null Tue 25 Dec 19:27:57 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 2i5i-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.8-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/2i5i-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.8-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 ============================================================ Tue 25 Dec 19:28:07 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/2i5i-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.8-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 354 and 0 Target number of residues in the AU: 354 Target solvent content: 0.6594 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-3.8-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.80 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: 29.446 3.800 Wilson plot Bfac: 83.92 5326 reflections ( 99.05 % complete ) and 0 restraints for refining 4641 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3429 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3218 (Rfree = 0.000) for 4641 atoms. Found 13 (25 requested) and removed 71 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.76 Search for helices and strands: 0 residues in 0 chains, 4623 seeds are put forward NCS extension: 0 residues added, 4623 seeds are put forward Round 1: 120 peptides, 28 chains. Longest chain 6 peptides. Score 0.198 Round 2: 140 peptides, 30 chains. Longest chain 10 peptides. Score 0.241 Round 3: 150 peptides, 30 chains. Longest chain 10 peptides. Score 0.276 Round 4: 166 peptides, 33 chains. Longest chain 10 peptides. Score 0.287 Round 5: 172 peptides, 33 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 5 Chains 33, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 9178 restraints for refining 3807 atoms. 8655 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2921 (Rfree = 0.000) for 3807 atoms. Found 13 (20 requested) and removed 42 (10 requested) atoms. Cycle 2: After refmac, R = 0.2737 (Rfree = 0.000) for 3729 atoms. Found 20 (20 requested) and removed 41 (10 requested) atoms. Cycle 3: After refmac, R = 0.2762 (Rfree = 0.000) for 3673 atoms. Found 20 (20 requested) and removed 36 (10 requested) atoms. Cycle 4: After refmac, R = 0.2739 (Rfree = 0.000) for 3625 atoms. Found 16 (20 requested) and removed 27 (10 requested) atoms. Cycle 5: After refmac, R = 0.2203 (Rfree = 0.000) for 3592 atoms. Found 14 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 3645 seeds are put forward NCS extension: 0 residues added, 3645 seeds are put forward Round 1: 112 peptides, 25 chains. Longest chain 8 peptides. Score 0.215 Round 2: 133 peptides, 25 chains. Longest chain 11 peptides. Score 0.292 Round 3: 143 peptides, 28 chains. Longest chain 12 peptides. Score 0.281 Round 4: 156 peptides, 29 chains. Longest chain 8 peptides. Score 0.311 Round 5: 165 peptides, 31 chains. Longest chain 12 peptides. Score 0.312 Taking the results from Round 5 Chains 31, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7197 restraints for refining 3207 atoms. 6692 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2400 (Rfree = 0.000) for 3207 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 7: After refmac, R = 0.2372 (Rfree = 0.000) for 3174 atoms. Found 17 (17 requested) and removed 35 (8 requested) atoms. Cycle 8: After refmac, R = 0.2379 (Rfree = 0.000) for 3145 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 9: After refmac, R = 0.2438 (Rfree = 0.000) for 3134 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.2507 (Rfree = 0.000) for 3127 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 0 residues added, 3190 seeds are put forward Round 1: 170 peptides, 36 chains. Longest chain 8 peptides. Score 0.258 Round 2: 205 peptides, 36 chains. Longest chain 11 peptides. Score 0.369 Round 3: 195 peptides, 36 chains. Longest chain 12 peptides. Score 0.339 Round 4: 191 peptides, 34 chains. Longest chain 12 peptides. Score 0.353 Round 5: 197 peptides, 35 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 2 Chains 36, Residues 169, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6362 restraints for refining 3088 atoms. 