Mon 24 Dec 01:01:01 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 2p8j-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.8-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/2p8j-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.8-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 01:01:05 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/2p8j-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.8-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 408 and 0 Target number of residues in the AU: 408 Target solvent content: 0.6584 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-3.8-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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 1.10 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 3.802 Wilson plot Bfac: 83.44 6663 reflections ( 98.27 % complete ) and 0 restraints for refining 3713 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3486 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3184 (Rfree = 0.000) for 3713 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 2.99 Search for helices and strands: 0 residues in 0 chains, 3782 seeds are put forward NCS extension: 0 residues added, 3782 seeds are put forward Round 1: 224 peptides, 38 chains. Longest chain 15 peptides. Score 0.377 Round 2: 242 peptides, 30 chains. Longest chain 19 peptides. Score 0.507 Round 3: 261 peptides, 33 chains. Longest chain 17 peptides. Score 0.519 Round 4: 266 peptides, 35 chains. Longest chain 18 peptides. Score 0.510 Round 5: 261 peptides, 30 chains. Longest chain 24 peptides. Score 0.548 Taking the results from Round 5 Chains 30, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6714 restraints for refining 3023 atoms. 5820 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2698 (Rfree = 0.000) for 3023 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 2: After refmac, R = 0.2525 (Rfree = 0.000) for 2987 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 3: After refmac, R = 0.2410 (Rfree = 0.000) for 2967 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 4: After refmac, R = 0.2512 (Rfree = 0.000) for 2949 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2413 (Rfree = 0.000) for 2937 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 2.99 Search for helices and strands: 0 residues in 0 chains, 3066 seeds are put forward NCS extension: 25 residues added (7 deleted due to clashes), 3091 seeds are put forward Round 1: 241 peptides, 35 chains. Longest chain 11 peptides. Score 0.452 Round 2: 255 peptides, 32 chains. Longest chain 14 peptides. Score 0.516 Round 3: 253 peptides, 28 chains. Longest chain 23 peptides. Score 0.551 Round 4: 266 peptides, 30 chains. Longest chain 16 peptides. Score 0.559 Round 5: 261 peptides, 33 chains. Longest chain 24 peptides. Score 0.519 Taking the results from Round 4 Chains 30, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6745 restraints for refining 3024 atoms. 5831 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2612 (Rfree = 0.000) for 3024 atoms. Found 11 (16 requested) and removed 17 (8 requested) atoms. Cycle 7: After refmac, R = 0.2528 (Rfree = 0.000) for 2989 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 8: After refmac, R = 0.2488 (Rfree = 0.000) for 2982 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2179 (Rfree = 0.000) for 2977 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.2133 (Rfree = 0.000) for 2961 atoms. Found 5 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 2.97 Search for helices and strands: 0 residues in 0 chains, 3052 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3068 seeds are put forward Round 1: 242 peptides, 37 chains. Longest chain 14 peptides. Score 0.433 Round 2: 277 peptides, 34 chains. Longest chain 18 peptides. Score 0.543 Round 3: 280 peptides, 31 chains. Longest chain 26 peptides. Score 0.578 Round 4: 277 peptides, 28 chains. Longest chain 20 peptides. Score 0.599 Round 5: 281 peptides, 32 chains. Longest chain 24 peptides. Score 0.570 Taking the results from Round 4 Chains 29, Residues 249, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6455 restraints for refining 3024 atoms. 5446 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2541 (Rfree = 0.000) for 3024 atoms. Found 11 (16 requested) and removed 15 (8 requested) atoms. Cycle 12: After refmac, R = 0.2333 (Rfree = 0.000) for 2984 atoms. Found 6 (16 requested) and removed 20 (8 requested) atoms. Cycle 13: After refmac, R = 0.2239 (Rfree = 0.000) for 2959 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. Cycle 14: After refmac, R = 0.2188 (Rfree = 0.000) for 2946 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.2175 (Rfree = 0.000) for 2936 atoms. Found 3 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 2.96 Search for helices and strands: 0 residues in 0 chains, 3045 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3067 seeds are put forward Round 1: 252 peptides, 36 chains. Longest chain 17 peptides. Score 0.468 Round 2: 270 peptides, 33 chains. Longest chain 22 peptides. Score 0.538 Round 3: 257 peptides, 30 chains. Longest chain 20 peptides. Score 0.540 Round 4: 279 peptides, 30 chains. Longest chain 23 peptides. Score 0.585 Round 5: 282 peptides, 31 chains. Longest chain 21 peptides. Score 0.582 Taking the results from Round 4 Chains 32, Residues 249, Estimated correctness of the model 0.0 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6233 restraints for refining 3023 atoms. 5150 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2456 (Rfree = 0.000) for 3023 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 17: After refmac, R = 0.2238 (Rfree = 0.000) for 2985 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2134 (Rfree = 0.000) for 2974 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2129 (Rfree = 0.000) for 2966 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.2195 (Rfree = 0.000) for 2952 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.00 Search for helices and strands: 0 residues in 0 chains, 3032 seeds are put forward NCS extension: 46 residues added (0 deleted due to clashes), 3078 seeds are put forward Round 1: 239 peptides, 35 chains. Longest chain 15 peptides. Score 0.448 Round 2: 266 peptides, 34 chains. Longest chain 21 peptides. Score 0.520 Round 3: 259 peptides, 30 chains. Longest chain 20 peptides. Score 0.544 Round 4: 263 peptides, 33 chains. Longest chain 18 peptides. Score 0.523 Round 5: 254 peptides, 29 chains. Longest chain 19 peptides. Score 0.544 Taking the results from Round 5 Chains 29, Residues 225, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6765 restraints for refining 3024 atoms. 