null Sun 23 Dec 22:23:05 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 2iiu-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-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/2iiu-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-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 22:23:15 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/2iiu-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-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 497 and 0 Target number of residues in the AU: 497 Target solvent content: 0.6475 Checking the provided sequence file Detected sequence length: 227 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 681 Adjusted target solvent content: 0.52 Input MTZ file: 2iiu-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: 155 Cell parameters: 99.900 99.900 397.311 90.000 90.000 120.000 Input sequence file: 2iiu-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5448 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: 132.437 3.801 Wilson plot Bfac: 76.41 7831 reflections ( 98.91 % complete ) and 0 restraints for refining 6045 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3671 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3539 (Rfree = 0.000) for 6045 atoms. Found 32 (33 requested) and removed 62 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 6099 seeds are put forward NCS extension: 0 residues added, 6099 seeds are put forward Round 1: 166 peptides, 36 chains. Longest chain 8 peptides. Score 0.230 Round 2: 223 peptides, 42 chains. Longest chain 10 peptides. Score 0.310 Round 3: 243 peptides, 47 chains. Longest chain 8 peptides. Score 0.307 Round 4: 256 peptides, 44 chains. Longest chain 13 peptides. Score 0.366 Round 5: 262 peptides, 46 chains. Longest chain 21 peptides. Score 0.360 Taking the results from Round 4 Chains 44, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11878 restraints for refining 4927 atoms. 11074 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2738 (Rfree = 0.000) for 4927 atoms. Found 26 (27 requested) and removed 29 (13 requested) atoms. Cycle 2: After refmac, R = 0.2526 (Rfree = 0.000) for 4856 atoms. Found 5 (27 requested) and removed 25 (13 requested) atoms. Cycle 3: After refmac, R = 0.2441 (Rfree = 0.000) for 4823 atoms. Found 5 (26 requested) and removed 21 (13 requested) atoms. Cycle 4: After refmac, R = 0.2435 (Rfree = 0.000) for 4796 atoms. Found 3 (26 requested) and removed 21 (13 requested) atoms. Cycle 5: After refmac, R = 0.2309 (Rfree = 0.000) for 4773 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 4968 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 4978 seeds are put forward Round 1: 229 peptides, 46 chains. Longest chain 11 peptides. Score 0.284 Round 2: 286 peptides, 48 chains. Longest chain 11 peptides. Score 0.394 Round 3: 283 peptides, 46 chains. Longest chain 12 peptides. Score 0.406 Round 4: 264 peptides, 43 chains. Longest chain 14 peptides. Score 0.394 Round 5: 277 peptides, 44 chains. Longest chain 14 peptides. Score 0.412 Taking the results from Round 5 Chains 44, Residues 233, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11734 restraints for refining 4912 atoms. 10846 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2487 (Rfree = 0.000) for 4912 atoms. Found 15 (26 requested) and removed 33 (13 requested) atoms. Cycle 7: After refmac, R = 0.2393 (Rfree = 0.000) for 4867 atoms. Found 10 (26 requested) and removed 18 (13 requested) atoms. Cycle 8: After refmac, R = 0.2362 (Rfree = 0.000) for 4853 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. Cycle 9: After refmac, R = 0.2361 (Rfree = 0.000) for 4841 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. Cycle 10: After refmac, R = 0.2333 (Rfree = 0.000) for 4831 atoms. Found 2 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 4997 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5018 seeds are put forward Round 1: 257 peptides, 51 chains. Longest chain 10 peptides. Score 0.300 Round 2: 264 peptides, 44 chains. Longest chain 13 peptides. Score 0.384 Round 3: 251 peptides, 40 chains. Longest chain 14 peptides. Score 0.394 Round 4: 256 peptides, 40 chains. Longest chain 13 peptides. Score 0.405 Round 5: 258 peptides, 45 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 4 Chains 40, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11938 restraints for refining 4928 atoms. 