Mon 24 Dec 00:36:10 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 2fna-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-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/2fna-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-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 00:36:14 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/2fna-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-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 510 and 0 Target number of residues in the AU: 510 Target solvent content: 0.6690 Checking the provided sequence file Detected sequence length: 357 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 714 Adjusted target solvent content: 0.54 Input MTZ file: 2fna-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: 4 Cell parameters: 55.380 108.390 70.600 90.000 100.307 90.000 Input sequence file: 2fna-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5712 target number of atoms Had to go as low as 0.80 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: 69.461 3.800 Wilson plot Bfac: 91.32 8052 reflections ( 98.50 % complete ) and 0 restraints for refining 6318 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3326 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3008 (Rfree = 0.000) for 6318 atoms. Found 34 (34 requested) and removed 53 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 6472 seeds are put forward NCS extension: 0 residues added, 6472 seeds are put forward Round 1: 294 peptides, 52 chains. Longest chain 13 peptides. Score 0.361 Round 2: 343 peptides, 50 chains. Longest chain 19 peptides. Score 0.471 Round 3: 350 peptides, 49 chains. Longest chain 22 peptides. Score 0.492 Round 4: 357 peptides, 50 chains. Longest chain 15 peptides. Score 0.496 Round 5: 370 peptides, 54 chains. Longest chain 22 peptides. Score 0.488 Taking the results from Round 4 Chains 50, Residues 307, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12644 restraints for refining 5163 atoms. 11466 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2274 (Rfree = 0.000) for 5163 atoms. Found 24 (28 requested) and removed 29 (14 requested) atoms. Cycle 2: After refmac, R = 0.2113 (Rfree = 0.000) for 5113 atoms. Found 14 (28 requested) and removed 21 (14 requested) atoms. Cycle 3: After refmac, R = 0.2047 (Rfree = 0.000) for 5082 atoms. Found 5 (28 requested) and removed 18 (14 requested) atoms. Cycle 4: After refmac, R = 0.1986 (Rfree = 0.000) for 5060 atoms. Found 6 (27 requested) and removed 14 (13 requested) atoms. Cycle 5: After refmac, R = 0.1852 (Rfree = 0.000) for 5043 atoms. Found 3 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 5246 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5264 seeds are put forward Round 1: 349 peptides, 58 chains. Longest chain 13 peptides. Score 0.418 Round 2: 348 peptides, 56 chains. Longest chain 16 peptides. Score 0.432 Round 3: 354 peptides, 50 chains. Longest chain 17 peptides. Score 0.491 Round 4: 363 peptides, 52 chains. Longest chain 16 peptides. Score 0.491 Round 5: 365 peptides, 51 chains. Longest chain 18 peptides. Score 0.502 Taking the results from Round 5 Chains 53, Residues 314, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 11901 restraints for refining 5164 atoms. 10641 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2098 (Rfree = 0.000) for 5164 atoms. Found 16 (28 requested) and removed 27 (14 requested) atoms. Cycle 7: After refmac, R = 0.1923 (Rfree = 0.000) for 5118 atoms. Found 3 (28 requested) and removed 18 (14 requested) atoms. Cycle 8: After refmac, R = 0.1901 (Rfree = 0.000) for 5093 atoms. Found 5 (28 requested) and removed 17 (14 requested) atoms. Cycle 9: After refmac, R = 0.1900 (Rfree = 0.000) for 5074 atoms. Found 4 (27 requested) and removed 16 (13 requested) atoms. Cycle 10: After refmac, R = 0.1792 (Rfree = 0.000) for 5058 atoms. Found 2 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 5227 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5247 seeds are put forward Round 1: 300 peptides, 56 chains. Longest chain 11 peptides. Score 0.338 Round 2: 333 peptides, 49 chains. Longest chain 16 peptides. Score 0.461 Round 3: 347 peptides, 47 chains. Longest chain 29 peptides. Score 0.502 Round 4: 345 peptides, 51 chains. Longest chain 19 peptides. Score 0.467 Round 5: 363 peptides, 46 chains. Longest chain 21 peptides. Score 0.536 Taking the results from Round 5 Chains 49, Residues 317, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 11546 restraints for refining 5162 atoms. 