null Mon 24 Dec 07:27:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2a9v-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.4-parrot-noncs ############### 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 07:27:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.4-parrot-noncs/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 518 and 0 Target number of residues in the AU: 518 Target solvent content: 0.6183 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 848 Adjusted target solvent content: 0.38 Input MTZ file: 2a9v-3.4-parrot-noncs.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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 6784 target number of atoms Had to go as low as 0.50 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: 137.806 3.400 Wilson plot Bfac: 60.53 10860 reflections ( 99.99 % complete ) and 0 restraints for refining 7486 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3772 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3658 (Rfree = 0.000) for 7486 atoms. Found 53 (56 requested) and removed 227 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 7425 seeds are put forward NCS extension: 0 residues added, 7425 seeds are put forward Round 1: 185 peptides, 41 chains. Longest chain 7 peptides. Score 0.227 Round 2: 251 peptides, 50 chains. Longest chain 10 peptides. Score 0.299 Round 3: 273 peptides, 54 chains. Longest chain 13 peptides. Score 0.312 Round 4: 291 peptides, 58 chains. Longest chain 9 peptides. Score 0.315 Round 5: 284 peptides, 53 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 5 Chains 53, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 15327 restraints for refining 6167 atoms. 14456 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3007 (Rfree = 0.000) for 6167 atoms. Found 31 (46 requested) and removed 129 (23 requested) atoms. Cycle 2: After refmac, R = 0.2849 (Rfree = 0.000) for 6017 atoms. Found 34 (45 requested) and removed 77 (22 requested) atoms. Cycle 3: After refmac, R = 0.2716 (Rfree = 0.000) for 5943 atoms. Found 27 (45 requested) and removed 39 (22 requested) atoms. Cycle 4: After refmac, R = 0.2339 (Rfree = 0.000) for 5904 atoms. Found 12 (44 requested) and removed 38 (22 requested) atoms. Cycle 5: After refmac, R = 0.2203 (Rfree = 0.000) for 5854 atoms. Found 10 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 3.72 Search for helices and strands: 0 residues in 0 chains, 6016 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6029 seeds are put forward Round 1: 271 peptides, 60 chains. Longest chain 10 peptides. Score 0.246 Round 2: 341 peptides, 63 chains. Longest chain 14 peptides. Score 0.380 Round 3: 312 peptides, 55 chains. Longest chain 15 peptides. Score 0.391 Round 4: 320 peptides, 55 chains. Longest chain 16 peptides. Score 0.409 Round 5: 335 peptides, 59 chains. Longest chain 11 peptides. Score 0.404 Taking the results from Round 4 Chains 56, Residues 265, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13471 restraints for refining 5844 atoms. 12373 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2724 (Rfree = 0.000) for 5844 atoms. Found 30 (44 requested) and removed 94 (22 requested) atoms. Cycle 7: After refmac, R = 0.2434 (Rfree = 0.000) for 5748 atoms. Found 25 (43 requested) and removed 40 (21 requested) atoms. Cycle 8: After refmac, R = 0.2383 (Rfree = 0.000) for 5712 atoms. Found 19 (43 requested) and removed 26 (21 requested) atoms. Cycle 9: After refmac, R = 0.2315 (Rfree = 0.000) for 5689 atoms. Found 13 (43 requested) and removed 35 (21 requested) atoms. Cycle 10: After refmac, R = 0.2257 (Rfree = 0.000) for 5657 atoms. Found 23 (42 requested) and removed 24 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 5846 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5861 seeds are put forward Round 1: 271 peptides, 59 chains. Longest chain 8 peptides. Score 0.256 Round 2: 309 peptides, 58 chains. Longest chain 11 peptides. Score 0.356 Round 3: 328 peptides, 56 chains. Longest chain 16 peptides. Score 0.416 Round 4: 299 peptides, 54 chains. Longest chain 14 peptides. Score 0.372 Round 5: 307 peptides, 55 chains. Longest chain 12 peptides. Score 0.380 Taking the results from Round 3 Chains 56, Residues 272, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13505 restraints for refining 5846 atoms. 