5668 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2400 (Rfree = 0.000) for 3088 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 12: After refmac, R = 0.2236 (Rfree = 0.000) for 3055 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.2379 (Rfree = 0.000) for 3032 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 14: After refmac, R = 0.2338 (Rfree = 0.000) for 2997 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 15: After refmac, R = 0.2321 (Rfree = 0.000) for 2985 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 3058 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3072 seeds are put forward Round 1: 170 peptides, 36 chains. Longest chain 10 peptides. Score 0.258 Round 2: 203 peptides, 39 chains. Longest chain 12 peptides. Score 0.324 Round 3: 192 peptides, 35 chains. Longest chain 11 peptides. Score 0.343 Round 4: 200 peptides, 36 chains. Longest chain 11 peptides. Score 0.354 Round 5: 211 peptides, 40 chains. Longest chain 12 peptides. Score 0.335 Taking the results from Round 4 Chains 36, Residues 164, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6715 restraints for refining 3153 atoms. 6040 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2805 (Rfree = 0.000) for 3153 atoms. Found 17 (17 requested) and removed 41 (8 requested) atoms. Cycle 17: After refmac, R = 0.2600 (Rfree = 0.000) for 3107 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 18: After refmac, R = 0.2124 (Rfree = 0.000) for 3073 atoms. Found 14 (16 requested) and removed 20 (8 requested) atoms. Cycle 19: After refmac, R = 0.2424 (Rfree = 0.000) for 3056 atoms. Found 16 (16 requested) and removed 53 (8 requested) atoms. Cycle 20: After refmac, R = 0.2276 (Rfree = 0.000) for 3004 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.77 Search for helices and strands: 0 residues in 0 chains, 3071 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3082 seeds are put forward Round 1: 188 peptides, 43 chains. Longest chain 7 peptides. Score 0.222 Round 2: 195 peptides, 37 chains. Longest chain 10 peptides. Score 0.325 Round 3: 184 peptides, 37 chains. Longest chain 9 peptides. Score 0.290 Round 4: 187 peptides, 37 chains. Longest chain 9 peptides. Score 0.300 Round 5: 200 peptides, 36 chains. Longest chain 15 peptides. Score 0.354 Taking the results from Round 5 Chains 37, Residues 164, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6944 restraints for refining 3229 atoms. 6292 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2760 (Rfree = 0.000) for 3229 atoms. Found 17 (17 requested) and removed 58 (8 requested) atoms. Cycle 22: After refmac, R = 0.2606 (Rfree = 0.000) for 3159 atoms. Found 17 (17 requested) and removed 36 (8 requested) atoms. Cycle 23: After refmac, R = 0.2490 (Rfree = 0.000) for 3123 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 24: After refmac, R = 0.2498 (Rfree = 0.000) for 3099 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.2462 (Rfree = 0.000) for 3087 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.79 Search for helices and strands: 0 residues in 0 chains, 3145 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3163 seeds are put forward Round 1: 142 peptides, 30 chains. Longest chain 9 peptides. Score 0.248 Round 2: 161 peptides, 30 chains. Longest chain 9 peptides. Score 0.313 Round 3: 140 peptides, 28 chains. Longest chain 9 peptides. Score 0.271 Round 4: 147 peptides, 27 chains. Longest chain 9 peptides. Score 0.310 Round 5: 143 peptides, 27 chains. Longest chain 10 peptides. Score 0.296 Taking the results from Round 2 Chains 30, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7036 restraints for refining 3124 atoms. 6542 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2645 (Rfree = 0.000) for 3124 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 27: After refmac, R = 0.2728 (Rfree = 0.000) for 3094 atoms. Found 17 (17 requested) and removed 32 (8 requested) atoms. Cycle 28: After refmac, R = 0.2573 (Rfree = 0.000) for 3069 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 29: After refmac, R = 0.2613 (Rfree = 0.000) for 3056 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 30: After refmac, R = 0.2103 (Rfree = 0.000) for 3044 atoms. Found 15 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.23 4.29 Search for helices and strands: 0 residues in 0 chains, 3078 seeds are put forward NCS extension: 0 residues added, 3078 seeds are put forward Round 1: 116 peptides, 26 chains. Longest chain 6 peptides. Score 0.214 Round 2: 141 peptides, 29 chains. Longest chain 8 peptides. Score 0.260 Round 3: 150 peptides, 29 chains. Longest chain 10 peptides. Score 0.291 Round 4: 168 peptides, 33 chains. Longest chain 11 peptides. Score 0.294 Round 5: 161 peptides, 31 chains. Longest chain 8 peptides. Score 0.299 Taking the results from Round 5 Chains 31, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6997 restraints for refining 3128 atoms. 