Sun 23 Dec 22:22:46 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 2p8j-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-3.4-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/2p8j-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-3.4-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 22:22:54 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/2p8j-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-3.4-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 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-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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-3.4-parrot-hancs.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 3695 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3287 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2963 (Rfree = 0.000) for 3695 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 2.76 Search for helices and strands: 0 residues in 0 chains, 3785 seeds are put forward NCS extension: 0 residues added, 3785 seeds are put forward Round 1: 280 peptides, 41 chains. Longest chain 14 peptides. Score 0.481 Round 2: 305 peptides, 35 chains. Longest chain 25 peptides. Score 0.590 Round 3: 295 peptides, 31 chains. Longest chain 27 peptides. Score 0.606 Round 4: 312 peptides, 31 chains. Longest chain 27 peptides. Score 0.637 Round 5: 325 peptides, 30 chains. Longest chain 38 peptides. Score 0.667 Taking the results from Round 5 Chains 34, Residues 295, Estimated correctness of the model 49.0 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5913 restraints for refining 3049 atoms. 4626 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2606 (Rfree = 0.000) for 3049 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 2: After refmac, R = 0.2378 (Rfree = 0.000) for 3012 atoms. Found 14 (22 requested) and removed 19 (11 requested) atoms. Cycle 3: After refmac, R = 0.2234 (Rfree = 0.000) for 2997 atoms. Found 12 (22 requested) and removed 14 (11 requested) atoms. Cycle 4: After refmac, R = 0.2164 (Rfree = 0.000) for 2991 atoms. Found 8 (22 requested) and removed 12 (11 requested) atoms. Cycle 5: After refmac, R = 0.2195 (Rfree = 0.000) for 2984 atoms. Found 7 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 2.71 Search for helices and strands: 0 residues in 0 chains, 3081 seeds are put forward NCS extension: 36 residues added (7 deleted due to clashes), 3117 seeds are put forward Round 1: 304 peptides, 35 chains. Longest chain 34 peptides. Score 0.588 Round 2: 325 peptides, 31 chains. Longest chain 32 peptides. Score 0.659 Round 3: 314 peptides, 27 chains. Longest chain 41 peptides. Score 0.673 Round 4: 322 peptides, 32 chains. Longest chain 22 peptides. Score 0.646 Round 5: 312 peptides, 29 chains. Longest chain 24 peptides. Score 0.654 Taking the results from Round 3 Chains 27, Residues 287, Estimated correctness of the model 50.7 % 5 chains (122 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5126 restraints for refining 3080 atoms. 3500 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2577 (Rfree = 0.000) for 3080 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 7: After refmac, R = 0.2395 (Rfree = 0.000) for 3056 atoms. Found 16 (23 requested) and removed 22 (11 requested) atoms. Cycle 8: After refmac, R = 0.2288 (Rfree = 0.000) for 3043 atoms. Found 6 (23 requested) and removed 15 (11 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2257 (Rfree = 0.000) for 3028 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. Cycle 10: After refmac, R = 0.2215 (Rfree = 0.000) for 3015 atoms. Found 6 (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, 3100 seeds are put forward NCS extension: 52 residues added (14 deleted due to clashes), 3152 seeds are put forward Round 1: 290 peptides, 33 chains. Longest chain 23 peptides. Score 0.579 Round 2: 317 peptides, 29 chains. Longest chain 34 peptides. Score 0.662 Round 3: 304 peptides, 27 chains. Longest chain 48 peptides. Score 0.656 Round 4: 318 peptides, 28 chains. Longest chain 29 peptides. Score 0.671 Round 5: 320 peptides, 27 chains. Longest chain 44 peptides. Score 0.682 Taking the results from Round 5 Chains 29, Residues 293, Estimated correctness of the model 53.1 % 5 chains (104 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5280 restraints for refining 3041 atoms. 