11114 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2552 (Rfree = 0.000) for 4928 atoms. Found 18 (27 requested) and removed 25 (13 requested) atoms. Cycle 12: After refmac, R = 0.2449 (Rfree = 0.000) for 4902 atoms. Found 3 (27 requested) and removed 18 (13 requested) atoms. Cycle 13: After refmac, R = 0.2426 (Rfree = 0.000) for 4882 atoms. Found 3 (26 requested) and removed 14 (13 requested) atoms. Cycle 14: After refmac, R = 0.2407 (Rfree = 0.000) for 4868 atoms. Found 6 (26 requested) and removed 16 (13 requested) atoms. Cycle 15: After refmac, R = 0.2378 (Rfree = 0.000) for 4858 atoms. Found 3 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 5017 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5032 seeds are put forward Round 1: 254 peptides, 50 chains. Longest chain 10 peptides. Score 0.303 Round 2: 272 peptides, 48 chains. Longest chain 10 peptides. Score 0.363 Round 3: 271 peptides, 44 chains. Longest chain 15 peptides. Score 0.399 Round 4: 265 peptides, 42 chains. Longest chain 14 peptides. Score 0.405 Round 5: 258 peptides, 37 chains. Longest chain 29 peptides. Score 0.438 Taking the results from Round 5 Chains 37, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11993 restraints for refining 4928 atoms. 11146 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2643 (Rfree = 0.000) for 4928 atoms. Found 14 (27 requested) and removed 15 (13 requested) atoms. Cycle 17: After refmac, R = 0.2564 (Rfree = 0.000) for 4916 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. Cycle 18: After refmac, R = 0.2521 (Rfree = 0.000) for 4905 atoms. Found 2 (26 requested) and removed 14 (13 requested) atoms. Cycle 19: After refmac, R = 0.2481 (Rfree = 0.000) for 4891 atoms. Found 7 (26 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.2452 (Rfree = 0.000) for 4883 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 5065 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 5090 seeds are put forward Round 1: 244 peptides, 46 chains. Longest chain 14 peptides. Score 0.319 Round 2: 263 peptides, 42 chains. Longest chain 19 peptides. Score 0.401 Round 3: 257 peptides, 39 chains. Longest chain 19 peptides. Score 0.417 Round 4: 272 peptides, 45 chains. Longest chain 15 peptides. Score 0.392 Round 5: 264 peptides, 44 chains. Longest chain 12 peptides. Score 0.384 Taking the results from Round 3 Chains 39, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11951 restraints for refining 4927 atoms. 11118 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2484 (Rfree = 0.000) for 4927 atoms. Found 13 (27 requested) and removed 18 (13 requested) atoms. Cycle 22: After refmac, R = 0.2429 (Rfree = 0.000) for 4906 atoms. Found 7 (27 requested) and removed 15 (13 requested) atoms. Cycle 23: After refmac, R = 0.2391 (Rfree = 0.000) for 4894 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Cycle 24: After refmac, R = 0.2382 (Rfree = 0.000) for 4886 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.2370 (Rfree = 0.000) for 4876 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 5018 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5039 seeds are put forward Round 1: 222 peptides, 44 chains. Longest chain 9 peptides. Score 0.287 Round 2: 247 peptides, 43 chains. Longest chain 11 peptides. Score 0.356 Round 3: 247 peptides, 40 chains. Longest chain 16 peptides. Score 0.386 Round 4: 251 peptides, 35 chains. Longest chain 15 peptides. Score 0.442 Round 5: 256 peptides, 40 chains. Longest chain 15 peptides. Score 0.405 Taking the results from Round 4 Chains 35, Residues 216, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11624 restraints for refining 4928 atoms. 10738 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2468 (Rfree = 0.000) for 4928 atoms. Found 17 (27 requested) and removed 19 (13 requested) atoms. Cycle 27: After refmac, R = 0.2342 (Rfree = 0.000) for 4908 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. Cycle 28: After refmac, R = 0.2284 (Rfree = 0.000) for 4893 atoms. Found 6 (26 requested) and removed 14 (13 requested) atoms. Cycle 29: After refmac, R = 0.2237 (Rfree = 0.000) for 4882 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.2206 (Rfree = 0.000) for 4868 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 5010 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5034 seeds are put forward Round 1: 223 peptides, 40 chains. Longest chain 11 peptides. Score 0.331 Round 2: 249 peptides, 41 chains. Longest chain 12 peptides. Score 0.380 Round 3: 253 peptides, 38 chains. Longest chain 14 peptides. Score 0.418 Round 4: 270 peptides, 42 chains. Longest chain 15 peptides. Score 0.416 Round 5: 264 peptides, 40 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 5 Chains 40, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11865 restraints for refining 4927 atoms. 