Mon 24 Dec 01:01:38 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.4-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 01:01:43 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.4-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 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-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-3.4-parrot-mrncs.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 3700 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3335 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2939 (Rfree = 0.000) for 3700 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3789 seeds are put forward NCS extension: 0 residues added, 3789 seeds are put forward Round 1: 266 peptides, 36 chains. Longest chain 16 peptides. Score 0.500 Round 2: 294 peptides, 38 chains. Longest chain 33 peptides. Score 0.541 Round 3: 290 peptides, 32 chains. Longest chain 32 peptides. Score 0.588 Round 4: 291 peptides, 30 chains. Longest chain 32 peptides. Score 0.608 Round 5: 301 peptides, 29 chains. Longest chain 36 peptides. Score 0.635 Taking the results from Round 5 Chains 29, Residues 272, Estimated correctness of the model 39.7 % 3 chains (73 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5773 restraints for refining 3138 atoms. 4408 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2567 (Rfree = 0.000) for 3138 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 2: After refmac, R = 0.2338 (Rfree = 0.000) for 3107 atoms. Found 10 (23 requested) and removed 20 (11 requested) atoms. Cycle 3: After refmac, R = 0.2239 (Rfree = 0.000) for 3085 atoms. Found 10 (23 requested) and removed 15 (11 requested) atoms. Cycle 4: After refmac, R = 0.2210 (Rfree = 0.000) for 3074 atoms. Found 12 (23 requested) and removed 11 (11 requested) atoms. Cycle 5: After refmac, R = 0.2213 (Rfree = 0.000) for 3069 atoms. Found 11 (23 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, 3167 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 3206 seeds are put forward Round 1: 291 peptides, 29 chains. Longest chain 37 peptides. Score 0.616 Round 2: 309 peptides, 30 chains. Longest chain 28 peptides. Score 0.640 Round 3: 307 peptides, 27 chains. Longest chain 34 peptides. Score 0.661 Round 4: 318 peptides, 31 chains. Longest chain 26 peptides. Score 0.647 Round 5: 317 peptides, 32 chains. Longest chain 30 peptides. Score 0.638 Taking the results from Round 3 Chains 28, Residues 280, Estimated correctness of the model 47.3 % 5 chains (102 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5437 restraints for refining 3040 atoms. 3924 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2562 (Rfree = 0.000) for 3040 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 7: After refmac, R = 0.2342 (Rfree = 0.000) for 3025 atoms. Found 12 (22 requested) and removed 13 (11 requested) atoms. Cycle 8: After refmac, R = 0.2245 (Rfree = 0.000) for 3016 atoms. Found 8 (22 requested) and removed 11 (11 requested) atoms. Cycle 9: After refmac, R = 0.2207 (Rfree = 0.000) for 3007 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.2152 (Rfree = 0.000) for 3001 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 3081 seeds are put forward NCS extension: 59 residues added (6 deleted due to clashes), 3140 seeds are put forward Round 1: 301 peptides, 31 chains. Longest chain 23 peptides. Score 0.617 Round 2: 305 peptides, 31 chains. Longest chain 31 peptides. Score 0.625 Round 3: 306 peptides, 33 chains. Longest chain 38 peptides. Score 0.609 Round 4: 308 peptides, 30 chains. Longest chain 31 peptides. Score 0.638 Round 5: 309 peptides, 32 chains. Longest chain 39 peptides. Score 0.623 Taking the results from Round 4 Chains 31, Residues 278, Estimated correctness of the model 40.6 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 6096 restraints for refining 3041 atoms. 4903 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2571 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 12: After refmac, R = 0.2322 (Rfree = 0.000) for 3038 atoms. Found 13 (23 requested) and removed 15 (11 requested) atoms. Cycle 13: After refmac, R = 0.2284 (Rfree = 0.000) for 3031 atoms. Found 5 (22 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.2236 (Rfree = 0.000) for 3019 atoms. Found 9 (22 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.2228 (Rfree = 0.000) for 3013 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3083 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 3124 seeds are put forward Round 1: 285 peptides, 33 chains. Longest chain 33 peptides. Score 0.569 Round 2: 302 peptides, 29 chains. Longest chain 24 peptides. Score 0.636 Round 3: 299 peptides, 32 chains. Longest chain 32 peptides. Score 0.605 Round 4: 309 peptides, 30 chains. Longest chain 29 peptides. Score 0.640 Round 5: 304 peptides, 25 chains. Longest chain 37 peptides. Score 0.672 Taking the results from Round 5 Chains 27, Residues 279, Estimated correctness of the model 50.4 % 3 chains (66 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5644 restraints for refining 3041 atoms. 