3688 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2633 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 12: After refmac, R = 0.2360 (Rfree = 0.000) for 3028 atoms. Found 15 (22 requested) and removed 15 (11 requested) atoms. Cycle 13: After refmac, R = 0.2286 (Rfree = 0.000) for 3025 atoms. Found 9 (22 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.2254 (Rfree = 0.000) for 3021 atoms. Found 10 (22 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.2244 (Rfree = 0.000) for 3015 atoms. Found 13 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 2.76 Search for helices and strands: 0 residues in 0 chains, 3111 seeds are put forward NCS extension: 24 residues added (18 deleted due to clashes), 3135 seeds are put forward Round 1: 285 peptides, 34 chains. Longest chain 41 peptides. Score 0.560 Round 2: 313 peptides, 31 chains. Longest chain 44 peptides. Score 0.639 Round 3: 298 peptides, 30 chains. Longest chain 28 peptides. Score 0.621 Round 4: 306 peptides, 33 chains. Longest chain 28 peptides. Score 0.609 Round 5: 305 peptides, 26 chains. Longest chain 39 peptides. Score 0.666 Taking the results from Round 5 Chains 28, Residues 279, Estimated correctness of the model 48.7 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 6100 restraints for refining 3040 atoms. 4848 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2582 (Rfree = 0.000) for 3040 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 17: After refmac, R = 0.2336 (Rfree = 0.000) for 3037 atoms. Found 15 (22 requested) and removed 13 (11 requested) atoms. Cycle 18: After refmac, R = 0.2257 (Rfree = 0.000) for 3031 atoms. Found 10 (22 requested) and removed 11 (11 requested) atoms. Cycle 19: After refmac, R = 0.2185 (Rfree = 0.000) for 3027 atoms. Found 14 (22 requested) and removed 13 (11 requested) atoms. Cycle 20: After refmac, R = 0.2137 (Rfree = 0.000) for 3027 atoms. Found 2 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 2.76 Search for helices and strands: 0 residues in 0 chains, 3101 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3125 seeds are put forward Round 1: 282 peptides, 32 chains. Longest chain 22 peptides. Score 0.572 Round 2: 302 peptides, 33 chains. Longest chain 44 peptides. Score 0.602 Round 3: 302 peptides, 29 chains. Longest chain 44 peptides. Score 0.636 Round 4: 305 peptides, 29 chains. Longest chain 45 peptides. Score 0.641 Round 5: 302 peptides, 30 chains. Longest chain 25 peptides. Score 0.628 Taking the results from Round 4 Chains 34, Residues 276, Estimated correctness of the model 41.5 % 4 chains (63 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5719 restraints for refining 3041 atoms. 4412 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2560 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 22: After refmac, R = 0.2383 (Rfree = 0.000) for 3020 atoms. Found 14 (22 requested) and removed 22 (11 requested) atoms. Cycle 23: After refmac, R = 0.2275 (Rfree = 0.000) for 3007 atoms. Found 11 (22 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.2251 (Rfree = 0.000) for 3002 atoms. Found 5 (22 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.2237 (Rfree = 0.000) for 2993 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 2.72 Search for helices and strands: 0 residues in 0 chains, 3076 seeds are put forward NCS extension: 23 residues added (8 deleted due to clashes), 3099 seeds are put forward Round 1: 279 peptides, 33 chains. Longest chain 26 peptides. Score 0.557 Round 2: 293 peptides, 28 chains. Longest chain 51 peptides. Score 0.629 Round 3: 293 peptides, 27 chains. Longest chain 42 peptides. Score 0.637 Round 4: 298 peptides, 29 chains. Longest chain 51 peptides. Score 0.629 Round 5: 301 peptides, 27 chains. Longest chain 43 peptides. Score 0.651 Taking the results from Round 5 Chains 28, Residues 274, Estimated correctness of the model 44.4 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 6140 restraints for refining 3041 atoms. 4993 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2578 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 27: After refmac, R = 0.2349 (Rfree = 0.000) for 3032 atoms. Found 14 (22 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.2282 (Rfree = 0.000) for 3025 atoms. Found 13 (22 requested) and removed 12 (11 requested) atoms. Cycle 29: After refmac, R = 0.2239 (Rfree = 0.000) for 3023 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. Cycle 30: After refmac, R = 0.2222 (Rfree = 0.000) for 3014 atoms. Found 13 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 3115 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3133 seeds are put forward Round 1: 284 peptides, 36 chains. Longest chain 42 peptides. Score 0.539 Round 2: 296 peptides, 27 chains. Longest chain 42 peptides. Score 0.643 Round 3: 302 peptides, 32 chains. Longest chain 42 peptides. Score 0.611 Round 4: 303 peptides, 29 chains. Longest chain 45 peptides. Score 0.638 Round 5: 286 peptides, 29 chains. Longest chain 27 peptides. Score 0.607 Taking the results from Round 2 Chains 30, Residues 269, Estimated correctness of the model 42.1 % 5 chains (83 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5549 restraints for refining 3040 atoms. 