Mon 24 Dec 07:50:19 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 2p8j-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.4-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/2p8j-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.4-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 07:50:23 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/2p8j-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.4-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 429 and 0 Target number of residues in the AU: 429 Target solvent content: 0.6408 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.65 Input MTZ file: 2p8j-3.4-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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 1.05 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: 72.625 3.400 Wilson plot Bfac: 72.40 9272 reflections ( 98.75 % complete ) and 0 restraints for refining 3694 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3336 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2812 (Rfree = 0.000) for 3694 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 2.76 Search for helices and strands: 0 residues in 0 chains, 3769 seeds are put forward NCS extension: 0 residues added, 3769 seeds are put forward Round 1: 273 peptides, 37 chains. Longest chain 21 peptides. Score 0.505 Round 2: 303 peptides, 36 chains. Longest chain 21 peptides. Score 0.577 Round 3: 303 peptides, 28 chains. Longest chain 33 peptides. Score 0.646 Round 4: 309 peptides, 29 chains. Longest chain 33 peptides. Score 0.648 Round 5: 322 peptides, 25 chains. Longest chain 39 peptides. Score 0.700 Taking the results from Round 5 Chains 26, Residues 297, Estimated correctness of the model 57.9 % 3 chains (82 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5209 restraints for refining 3040 atoms. 3695 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2747 (Rfree = 0.000) for 3040 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 2: After refmac, R = 0.2465 (Rfree = 0.000) for 3008 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 3: After refmac, R = 0.2426 (Rfree = 0.000) for 2994 atoms. Found 19 (22 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.2345 (Rfree = 0.000) for 2995 atoms. Found 11 (22 requested) and removed 15 (11 requested) atoms. Cycle 5: After refmac, R = 0.2286 (Rfree = 0.000) for 2982 atoms. Found 21 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 2.72 Search for helices and strands: 0 residues in 0 chains, 3090 seeds are put forward NCS extension: 42 residues added (15 deleted due to clashes), 3132 seeds are put forward Round 1: 307 peptides, 32 chains. Longest chain 35 peptides. Score 0.620 Round 2: 306 peptides, 29 chains. Longest chain 47 peptides. Score 0.643 Round 3: 323 peptides, 28 chains. Longest chain 33 peptides. Score 0.679 Round 4: 310 peptides, 28 chains. Longest chain 51 peptides. Score 0.658 Round 5: 330 peptides, 27 chains. Longest chain 51 peptides. Score 0.698 Taking the results from Round 5 Chains 28, Residues 303, Estimated correctness of the model 57.4 % 2 chains (75 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5330 restraints for refining 3040 atoms. 3799 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2588 (Rfree = 0.000) for 3040 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 7: After refmac, R = 0.2378 (Rfree = 0.000) for 3020 atoms. Found 20 (22 requested) and removed 13 (11 requested) atoms. Cycle 8: After refmac, R = 0.2299 (Rfree = 0.000) for 3017 atoms. Found 8 (22 requested) and removed 11 (11 requested) atoms. Cycle 9: After refmac, R = 0.2230 (Rfree = 0.000) for 3008 atoms. Found 10 (22 requested) and removed 11 (11 requested) atoms. Cycle 10: After refmac, R = 0.2190 (Rfree = 0.000) for 3005 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.72 Search for helices and strands: 0 residues in 0 chains, 3114 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3133 seeds are put forward Round 1: 307 peptides, 34 chains. Longest chain 19 peptides. Score 0.603 Round 2: 320 peptides, 29 chains. Longest chain 38 peptides. Score 0.667 Round 3: 313 peptides, 26 chains. Longest chain 42 peptides. Score 0.679 Round 4: 316 peptides, 26 chains. Longest chain 38 peptides. Score 0.684 Round 5: 321 peptides, 27 chains. Longest chain 28 peptides. Score 0.684 Taking the results from Round 5 Chains 30, Residues 294, Estimated correctness of the model 53.7 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 6075 restraints for refining 3040 atoms. 