Mon 24 Dec 00:51:40 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 2op5-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.6-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/2op5-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.6-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 00:51:45 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/2op5-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.6-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 484 and 0 Target number of residues in the AU: 484 Target solvent content: 0.6225 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-3.6-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: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.75 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: 73.087 3.600 Wilson plot Bfac: 62.34 8519 reflections ( 99.80 % complete ) and 0 restraints for refining 6187 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3307 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2992 (Rfree = 0.000) for 6187 atoms. Found 24 (39 requested) and removed 59 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.60 Search for helices and strands: 0 residues in 0 chains, 6281 seeds are put forward NCS extension: 0 residues added, 6281 seeds are put forward Round 1: 270 peptides, 49 chains. Longest chain 14 peptides. Score 0.363 Round 2: 322 peptides, 47 chains. Longest chain 16 peptides. Score 0.498 Round 3: 337 peptides, 44 chains. Longest chain 17 peptides. Score 0.554 Round 4: 344 peptides, 45 chains. Longest chain 18 peptides. Score 0.559 Round 5: 375 peptides, 56 chains. Longest chain 22 peptides. Score 0.525 Taking the results from Round 4 Chains 45, Residues 299, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11748 restraints for refining 5087 atoms. 10597 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2456 (Rfree = 0.000) for 5087 atoms. Found 17 (32 requested) and removed 38 (16 requested) atoms. Cycle 2: After refmac, R = 0.2493 (Rfree = 0.000) for 4998 atoms. Found 14 (32 requested) and removed 29 (16 requested) atoms. Cycle 3: After refmac, R = 0.2471 (Rfree = 0.000) for 4939 atoms. Found 12 (31 requested) and removed 21 (15 requested) atoms. Cycle 4: After refmac, R = 0.2418 (Rfree = 0.000) for 4891 atoms. Found 14 (31 requested) and removed 20 (15 requested) atoms. Cycle 5: After refmac, R = 0.2477 (Rfree = 0.000) for 4874 atoms. Found 16 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 5061 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5074 seeds are put forward Round 1: 277 peptides, 50 chains. Longest chain 14 peptides. Score 0.369 Round 2: 353 peptides, 58 chains. Longest chain 15 peptides. Score 0.463 Round 3: 377 peptides, 58 chains. Longest chain 17 peptides. Score 0.512 Round 4: 380 peptides, 55 chains. Longest chain 17 peptides. Score 0.543 Round 5: 409 peptides, 63 chains. Longest chain 23 peptides. Score 0.532 Taking the results from Round 4 Chains 55, Residues 325, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 10783 restraints for refining 4778 atoms. 9503 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2414 (Rfree = 0.000) for 4778 atoms. Found 29 (30 requested) and removed 39 (15 requested) atoms. Cycle 7: After refmac, R = 0.2203 (Rfree = 0.000) for 4738 atoms. Found 7 (30 requested) and removed 31 (15 requested) atoms. Cycle 8: After refmac, R = 0.2199 (Rfree = 0.000) for 4699 atoms. Found 5 (30 requested) and removed 20 (15 requested) atoms. Cycle 9: After refmac, R = 0.2126 (Rfree = 0.000) for 4680 atoms. Found 10 (30 requested) and removed 19 (15 requested) atoms. Cycle 10: After refmac, R = 0.2107 (Rfree = 0.000) for 4667 atoms. Found 9 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 4820 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4840 seeds are put forward Round 1: 324 peptides, 57 chains. Longest chain 22 peptides. Score 0.409 Round 2: 352 peptides, 52 chains. Longest chain 22 peptides. Score 0.514 Round 3: 376 peptides, 54 chains. Longest chain 22 peptides. Score 0.544 Round 4: 389 peptides, 51 chains. Longest chain 22 peptides. Score 0.591 Round 5: 362 peptides, 46 chains. Longest chain 22 peptides. Score 0.583 Taking the results from Round 4 Chains 51, Residues 338, Estimated correctness of the model 11.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11088 restraints for refining 4937 atoms. 