Mon 24 Dec 00:35:24 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1z82-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-mrncs ############### 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 00:35:29 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/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-mrncs/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 410 and 0 Target number of residues in the AU: 410 Target solvent content: 0.6357 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-3.4-parrot-mrncs.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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.65 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: 29.850 3.400 Wilson plot Bfac: 69.58 8387 reflections ( 99.63 % complete ) and 0 restraints for refining 5922 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3003 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2776 (Rfree = 0.000) for 5922 atoms. Found 44 (44 requested) and removed 46 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.78 Search for helices and strands: 0 residues in 0 chains, 6063 seeds are put forward NCS extension: 0 residues added, 6063 seeds are put forward Round 1: 223 peptides, 46 chains. Longest chain 9 peptides. Score 0.287 Round 2: 304 peptides, 51 chains. Longest chain 19 peptides. Score 0.448 Round 3: 325 peptides, 58 chains. Longest chain 14 peptides. Score 0.426 Round 4: 368 peptides, 59 chains. Longest chain 19 peptides. Score 0.517 Round 5: 390 peptides, 59 chains. Longest chain 19 peptides. Score 0.563 Taking the results from Round 5 Chains 60, Residues 331, Estimated correctness of the model 16.1 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10990 restraints for refining 4873 atoms. 9659 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2243 (Rfree = 0.000) for 4873 atoms. Found 33 (36 requested) and removed 38 (18 requested) atoms. Cycle 2: After refmac, R = 0.2059 (Rfree = 0.000) for 4791 atoms. Found 15 (36 requested) and removed 25 (18 requested) atoms. Cycle 3: After refmac, R = 0.1844 (Rfree = 0.000) for 4748 atoms. Found 3 (36 requested) and removed 19 (18 requested) atoms. Cycle 4: After refmac, R = 0.1954 (Rfree = 0.000) for 4717 atoms. Found 15 (35 requested) and removed 20 (17 requested) atoms. Cycle 5: After refmac, R = 0.1999 (Rfree = 0.000) for 4703 atoms. Found 12 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 4892 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 4904 seeds are put forward Round 1: 301 peptides, 56 chains. Longest chain 11 peptides. Score 0.386 Round 2: 342 peptides, 51 chains. Longest chain 20 peptides. Score 0.535 Round 3: 371 peptides, 51 chains. Longest chain 22 peptides. Score 0.595 Round 4: 341 peptides, 48 chains. Longest chain 22 peptides. Score 0.561 Round 5: 358 peptides, 47 chains. Longest chain 33 peptides. Score 0.604 Taking the results from Round 5 Chains 52, Residues 311, Estimated correctness of the model 30.0 % 5 chains (61 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10599 restraints for refining 4834 atoms. 9190 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2322 (Rfree = 0.000) for 4834 atoms. Found 26 (36 requested) and removed 48 (18 requested) atoms. Cycle 7: After refmac, R = 0.2088 (Rfree = 0.000) for 4786 atoms. Found 21 (36 requested) and removed 29 (18 requested) atoms. Cycle 8: After refmac, R = 0.2053 (Rfree = 0.000) for 4762 atoms. Found 18 (36 requested) and removed 25 (18 requested) atoms. Cycle 9: After refmac, R = 0.1953 (Rfree = 0.000) for 4738 atoms. Found 12 (35 requested) and removed 26 (17 requested) atoms. Cycle 10: After refmac, R = 0.1938 (Rfree = 0.000) for 4708 atoms. Found 10 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 4892 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4910 seeds are put forward Round 1: 293 peptides, 54 chains. Longest chain 13 peptides. Score 0.388 Round 2: 339 peptides, 50 chains. Longest chain 19 peptides. Score 0.538 Round 3: 334 peptides, 47 chains. Longest chain 20 peptides. Score 0.556 Round 4: 376 peptides, 58 chains. Longest chain 22 peptides. Score 0.543 Round 5: 374 peptides, 52 chains. Longest chain 21 peptides. Score 0.592 Taking the results from Round 5 Chains 53, Residues 322, Estimated correctness of the model 26.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10853 restraints for refining 4813 atoms. 