null Sun 23 Dec 22:22:49 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 2op5-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2op5-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2op5-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-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/2op5-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-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 22:22:59 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/hancs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-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 458 and 0 Target number of residues in the AU: 458 Target solvent content: 0.6428 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: 2op5-4.0-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: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-4.0-parrot-hancs.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 4.000 Wilson plot Bfac: 73.49 6261 reflections ( 99.73 % complete ) and 0 restraints for refining 6215 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3379 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3314 (Rfree = 0.000) for 6215 atoms. Found 27 (29 requested) and removed 43 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.87 Search for helices and strands: 0 residues in 0 chains, 6339 seeds are put forward NCS extension: 0 residues added, 6339 seeds are put forward Round 1: 196 peptides, 42 chains. Longest chain 8 peptides. Score 0.248 Round 2: 270 peptides, 50 chains. Longest chain 10 peptides. Score 0.352 Round 3: 300 peptides, 51 chains. Longest chain 10 peptides. Score 0.413 Round 4: 309 peptides, 48 chains. Longest chain 16 peptides. Score 0.462 Round 5: 321 peptides, 49 chains. Longest chain 14 peptides. Score 0.478 Taking the results from Round 5 Chains 49, Residues 272, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 12255 restraints for refining 5072 atoms. 11216 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2749 (Rfree = 0.000) for 5072 atoms. Found 9 (24 requested) and removed 51 (12 requested) atoms. Cycle 2: After refmac, R = 0.2612 (Rfree = 0.000) for 4931 atoms. Found 7 (23 requested) and removed 46 (11 requested) atoms. Cycle 3: After refmac, R = 0.2414 (Rfree = 0.000) for 4824 atoms. Found 6 (23 requested) and removed 25 (11 requested) atoms. Cycle 4: After refmac, R = 0.2283 (Rfree = 0.000) for 4760 atoms. Found 4 (22 requested) and removed 22 (11 requested) atoms. Cycle 5: After refmac, R = 0.2243 (Rfree = 0.000) for 4719 atoms. Found 8 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.81 Search for helices and strands: 0 residues in 0 chains, 4863 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4880 seeds are put forward Round 1: 255 peptides, 51 chains. Longest chain 9 peptides. Score 0.305 Round 2: 297 peptides, 56 chains. Longest chain 9 peptides. Score 0.356 Round 3: 317 peptides, 53 chains. Longest chain 18 peptides. Score 0.432 Round 4: 331 peptides, 52 chains. Longest chain 14 peptides. Score 0.471 Round 5: 333 peptides, 51 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 5 Chains 51, Residues 282, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11027 restraints for refining 4748 atoms. 9950 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2719 (Rfree = 0.000) for 4748 atoms. Found 18 (22 requested) and removed 51 (11 requested) atoms. Cycle 7: After refmac, R = 0.2252 (Rfree = 0.000) for 4681 atoms. Found 13 (22 requested) and removed 27 (11 requested) atoms. Cycle 8: After refmac, R = 0.2204 (Rfree = 0.000) for 4629 atoms. Found 4 (22 requested) and removed 17 (11 requested) atoms. Cycle 9: After refmac, R = 0.1867 (Rfree = 0.000) for 4584 atoms. Found 6 (21 requested) and removed 23 (10 requested) atoms. Cycle 10: After refmac, R = 0.2026 (Rfree = 0.000) for 4557 atoms. Found 7 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.90 Search for helices and strands: 0 residues in 0 chains, 4726 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4743 seeds are put forward Round 1: 263 peptides, 55 chains. Longest chain 11 peptides. Score 0.282 Round 2: 310 peptides, 53 chains. Longest chain 11 peptides. Score 0.416 Round 3: 299 peptides, 51 chains. Longest chain 14 peptides. Score 0.411 Round 4: 309 peptides, 54 chains. Longest chain 16 peptides. Score 0.404 Round 5: 299 peptides, 48 chains. Longest chain 13 peptides. Score 0.440 Taking the results from Round 5 Chains 48, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11609 restraints for refining 4892 atoms. 