4251 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2646 (Rfree = 0.000) for 3041 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 17: After refmac, R = 0.2427 (Rfree = 0.000) for 3024 atoms. Found 10 (22 requested) and removed 19 (11 requested) atoms. Cycle 18: After refmac, R = 0.2360 (Rfree = 0.000) for 3013 atoms. Found 9 (22 requested) and removed 11 (11 requested) atoms. Cycle 19: After refmac, R = 0.2315 (Rfree = 0.000) for 3011 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.2281 (Rfree = 0.000) for 3005 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3094 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3118 seeds are put forward Round 1: 283 peptides, 29 chains. Longest chain 28 peptides. Score 0.602 Round 2: 284 peptides, 28 chains. Longest chain 32 peptides. Score 0.612 Round 3: 293 peptides, 26 chains. Longest chain 30 peptides. Score 0.646 Round 4: 300 peptides, 30 chains. Longest chain 34 peptides. Score 0.624 Round 5: 315 peptides, 23 chains. Longest chain 36 peptides. Score 0.705 Taking the results from Round 5 Chains 26, Residues 292, Estimated correctness of the model 59.1 % 5 chains (107 residues) have been docked in sequence Building loops using Loopy2018 26 chains (292 residues) following loop building 5 chains (107 residues) in sequence following loop building ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5200 restraints for refining 3053 atoms. 3590 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2681 (Rfree = 0.000) for 3053 atoms. Found 23 (23 requested) and removed 36 (11 requested) atoms. Cycle 22: After refmac, R = 0.2459 (Rfree = 0.000) for 3032 atoms. Found 12 (22 requested) and removed 17 (11 requested) atoms. Cycle 23: After refmac, R = 0.2473 (Rfree = 0.000) for 3018 atoms. Found 17 (21 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.2348 (Rfree = 0.000) for 3020 atoms. Found 5 (21 requested) and removed 13 (11 requested) atoms. Cycle 25: After refmac, R = 0.2322 (Rfree = 0.000) for 3005 atoms. Found 6 (20 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3092 seeds are put forward NCS extension: 43 residues added (6 deleted due to clashes), 3135 seeds are put forward Round 1: 272 peptides, 30 chains. Longest chain 22 peptides. Score 0.571 Round 2: 287 peptides, 24 chains. Longest chain 25 peptides. Score 0.652 Round 3: 288 peptides, 29 chains. Longest chain 39 peptides. Score 0.611 Round 4: 307 peptides, 23 chains. Longest chain 41 peptides. Score 0.693 Round 5: 298 peptides, 27 chains. Longest chain 23 peptides. Score 0.646 Taking the results from Round 4 Chains 29, Residues 284, Estimated correctness of the model 56.1 % 8 chains (143 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 4992 restraints for refining 3092 atoms. 3299 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2688 (Rfree = 0.000) for 3092 atoms. Found 21 (21 requested) and removed 27 (11 requested) atoms. Cycle 27: After refmac, R = 0.2511 (Rfree = 0.000) for 3070 atoms. Found 16 (21 requested) and removed 17 (11 requested) atoms. Cycle 28: After refmac, R = 0.2445 (Rfree = 0.000) for 3062 atoms. Found 17 (21 requested) and removed 16 (11 requested) atoms. Cycle 29: After refmac, R = 0.2359 (Rfree = 0.000) for 3057 atoms. Found 11 (21 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.2273 (Rfree = 0.000) for 3048 atoms. Found 10 (21 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3145 seeds are put forward NCS extension: 35 residues added (9 deleted due to clashes), 3180 seeds are put forward Round 1: 278 peptides, 33 chains. Longest chain 41 peptides. Score 0.555 Round 2: 282 peptides, 27 chains. Longest chain 35 peptides. Score 0.618 Round 3: 304 peptides, 29 chains. Longest chain 39 peptides. Score 0.640 Round 4: 306 peptides, 26 chains. Longest chain 31 peptides. Score 0.668 Round 5: 304 peptides, 27 chains. Longest chain 39 peptides. Score 0.656 Taking the results from Round 4 Chains 27, Residues 280, Estimated correctness of the model 49.3 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5716 restraints for refining 3040 atoms. 