null Mon 24 Dec 08:01:48 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-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 08:01:53 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-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 502 and 0 Target number of residues in the AU: 502 Target solvent content: 0.6301 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 66.39 7872 reflections ( 99.99 % complete ) and 0 restraints for refining 7493 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3827 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3624 (Rfree = 0.000) for 7493 atoms. Found 41 (41 requested) and removed 233 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 4.10 Search for helices and strands: 0 residues in 0 chains, 7396 seeds are put forward NCS extension: 0 residues added, 7396 seeds are put forward Round 1: 142 peptides, 32 chains. Longest chain 8 peptides. Score 0.210 Round 2: 176 peptides, 37 chains. Longest chain 8 peptides. Score 0.248 Round 3: 195 peptides, 39 chains. Longest chain 9 peptides. Score 0.276 Round 4: 212 peptides, 42 chains. Longest chain 10 peptides. Score 0.287 Round 5: 215 peptides, 43 chains. Longest chain 10 peptides. Score 0.284 Taking the results from Round 4 Chains 42, Residues 170, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 15585 restraints for refining 6137 atoms. 14919 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3046 (Rfree = 0.000) for 6137 atoms. Found 33 (33 requested) and removed 79 (16 requested) atoms. Cycle 2: After refmac, R = 0.2894 (Rfree = 0.000) for 6002 atoms. Found 33 (33 requested) and removed 67 (16 requested) atoms. Cycle 3: After refmac, R = 0.2701 (Rfree = 0.000) for 5924 atoms. Found 32 (32 requested) and removed 42 (16 requested) atoms. Cycle 4: After refmac, R = 0.2155 (Rfree = 0.000) for 5872 atoms. Found 16 (32 requested) and removed 34 (16 requested) atoms. Cycle 5: After refmac, R = 0.1957 (Rfree = 0.000) for 5827 atoms. Found 6 (32 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 4.05 Search for helices and strands: 0 residues in 0 chains, 5943 seeds are put forward NCS extension: 4 residues added (2 deleted due to clashes), 5947 seeds are put forward Round 1: 178 peptides, 40 chains. Longest chain 7 peptides. Score 0.219 Round 2: 234 peptides, 49 chains. Longest chain 8 peptides. Score 0.268 Round 3: 279 peptides, 55 chains. Longest chain 11 peptides. Score 0.316 Round 4: 288 peptides, 54 chains. Longest chain 11 peptides. Score 0.347 Round 5: 295 peptides, 51 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 5 Chains 51, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13582 restraints for refining 5618 atoms. 12657 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2438 (Rfree = 0.000) for 5618 atoms. Found 30 (30 requested) and removed 67 (15 requested) atoms. Cycle 7: After refmac, R = 0.2300 (Rfree = 0.000) for 5531 atoms. Found 30 (30 requested) and removed 62 (15 requested) atoms. Cycle 8: After refmac, R = 0.2304 (Rfree = 0.000) for 5475 atoms. Found 30 (30 requested) and removed 42 (15 requested) atoms. Cycle 9: After refmac, R = 0.2201 (Rfree = 0.000) for 5444 atoms. Found 30 (30 requested) and removed 36 (15 requested) atoms. Cycle 10: After refmac, R = 0.2181 (Rfree = 0.000) for 5414 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 5583 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5600 seeds are put forward Round 1: 246 peptides, 53 chains. Longest chain 9 peptides. Score 0.256 Round 2: 255 peptides, 49 chains. Longest chain 8 peptides. Score 0.319 Round 3: 269 peptides, 47 chains. Longest chain 13 peptides. Score 0.372 Round 4: 280 peptides, 51 chains. Longest chain 16 peptides. Score 0.358 Round 5: 285 peptides, 46 chains. Longest chain 16 peptides. Score 0.417 Taking the results from Round 5 Chains 46, Residues 239, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13482 restraints for refining 5627 atoms. 