null Sun 23 Dec 22:23:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2a9v-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:18 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/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-parrot-hancs/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-hancs.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-hancs.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 7499 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3817 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3494 (Rfree = 0.000) for 7499 atoms. Found 41 (41 requested) and removed 272 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 4.08 Search for helices and strands: 0 residues in 0 chains, 7364 seeds are put forward NCS extension: 0 residues added, 7364 seeds are put forward Round 1: 177 peptides, 38 chains. Longest chain 7 peptides. Score 0.239 Round 2: 201 peptides, 40 chains. Longest chain 10 peptides. Score 0.280 Round 3: 223 peptides, 42 chains. Longest chain 11 peptides. Score 0.314 Round 4: 251 peptides, 45 chains. Longest chain 11 peptides. Score 0.350 Round 5: 237 peptides, 44 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 4 Chains 46, Residues 206, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 15268 restraints for refining 6133 atoms. 14450 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2765 (Rfree = 0.000) for 6133 atoms. Found 9 (33 requested) and removed 89 (16 requested) atoms. Cycle 2: After refmac, R = 0.2588 (Rfree = 0.000) for 5972 atoms. Found 18 (33 requested) and removed 80 (16 requested) atoms. Cycle 3: After refmac, R = 0.2491 (Rfree = 0.000) for 5854 atoms. Found 19 (32 requested) and removed 53 (16 requested) atoms. Cycle 4: After refmac, R = 0.2452 (Rfree = 0.000) for 5770 atoms. Found 21 (32 requested) and removed 59 (16 requested) atoms. Cycle 5: After refmac, R = 0.1936 (Rfree = 0.000) for 5712 atoms. Found 6 (31 requested) and removed 36 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 5818 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5830 seeds are put forward Round 1: 208 peptides, 47 chains. Longest chain 7 peptides. Score 0.222 Round 2: 280 peptides, 56 chains. Longest chain 9 peptides. Score 0.308 Round 3: 281 peptides, 52 chains. Longest chain 8 peptides. Score 0.350 Round 4: 295 peptides, 54 chains. Longest chain 15 peptides. Score 0.363 Round 5: 290 peptides, 54 chains. Longest chain 11 peptides. Score 0.351 Taking the results from Round 4 Chains 54, Residues 241, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13123 restraints for refining 5582 atoms. 12179 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2286 (Rfree = 0.000) for 5582 atoms. Found 18 (30 requested) and removed 100 (15 requested) atoms. Cycle 7: After refmac, R = 0.2163 (Rfree = 0.000) for 5465 atoms. Found 18 (30 requested) and removed 46 (15 requested) atoms. Cycle 8: After refmac, R = 0.2099 (Rfree = 0.000) for 5423 atoms. Found 14 (29 requested) and removed 50 (14 requested) atoms. Cycle 9: After refmac, R = 0.2041 (Rfree = 0.000) for 5372 atoms. Found 20 (29 requested) and removed 46 (14 requested) atoms. Cycle 10: After refmac, R = 0.1996 (Rfree = 0.000) for 5330 atoms. Found 21 (29 requested) and removed 33 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 5496 seeds are put forward NCS extension: 0 residues added, 5496 seeds are put forward Round 1: 253 peptides, 53 chains. Longest chain 9 peptides. Score 0.273 Round 2: 282 peptides, 52 chains. Longest chain 13 peptides. Score 0.353 Round 3: 280 peptides, 50 chains. Longest chain 13 peptides. Score 0.368 Round 4: 299 peptides, 55 chains. Longest chain 11 peptides. Score 0.362 Round 5: 286 peptides, 48 chains. Longest chain 11 peptides. Score 0.400 Taking the results from Round 5 Chains 48, Residues 238, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13602 restraints for refining 5730 atoms. 