6508 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2606 (Rfree = 0.000) for 3128 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 32: After refmac, R = 0.2668 (Rfree = 0.000) for 3099 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 33: After refmac, R = 0.2111 (Rfree = 0.000) for 3063 atoms. Found 7 (16 requested) and removed 21 (8 requested) atoms. Cycle 34: After refmac, R = 0.2040 (Rfree = 0.000) for 3033 atoms. Found 5 (16 requested) and removed 14 (8 requested) atoms. Cycle 35: After refmac, R = 0.2019 (Rfree = 0.000) for 3012 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.93 3.98 Search for helices and strands: 0 residues in 0 chains, 3067 seeds are put forward NCS extension: 0 residues added, 3067 seeds are put forward Round 1: 127 peptides, 30 chains. Longest chain 6 peptides. Score 0.194 Round 2: 153 peptides, 33 chains. Longest chain 7 peptides. Score 0.243 Round 3: 172 peptides, 34 chains. Longest chain 10 peptides. Score 0.293 Round 4: 159 peptides, 33 chains. Longest chain 9 peptides. Score 0.264 Round 5: 175 peptides, 33 chains. Longest chain 12 peptides. Score 0.316 Taking the results from Round 5 Chains 33, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6927 restraints for refining 3120 atoms. 6392 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2451 (Rfree = 0.000) for 3120 atoms. Found 17 (17 requested) and removed 48 (8 requested) atoms. Cycle 37: After refmac, R = 0.2681 (Rfree = 0.000) for 3071 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 38: After refmac, R = 0.2536 (Rfree = 0.000) for 3047 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 39: After refmac, R = 0.2657 (Rfree = 0.000) for 3030 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 40: After refmac, R = 0.2573 (Rfree = 0.000) for 3010 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 5.49 5.56 Search for helices and strands: 0 residues in 0 chains, 3068 seeds are put forward NCS extension: 0 residues added, 3068 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 8 peptides. Score 0.236 Round 2: 136 peptides, 26 chains. Longest chain 10 peptides. Score 0.287 Round 3: 149 peptides, 29 chains. Longest chain 8 peptides. Score 0.287 Round 4: 152 peptides, 28 chains. Longest chain 10 peptides. Score 0.312 Round 5: 147 peptides, 29 chains. Longest chain 8 peptides. Score 0.280 Taking the results from Round 4 Chains 28, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6714 restraints for refining 3012 atoms. 6246 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2555 (Rfree = 0.000) for 3012 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. Cycle 42: After refmac, R = 0.2494 (Rfree = 0.000) for 2974 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 43: After refmac, R = 0.2463 (Rfree = 0.000) for 2956 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 44: After refmac, R = 0.2285 (Rfree = 0.000) for 2940 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 45: After refmac, R = 0.2276 (Rfree = 0.000) for 2932 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 2982 seeds are put forward NCS extension: 0 residues added, 2982 seeds are put forward Round 1: 154 peptides, 34 chains. Longest chain 7 peptides. Score 0.232 Round 2: 157 peptides, 30 chains. Longest chain 15 peptides. Score 0.300 Round 3: 150 peptides, 27 chains. Longest chain 10 peptides. Score 0.319 Round 4: 164 peptides, 30 chains. Longest chain 12 peptides. Score 0.323 Round 5: 158 peptides, 28 chains. Longest chain 10 peptides. Score 0.331 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 130, 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 2i5i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5326 reflections ( 99.05 % complete ) and 7232 restraints for refining 3175 atoms. 6740 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2566 (Rfree = 0.000) for 3175 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2377 (Rfree = 0.000) for 3140 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2350 (Rfree = 0.000) for 3118 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2417 (Rfree = 0.000) for 3102 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:26:27 GMT 2018 Job finished. TimeTaking 58.51 Used memory is bytes: 23355592