4171 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2566 (Rfree = 0.000) for 3040 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 32: After refmac, R = 0.2384 (Rfree = 0.000) for 3030 atoms. Found 14 (22 requested) and removed 16 (11 requested) atoms. Cycle 33: After refmac, R = 0.2349 (Rfree = 0.000) for 3026 atoms. Found 11 (22 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.2320 (Rfree = 0.000) for 3019 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.2273 (Rfree = 0.000) for 3008 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 2.72 Search for helices and strands: 0 residues in 0 chains, 3121 seeds are put forward NCS extension: 62 residues added (3 deleted due to clashes), 3183 seeds are put forward Round 1: 288 peptides, 36 chains. Longest chain 19 peptides. Score 0.547 Round 2: 291 peptides, 31 chains. Longest chain 40 peptides. Score 0.599 Round 3: 301 peptides, 32 chains. Longest chain 29 peptides. Score 0.609 Round 4: 305 peptides, 32 chains. Longest chain 24 peptides. Score 0.616 Round 5: 306 peptides, 30 chains. Longest chain 31 peptides. Score 0.635 Taking the results from Round 5 Chains 30, Residues 276, Estimated correctness of the model 39.7 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 6094 restraints for refining 3041 atoms. 4902 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2563 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 37: After refmac, R = 0.2365 (Rfree = 0.000) for 3027 atoms. Found 10 (23 requested) and removed 14 (11 requested) atoms. Cycle 38: After refmac, R = 0.2335 (Rfree = 0.000) for 3017 atoms. Found 9 (22 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.2271 (Rfree = 0.000) for 3012 atoms. Found 4 (22 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.2258 (Rfree = 0.000) for 3002 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3106 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3126 seeds are put forward Round 1: 280 peptides, 30 chains. Longest chain 46 peptides. Score 0.587 Round 2: 308 peptides, 29 chains. Longest chain 41 peptides. Score 0.647 Round 3: 303 peptides, 30 chains. Longest chain 27 peptides. Score 0.630 Round 4: 311 peptides, 29 chains. Longest chain 42 peptides. Score 0.652 Round 5: 302 peptides, 30 chains. Longest chain 45 peptides. Score 0.628 Taking the results from Round 4 Chains 31, Residues 282, Estimated correctness of the model 44.7 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5862 restraints for refining 3041 atoms. 4570 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2536 (Rfree = 0.000) for 3041 atoms. Found 20 (22 requested) and removed 13 (11 requested) atoms. Cycle 42: After refmac, R = 0.2673 (Rfree = 0.000) for 3039 atoms. Found 21 (23 requested) and removed 20 (11 requested) atoms. Cycle 43: After refmac, R = 0.2250 (Rfree = 0.000) for 3026 atoms. Found 7 (22 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.2194 (Rfree = 0.000) for 3018 atoms. Found 12 (22 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.2152 (Rfree = 0.000) for 3014 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.71 Search for helices and strands: 0 residues in 0 chains, 3113 seeds are put forward NCS extension: 50 residues added (13 deleted due to clashes), 3163 seeds are put forward Round 1: 294 peptides, 36 chains. Longest chain 25 peptides. Score 0.559 Round 2: 307 peptides, 32 chains. Longest chain 21 peptides. Score 0.620 Round 3: 317 peptides, 29 chains. Longest chain 42 peptides. Score 0.662 Round 4: 313 peptides, 29 chains. Longest chain 24 peptides. Score 0.655 Round 5: 311 peptides, 31 chains. Longest chain 39 peptides. Score 0.635 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 288, Estimated correctness of the model 47.6 % 2 chains (35 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 30 chains (288 residues) following loop building 2 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9272 reflections ( 98.75 % complete ) and 5885 restraints for refining 3041 atoms. 4615 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2466 (Rfree = 0.000) for 3041 atoms. Found 0 (22 requested) and removed 7 (11 requested) atoms. Cycle 47: After refmac, R = 0.2428 (Rfree = 0.000) for 3029 atoms. Found 0 (22 requested) and removed 9 (11 requested) atoms. Cycle 48: After refmac, R = 0.2267 (Rfree = 0.000) for 3014 atoms. Found 0 (22 requested) and removed 2 (11 requested) atoms. Cycle 49: After refmac, R = 0.2273 (Rfree = 0.000) for 3007 atoms. Found 0 (22 requested) and removed 1 (11 requested) atoms. Writing output files ... TimeTaking 60.38