12646 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2277 (Rfree = 0.000) for 5730 atoms. Found 17 (31 requested) and removed 78 (15 requested) atoms. Cycle 12: After refmac, R = 0.2217 (Rfree = 0.000) for 5636 atoms. Found 31 (31 requested) and removed 46 (15 requested) atoms. Cycle 13: After refmac, R = 0.2158 (Rfree = 0.000) for 5595 atoms. Found 30 (30 requested) and removed 47 (15 requested) atoms. Cycle 14: After refmac, R = 0.2073 (Rfree = 0.000) for 5552 atoms. Found 30 (30 requested) and removed 41 (15 requested) atoms. Cycle 15: After refmac, R = 0.1813 (Rfree = 0.000) for 5522 atoms. Found 22 (30 requested) and removed 38 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 5667 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 5670 seeds are put forward Round 1: 224 peptides, 50 chains. Longest chain 7 peptides. Score 0.231 Round 2: 285 peptides, 54 chains. Longest chain 10 peptides. Score 0.340 Round 3: 270 peptides, 47 chains. Longest chain 11 peptides. Score 0.374 Round 4: 294 peptides, 54 chains. Longest chain 12 peptides. Score 0.361 Round 5: 297 peptides, 47 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 5 Chains 47, Residues 250, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13616 restraints for refining 5793 atoms. 12658 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2095 (Rfree = 0.000) for 5793 atoms. Found 23 (31 requested) and removed 66 (15 requested) atoms. Cycle 17: After refmac, R = 0.2058 (Rfree = 0.000) for 5722 atoms. Found 28 (31 requested) and removed 57 (15 requested) atoms. Cycle 18: After refmac, R = 0.2114 (Rfree = 0.000) for 5667 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 19: After refmac, R = 0.2077 (Rfree = 0.000) for 5643 atoms. Found 31 (31 requested) and removed 42 (15 requested) atoms. Cycle 20: After refmac, R = 0.1654 (Rfree = 0.000) for 5618 atoms. Found 12 (30 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 5748 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5764 seeds are put forward Round 1: 224 peptides, 48 chains. Longest chain 9 peptides. Score 0.253 Round 2: 261 peptides, 45 chains. Longest chain 16 peptides. Score 0.374 Round 3: 279 peptides, 46 chains. Longest chain 15 peptides. Score 0.404 Round 4: 264 peptides, 44 chains. Longest chain 15 peptides. Score 0.390 Round 5: 256 peptides, 40 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 5 Chains 40, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13913 restraints for refining 5802 atoms. 13089 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2213 (Rfree = 0.000) for 5802 atoms. Found 31 (31 requested) and removed 63 (15 requested) atoms. Cycle 22: After refmac, R = 0.2049 (Rfree = 0.000) for 5743 atoms. Found 31 (31 requested) and removed 52 (15 requested) atoms. Cycle 23: After refmac, R = 0.2033 (Rfree = 0.000) for 5706 atoms. Found 29 (31 requested) and removed 35 (15 requested) atoms. Cycle 24: After refmac, R = 0.1956 (Rfree = 0.000) for 5689 atoms. Found 30 (31 requested) and removed 34 (15 requested) atoms. Cycle 25: After refmac, R = 0.1536 (Rfree = 0.000) for 5673 atoms. Found 7 (31 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 5794 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5810 seeds are put forward Round 1: 214 peptides, 47 chains. Longest chain 8 peptides. Score 0.238 Round 2: 242 peptides, 46 chains. Longest chain 10 peptides. Score 0.319 Round 3: 266 peptides, 49 chains. Longest chain 14 peptides. Score 0.345 Round 4: 265 peptides, 49 chains. Longest chain 10 peptides. Score 0.343 Round 5: 261 peptides, 50 chains. Longest chain 11 peptides. Score 0.323 Taking the results from Round 3 Chains 49, Residues 217, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13371 restraints for refining 5723 atoms. 12533 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1927 (Rfree = 0.000) for 5723 atoms. Found 22 (31 requested) and removed 59 (15 requested) atoms. Cycle 27: After refmac, R = 0.1874 (Rfree = 0.000) for 5660 atoms. Found 26 (31 requested) and removed 34 (15 requested) atoms. Cycle 28: After refmac, R = 0.1933 (Rfree = 0.000) for 5632 atoms. Found 25 (31 requested) and removed 33 (15 requested) atoms. Cycle 29: After refmac, R = 0.1952 (Rfree = 0.000) for 5615 atoms. Found 30 (30 requested) and removed 37 (15 requested) atoms. Cycle 30: After refmac, R = 0.1453 (Rfree = 0.000) for 5596 atoms. Found 7 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 5752 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 5777 seeds are put forward Round 1: 213 peptides, 45 chains. Longest chain 9 peptides. Score 0.257 Round 2: 231 peptides, 42 chains. Longest chain 11 peptides. Score 0.334 Round 3: 248 peptides, 44 chains. Longest chain 12 peptides. Score 0.354 Round 4: 256 peptides, 47 chains. Longest chain 12 peptides. Score 0.342 Round 5: 236 peptides, 41 chains. Longest chain 13 peptides. Score 0.356 Taking the results from Round 5 Chains 42, Residues 195, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13477 restraints for refining 5758 atoms. 