10653 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2405 (Rfree = 0.000) for 4892 atoms. Found 18 (23 requested) and removed 43 (11 requested) atoms. Cycle 12: After refmac, R = 0.2186 (Rfree = 0.000) for 4833 atoms. Found 11 (23 requested) and removed 25 (11 requested) atoms. Cycle 13: After refmac, R = 0.2145 (Rfree = 0.000) for 4787 atoms. Found 13 (22 requested) and removed 25 (11 requested) atoms. Cycle 14: After refmac, R = 0.1861 (Rfree = 0.000) for 4759 atoms. Found 5 (22 requested) and removed 19 (11 requested) atoms. Cycle 15: After refmac, R = 0.1977 (Rfree = 0.000) for 4726 atoms. Found 9 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 4859 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4876 seeds are put forward Round 1: 258 peptides, 53 chains. Longest chain 9 peptides. Score 0.291 Round 2: 292 peptides, 52 chains. Longest chain 16 peptides. Score 0.384 Round 3: 275 peptides, 45 chains. Longest chain 14 peptides. Score 0.415 Round 4: 289 peptides, 50 chains. Longest chain 16 peptides. Score 0.397 Round 5: 301 peptides, 50 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 5 Chains 50, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11829 restraints for refining 4974 atoms. 10875 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2425 (Rfree = 0.000) for 4974 atoms. Found 8 (23 requested) and removed 39 (11 requested) atoms. Cycle 17: After refmac, R = 0.2245 (Rfree = 0.000) for 4883 atoms. Found 17 (23 requested) and removed 42 (11 requested) atoms. Cycle 18: After refmac, R = 0.2040 (Rfree = 0.000) for 4821 atoms. Found 8 (23 requested) and removed 24 (11 requested) atoms. Cycle 19: After refmac, R = 0.2098 (Rfree = 0.000) for 4771 atoms. Found 13 (22 requested) and removed 22 (11 requested) atoms. Cycle 20: After refmac, R = 0.1985 (Rfree = 0.000) for 4739 atoms. Found 9 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 4889 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4906 seeds are put forward Round 1: 222 peptides, 46 chains. Longest chain 9 peptides. Score 0.273 Round 2: 279 peptides, 50 chains. Longest chain 12 peptides. Score 0.374 Round 3: 298 peptides, 53 chains. Longest chain 10 peptides. Score 0.388 Round 4: 300 peptides, 50 chains. Longest chain 16 peptides. Score 0.423 Round 5: 293 peptides, 48 chains. Longest chain 12 peptides. Score 0.426 Taking the results from Round 5 Chains 48, Residues 245, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11492 restraints for refining 4884 atoms. 10560 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2342 (Rfree = 0.000) for 4884 atoms. Found 16 (23 requested) and removed 41 (11 requested) atoms. Cycle 22: After refmac, R = 0.1943 (Rfree = 0.000) for 4831 atoms. Found 5 (23 requested) and removed 24 (11 requested) atoms. Cycle 23: After refmac, R = 0.1703 (Rfree = 0.000) for 4789 atoms. Found 5 (22 requested) and removed 17 (11 requested) atoms. Cycle 24: After refmac, R = 0.1636 (Rfree = 0.000) for 4771 atoms. Found 3 (22 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.1639 (Rfree = 0.000) for 4756 atoms. Found 3 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 4888 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4903 seeds are put forward Round 1: 251 peptides, 48 chains. Longest chain 12 peptides. Score 0.326 Round 2: 264 peptides, 42 chains. Longest chain 14 peptides. Score 0.420 Round 3: 269 peptides, 44 chains. Longest chain 18 peptides. Score 0.411 Round 4: 260 peptides, 42 chains. Longest chain 13 peptides. Score 0.411 Round 5: 297 peptides, 43 chains. Longest chain 14 peptides. Score 0.483 Taking the results from Round 5 Chains 43, Residues 254, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11527 restraints for refining 4989 atoms. 10528 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2389 (Rfree = 0.000) for 4989 atoms. Found 17 (23 requested) and removed 47 (11 requested) atoms. Cycle 27: After refmac, R = 0.2196 (Rfree = 0.000) for 4934 atoms. Found 15 (23 requested) and removed 33 (11 requested) atoms. Cycle 28: After refmac, R = 0.2029 (Rfree = 0.000) for 4890 atoms. Found 11 (23 requested) and removed 36 (11 requested) atoms. Cycle 29: After refmac, R = 0.1851 (Rfree = 0.000) for 4846 atoms. Found 10 (23 requested) and removed 28 (11 requested) atoms. Cycle 30: After refmac, R = 0.1735 (Rfree = 0.000) for 4812 atoms. Found 11 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 4951 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4969 seeds are put forward Round 1: 212 peptides, 47 chains. Longest chain 11 peptides. Score 0.235 Round 2: 243 peptides, 45 chains. Longest chain 12 peptides. Score 0.338 Round 3: 264 peptides, 48 chains. Longest chain 17 peptides. Score 0.359 Round 4: 264 peptides, 44 chains. Longest chain 17 peptides. Score 0.400 Round 5: 271 peptides, 43 chains. Longest chain 13 peptides. Score 0.426 Taking the results from Round 5 Chains 43, Residues 228, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11599 restraints for refining 4971 atoms. 