After refmac, R = 0.2397 (Rfree = 0.000) for 2775 atoms. Found 10 (13 requested) and removed 18 (6 requested) atoms. Cycle 39: After refmac, R = 0.2610 (Rfree = 0.000) for 2760 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 40: After refmac, R = 0.2445 (Rfree = 0.000) for 2751 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 4.05 Search for helices and strands: 0 residues in 0 chains, 2828 seeds are put forward NCS extension: 0 residues added, 2828 seeds are put forward Round 1: 117 peptides, 25 chains. Longest chain 8 peptides. Score 0.245 Round 2: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.327 Round 3: 143 peptides, 27 chains. Longest chain 10 peptides. Score 0.318 Round 4: 151 peptides, 27 chains. Longest chain 9 peptides. Score 0.349 Round 5: 142 peptides, 27 chains. Longest chain 9 peptides. Score 0.314 Taking the results from Round 4 Chains 27, Residues 124, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3613 reflections ( 95.46 % complete ) and 6020 restraints for refining 2847 atoms. 5533 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2786 (Rfree = 0.000) for 2847 atoms. Found 13 (13 requested) and removed 33 (6 requested) atoms. Cycle 42: After refmac, R = 0.3007 (Rfree = 0.000) for 2819 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 43: After refmac, R = 0.3073 (Rfree = 0.000) for 2807 atoms. Found 13 (13 requested) and removed 35 (6 requested) atoms. Cycle 44: After refmac, R = 0.2786 (Rfree = 0.000) for 2782 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 45: After refmac, R = 0.2998 (Rfree = 0.000) for 2771 atoms. Found 13 (13 requested) and removed 33 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.88 Search for helices and strands: 0 residues in 0 chains, 2828 seeds are put forward NCS extension: 0 residues added, 2828 seeds are put forward Round 1: 95 peptides, 22 chains. Longest chain 6 peptides. Score 0.201 Round 2: 111 peptides, 21 chains. Longest chain 8 peptides. Score 0.293 Round 3: 122 peptides, 22 chains. Longest chain 10 peptides. Score 0.321 Round 4: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.312 Round 5: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.326 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 91, 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 2pke-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3613 reflections ( 95.46 % complete ) and 6263 restraints for refining 2822 atoms. 5918 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2781 (Rfree = 0.000) for 2822 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3256 (Rfree = 0.000) for 2802 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2835 (Rfree = 0.000) for 2787 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2939 (Rfree = 0.000) for 2773 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:23 GMT 2018 Job finished. TimeTaking 47.52 Used memory is bytes: 15367704