12432 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2331 (Rfree = 0.000) for 5846 atoms. Found 25 (44 requested) and removed 53 (22 requested) atoms. Cycle 12: After refmac, R = 0.2203 (Rfree = 0.000) for 5801 atoms. Found 12 (43 requested) and removed 33 (21 requested) atoms. Cycle 13: After refmac, R = 0.2125 (Rfree = 0.000) for 5770 atoms. Found 16 (43 requested) and removed 30 (21 requested) atoms. Cycle 14: After refmac, R = 0.2078 (Rfree = 0.000) for 5745 atoms. Found 21 (43 requested) and removed 29 (21 requested) atoms. Cycle 15: After refmac, R = 0.2080 (Rfree = 0.000) for 5725 atoms. Found 18 (43 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.73 Search for helices and strands: 0 residues in 0 chains, 5864 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5881 seeds are put forward Round 1: 250 peptides, 54 chains. Longest chain 8 peptides. Score 0.255 Round 2: 290 peptides, 57 chains. Longest chain 10 peptides. Score 0.322 Round 3: 289 peptides, 52 chains. Longest chain 13 peptides. Score 0.369 Round 4: 297 peptides, 52 chains. Longest chain 14 peptides. Score 0.387 Round 5: 293 peptides, 54 chains. Longest chain 16 peptides. Score 0.358 Taking the results from Round 4 Chains 53, Residues 245, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13599 restraints for refining 5879 atoms. 12600 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2240 (Rfree = 0.000) for 5879 atoms. Found 29 (44 requested) and removed 71 (22 requested) atoms. Cycle 17: After refmac, R = 0.2050 (Rfree = 0.000) for 5812 atoms. Found 22 (44 requested) and removed 37 (22 requested) atoms. Cycle 18: After refmac, R = 0.2003 (Rfree = 0.000) for 5783 atoms. Found 14 (43 requested) and removed 27 (21 requested) atoms. Cycle 19: After refmac, R = 0.1974 (Rfree = 0.000) for 5755 atoms. Found 18 (43 requested) and removed 27 (21 requested) atoms. Cycle 20: After refmac, R = 0.1888 (Rfree = 0.000) for 5737 atoms. Found 17 (43 requested) and removed 24 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.72 Search for helices and strands: 0 residues in 0 chains, 5870 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5890 seeds are put forward Round 1: 241 peptides, 51 chains. Longest chain 9 peptides. Score 0.264 Round 2: 274 peptides, 50 chains. Longest chain 15 peptides. Score 0.354 Round 3: 269 peptides, 50 chains. Longest chain 13 peptides. Score 0.342 Round 4: 279 peptides, 50 chains. Longest chain 14 peptides. Score 0.365 Round 5: 277 peptides, 49 chains. Longest chain 14 peptides. Score 0.371 Taking the results from Round 5 Chains 49, Residues 228, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13717 restraints for refining 5876 atoms. 12841 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2063 (Rfree = 0.000) for 5876 atoms. Found 25 (44 requested) and removed 47 (22 requested) atoms. Cycle 22: After refmac, R = 0.1879 (Rfree = 0.000) for 5837 atoms. Found 24 (44 requested) and removed 30 (22 requested) atoms. Cycle 23: After refmac, R = 0.1816 (Rfree = 0.000) for 5819 atoms. Found 13 (44 requested) and removed 30 (22 requested) atoms. Cycle 24: After refmac, R = 0.1770 (Rfree = 0.000) for 5799 atoms. Found 17 (43 requested) and removed 25 (21 requested) atoms. Cycle 25: After refmac, R = 0.1787 (Rfree = 0.000) for 5783 atoms. Found 16 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.73 Search for helices and strands: 0 residues in 0 chains, 5939 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5959 seeds are put forward Round 1: 273 peptides, 59 chains. Longest chain 9 peptides. Score 0.261 Round 2: 314 peptides, 61 chains. Longest chain 14 peptides. Score 0.339 Round 3: 318 peptides, 60 chains. Longest chain 11 peptides. Score 0.357 Round 4: 330 peptides, 58 chains. Longest chain 15 peptides. Score 0.402 Round 5: 318 peptides, 54 chains. Longest chain 15 peptides. Score 0.414 Taking the results from Round 5 Chains 54, Residues 264, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13832 restraints for refining 5929 atoms. 12817 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2139 (Rfree = 0.000) for 5929 atoms. Found 30 (44 requested) and removed 55 (22 requested) atoms. Cycle 27: After refmac, R = 0.1944 (Rfree = 0.000) for 5892 atoms. Found 19 (44 requested) and removed 36 (22 requested) atoms. Cycle 28: After refmac, R = 0.1937 (Rfree = 0.000) for 5870 atoms. Found 13 (44 requested) and removed 30 (22 requested) atoms. Cycle 29: After refmac, R = 0.1864 (Rfree = 0.000) for 5852 atoms. Found 16 (44 requested) and removed 23 (22 requested) atoms. Cycle 30: After refmac, R = 0.1866 (Rfree = 0.000) for 5844 atoms. Found 19 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.72 Search for helices and strands: 0 residues in 0 chains, 6018 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6040 seeds are put forward Round 1: 265 peptides, 54 chains. Longest chain 8 peptides. Score 0.292 Round 2: 296 peptides, 55 chains. Longest chain 10 peptides. Score 0.355 Round 3: 303 peptides, 51 chains. Longest chain 14 peptides. Score 0.409 Round 4: 304 peptides, 53 chains. Longest chain 16 peptides. Score 0.393 Round 5: 309 peptides, 49 chains. Longest chain 20 peptides. Score 0.440 Taking the results from Round 5 Chains 50, Residues 260, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14035 restraints for refining 6053 atoms. 