12532 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2223 (Rfree = 0.000) for 5627 atoms. Found 30 (30 requested) and removed 63 (15 requested) atoms. Cycle 12: After refmac, R = 0.2167 (Rfree = 0.000) for 5571 atoms. Found 30 (30 requested) and removed 37 (15 requested) atoms. Cycle 13: After refmac, R = 0.2176 (Rfree = 0.000) for 5548 atoms. Found 30 (30 requested) and removed 41 (15 requested) atoms. Cycle 14: After refmac, R = 0.1981 (Rfree = 0.000) for 5521 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 15: After refmac, R = 0.1894 (Rfree = 0.000) for 5508 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 5629 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5651 seeds are put forward Round 1: 253 peptides, 54 chains. Longest chain 9 peptides. Score 0.263 Round 2: 261 peptides, 48 chains. Longest chain 11 peptides. Score 0.344 Round 3: 287 peptides, 51 chains. Longest chain 15 peptides. Score 0.374 Round 4: 273 peptides, 46 chains. Longest chain 17 peptides. Score 0.391 Round 5: 284 peptides, 52 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 4 Chains 46, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13952 restraints for refining 5758 atoms. 13090 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2252 (Rfree = 0.000) for 5758 atoms. Found 31 (31 requested) and removed 64 (15 requested) atoms. Cycle 17: After refmac, R = 0.2006 (Rfree = 0.000) for 5704 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 18: After refmac, R = 0.1904 (Rfree = 0.000) for 5674 atoms. Found 29 (31 requested) and removed 36 (15 requested) atoms. Cycle 19: After refmac, R = 0.1531 (Rfree = 0.000) for 5651 atoms. Found 6 (31 requested) and removed 20 (15 requested) atoms. Cycle 20: After refmac, R = 0.1449 (Rfree = 0.000) for 5628 atoms. Found 3 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 5768 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 5795 seeds are put forward Round 1: 239 peptides, 51 chains. Longest chain 8 peptides. Score 0.259 Round 2: 278 peptides, 52 chains. Longest chain 13 peptides. Score 0.343 Round 3: 290 peptides, 48 chains. Longest chain 12 peptides. Score 0.409 Round 4: 300 peptides, 48 chains. Longest chain 12 peptides. Score 0.431 Round 5: 302 peptides, 47 chains. Longest chain 16 peptides. Score 0.444 Taking the results from Round 5 Chains 47, Residues 255, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 14007 restraints for refining 5886 atoms. 13034 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2069 (Rfree = 0.000) for 5886 atoms. Found 32 (32 requested) and removed 63 (16 requested) atoms. Cycle 22: After refmac, R = 0.2121 (Rfree = 0.000) for 5835 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. Cycle 23: After refmac, R = 0.1992 (Rfree = 0.000) for 5807 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 24: After refmac, R = 0.1521 (Rfree = 0.000) for 5788 atoms. Found 12 (31 requested) and removed 22 (15 requested) atoms. Cycle 25: After refmac, R = 0.1436 (Rfree = 0.000) for 5762 atoms. Found 5 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 4.04 Search for helices and strands: 0 residues in 0 chains, 5895 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5908 seeds are put forward Round 1: 233 peptides, 49 chains. Longest chain 11 peptides. Score 0.265 Round 2: 274 peptides, 50 chains. Longest chain 12 peptides. Score 0.354 Round 3: 273 peptides, 48 chains. Longest chain 16 peptides. Score 0.371 Round 4: 300 peptides, 49 chains. Longest chain 11 peptides. Score 0.421 Round 5: 307 peptides, 48 chains. Longest chain 15 peptides. Score 0.446 Taking the results from Round 5 Chains 48, Residues 259, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13850 restraints for refining 5923 atoms. 12821 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2066 (Rfree = 0.000) for 5923 atoms. Found 31 (32 requested) and removed 60 (16 requested) atoms. Cycle 27: After refmac, R = 0.2000 (Rfree = 0.000) for 5865 atoms. Found 32 (32 requested) and removed 37 (16 requested) atoms. Cycle 28: After refmac, R = 0.2043 (Rfree = 0.000) for 5838 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 29: After refmac, R = 0.1971 (Rfree = 0.000) for 5812 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 30: After refmac, R = 0.1979 (Rfree = 0.000) for 5801 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 5976 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5999 seeds are put forward Round 1: 212 peptides, 46 chains. Longest chain 9 peptides. Score 0.243 Round 2: 234 peptides, 44 chains. Longest chain 12 peptides. Score 0.320 Round 3: 251 peptides, 44 chains. Longest chain 13 peptides. Score 0.361 Round 4: 265 peptides, 44 chains. Longest chain 17 peptides. Score 0.393 Round 5: 274 peptides, 47 chains. Longest chain 14 peptides. Score 0.383 Taking the results from Round 4 Chains 44, Residues 221, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 14136 restraints for refining 5906 atoms. 