null Sun 23 Dec 22:23:08 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-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/2p8j-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-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 ============================================================ Sun 23 Dec 22:23:18 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-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 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-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-3.8-parrot-hancs.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 3749 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3497 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3185 (Rfree = 0.000) for 3749 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 2.97 Search for helices and strands: 0 residues in 0 chains, 3820 seeds are put forward NCS extension: 0 residues added, 3820 seeds are put forward Round 1: 217 peptides, 36 chains. Longest chain 17 peptides. Score 0.382 Round 2: 249 peptides, 33 chains. Longest chain 19 peptides. Score 0.492 Round 3: 268 peptides, 32 chains. Longest chain 22 peptides. Score 0.544 Round 4: 251 peptides, 30 chains. Longest chain 19 peptides. Score 0.527 Round 5: 268 peptides, 33 chains. Longest chain 19 peptides. Score 0.534 Taking the results from Round 3 Chains 32, Residues 236, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6448 restraints for refining 3023 atoms. 5440 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2551 (Rfree = 0.000) for 3023 atoms. Found 12 (16 requested) and removed 19 (8 requested) atoms. Cycle 2: After refmac, R = 0.2403 (Rfree = 0.000) for 2957 atoms. Found 11 (16 requested) and removed 15 (8 requested) atoms. Cycle 3: After refmac, R = 0.2402 (Rfree = 0.000) for 2938 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 4: After refmac, R = 0.2321 (Rfree = 0.000) for 2924 atoms. Found 14 (16 requested) and removed 16 (8 requested) atoms. Cycle 5: After refmac, R = 0.2227 (Rfree = 0.000) for 2916 atoms. Found 9 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 2.95 Search for helices and strands: 0 residues in 0 chains, 3023 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3048 seeds are put forward Round 1: 257 peptides, 38 chains. Longest chain 18 peptides. Score 0.459 Round 2: 275 peptides, 32 chains. Longest chain 28 peptides. Score 0.558 Round 3: 275 peptides, 31 chains. Longest chain 31 peptides. Score 0.568 Round 4: 285 peptides, 32 chains. Longest chain 20 peptides. Score 0.578 Round 5: 275 peptides, 27 chains. Longest chain 28 peptides. Score 0.604 Taking the results from Round 5 Chains 27, Residues 248, Estimated correctness of the model 0.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6553 restraints for refining 3023 atoms. 5588 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2413 (Rfree = 0.000) for 3023 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 7: After refmac, R = 0.2158 (Rfree = 0.000) for 2995 atoms. Found 10 (16 requested) and removed 17 (8 requested) atoms. Cycle 8: After refmac, R = 0.2115 (Rfree = 0.000) for 2978 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.2053 (Rfree = 0.000) for 2968 atoms. Found 7 (16 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.2022 (Rfree = 0.000) for 2960 atoms. Found 4 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 2.93 Search for helices and strands: 0 residues in 0 chains, 3090 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3111 seeds are put forward Round 1: 248 peptides, 37 chains. Longest chain 18 peptides. Score 0.448 Round 2: 274 peptides, 32 chains. Longest chain 23 peptides. Score 0.556 Round 3: 285 peptides, 33 chains. Longest chain 20 peptides. Score 0.569 Round 4: 294 peptides, 36 chains. Longest chain 22 peptides. Score 0.559 Round 5: 267 peptides, 28 chains. Longest chain 26 peptides. Score 0.580 Taking the results from Round 5 Chains 28, Residues 239, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6529 restraints for refining 3024 atoms. 5601 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2556 (Rfree = 0.000) for 3024 atoms. Found 15 (16 requested) and removed 15 (8 requested) atoms. Cycle 12: After refmac, R = 0.2218 (Rfree = 0.000) for 2992 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2133 (Rfree = 0.000) for 2973 atoms. Found 6 (16 requested) and removed 16 (8 requested) atoms. Cycle 14: After refmac, R = 0.2012 (Rfree = 0.000) for 2960 atoms. Found 4 (16 requested) and removed 15 (8 requested) atoms. Cycle 15: After refmac, R = 0.2007 (Rfree = 0.000) for 2947 atoms. Found 7 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 2.94 Search for helices and strands: 0 residues in 0 chains, 3054 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3087 seeds are put forward Round 1: 246 peptides, 38 chains. Longest chain 16 peptides. Score 0.432 Round 2: 266 peptides, 31 chains. Longest chain 25 peptides. Score 0.549 Round 3: 271 peptides, 28 chains. Longest chain 22 peptides. Score 0.588 Round 4: 260 peptides, 29 chains. Longest chain 20 peptides. Score 0.556 Round 5: 261 peptides, 29 chains. Longest chain 20 peptides. Score 0.558 Taking the results from Round 3 Chains 28, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6553 restraints for refining 3024 atoms. 5609 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2451 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 17: After refmac, R = 0.2201 (Rfree = 0.000) for 3021 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.2098 (Rfree = 0.000) for 3004 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.2071 (Rfree = 0.000) for 2992 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2079 (Rfree = 0.000) for 2984 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 2.96 Search for helices and strands: 0 residues in 0 chains, 3104 seeds are put forward NCS extension: 33 residues added (6 deleted due to clashes), 3137 seeds are put forward Round 1: 238 peptides, 34 chains. Longest chain 19 peptides. Score 0.456 Round 2: 258 peptides, 34 chains. Longest chain 19 peptides. Score 0.502 Round 3: 278 peptides, 34 chains. Longest chain 16 peptides. Score 0.545 Round 4: 276 peptides, 31 chains. Longest chain 26 peptides. Score 0.570 Round 5: 269 peptides, 31 chains. Longest chain 20 peptides. Score 0.555 Taking the results from Round 4 Chains 33, Residues 245, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6564 restraints for refining 3024 atoms. 