4823 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2500 (Rfree = 0.000) for 3040 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 12: After refmac, R = 0.2409 (Rfree = 0.000) for 3037 atoms. Found 12 (23 requested) and removed 15 (11 requested) atoms. Cycle 13: After refmac, R = 0.2252 (Rfree = 0.000) for 3029 atoms. Found 5 (22 requested) and removed 14 (11 requested) atoms. Cycle 14: After refmac, R = 0.2206 (Rfree = 0.000) for 3019 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.2166 (Rfree = 0.000) for 3010 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 3115 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3134 seeds are put forward Round 1: 294 peptides, 37 chains. Longest chain 25 peptides. Score 0.550 Round 2: 301 peptides, 30 chains. Longest chain 29 peptides. Score 0.626 Round 3: 300 peptides, 26 chains. Longest chain 45 peptides. Score 0.658 Round 4: 312 peptides, 30 chains. Longest chain 40 peptides. Score 0.645 Round 5: 292 peptides, 32 chains. Longest chain 22 peptides. Score 0.592 Taking the results from Round 3 Chains 28, Residues 274, Estimated correctness of the model 46.5 % 3 chains (83 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5383 restraints for refining 3041 atoms. 3938 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2577 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 17: After refmac, R = 0.2397 (Rfree = 0.000) for 3030 atoms. Found 19 (22 requested) and removed 16 (11 requested) atoms. Cycle 18: After refmac, R = 0.2333 (Rfree = 0.000) for 3022 atoms. Found 13 (22 requested) and removed 13 (11 requested) atoms. Cycle 19: After refmac, R = 0.2300 (Rfree = 0.000) for 3021 atoms. Found 4 (22 requested) and removed 13 (11 requested) atoms. Cycle 20: After refmac, R = 0.2274 (Rfree = 0.000) for 3008 atoms. Found 4 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 2.75 Search for helices and strands: 0 residues in 0 chains, 3087 seeds are put forward NCS extension: 53 residues added (1 deleted due to clashes), 3140 seeds are put forward Round 1: 273 peptides, 35 chains. Longest chain 19 peptides. Score 0.525 Round 2: 298 peptides, 30 chains. Longest chain 35 peptides. Score 0.621 Round 3: 282 peptides, 29 chains. Longest chain 24 peptides. Score 0.600 Round 4: 305 peptides, 32 chains. Longest chain 25 peptides. Score 0.616 Round 5: 303 peptides, 30 chains. Longest chain 51 peptides. Score 0.630 Taking the results from Round 5 Chains 31, Residues 273, Estimated correctness of the model 38.2 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5817 restraints for refining 3041 atoms. 4548 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2601 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 22: After refmac, R = 0.2394 (Rfree = 0.000) for 3034 atoms. Found 15 (22 requested) and removed 19 (11 requested) atoms. Cycle 23: After refmac, R = 0.2297 (Rfree = 0.000) for 3023 atoms. Found 7 (22 requested) and removed 11 (11 requested) atoms. Cycle 24: After refmac, R = 0.2287 (Rfree = 0.000) for 3015 atoms. Found 18 (22 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.2241 (Rfree = 0.000) for 3017 atoms. Found 9 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 2.74 Search for helices and strands: 0 residues in 0 chains, 3106 seeds are put forward NCS extension: 88 residues added (2 deleted due to clashes), 3194 seeds are put forward Round 1: 277 peptides, 34 chains. Longest chain 23 peptides. Score 0.543 Round 2: 292 peptides, 30 chains. Longest chain 25 peptides. Score 0.610 Round 3: 288 peptides, 34 chains. Longest chain 23 peptides. Score 0.566 Round 4: 289 peptides, 32 chains. Longest chain 24 peptides. Score 0.586 Round 5: 307 peptides, 31 chains. Longest chain 30 peptides. Score 0.628 Taking the results from Round 5 Chains 34, Residues 276, Estimated correctness of the model 37.5 % 6 chains (96 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5355 restraints for refining 3098 atoms. 3858 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2681 (Rfree = 0.000) for 3098 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 27: After refmac, R = 0.2479 (Rfree = 0.000) for 3073 atoms. Found 19 (23 requested) and removed 16 (11 requested) atoms. Cycle 28: After refmac, R = 0.2412 (Rfree = 0.000) for 3071 atoms. Found 14 (23 requested) and removed 13 (11 requested) atoms. Cycle 29: After refmac, R = 0.2298 (Rfree = 0.000) for 3068 atoms. Found 11 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2244 (Rfree = 0.000) for 3058 atoms. Found 6 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3137 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3160 seeds are put forward Round 1: 258 peptides, 36 chains. Longest chain 18 peptides. Score 0.482 Round 2: 271 peptides, 31 chains. Longest chain 23 peptides. Score 0.559 Round 3: 281 peptides, 31 chains. Longest chain 33 peptides. Score 0.580 Round 4: 274 peptides, 26 chains. Longest chain 43 peptides. Score 0.612 Round 5: 262 peptides, 26 chains. Longest chain 33 peptides. Score 0.589 Taking the results from Round 4 Chains 28, Residues 248, Estimated correctness of the model 32.5 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 6271 restraints for refining 3041 atoms. 