12690 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2023 (Rfree = 0.000) for 5758 atoms. Found 17 (31 requested) and removed 73 (15 requested) atoms. Cycle 32: After refmac, R = 0.2024 (Rfree = 0.000) for 5684 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 33: After refmac, R = 0.1556 (Rfree = 0.000) for 5659 atoms. Found 4 (31 requested) and removed 29 (15 requested) atoms. Cycle 34: After refmac, R = 0.1441 (Rfree = 0.000) for 5624 atoms. Found 8 (30 requested) and removed 22 (15 requested) atoms. Cycle 35: After refmac, R = 0.1787 (Rfree = 0.000) for 5600 atoms. Found 28 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 4.05 Search for helices and strands: 0 residues in 0 chains, 5743 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5761 seeds are put forward Round 1: 212 peptides, 44 chains. Longest chain 11 peptides. Score 0.265 Round 2: 231 peptides, 43 chains. Longest chain 11 peptides. Score 0.323 Round 3: 223 peptides, 44 chains. Longest chain 9 peptides. Score 0.293 Round 4: 231 peptides, 40 chains. Longest chain 14 peptides. Score 0.355 Round 5: 232 peptides, 43 chains. Longest chain 11 peptides. Score 0.326 Taking the results from Round 4 Chains 40, Residues 191, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13268 restraints for refining 5720 atoms. 12512 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1961 (Rfree = 0.000) for 5720 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. Cycle 37: After refmac, R = 0.1778 (Rfree = 0.000) for 5683 atoms. Found 27 (31 requested) and removed 41 (15 requested) atoms. Cycle 38: After refmac, R = 0.1786 (Rfree = 0.000) for 5657 atoms. Found 30 (31 requested) and removed 27 (15 requested) atoms. Cycle 39: After refmac, R = 0.1829 (Rfree = 0.000) for 5653 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 40: After refmac, R = 0.1739 (Rfree = 0.000) for 5649 atoms. Found 30 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 4.04 Search for helices and strands: 0 residues in 0 chains, 5819 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5835 seeds are put forward Round 1: 186 peptides, 41 chains. Longest chain 8 peptides. Score 0.229 Round 2: 218 peptides, 42 chains. Longest chain 10 peptides. Score 0.302 Round 3: 247 peptides, 46 chains. Longest chain 9 peptides. Score 0.331 Round 4: 251 peptides, 43 chains. Longest chain 13 peptides. Score 0.371 Round 5: 239 peptides, 43 chains. Longest chain 11 peptides. Score 0.343 Taking the results from Round 4 Chains 43, Residues 208, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13515 restraints for refining 5819 atoms. 12692 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1872 (Rfree = 0.000) for 5819 atoms. Found 32 (32 requested) and removed 49 (16 requested) atoms. Cycle 42: After refmac, R = 0.1983 (Rfree = 0.000) for 5776 atoms. Found 31 (31 requested) and removed 46 (15 requested) atoms. Cycle 43: After refmac, R = 0.1931 (Rfree = 0.000) for 5750 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 44: After refmac, R = 0.1896 (Rfree = 0.000) for 5742 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 45: After refmac, R = 0.1853 (Rfree = 0.000) for 5725 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 4.07 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: 185 peptides, 43 chains. Longest chain 6 peptides. Score 0.204 Round 2: 210 peptides, 41 chains. Longest chain 10 peptides. Score 0.292 Round 3: 195 peptides, 36 chains. Longest chain 10 peptides. Score 0.309 Round 4: 212 peptides, 39 chains. Longest chain 10 peptides. Score 0.319 Round 5: 202 peptides, 37 chains. Longest chain 10 peptides. Score 0.316 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 173, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2a9v-3_warpNtrace.pdb as input Building loops using Loopy2018 39 chains (173 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7872 reflections ( 99.99 % complete ) and 13610 restraints for refining 5745 atoms. 12950 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1805 (Rfree = 0.000) for 5745 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.1974 (Rfree = 0.000) for 5717 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1824 (Rfree = 0.000) for 5690 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1889 (Rfree = 0.000) for 5667 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:41:37 GMT 2018 Job finished. TimeTaking 78.48 Used memory is bytes: 2621592