9787 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2444 (Rfree = 0.000) for 4937 atoms. Found 15 (31 requested) and removed 48 (15 requested) atoms. Cycle 12: After refmac, R = 0.2275 (Rfree = 0.000) for 4886 atoms. Found 10 (31 requested) and removed 27 (15 requested) atoms. Cycle 13: After refmac, R = 0.2321 (Rfree = 0.000) for 4864 atoms. Found 6 (31 requested) and removed 26 (15 requested) atoms. Cycle 14: After refmac, R = 0.2217 (Rfree = 0.000) for 4843 atoms. Found 7 (31 requested) and removed 20 (15 requested) atoms. Cycle 15: After refmac, R = 0.2181 (Rfree = 0.000) for 4825 atoms. Found 3 (30 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 4950 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 4974 seeds are put forward Round 1: 310 peptides, 54 chains. Longest chain 13 peptides. Score 0.406 Round 2: 340 peptides, 51 chains. Longest chain 27 peptides. Score 0.499 Round 3: 341 peptides, 50 chains. Longest chain 19 peptides. Score 0.510 Round 4: 336 peptides, 48 chains. Longest chain 17 peptides. Score 0.517 Round 5: 332 peptides, 48 chains. Longest chain 18 peptides. Score 0.509 Taking the results from Round 4 Chains 48, Residues 288, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 12204 restraints for refining 5091 atoms. 11100 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2370 (Rfree = 0.000) for 5091 atoms. Found 19 (32 requested) and removed 33 (16 requested) atoms. Cycle 17: After refmac, R = 0.2319 (Rfree = 0.000) for 5062 atoms. Found 18 (32 requested) and removed 37 (16 requested) atoms. Cycle 18: After refmac, R = 0.2231 (Rfree = 0.000) for 5027 atoms. Found 29 (32 requested) and removed 35 (16 requested) atoms. Cycle 19: After refmac, R = 0.2016 (Rfree = 0.000) for 5009 atoms. Found 14 (32 requested) and removed 20 (16 requested) atoms. Cycle 20: After refmac, R = 0.2093 (Rfree = 0.000) for 4988 atoms. Found 22 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 5173 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5190 seeds are put forward Round 1: 289 peptides, 54 chains. Longest chain 17 peptides. Score 0.357 Round 2: 323 peptides, 52 chains. Longest chain 17 peptides. Score 0.454 Round 3: 313 peptides, 46 chains. Longest chain 19 peptides. Score 0.489 Round 4: 317 peptides, 46 chains. Longest chain 19 peptides. Score 0.497 Round 5: 313 peptides, 43 chains. Longest chain 19 peptides. Score 0.516 Taking the results from Round 5 Chains 43, Residues 270, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11935 restraints for refining 5091 atoms. 10898 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2253 (Rfree = 0.000) for 5091 atoms. Found 19 (32 requested) and removed 26 (16 requested) atoms. Cycle 22: After refmac, R = 0.2174 (Rfree = 0.000) for 5059 atoms. Found 19 (32 requested) and removed 28 (16 requested) atoms. Cycle 23: After refmac, R = 0.1992 (Rfree = 0.000) for 5030 atoms. Found 10 (32 requested) and removed 20 (16 requested) atoms. Cycle 24: After refmac, R = 0.2048 (Rfree = 0.000) for 5013 atoms. Found 18 (32 requested) and removed 20 (16 requested) atoms. Cycle 25: After refmac, R = 0.1775 (Rfree = 0.000) for 5006 atoms. Found 5 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 5147 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5165 seeds are put forward Round 1: 231 peptides, 43 chains. Longest chain 10 peptides. Score 0.330 Round 2: 272 peptides, 42 chains. Longest chain 21 peptides. Score 0.438 Round 3: 292 peptides, 46 chains. Longest chain 20 peptides. Score 0.444 Round 4: 290 peptides, 47 chains. Longest chain 13 peptides. Score 0.429 Round 5: 308 peptides, 44 chains. Longest chain 20 peptides. Score 0.497 Taking the results from Round 5 Chains 44, Residues 264, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11835 restraints for refining 5091 atoms. 10823 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2080 (Rfree = 0.000) for 5091 atoms. Found 20 (32 requested) and removed 38 (16 requested) atoms. Cycle 27: After refmac, R = 0.1991 (Rfree = 0.000) for 5062 atoms. Found 10 (32 requested) and removed 23 (16 requested) atoms. Cycle 28: After refmac, R = 0.1990 (Rfree = 0.000) for 5041 atoms. Found 14 (32 requested) and removed 28 (16 requested) atoms. Cycle 29: After refmac, R = 0.1870 (Rfree = 0.000) for 5021 atoms. Found 10 (32 requested) and removed 21 (16 requested) atoms. Cycle 30: After refmac, R = 0.1621 (Rfree = 0.000) for 5003 atoms. Found 3 (32 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 5150 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 5164 seeds are put forward Round 1: 236 peptides, 47 chains. Longest chain 10 peptides. Score 0.299 Round 2: 271 peptides, 43 chains. Longest chain 14 peptides. Score 0.426 Round 3: 265 peptides, 45 chains. Longest chain 13 peptides. Score 0.392 Round 4: 284 peptides, 42 chains. Longest chain 16 peptides. Score 0.465 Round 5: 293 peptides, 46 chains. Longest chain 14 peptides. Score 0.446 Taking the results from Round 4 Chains 42, Residues 242, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 12120 restraints for refining 5091 atoms. 