11009 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2448 (Rfree = 0.000) for 4927 atoms. Found 20 (27 requested) and removed 19 (13 requested) atoms. Cycle 32: After refmac, R = 0.2309 (Rfree = 0.000) for 4915 atoms. Found 7 (27 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.2263 (Rfree = 0.000) for 4905 atoms. Found 8 (26 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.2242 (Rfree = 0.000) for 4898 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.2235 (Rfree = 0.000) for 4880 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 5053 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5065 seeds are put forward Round 1: 221 peptides, 46 chains. Longest chain 8 peptides. Score 0.264 Round 2: 253 peptides, 43 chains. Longest chain 15 peptides. Score 0.370 Round 3: 255 peptides, 44 chains. Longest chain 15 peptides. Score 0.364 Round 4: 251 peptides, 42 chains. Longest chain 12 peptides. Score 0.375 Round 5: 260 peptides, 43 chains. Longest chain 18 peptides. Score 0.385 Taking the results from Round 5 Chains 43, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 11933 restraints for refining 4928 atoms. 11108 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2451 (Rfree = 0.000) for 4928 atoms. Found 18 (27 requested) and removed 14 (13 requested) atoms. Cycle 37: After refmac, R = 0.2367 (Rfree = 0.000) for 4923 atoms. Found 13 (27 requested) and removed 15 (13 requested) atoms. Cycle 38: After refmac, R = 0.2323 (Rfree = 0.000) for 4917 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.2315 (Rfree = 0.000) for 4907 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2301 (Rfree = 0.000) for 4897 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 5077 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 5089 seeds are put forward Round 1: 220 peptides, 43 chains. Longest chain 11 peptides. Score 0.293 Round 2: 233 peptides, 40 chains. Longest chain 13 peptides. Score 0.354 Round 3: 220 peptides, 35 chains. Longest chain 12 peptides. Score 0.375 Round 4: 219 peptides, 34 chains. Longest chain 14 peptides. Score 0.383 Round 5: 215 peptides, 35 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 4 Chains 34, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7831 reflections ( 98.91 % complete ) and 12189 restraints for refining 4928 atoms. 11483 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2471 (Rfree = 0.000) for 4928 atoms. Found 22 (27 requested) and removed 14 (13 requested) atoms. Cycle 42: After refmac, R = 0.2362 (Rfree = 0.000) for 4929 atoms. Found 4 (27 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.2336 (Rfree = 0.000) for 4915 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. Cycle 44: After refmac, R = 0.2330 (Rfree = 0.000) for 4904 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.2316 (Rfree = 0.000) for 4893 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 5066 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5086 seeds are put forward Round 1: 201 peptides, 42 chains. Longest chain 8 peptides. Score 0.256 Round 2: 227 peptides, 42 chains. Longest chain 12 peptides. Score 0.320 Round 3: 240 peptides, 40 chains. Longest chain 16 peptides. Score 0.370 Round 4: 221 peptides, 39 chains. Longest chain 14 peptides. Score 0.336 Round 5: 237 peptides, 40 chains. Longest chain 17 peptides. Score 0.363 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 200, 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 2iiu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7831 reflections ( 98.91 % complete ) and 11941 restraints for refining 4909 atoms. 11181 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2524 (Rfree = 0.000) for 4909 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2425 (Rfree = 0.000) for 4890 atoms. Found 0 (26 requested) and removed 11 (13 requested) atoms. Cycle 48: After refmac, R = 0.2425 (Rfree = 0.000) for 4872 atoms. Found 0 (26 requested) and removed 4 (13 requested) atoms. Cycle 49: After refmac, R = 0.2413 (Rfree = 0.000) for 4868 atoms. Found 0 (26 requested) and removed 0 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:38:29 GMT 2018 Job finished. TimeTaking 75.4 Used memory is bytes: 18203744