null Sun 23 Dec 22:23:02 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 2ajr-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-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/2ajr-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-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 22:23:12 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/2ajr-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-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 529 and 0 Target number of residues in the AU: 529 Target solvent content: 0.6574 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 662 Adjusted target solvent content: 0.57 Input MTZ file: 2ajr-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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5296 target number of atoms Had to go as low as 0.70 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: 29.168 4.000 Wilson plot Bfac: 83.11 7545 reflections ( 99.38 % complete ) and 0 restraints for refining 5839 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3738 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3670 (Rfree = 0.000) for 5839 atoms. Found 27 (27 requested) and removed 42 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 5906 seeds are put forward NCS extension: 0 residues added, 5906 seeds are put forward Round 1: 177 peptides, 40 chains. Longest chain 6 peptides. Score 0.212 Round 2: 250 peptides, 47 chains. Longest chain 12 peptides. Score 0.313 Round 3: 269 peptides, 51 chains. Longest chain 11 peptides. Score 0.317 Round 4: 297 peptides, 49 chains. Longest chain 13 peptides. Score 0.393 Round 5: 293 peptides, 49 chains. Longest chain 14 peptides. Score 0.385 Taking the results from Round 4 Chains 49, Residues 248, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 11510 restraints for refining 4763 atoms. 10555 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3316 (Rfree = 0.000) for 4763 atoms. Found 22 (22 requested) and removed 51 (11 requested) atoms. Cycle 2: After refmac, R = 0.3063 (Rfree = 0.000) for 4623 atoms. Found 22 (22 requested) and removed 38 (11 requested) atoms. Cycle 3: After refmac, R = 0.2983 (Rfree = 0.000) for 4530 atoms. Found 21 (21 requested) and removed 40 (10 requested) atoms. Cycle 4: After refmac, R = 0.3049 (Rfree = 0.000) for 4461 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 5: After refmac, R = 0.2921 (Rfree = 0.000) for 4417 atoms. Found 21 (21 requested) and removed 37 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.30 Search for helices and strands: 0 residues in 0 chains, 4529 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4544 seeds are put forward Round 1: 252 peptides, 48 chains. Longest chain 10 peptides. Score 0.308 Round 2: 288 peptides, 49 chains. Longest chain 14 peptides. Score 0.375 Round 3: 320 peptides, 51 chains. Longest chain 14 peptides. Score 0.420 Round 4: 314 peptides, 48 chains. Longest chain 13 peptides. Score 0.434 Round 5: 317 peptides, 46 chains. Longest chain 14 peptides. Score 0.456 Taking the results from Round 5 Chains 46, Residues 271, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10213 restraints for refining 4559 atoms. 9045 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2829 (Rfree = 0.000) for 4559 atoms. Found 21 (21 requested) and removed 45 (10 requested) atoms. Cycle 7: After refmac, R = 0.2666 (Rfree = 0.000) for 4494 atoms. Found 21 (21 requested) and removed 33 (10 requested) atoms. Cycle 8: After refmac, R = 0.2529 (Rfree = 0.000) for 4442 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 9: After refmac, R = 0.2476 (Rfree = 0.000) for 4402 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 10: After refmac, R = 0.2462 (Rfree = 0.000) for 4378 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 4509 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4532 seeds are put forward Round 1: 284 peptides, 55 chains. Longest chain 11 peptides. Score 0.313 Round 2: 319 peptides, 47 chains. Longest chain 22 peptides. Score 0.452 Round 3: 318 peptides, 47 chains. Longest chain 17 peptides. Score 0.450 Round 4: 324 peptides, 49 chains. Longest chain 14 peptides. Score 0.444 Round 5: 333 peptides, 42 chains. Longest chain 20 peptides. Score 0.517 Taking the results from Round 5 Chains 44, Residues 291, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10651 restraints for refining 4749 atoms. 