9573 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2124 (Rfree = 0.000) for 4813 atoms. Found 29 (36 requested) and removed 36 (18 requested) atoms. Cycle 12: After refmac, R = 0.1971 (Rfree = 0.000) for 4778 atoms. Found 15 (36 requested) and removed 26 (18 requested) atoms. Cycle 13: After refmac, R = 0.2002 (Rfree = 0.000) for 4758 atoms. Found 22 (35 requested) and removed 28 (17 requested) atoms. Cycle 14: After refmac, R = 0.1776 (Rfree = 0.000) for 4741 atoms. Found 10 (35 requested) and removed 24 (17 requested) atoms. Cycle 15: After refmac, R = 0.1894 (Rfree = 0.000) for 4720 atoms. Found 15 (35 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.81 Search for helices and strands: 0 residues in 0 chains, 4956 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4980 seeds are put forward Round 1: 280 peptides, 50 chains. Longest chain 12 peptides. Score 0.398 Round 2: 326 peptides, 51 chains. Longest chain 27 peptides. Score 0.500 Round 3: 314 peptides, 47 chains. Longest chain 17 peptides. Score 0.512 Round 4: 312 peptides, 44 chains. Longest chain 18 peptides. Score 0.537 Round 5: 323 peptides, 47 chains. Longest chain 19 peptides. Score 0.532 Taking the results from Round 4 Chains 46, Residues 268, Estimated correctness of the model 6.8 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10691 restraints for refining 4752 atoms. 9593 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1941 (Rfree = 0.000) for 4752 atoms. Found 27 (35 requested) and removed 31 (17 requested) atoms. Cycle 17: After refmac, R = 0.2046 (Rfree = 0.000) for 4736 atoms. Found 32 (35 requested) and removed 29 (17 requested) atoms. Cycle 18: After refmac, R = 0.1834 (Rfree = 0.000) for 4726 atoms. Found 26 (35 requested) and removed 26 (17 requested) atoms. Cycle 19: After refmac, R = 0.1740 (Rfree = 0.000) for 4718 atoms. Found 16 (35 requested) and removed 27 (17 requested) atoms. Cycle 20: After refmac, R = 0.1679 (Rfree = 0.000) for 4698 atoms. Found 21 (35 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.80 Search for helices and strands: 0 residues in 0 chains, 4919 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 4932 seeds are put forward Round 1: 248 peptides, 48 chains. Longest chain 12 peptides. Score 0.335 Round 2: 288 peptides, 48 chains. Longest chain 11 peptides. Score 0.440 Round 3: 312 peptides, 47 chains. Longest chain 20 peptides. Score 0.508 Round 4: 310 peptides, 49 chains. Longest chain 14 peptides. Score 0.483 Round 5: 311 peptides, 51 chains. Longest chain 11 peptides. Score 0.465 Taking the results from Round 3 Chains 48, Residues 265, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10421 restraints for refining 4696 atoms. 9363 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2371 (Rfree = 0.000) for 4696 atoms. Found 35 (35 requested) and removed 42 (17 requested) atoms. Cycle 22: After refmac, R = 0.1920 (Rfree = 0.000) for 4672 atoms. Found 24 (35 requested) and removed 25 (17 requested) atoms. Cycle 23: After refmac, R = 0.1999 (Rfree = 0.000) for 4663 atoms. Found 29 (35 requested) and removed 26 (17 requested) atoms. Cycle 24: After refmac, R = 0.1904 (Rfree = 0.000) for 4654 atoms. Found 13 (35 requested) and removed 24 (17 requested) atoms. Cycle 25: After refmac, R = 0.1799 (Rfree = 0.000) for 4630 atoms. Found 20 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.74 Search for helices and strands: 0 residues in 0 chains, 4818 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4834 seeds are put forward Round 1: 234 peptides, 46 chains. Longest chain 13 peptides. Score 0.319 Round 2: 266 peptides, 44 chains. Longest chain 16 peptides. Score 0.428 Round 3: 289 peptides, 50 chains. Longest chain 13 peptides. Score 0.421 Round 4: 284 peptides, 50 chains. Longest chain 13 peptides. Score 0.408 Round 5: 287 peptides, 49 chains. Longest chain 14 peptides. Score 0.427 Taking the results from Round 2 Chains 44, Residues 222, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10338 restraints for refining 4555 atoms. 9444 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1833 (Rfree = 0.000) for 4555 atoms. Found 32 (34 requested) and removed 25 (17 requested) atoms. Cycle 27: After refmac, R = 0.1711 (Rfree = 0.000) for 4555 atoms. Found 13 (34 requested) and removed 21 (17 requested) atoms. Cycle 28: After refmac, R = 0.1669 (Rfree = 0.000) for 4540 atoms. Found 8 (34 requested) and removed 23 (17 requested) atoms. Cycle 29: After refmac, R = 0.1629 (Rfree = 0.000) for 4517 atoms. Found 12 (34 requested) and removed 20 (17 requested) atoms. Cycle 30: After refmac, R = 0.1609 (Rfree = 0.000) for 4507 atoms. Found 7 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 4684 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 4706 seeds are put forward Round 1: 243 peptides, 46 chains. Longest chain 13 peptides. Score 0.344 Round 2: 278 peptides, 48 chains. Longest chain 11 peptides. Score 0.415 Round 3: 271 peptides, 42 chains. Longest chain 14 peptides. Score 0.462 Round 4: 296 peptides, 48 chains. Longest chain 13 peptides. Score 0.460 Round 5: 291 peptides, 44 chains. Longest chain 14 peptides. Score 0.489 Taking the results from Round 5 Chains 46, Residues 247, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10305 restraints for refining 4631 atoms. 