10210 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2170 (Rfree = 0.000) for 5162 atoms. Found 14 (28 requested) and removed 21 (14 requested) atoms. Cycle 12: After refmac, R = 0.1894 (Rfree = 0.000) for 5109 atoms. Found 6 (28 requested) and removed 18 (14 requested) atoms. Cycle 13: After refmac, R = 0.1831 (Rfree = 0.000) for 5083 atoms. Found 7 (28 requested) and removed 16 (14 requested) atoms. Cycle 14: After refmac, R = 0.1762 (Rfree = 0.000) for 5060 atoms. Found 3 (27 requested) and removed 14 (13 requested) atoms. Cycle 15: After refmac, R = 0.1773 (Rfree = 0.000) for 5042 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 5231 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 5258 seeds are put forward Round 1: 286 peptides, 53 chains. Longest chain 14 peptides. Score 0.335 Round 2: 349 peptides, 56 chains. Longest chain 20 peptides. Score 0.434 Round 3: 358 peptides, 56 chains. Longest chain 17 peptides. Score 0.451 Round 4: 367 peptides, 50 chains. Longest chain 18 peptides. Score 0.513 Round 5: 354 peptides, 51 chains. Longest chain 18 peptides. Score 0.483 Taking the results from Round 4 Chains 50, Residues 317, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 11936 restraints for refining 5164 atoms. 10718 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2020 (Rfree = 0.000) for 5164 atoms. Found 18 (28 requested) and removed 22 (14 requested) atoms. Cycle 17: After refmac, R = 0.1914 (Rfree = 0.000) for 5127 atoms. Found 17 (28 requested) and removed 18 (14 requested) atoms. Cycle 18: After refmac, R = 0.1929 (Rfree = 0.000) for 5111 atoms. Found 21 (28 requested) and removed 19 (14 requested) atoms. Cycle 19: After refmac, R = 0.1802 (Rfree = 0.000) for 5103 atoms. Found 11 (28 requested) and removed 17 (14 requested) atoms. Cycle 20: After refmac, R = 0.1906 (Rfree = 0.000) for 5089 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 5301 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 5328 seeds are put forward Round 1: 328 peptides, 57 chains. Longest chain 12 peptides. Score 0.386 Round 2: 335 peptides, 51 chains. Longest chain 20 peptides. Score 0.449 Round 3: 346 peptides, 54 chains. Longest chain 19 peptides. Score 0.445 Round 4: 349 peptides, 50 chains. Longest chain 24 peptides. Score 0.482 Round 5: 351 peptides, 51 chains. Longest chain 18 peptides. Score 0.478 Taking the results from Round 4 Chains 50, Residues 299, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12060 restraints for refining 5165 atoms. 10914 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2005 (Rfree = 0.000) for 5165 atoms. Found 13 (28 requested) and removed 25 (14 requested) atoms. Cycle 22: After refmac, R = 0.1888 (Rfree = 0.000) for 5125 atoms. Found 16 (28 requested) and removed 19 (14 requested) atoms. Cycle 23: After refmac, R = 0.1915 (Rfree = 0.000) for 5107 atoms. Found 16 (28 requested) and removed 17 (14 requested) atoms. Cycle 24: After refmac, R = 0.1795 (Rfree = 0.000) for 5095 atoms. Found 6 (28 requested) and removed 18 (14 requested) atoms. Cycle 25: After refmac, R = 0.1535 (Rfree = 0.000) for 5076 atoms. Found 2 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 5254 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 5286 seeds are put forward Round 1: 291 peptides, 58 chains. Longest chain 9 peptides. Score 0.301 Round 2: 317 peptides, 49 chains. Longest chain 14 peptides. Score 0.432 Round 3: 319 peptides, 53 chains. Longest chain 20 peptides. Score 0.402 Round 4: 329 peptides, 48 chains. Longest chain 22 peptides. Score 0.462 Round 5: 320 peptides, 54 chains. Longest chain 15 peptides. Score 0.395 Taking the results from Round 4 Chains 48, Residues 281, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12197 restraints for refining 5165 atoms. 11121 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1979 (Rfree = 0.000) for 5165 atoms. Found 12 (28 requested) and removed 18 (14 requested) atoms. Cycle 27: After refmac, R = 0.1872 (Rfree = 0.000) for 5133 atoms. Found 12 (28 requested) and removed 17 (14 requested) atoms. Cycle 28: After refmac, R = 0.1804 (Rfree = 0.000) for 5112 atoms. Found 11 (28 requested) and removed 19 (14 requested) atoms. Cycle 29: After refmac, R = 0.1737 (Rfree = 0.000) for 5097 atoms. Found 9 (28 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.1454 (Rfree = 0.000) for 5086 atoms. Found 1 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 5275 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 5305 seeds are put forward Round 1: 271 peptides, 53 chains. Longest chain 10 peptides. Score 0.304 Round 2: 308 peptides, 56 chains. Longest chain 15 peptides. Score 0.354 Round 3: 295 peptides, 51 chains. Longest chain 15 peptides. Score 0.372 Round 4: 331 peptides, 53 chains. Longest chain 11 peptides. Score 0.425 Round 5: 316 peptides, 46 chains. Longest chain 16 peptides. Score 0.455 Taking the results from Round 5 Chains 46, Residues 270, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12193 restraints for refining 5165 atoms. 