9432 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2777 (Rfree = 0.000) for 4749 atoms. Found 22 (22 requested) and removed 49 (11 requested) atoms. Cycle 12: After refmac, R = 0.2692 (Rfree = 0.000) for 4661 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 13: After refmac, R = 0.2628 (Rfree = 0.000) for 4608 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. Cycle 14: After refmac, R = 0.2275 (Rfree = 0.000) for 4550 atoms. Found 16 (21 requested) and removed 19 (10 requested) atoms. Cycle 15: After refmac, R = 0.2144 (Rfree = 0.000) for 4525 atoms. Found 6 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 4611 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4629 seeds are put forward Round 1: 263 peptides, 52 chains. Longest chain 12 peptides. Score 0.295 Round 2: 293 peptides, 49 chains. Longest chain 12 peptides. Score 0.385 Round 3: 282 peptides, 46 chains. Longest chain 12 peptides. Score 0.389 Round 4: 307 peptides, 46 chains. Longest chain 20 peptides. Score 0.438 Round 5: 307 peptides, 49 chains. Longest chain 15 peptides. Score 0.412 Taking the results from Round 4 Chains 46, Residues 261, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10372 restraints for refining 4718 atoms. 9269 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2823 (Rfree = 0.000) for 4718 atoms. Found 22 (22 requested) and removed 64 (11 requested) atoms. Cycle 17: After refmac, R = 0.2670 (Rfree = 0.000) for 4621 atoms. Found 22 (22 requested) and removed 47 (11 requested) atoms. Cycle 18: After refmac, R = 0.2668 (Rfree = 0.000) for 4545 atoms. Found 21 (21 requested) and removed 28 (10 requested) atoms. Cycle 19: After refmac, R = 0.2501 (Rfree = 0.000) for 4505 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 20: After refmac, R = 0.2491 (Rfree = 0.000) for 4469 atoms. Found 21 (21 requested) and removed 40 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.40 Search for helices and strands: 0 residues in 0 chains, 4567 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4584 seeds are put forward Round 1: 286 peptides, 55 chains. Longest chain 11 peptides. Score 0.317 Round 2: 298 peptides, 51 chains. Longest chain 13 peptides. Score 0.377 Round 3: 292 peptides, 52 chains. Longest chain 15 peptides. Score 0.357 Round 4: 305 peptides, 47 chains. Longest chain 21 peptides. Score 0.426 Round 5: 310 peptides, 50 chains. Longest chain 14 peptides. Score 0.410 Taking the results from Round 4 Chains 47, Residues 258, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10889 restraints for refining 4778 atoms. 9880 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2898 (Rfree = 0.000) for 4778 atoms. Found 22 (22 requested) and removed 115 (11 requested) atoms. Cycle 22: After refmac, R = 0.2703 (Rfree = 0.000) for 4645 atoms. Found 22 (22 requested) and removed 39 (11 requested) atoms. Cycle 23: After refmac, R = 0.2633 (Rfree = 0.000) for 4598 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 24: After refmac, R = 0.2603 (Rfree = 0.000) for 4564 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 25: After refmac, R = 0.2598 (Rfree = 0.000) for 4549 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 4678 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 4707 seeds are put forward Round 1: 217 peptides, 47 chains. Longest chain 8 peptides. Score 0.239 Round 2: 294 peptides, 50 chains. Longest chain 13 peptides. Score 0.378 Round 3: 289 peptides, 52 chains. Longest chain 11 peptides. Score 0.350 Round 4: 321 peptides, 55 chains. Longest chain 12 peptides. Score 0.389 Round 5: 313 peptides, 52 chains. Longest chain 15 peptides. Score 0.399 Taking the results from Round 5 Chains 52, Residues 261, Estimated correctness of the model 0.0 % 7 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10657 restraints for refining 4781 atoms. 9580 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2620 (Rfree = 0.000) for 4781 atoms. Found 22 (22 requested) and removed 62 (11 requested) atoms. Cycle 27: After refmac, R = 0.2538 (Rfree = 0.000) for 4683 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 28: After refmac, R = 0.2141 (Rfree = 0.000) for 4647 atoms. Found 12 (22 requested) and removed 20 (11 requested) atoms. Cycle 29: After refmac, R = 0.2151 (Rfree = 0.000) for 4620 atoms. Found 6 (22 requested) and removed 21 (11 requested) atoms. Cycle 30: After refmac, R = 0.2047 (Rfree = 0.000) for 4596 atoms. Found 10 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 4688 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 4714 seeds are put forward Round 1: 229 peptides, 46 chains. Longest chain 11 peptides. Score 0.276 Round 2: 274 peptides, 49 chains. Longest chain 14 peptides. Score 0.346 Round 3: 264 peptides, 48 chains. Longest chain 9 peptides. Score 0.334 Round 4: 263 peptides, 45 chains. Longest chain 11 peptides. Score 0.360 Round 5: 275 peptides, 42 chains. Longest chain 19 peptides. Score 0.411 Taking the results from Round 5 Chains 44, Residues 233, Estimated correctness of the model 0.0 % 6 chains (48 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10371 restraints for refining 4783 atoms. 