9269 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1906 (Rfree = 0.000) for 4631 atoms. Found 26 (34 requested) and removed 25 (17 requested) atoms. Cycle 32: After refmac, R = 0.1917 (Rfree = 0.000) for 4616 atoms. Found 27 (34 requested) and removed 23 (17 requested) atoms. Cycle 33: After refmac, R = 0.1753 (Rfree = 0.000) for 4610 atoms. Found 16 (34 requested) and removed 22 (17 requested) atoms. Cycle 34: After refmac, R = 0.1825 (Rfree = 0.000) for 4597 atoms. Found 21 (34 requested) and removed 20 (17 requested) atoms. Cycle 35: After refmac, R = 0.1772 (Rfree = 0.000) for 4595 atoms. Found 19 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 4799 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4813 seeds are put forward Round 1: 221 peptides, 44 chains. Longest chain 11 peptides. Score 0.306 Round 2: 268 peptides, 49 chains. Longest chain 12 peptides. Score 0.377 Round 3: 273 peptides, 48 chains. Longest chain 12 peptides. Score 0.402 Round 4: 273 peptides, 45 chains. Longest chain 13 peptides. Score 0.435 Round 5: 270 peptides, 43 chains. Longest chain 14 peptides. Score 0.449 Taking the results from Round 5 Chains 43, Residues 227, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10658 restraints for refining 4709 atoms. 9733 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1836 (Rfree = 0.000) for 4709 atoms. Found 17 (35 requested) and removed 31 (17 requested) atoms. Cycle 37: After refmac, R = 0.1772 (Rfree = 0.000) for 4685 atoms. Found 12 (35 requested) and removed 21 (17 requested) atoms. Cycle 38: After refmac, R = 0.1729 (Rfree = 0.000) for 4673 atoms. Found 17 (35 requested) and removed 19 (17 requested) atoms. Cycle 39: After refmac, R = 0.1714 (Rfree = 0.000) for 4660 atoms. Found 17 (35 requested) and removed 21 (17 requested) atoms. Cycle 40: After refmac, R = 0.1638 (Rfree = 0.000) for 4655 atoms. Found 13 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.74 Search for helices and strands: 0 residues in 0 chains, 4836 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4856 seeds are put forward Round 1: 185 peptides, 38 chains. Longest chain 9 peptides. Score 0.274 Round 2: 218 peptides, 39 chains. Longest chain 11 peptides. Score 0.358 Round 3: 237 peptides, 42 chains. Longest chain 11 peptides. Score 0.375 Round 4: 226 peptides, 39 chains. Longest chain 12 peptides. Score 0.380 Round 5: 250 peptides, 41 chains. Longest chain 14 peptides. Score 0.421 Taking the results from Round 5 Chains 41, Residues 209, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10777 restraints for refining 4715 atoms. 9941 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1860 (Rfree = 0.000) for 4715 atoms. Found 21 (35 requested) and removed 36 (17 requested) atoms. Cycle 42: After refmac, R = 0.1776 (Rfree = 0.000) for 4693 atoms. Found 23 (35 requested) and removed 21 (17 requested) atoms. Cycle 43: After refmac, R = 0.1719 (Rfree = 0.000) for 4684 atoms. Found 17 (35 requested) and removed 22 (17 requested) atoms. Cycle 44: After refmac, R = 0.1667 (Rfree = 0.000) for 4675 atoms. Found 18 (35 requested) and removed 18 (17 requested) atoms. Cycle 45: After refmac, R = 0.1622 (Rfree = 0.000) for 4671 atoms. Found 10 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 4854 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4869 seeds are put forward Round 1: 176 peptides, 35 chains. Longest chain 11 peptides. Score 0.285 Round 2: 243 peptides, 44 chains. Longest chain 11 peptides. Score 0.368 Round 3: 247 peptides, 41 chains. Longest chain 12 peptides. Score 0.413 Round 4: 240 peptides, 40 chains. Longest chain 12 peptides. Score 0.406 Round 5: 235 peptides, 39 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 206, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8387 reflections ( 99.63 % complete ) and 10344 restraints for refining 4604 atoms. 9538 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1789 (Rfree = 0.000) for 4604 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1721 (Rfree = 0.000) for 4577 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1672 (Rfree = 0.000) for 4555 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1651 (Rfree = 0.000) for 4533 atoms. TimeTaking 57.7