5168 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2496 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 32: After refmac, R = 0.2303 (Rfree = 0.000) for 3045 atoms. Found 8 (23 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.2237 (Rfree = 0.000) for 3035 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.2222 (Rfree = 0.000) for 3024 atoms. Found 7 (22 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.2228 (Rfree = 0.000) for 3019 atoms. Found 11 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 3131 seeds are put forward NCS extension: 58 residues added (4 deleted due to clashes), 3189 seeds are put forward Round 1: 263 peptides, 37 chains. Longest chain 19 peptides. Score 0.483 Round 2: 298 peptides, 34 chains. Longest chain 24 peptides. Score 0.585 Round 3: 277 peptides, 28 chains. Longest chain 22 peptides. Score 0.599 Round 4: 272 peptides, 30 chains. Longest chain 19 peptides. Score 0.571 Round 5: 280 peptides, 31 chains. Longest chain 26 peptides. Score 0.578 Taking the results from Round 3 Chains 29, Residues 249, Estimated correctness of the model 28.3 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 6106 restraints for refining 3041 atoms. 4979 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2503 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 37: After refmac, R = 0.2330 (Rfree = 0.000) for 3030 atoms. Found 15 (22 requested) and removed 14 (11 requested) atoms. Cycle 38: After refmac, R = 0.2289 (Rfree = 0.000) for 3026 atoms. Found 12 (22 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.2254 (Rfree = 0.000) for 3020 atoms. Found 10 (22 requested) and removed 16 (11 requested) atoms. Cycle 40: After refmac, R = 0.2252 (Rfree = 0.000) for 3009 atoms. Found 13 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 2.69 Search for helices and strands: 0 residues in 0 chains, 3109 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3132 seeds are put forward Round 1: 253 peptides, 37 chains. Longest chain 17 peptides. Score 0.460 Round 2: 267 peptides, 34 chains. Longest chain 23 peptides. Score 0.522 Round 3: 257 peptides, 29 chains. Longest chain 22 peptides. Score 0.550 Round 4: 258 peptides, 32 chains. Longest chain 23 peptides. Score 0.522 Round 5: 263 peptides, 24 chains. Longest chain 35 peptides. Score 0.609 Taking the results from Round 5 Chains 24, Residues 239, Estimated correctness of the model 31.6 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 6126 restraints for refining 3041 atoms. 5042 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2599 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 42: After refmac, R = 0.2439 (Rfree = 0.000) for 3038 atoms. Found 11 (23 requested) and removed 13 (11 requested) atoms. Cycle 43: After refmac, R = 0.2438 (Rfree = 0.000) for 3030 atoms. Found 14 (22 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.2390 (Rfree = 0.000) for 3028 atoms. Found 16 (22 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.2302 (Rfree = 0.000) for 3028 atoms. Found 14 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 2.69 Search for helices and strands: 0 residues in 0 chains, 3103 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 3133 seeds are put forward Round 1: 237 peptides, 30 chains. Longest chain 22 peptides. Score 0.496 Round 2: 263 peptides, 31 chains. Longest chain 20 peptides. Score 0.543 Round 3: 252 peptides, 30 chains. Longest chain 23 peptides. Score 0.529 Round 4: 269 peptides, 30 chains. Longest chain 25 peptides. Score 0.565 Round 5: 281 peptides, 32 chains. Longest chain 27 peptides. Score 0.570 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 249, Estimated correctness of the model 18.6 % 2 chains (32 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2p8j-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (249 residues) following loop building 2 chains (32 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9272 reflections ( 98.75 % complete ) and 6179 restraints for refining 3041 atoms. 5058 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2611 (Rfree = 0.000) for 3041 atoms. Found 0 (22 requested) and removed 10 (11 requested) atoms. Cycle 47: After refmac, R = 0.2628 (Rfree = 0.000) for 3020 atoms. Found 0 (22 requested) and removed 3 (11 requested) atoms. Cycle 48: After refmac, R = 0.2442 (Rfree = 0.000) for 3013 atoms. Found 0 (22 requested) and removed 5 (11 requested) atoms. Cycle 49: After refmac, R = 0.2400 (Rfree = 0.000) for 3000 atoms. TimeTaking 44.38