13291 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2063 (Rfree = 0.000) for 5906 atoms. Found 32 (32 requested) and removed 76 (16 requested) atoms. Cycle 32: After refmac, R = 0.2139 (Rfree = 0.000) for 5845 atoms. Found 32 (32 requested) and removed 54 (16 requested) atoms. Cycle 33: After refmac, R = 0.1997 (Rfree = 0.000) for 5812 atoms. Found 32 (32 requested) and removed 49 (16 requested) atoms. Cycle 34: After refmac, R = 0.2047 (Rfree = 0.000) for 5786 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 35: After refmac, R = 0.1564 (Rfree = 0.000) for 5772 atoms. Found 10 (31 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 5936 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 5961 seeds are put forward Round 1: 209 peptides, 47 chains. Longest chain 7 peptides. Score 0.224 Round 2: 245 peptides, 48 chains. Longest chain 9 peptides. Score 0.305 Round 3: 272 peptides, 52 chains. Longest chain 13 peptides. Score 0.329 Round 4: 272 peptides, 48 chains. Longest chain 10 peptides. Score 0.369 Round 5: 274 peptides, 49 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 4 Chains 48, Residues 224, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13621 restraints for refining 5876 atoms. 12729 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1974 (Rfree = 0.000) for 5876 atoms. Found 28 (32 requested) and removed 48 (16 requested) atoms. Cycle 37: After refmac, R = 0.2115 (Rfree = 0.000) for 5838 atoms. Found 32 (32 requested) and removed 42 (16 requested) atoms. Cycle 38: After refmac, R = 0.2066 (Rfree = 0.000) for 5815 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 39: After refmac, R = 0.1615 (Rfree = 0.000) for 5794 atoms. Found 11 (31 requested) and removed 31 (15 requested) atoms. Cycle 40: After refmac, R = 0.1550 (Rfree = 0.000) for 5764 atoms. Found 9 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 4.05 Search for helices and strands: 0 residues in 0 chains, 5929 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 5940 seeds are put forward Round 1: 208 peptides, 47 chains. Longest chain 8 peptides. Score 0.222 Round 2: 219 peptides, 43 chains. Longest chain 8 peptides. Score 0.294 Round 3: 237 peptides, 43 chains. Longest chain 10 peptides. Score 0.338 Round 4: 242 peptides, 42 chains. Longest chain 14 peptides. Score 0.360 Round 5: 249 peptides, 44 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 4 Chains 42, Residues 200, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13654 restraints for refining 5809 atoms. 12874 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2068 (Rfree = 0.000) for 5809 atoms. Found 31 (31 requested) and removed 53 (15 requested) atoms. Cycle 42: After refmac, R = 0.2071 (Rfree = 0.000) for 5770 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 43: After refmac, R = 0.2094 (Rfree = 0.000) for 5761 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 44: After refmac, R = 0.1994 (Rfree = 0.000) for 5746 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 45: After refmac, R = 0.2065 (Rfree = 0.000) for 5741 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 4.04 Search for helices and strands: 0 residues in 0 chains, 5937 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5957 seeds are put forward Round 1: 180 peptides, 41 chains. Longest chain 6 peptides. Score 0.213 Round 2: 191 peptides, 38 chains. Longest chain 8 peptides. Score 0.276 Round 3: 206 peptides, 39 chains. Longest chain 10 peptides. Score 0.304 Round 4: 214 peptides, 39 chains. Longest chain 10 peptides. Score 0.324 Round 5: 202 peptides, 39 chains. Longest chain 9 peptides. Score 0.294 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 175, 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. 7872 reflections ( 99.99 % complete ) and 13658 restraints for refining 5716 atoms. 12997 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2071 (Rfree = 0.000) for 5716 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2127 (Rfree = 0.000) for 5687 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1977 (Rfree = 0.000) for 5665 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1636 (Rfree = 0.000) for 5644 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:02:08 GMT 2018 Job finished. TimeTaking 60.34 Used memory is bytes: 13149120