11159 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1858 (Rfree = 0.000) for 5165 atoms. Found 13 (28 requested) and removed 15 (14 requested) atoms. Cycle 32: After refmac, R = 0.1717 (Rfree = 0.000) for 5149 atoms. Found 8 (28 requested) and removed 17 (14 requested) atoms. Cycle 33: After refmac, R = 0.1669 (Rfree = 0.000) for 5123 atoms. Found 11 (28 requested) and removed 19 (14 requested) atoms. Cycle 34: After refmac, R = 0.1647 (Rfree = 0.000) for 5104 atoms. Found 7 (28 requested) and removed 16 (14 requested) atoms. Cycle 35: After refmac, R = 0.1613 (Rfree = 0.000) for 5092 atoms. Found 17 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 5236 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 5250 seeds are put forward Round 1: 260 peptides, 51 chains. Longest chain 11 peptides. Score 0.298 Round 2: 281 peptides, 50 chains. Longest chain 13 peptides. Score 0.352 Round 3: 275 peptides, 47 chains. Longest chain 12 peptides. Score 0.366 Round 4: 277 peptides, 46 chains. Longest chain 15 peptides. Score 0.379 Round 5: 270 peptides, 44 chains. Longest chain 17 peptides. Score 0.383 Taking the results from Round 5 Chains 44, Residues 226, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12267 restraints for refining 5165 atoms. 11407 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2018 (Rfree = 0.000) for 5165 atoms. Found 28 (28 requested) and removed 17 (14 requested) atoms. Cycle 37: After refmac, R = 0.1851 (Rfree = 0.000) for 5161 atoms. Found 20 (28 requested) and removed 18 (14 requested) atoms. Cycle 38: After refmac, R = 0.1770 (Rfree = 0.000) for 5156 atoms. Found 16 (28 requested) and removed 16 (14 requested) atoms. Cycle 39: After refmac, R = 0.1736 (Rfree = 0.000) for 5145 atoms. Found 18 (28 requested) and removed 19 (14 requested) atoms. Cycle 40: After refmac, R = 0.1712 (Rfree = 0.000) for 5132 atoms. Found 24 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 5308 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 5334 seeds are put forward Round 1: 240 peptides, 51 chains. Longest chain 15 peptides. Score 0.253 Round 2: 283 peptides, 53 chains. Longest chain 11 peptides. Score 0.329 Round 3: 284 peptides, 51 chains. Longest chain 13 peptides. Score 0.349 Round 4: 273 peptides, 49 chains. Longest chain 13 peptides. Score 0.344 Round 5: 278 peptides, 48 chains. Longest chain 15 peptides. Score 0.364 Taking the results from Round 5 Chains 48, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8052 reflections ( 98.50 % complete ) and 12320 restraints for refining 5164 atoms. 11448 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1938 (Rfree = 0.000) for 5164 atoms. Found 15 (28 requested) and removed 14 (14 requested) atoms. Cycle 42: After refmac, R = 0.1889 (Rfree = 0.000) for 5151 atoms. Found 19 (28 requested) and removed 20 (14 requested) atoms. Cycle 43: After refmac, R = 0.1852 (Rfree = 0.000) for 5146 atoms. Found 23 (28 requested) and removed 16 (14 requested) atoms. Cycle 44: After refmac, R = 0.1811 (Rfree = 0.000) for 5141 atoms. Found 27 (28 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.1689 (Rfree = 0.000) for 5139 atoms. Found 24 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 5304 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5324 seeds are put forward Round 1: 212 peptides, 45 chains. Longest chain 10 peptides. Score 0.247 Round 2: 237 peptides, 43 chains. Longest chain 14 peptides. Score 0.323 Round 3: 252 peptides, 44 chains. Longest chain 19 peptides. Score 0.346 Round 4: 225 peptides, 41 chains. Longest chain 14 peptides. Score 0.316 Round 5: 241 peptides, 45 chains. Longest chain 17 peptides. Score 0.313 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 208, 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 2fna-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8052 reflections ( 98.50 % complete ) and 12388 restraints for refining 5165 atoms. 11600 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1873 (Rfree = 0.000) for 5165 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1920 (Rfree = 0.000) for 5132 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1808 (Rfree = 0.000) for 5106 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1446 (Rfree = 0.000) for 5087 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... TimeTaking 49.07