11194 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2019 (Rfree = 0.000) for 5091 atoms. Found 23 (32 requested) and removed 28 (16 requested) atoms. Cycle 32: After refmac, R = 0.2042 (Rfree = 0.000) for 5072 atoms. Found 13 (32 requested) and removed 31 (16 requested) atoms. Cycle 33: After refmac, R = 0.1964 (Rfree = 0.000) for 5049 atoms. Found 5 (32 requested) and removed 24 (16 requested) atoms. Cycle 34: After refmac, R = 0.1967 (Rfree = 0.000) for 5027 atoms. Found 11 (32 requested) and removed 24 (16 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1939 (Rfree = 0.000) for 5012 atoms. Found 12 (32 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 5145 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5162 seeds are put forward Round 1: 247 peptides, 51 chains. Longest chain 12 peptides. Score 0.284 Round 2: 277 peptides, 46 chains. Longest chain 12 peptides. Score 0.410 Round 3: 265 peptides, 44 chains. Longest chain 11 peptides. Score 0.402 Round 4: 280 peptides, 43 chains. Longest chain 18 peptides. Score 0.446 Round 5: 265 peptides, 42 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 4 Chains 43, Residues 237, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 12176 restraints for refining 5091 atoms. 11271 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2327 (Rfree = 0.000) for 5091 atoms. Found 19 (32 requested) and removed 32 (16 requested) atoms. Cycle 37: After refmac, R = 0.2207 (Rfree = 0.000) for 5067 atoms. Found 23 (32 requested) and removed 29 (16 requested) atoms. Cycle 38: After refmac, R = 0.2095 (Rfree = 0.000) for 5051 atoms. Found 13 (32 requested) and removed 19 (16 requested) atoms. Cycle 39: After refmac, R = 0.2062 (Rfree = 0.000) for 5043 atoms. Found 18 (32 requested) and removed 26 (16 requested) atoms. Cycle 40: After refmac, R = 0.1966 (Rfree = 0.000) for 5030 atoms. Found 7 (32 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.52 Search for helices and strands: 0 residues in 0 chains, 5185 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 5201 seeds are put forward Round 1: 213 peptides, 41 chains. Longest chain 11 peptides. Score 0.306 Round 2: 244 peptides, 43 chains. Longest chain 10 peptides. Score 0.362 Round 3: 250 peptides, 42 chains. Longest chain 12 peptides. Score 0.387 Round 4: 255 peptides, 39 chains. Longest chain 11 peptides. Score 0.430 Round 5: 259 peptides, 37 chains. Longest chain 14 peptides. Score 0.459 Taking the results from Round 5 Chains 37, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11961 restraints for refining 5091 atoms. 11110 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2094 (Rfree = 0.000) for 5091 atoms. Found 23 (32 requested) and removed 27 (16 requested) atoms. Cycle 42: After refmac, R = 0.2055 (Rfree = 0.000) for 5083 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. Cycle 43: After refmac, R = 0.1875 (Rfree = 0.000) for 5083 atoms. Found 22 (32 requested) and removed 25 (16 requested) atoms. Cycle 44: After refmac, R = 0.1564 (Rfree = 0.000) for 5074 atoms. Found 5 (32 requested) and removed 18 (16 requested) atoms. Cycle 45: After refmac, R = 0.1502 (Rfree = 0.000) for 5061 atoms. Found 3 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 5211 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5228 seeds are put forward Round 1: 198 peptides, 40 chains. Longest chain 10 peptides. Score 0.277 Round 2: 231 peptides, 37 chains. Longest chain 17 peptides. Score 0.394 Round 3: 246 peptides, 38 chains. Longest chain 17 peptides. Score 0.419 Round 4: 255 peptides, 40 chains. Longest chain 18 peptides. Score 0.420 Round 5: 252 peptides, 39 chains. Longest chain 12 peptides. Score 0.423 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 213, 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 2op5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8519 reflections ( 99.80 % complete ) and 12031 restraints for refining 5091 atoms. 11218 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1947 (Rfree = 0.000) for 5091 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1965 (Rfree = 0.000) for 5064 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2043 (Rfree = 0.000) for 5046 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1948 (Rfree = 0.000) for 5026 atoms. TimeTaking 61.05