5894 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2674 (Rfree = 0.000) for 3024 atoms. Found 14 (16 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.2406 (Rfree = 0.000) for 2986 atoms. Found 13 (16 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2297 (Rfree = 0.000) for 2978 atoms. Found 13 (16 requested) and removed 14 (8 requested) atoms. Cycle 24: After refmac, R = 0.2197 (Rfree = 0.000) for 2961 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.1916 (Rfree = 0.000) for 2957 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 2.95 Search for helices and strands: 0 residues in 0 chains, 3064 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3097 seeds are put forward Round 1: 245 peptides, 39 chains. Longest chain 14 peptides. Score 0.419 Round 2: 283 peptides, 36 chains. Longest chain 25 peptides. Score 0.537 Round 3: 267 peptides, 35 chains. Longest chain 25 peptides. Score 0.512 Round 4: 268 peptides, 36 chains. Longest chain 18 peptides. Score 0.504 Round 5: 258 peptides, 27 chains. Longest chain 23 peptides. Score 0.571 Taking the results from Round 5 Chains 27, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6665 restraints for refining 3024 atoms. 5768 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2464 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 27: After refmac, R = 0.2224 (Rfree = 0.000) for 2998 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 28: After refmac, R = 0.2075 (Rfree = 0.000) for 2988 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2071 (Rfree = 0.000) for 2975 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1986 (Rfree = 0.000) for 2967 atoms. Found 4 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 2.94 Search for helices and strands: 0 residues in 0 chains, 3061 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 3091 seeds are put forward Round 1: 248 peptides, 43 chains. Longest chain 13 peptides. Score 0.383 Round 2: 267 peptides, 35 chains. Longest chain 23 peptides. Score 0.512 Round 3: 268 peptides, 35 chains. Longest chain 20 peptides. Score 0.514 Round 4: 261 peptides, 36 chains. Longest chain 18 peptides. Score 0.489 Round 5: 277 peptides, 37 chains. Longest chain 22 peptides. Score 0.514 Taking the results from Round 5 Chains 38, Residues 240, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6427 restraints for refining 3024 atoms. 5447 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2595 (Rfree = 0.000) for 3024 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. Cycle 32: After refmac, R = 0.2252 (Rfree = 0.000) for 3008 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.2177 (Rfree = 0.000) for 2998 atoms. Found 14 (16 requested) and removed 12 (8 requested) atoms. Cycle 34: After refmac, R = 0.2146 (Rfree = 0.000) for 2987 atoms. Found 13 (16 requested) and removed 14 (8 requested) atoms. Cycle 35: After refmac, R = 0.2138 (Rfree = 0.000) for 2976 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 2.91 Search for helices and strands: 0 residues in 0 chains, 3110 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3127 seeds are put forward Round 1: 214 peptides, 39 chains. Longest chain 12 peptides. Score 0.339 Round 2: 233 peptides, 33 chains. Longest chain 23 peptides. Score 0.455 Round 3: 250 peptides, 38 chains. Longest chain 15 peptides. Score 0.442 Round 4: 255 peptides, 36 chains. Longest chain 21 peptides. Score 0.475 Round 5: 248 peptides, 33 chains. Longest chain 21 peptides. Score 0.490 Taking the results from Round 5 Chains 33, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6657 restraints for refining 3024 atoms. 5830 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2422 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 37: After refmac, R = 0.2240 (Rfree = 0.000) for 2996 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2148 (Rfree = 0.000) for 2988 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. Cycle 39: After refmac, R = 0.2063 (Rfree = 0.000) for 2980 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2008 (Rfree = 0.000) for 2974 atoms. Found 0 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 3073 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3086 seeds are put forward Round 1: 203 peptides, 37 chains. Longest chain 12 peptides. Score 0.332 Round 2: 226 peptides, 33 chains. Longest chain 21 peptides. Score 0.438 Round 3: 231 peptides, 32 chains. Longest chain 21 peptides. Score 0.461 Round 4: 249 peptides, 35 chains. Longest chain 21 peptides. Score 0.471 Round 5: 256 peptides, 31 chains. Longest chain 18 peptides. Score 0.528 Taking the results from Round 5 Chains 31, Residues 225, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6640 restraints for refining 3022 atoms. 5771 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2576 (Rfree = 0.000) for 3022 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 42: After refmac, R = 0.2398 (Rfree = 0.000) for 3009 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2379 (Rfree = 0.000) for 2996 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 44: After refmac, R = 0.2394 (Rfree = 0.000) for 2993 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.2315 (Rfree = 0.000) for 2983 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 3112 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 3124 seeds are put forward Round 1: 209 peptides, 39 chains. Longest chain 10 peptides. Score 0.325 Round 2: 225 peptides, 36 chains. Longest chain 13 peptides. Score 0.402 Round 3: 239 peptides, 37 chains. Longest chain 20 peptides. Score 0.426 Round 4: 245 peptides, 39 chains. Longest chain 14 peptides. Score 0.419 Round 5: 257 peptides, 37 chains. Longest chain 18 peptides. Score 0.469 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 220, 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 2p8j-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6663 reflections ( 98.27 % complete ) and 6699 restraints for refining 3024 atoms. 5856 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2291 (Rfree = 0.000) for 3024 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2271 (Rfree = 0.000) for 3003 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2365 (Rfree = 0.000) for 2988 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2261 (Rfree = 0.000) for 2972 atoms. TimeTaking 36.95