5584 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2492 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 22: After refmac, R = 0.2271 (Rfree = 0.000) for 3007 atoms. Found 11 (16 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.2154 (Rfree = 0.000) for 2999 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2066 (Rfree = 0.000) for 2991 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.1990 (Rfree = 0.000) for 2976 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 2.96 Search for helices and strands: 0 residues in 0 chains, 3064 seeds are put forward NCS extension: 20 residues added (8 deleted due to clashes), 3084 seeds are put forward Round 1: 244 peptides, 33 chains. Longest chain 20 peptides. Score 0.481 Round 2: 270 peptides, 32 chains. Longest chain 17 peptides. Score 0.548 Round 3: 274 peptides, 34 chains. Longest chain 20 peptides. Score 0.537 Round 4: 284 peptides, 31 chains. Longest chain 22 peptides. Score 0.585 Round 5: 266 peptides, 35 chains. Longest chain 16 peptides. Score 0.510 Taking the results from Round 4 Chains 31, Residues 253, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6348 restraints for refining 3022 atoms. 5300 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2436 (Rfree = 0.000) for 3022 atoms. Found 12 (16 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.2247 (Rfree = 0.000) for 3002 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2128 (Rfree = 0.000) for 2992 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.2100 (Rfree = 0.000) for 2981 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2037 (Rfree = 0.000) for 2978 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 2.98 Search for helices and strands: 0 residues in 0 chains, 3062 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3080 seeds are put forward Round 1: 245 peptides, 36 chains. Longest chain 17 peptides. Score 0.451 Round 2: 261 peptides, 35 chains. Longest chain 16 peptides. Score 0.499 Round 3: 264 peptides, 34 chains. Longest chain 17 peptides. Score 0.515 Round 4: 278 peptides, 38 chains. Longest chain 17 peptides. Score 0.506 Round 5: 259 peptides, 34 chains. Longest chain 21 peptides. Score 0.504 Taking the results from Round 3 Chains 35, Residues 230, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6484 restraints for refining 3023 atoms. 5569 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2425 (Rfree = 0.000) for 3023 atoms. Found 10 (16 requested) and removed 14 (8 requested) atoms. Cycle 32: After refmac, R = 0.2288 (Rfree = 0.000) for 3005 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 33: After refmac, R = 0.2192 (Rfree = 0.000) for 2997 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.2194 (Rfree = 0.000) for 2999 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2108 (Rfree = 0.000) for 2995 atoms. Found 12 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 2.99 Search for helices and strands: 0 residues in 0 chains, 3126 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3146 seeds are put forward Round 1: 226 peptides, 34 chains. Longest chain 13 peptides. Score 0.427 Round 2: 251 peptides, 35 chains. Longest chain 17 peptides. Score 0.476 Round 3: 257 peptides, 35 chains. Longest chain 21 peptides. Score 0.490 Round 4: 254 peptides, 34 chains. Longest chain 19 peptides. Score 0.493 Round 5: 253 peptides, 32 chains. Longest chain 18 peptides. Score 0.511 Taking the results from Round 5 Chains 32, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6699 restraints for refining 3024 atoms. 5847 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2581 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 37: After refmac, R = 0.2351 (Rfree = 0.000) for 3006 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.2352 (Rfree = 0.000) for 2998 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 39: After refmac, R = 0.2234 (Rfree = 0.000) for 2990 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 40: After refmac, R = 0.2214 (Rfree = 0.000) for 2987 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 2.99 Search for helices and strands: 0 residues in 0 chains, 3105 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3130 seeds are put forward Round 1: 223 peptides, 42 chains. Longest chain 10 peptides. Score 0.328 Round 2: 240 peptides, 33 chains. Longest chain 19 peptides. Score 0.471 Round 3: 230 peptides, 29 chains. Longest chain 15 peptides. Score 0.491 Round 4: 240 peptides, 31 chains. Longest chain 19 peptides. Score 0.492 Round 5: 250 peptides, 33 chains. Longest chain 19 peptides. Score 0.494 Taking the results from Round 5 Chains 33, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6727 restraints for refining 3023 atoms. 5892 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2627 (Rfree = 0.000) for 3023 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 42: After refmac, R = 0.2334 (Rfree = 0.000) for 3004 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2132 (Rfree = 0.000) for 2999 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.1939 (Rfree = 0.000) for 2986 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.2012 (Rfree = 0.000) for 2976 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 2.99 Search for helices and strands: 0 residues in 0 chains, 3096 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3123 seeds are put forward Round 1: 215 peptides, 37 chains. Longest chain 17 peptides. Score 0.365 Round 2: 235 peptides, 36 chains. Longest chain 18 peptides. Score 0.427 Round 3: 215 peptides, 29 chains. Longest chain 19 peptides. Score 0.455 Round 4: 246 peptides, 32 chains. Longest chain 21 peptides. Score 0.496 Round 5: 236 peptides, 31 chains. Longest chain 21 peptides. Score 0.483 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 214, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 4 % 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 6727 restraints for refining 3023 atoms. 5878 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2537 (Rfree = 0.000) for 3023 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2263 (Rfree = 0.000) for 3001 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2186 (Rfree = 0.000) for 2989 atoms. Found 0 (16 requested) and removed 5 (8 requested) atoms. Cycle 49: After refmac, R = 0.2154 (Rfree = 0.000) for 2982 atoms. Found 0 (16 requested) and removed 5 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:18:41 GMT 2018 Job finished. TimeTaking 55.55 Used memory is bytes: 19380904