10704 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1801 (Rfree = 0.000) for 4971 atoms. Found 18 (23 requested) and removed 35 (11 requested) atoms. Cycle 32: After refmac, R = 0.1691 (Rfree = 0.000) for 4930 atoms. Found 7 (23 requested) and removed 20 (11 requested) atoms. Cycle 33: After refmac, R = 0.1600 (Rfree = 0.000) for 4900 atoms. Found 5 (23 requested) and removed 16 (11 requested) atoms. Cycle 34: After refmac, R = 0.1738 (Rfree = 0.000) for 4879 atoms. Found 9 (23 requested) and removed 17 (11 requested) atoms. Cycle 35: After refmac, R = 0.1715 (Rfree = 0.000) for 4853 atoms. Found 5 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 4964 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4983 seeds are put forward Round 1: 212 peptides, 47 chains. Longest chain 8 peptides. Score 0.235 Round 2: 240 peptides, 46 chains. Longest chain 13 peptides. Score 0.320 Round 3: 230 peptides, 43 chains. Longest chain 13 peptides. Score 0.327 Round 4: 231 peptides, 43 chains. Longest chain 13 peptides. Score 0.330 Round 5: 228 peptides, 42 chains. Longest chain 12 peptides. Score 0.333 Taking the results from Round 5 Chains 42, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 12302 restraints for refining 5031 atoms. 11600 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2138 (Rfree = 0.000) for 5031 atoms. Found 15 (23 requested) and removed 39 (11 requested) atoms. Cycle 37: After refmac, R = 0.1947 (Rfree = 0.000) for 4978 atoms. Found 14 (23 requested) and removed 32 (11 requested) atoms. Cycle 38: After refmac, R = 0.2024 (Rfree = 0.000) for 4944 atoms. Found 15 (23 requested) and removed 20 (11 requested) atoms. Cycle 39: After refmac, R = 0.2003 (Rfree = 0.000) for 4915 atoms. Found 19 (23 requested) and removed 27 (11 requested) atoms. Cycle 40: After refmac, R = 0.2012 (Rfree = 0.000) for 4895 atoms. Found 14 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 4995 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5011 seeds are put forward Round 1: 177 peptides, 42 chains. Longest chain 6 peptides. Score 0.194 Round 2: 206 peptides, 42 chains. Longest chain 10 peptides. Score 0.276 Round 3: 209 peptides, 40 chains. Longest chain 13 peptides. Score 0.306 Round 4: 211 peptides, 38 chains. Longest chain 11 peptides. Score 0.334 Round 5: 219 peptides, 39 chains. Longest chain 11 peptides. Score 0.343 Taking the results from Round 5 Chains 39, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11263 restraints for refining 4823 atoms. 10582 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2172 (Rfree = 0.000) for 4823 atoms. Found 17 (22 requested) and removed 33 (11 requested) atoms. Cycle 42: After refmac, R = 0.2122 (Rfree = 0.000) for 4779 atoms. Found 18 (22 requested) and removed 23 (11 requested) atoms. Cycle 43: After refmac, R = 0.1969 (Rfree = 0.000) for 4756 atoms. Found 13 (22 requested) and removed 25 (11 requested) atoms. Cycle 44: After refmac, R = 0.2123 (Rfree = 0.000) for 4732 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 45: After refmac, R = 0.1834 (Rfree = 0.000) for 4717 atoms. Found 11 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 4830 seeds are put forward NCS extension: 0 residues added, 4830 seeds are put forward Round 1: 152 peptides, 35 chains. Longest chain 7 peptides. Score 0.205 Round 2: 202 peptides, 42 chains. Longest chain 14 peptides. Score 0.265 Round 3: 204 peptides, 40 chains. Longest chain 11 peptides. Score 0.293 Round 4: 204 peptides, 38 chains. Longest chain 8 peptides. Score 0.316 Round 5: 217 peptides, 40 chains. Longest chain 11 peptides. Score 0.327 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 177, 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 2op5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6261 reflections ( 99.73 % complete ) and 10950 restraints for refining 4721 atoms. 10282 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2336 (Rfree = 0.000) for 4721 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2084 (Rfree = 0.000) for 4685 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1726 (Rfree = 0.000) for 4654 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1747 (Rfree = 0.000) for 4634 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:28:15 GMT 2018 Job finished. TimeTaking 65.43 Used memory is bytes: 13027104