12997 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2095 (Rfree = 0.000) for 6053 atoms. Found 24 (45 requested) and removed 55 (22 requested) atoms. Cycle 32: After refmac, R = 0.1883 (Rfree = 0.000) for 6014 atoms. Found 10 (45 requested) and removed 28 (22 requested) atoms. Cycle 33: After refmac, R = 0.1885 (Rfree = 0.000) for 5990 atoms. Found 8 (45 requested) and removed 38 (22 requested) atoms. Cycle 34: After refmac, R = 0.1871 (Rfree = 0.000) for 5955 atoms. Found 24 (45 requested) and removed 28 (22 requested) atoms. Cycle 35: After refmac, R = 0.1906 (Rfree = 0.000) for 5942 atoms. Found 23 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.71 Search for helices and strands: 0 residues in 0 chains, 6117 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6141 seeds are put forward Round 1: 240 peptides, 50 chains. Longest chain 9 peptides. Score 0.272 Round 2: 263 peptides, 48 chains. Longest chain 13 peptides. Score 0.348 Round 3: 273 peptides, 47 chains. Longest chain 12 peptides. Score 0.381 Round 4: 262 peptides, 44 chains. Longest chain 16 peptides. Score 0.386 Round 5: 271 peptides, 45 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 5 Chains 45, Residues 226, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14632 restraints for refining 6122 atoms. 13773 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1979 (Rfree = 0.000) for 6122 atoms. Found 28 (46 requested) and removed 45 (23 requested) atoms. Cycle 37: After refmac, R = 0.1931 (Rfree = 0.000) for 6098 atoms. Found 20 (46 requested) and removed 32 (23 requested) atoms. Cycle 38: After refmac, R = 0.1886 (Rfree = 0.000) for 6081 atoms. Found 30 (45 requested) and removed 29 (22 requested) atoms. Cycle 39: After refmac, R = 0.1831 (Rfree = 0.000) for 6080 atoms. Found 21 (45 requested) and removed 32 (22 requested) atoms. Cycle 40: After refmac, R = 0.1788 (Rfree = 0.000) for 6063 atoms. Found 19 (45 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.73 Search for helices and strands: 0 residues in 0 chains, 6228 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6245 seeds are put forward Round 1: 229 peptides, 51 chains. Longest chain 8 peptides. Score 0.234 Round 2: 254 peptides, 50 chains. Longest chain 12 peptides. Score 0.307 Round 3: 258 peptides, 51 chains. Longest chain 10 peptides. Score 0.306 Round 4: 256 peptides, 46 chains. Longest chain 10 peptides. Score 0.352 Round 5: 261 peptides, 47 chains. Longest chain 12 peptides. Score 0.354 Taking the results from Round 5 Chains 47, Residues 214, Estimated correctness of the model 0.0 % 4 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14678 restraints for refining 6168 atoms. 13843 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1915 (Rfree = 0.000) for 6168 atoms. Found 29 (46 requested) and removed 42 (23 requested) atoms. Cycle 42: After refmac, R = 0.1844 (Rfree = 0.000) for 6149 atoms. Found 18 (46 requested) and removed 33 (23 requested) atoms. Cycle 43: After refmac, R = 0.1857 (Rfree = 0.000) for 6131 atoms. Found 33 (46 requested) and removed 30 (23 requested) atoms. Cycle 44: After refmac, R = 0.1866 (Rfree = 0.000) for 6130 atoms. Found 28 (46 requested) and removed 31 (23 requested) atoms. Cycle 45: After refmac, R = 0.1852 (Rfree = 0.000) for 6127 atoms. Found 30 (46 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 6285 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6301 seeds are put forward Round 1: 195 peptides, 43 chains. Longest chain 8 peptides. Score 0.231 Round 2: 229 peptides, 42 chains. Longest chain 10 peptides. Score 0.329 Round 3: 242 peptides, 43 chains. Longest chain 15 peptides. Score 0.350 Round 4: 239 peptides, 42 chains. Longest chain 13 peptides. Score 0.353 Round 5: 249 peptides, 42 chains. Longest chain 13 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 207, 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 2a9v-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10860 reflections ( 99.99 % complete ) and 14802 restraints for refining 6167 atoms. 14016 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2067 (Rfree = 0.000) for 6167 atoms. Found 0 (46 requested) and removed 22 (23 requested) atoms. Cycle 47: After refmac, R = 0.2081 (Rfree = 0.000) for 6140 atoms. Found 0 (46 requested) and removed 16 (23 requested) atoms. Cycle 48: After refmac, R = 0.1985 (Rfree = 0.000) for 6117 atoms. Found 0 (46 requested) and removed 18 (23 requested) atoms. Cycle 49: After refmac, R = 0.2022 (Rfree = 0.000) for 6094 atoms. Found 0 (46 requested) and removed 19 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:39:10 GMT 2018 Job finished. TimeTaking 71.27 Used memory is bytes: 20623296