4374 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2537 (Rfree = 0.000) for 3040 atoms. Found 20 (20 requested) and removed 20 (11 requested) atoms. Cycle 32: After refmac, R = 0.2322 (Rfree = 0.000) for 3027 atoms. Found 13 (20 requested) and removed 14 (11 requested) atoms. Cycle 33: After refmac, R = 0.2289 (Rfree = 0.000) for 3017 atoms. Found 12 (20 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.2214 (Rfree = 0.000) for 3013 atoms. Found 2 (20 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.2183 (Rfree = 0.000) for 3002 atoms. Found 3 (20 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.74 Search for helices and strands: 0 residues in 0 chains, 3094 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3123 seeds are put forward Round 1: 277 peptides, 30 chains. Longest chain 32 peptides. Score 0.581 Round 2: 296 peptides, 27 chains. Longest chain 30 peptides. Score 0.643 Round 3: 287 peptides, 27 chains. Longest chain 43 peptides. Score 0.627 Round 4: 290 peptides, 26 chains. Longest chain 28 peptides. Score 0.640 Round 5: 283 peptides, 27 chains. Longest chain 36 peptides. Score 0.619 Taking the results from Round 2 Chains 29, Residues 269, Estimated correctness of the model 42.1 % 3 chains (71 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5644 restraints for refining 3041 atoms. 4293 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2463 (Rfree = 0.000) for 3041 atoms. Found 20 (20 requested) and removed 20 (11 requested) atoms. Cycle 37: After refmac, R = 0.2297 (Rfree = 0.000) for 3036 atoms. Found 19 (20 requested) and removed 14 (11 requested) atoms. Cycle 38: After refmac, R = 0.2293 (Rfree = 0.000) for 3037 atoms. Found 9 (20 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.2268 (Rfree = 0.000) for 3034 atoms. Found 6 (20 requested) and removed 15 (11 requested) atoms. Cycle 40: After refmac, R = 0.2233 (Rfree = 0.000) for 3019 atoms. Found 12 (20 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 2.71 Search for helices and strands: 0 residues in 0 chains, 3110 seeds are put forward NCS extension: 22 residues added (7 deleted due to clashes), 3132 seeds are put forward Round 1: 253 peptides, 36 chains. Longest chain 19 peptides. Score 0.470 Round 2: 275 peptides, 29 chains. Longest chain 31 peptides. Score 0.586 Round 3: 281 peptides, 26 chains. Longest chain 41 peptides. Score 0.624 Round 4: 274 peptides, 27 chains. Longest chain 29 peptides. Score 0.602 Round 5: 278 peptides, 29 chains. Longest chain 27 peptides. Score 0.592 Taking the results from Round 3 Chains 30, Residues 255, Estimated correctness of the model 36.3 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ 9272 reflections ( 98.75 % complete ) and 5771 restraints for refining 3041 atoms. 4533 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2438 (Rfree = 0.000) for 3041 atoms. Found 20 (20 requested) and removed 16 (11 requested) atoms. Cycle 42: After refmac, R = 0.2306 (Rfree = 0.000) for 3036 atoms. Found 9 (20 requested) and removed 12 (11 requested) atoms. Cycle 43: After refmac, R = 0.2511 (Rfree = 0.000) for 3026 atoms. Found 20 (20 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.2186 (Rfree = 0.000) for 3026 atoms. Found 12 (20 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.2231 (Rfree = 0.000) for 3021 atoms. Found 15 (20 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, 3123 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3149 seeds are put forward Round 1: 269 peptides, 37 chains. Longest chain 23 peptides. Score 0.496 Round 2: 283 peptides, 29 chains. Longest chain 27 peptides. Score 0.602 Round 3: 294 peptides, 28 chains. Longest chain 44 peptides. Score 0.631 Round 4: 300 peptides, 24 chains. Longest chain 33 peptides. Score 0.674 Round 5: 291 peptides, 27 chains. Longest chain 31 peptides. Score 0.634 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 276, Estimated correctness of the model 50.9 % 2 chains (34 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 25 chains (276 residues) following loop building 2 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9272 reflections ( 98.75 % complete ) and 6004 restraints for refining 3041 atoms. 4768 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2415 (Rfree = 0.000) for 3041 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2376 (Rfree = 0.000) for 3022 atoms. Found 0 (20 requested) and removed 4 (11 requested) atoms. Cycle 48: After refmac, R = 0.2383 (Rfree = 0.000) for 3011 atoms. Found 0 (20 requested) and removed 5 (11 requested) atoms. Cycle 49: After refmac, R = 0.2382 (Rfree = 0.000) for 3005 atoms. TimeTaking 48.65