9313 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2794 (Rfree = 0.000) for 4783 atoms. Found 22 (22 requested) and removed 61 (11 requested) atoms. Cycle 32: After refmac, R = 0.2449 (Rfree = 0.000) for 4710 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 33: After refmac, R = 0.2291 (Rfree = 0.000) for 4664 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. Cycle 34: After refmac, R = 0.2191 (Rfree = 0.000) for 4628 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 35: After refmac, R = 0.1931 (Rfree = 0.000) for 4602 atoms. Found 11 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 4699 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4721 seeds are put forward Round 1: 244 peptides, 55 chains. Longest chain 6 peptides. Score 0.224 Round 2: 282 peptides, 53 chains. Longest chain 12 peptides. Score 0.327 Round 3: 269 peptides, 48 chains. Longest chain 19 peptides. Score 0.345 Round 4: 273 peptides, 48 chains. Longest chain 14 peptides. Score 0.353 Round 5: 261 peptides, 44 chains. Longest chain 15 peptides. Score 0.365 Taking the results from Round 5 Chains 45, Residues 217, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10960 restraints for refining 4782 atoms. 10083 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2552 (Rfree = 0.000) for 4782 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 37: After refmac, R = 0.2426 (Rfree = 0.000) for 4739 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 38: After refmac, R = 0.1990 (Rfree = 0.000) for 4696 atoms. Found 10 (22 requested) and removed 18 (11 requested) atoms. Cycle 39: After refmac, R = 0.1856 (Rfree = 0.000) for 4675 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 40: After refmac, R = 0.1762 (Rfree = 0.000) for 4666 atoms. Found 4 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 4748 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 4761 seeds are put forward Round 1: 214 peptides, 46 chains. Longest chain 8 peptides. Score 0.241 Round 2: 260 peptides, 46 chains. Longest chain 15 peptides. Score 0.344 Round 3: 242 peptides, 41 chains. Longest chain 14 peptides. Score 0.352 Round 4: 247 peptides, 44 chains. Longest chain 15 peptides. Score 0.335 Round 5: 241 peptides, 38 chains. Longest chain 15 peptides. Score 0.378 Taking the results from Round 5 Chains 38, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 11110 restraints for refining 4781 atoms. 10336 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2559 (Rfree = 0.000) for 4781 atoms. Found 22 (22 requested) and removed 45 (11 requested) atoms. Cycle 42: After refmac, R = 0.2420 (Rfree = 0.000) for 4739 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 43: After refmac, R = 0.2470 (Rfree = 0.000) for 4716 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 44: After refmac, R = 0.2290 (Rfree = 0.000) for 4690 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 45: After refmac, R = 0.2322 (Rfree = 0.000) for 4671 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 4772 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 4791 seeds are put forward Round 1: 193 peptides, 42 chains. Longest chain 9 peptides. Score 0.231 Round 2: 247 peptides, 48 chains. Longest chain 9 peptides. Score 0.297 Round 3: 246 peptides, 45 chains. Longest chain 13 peptides. Score 0.324 Round 4: 263 peptides, 46 chains. Longest chain 13 peptides. Score 0.350 Round 5: 245 peptides, 40 chains. Longest chain 15 peptides. Score 0.368 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 205, 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 2ajr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7545 reflections ( 99.38 % complete ) and 10920 restraints for refining 4782 atoms. 10140 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2370 (Rfree = 0.000) for 4782 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2463 (Rfree = 0.000) for 4739 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2433 (Rfree = 0.000) for 4708 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2479 (Rfree = 0.000) for 4679 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:31:00 GMT 2018 Job finished. TimeTaking 67.96 Used memory is bytes: 6782072