null Mon 24 Dec 07:31:28 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkz-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-noncs ############### 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 07:31:37 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-noncs/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 627 and 0 Target number of residues in the AU: 627 Target solvent content: 0.5993 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-3.8-parrot-noncs.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: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.60 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: 19.959 3.800 Wilson plot Bfac: 52.34 8080 reflections ( 96.28 % complete ) and 0 restraints for refining 7309 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.2986 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3002 (Rfree = 0.000) for 7309 atoms. Found 40 (40 requested) and removed 50 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.36 Search for helices and strands: 0 residues in 0 chains, 7403 seeds are put forward NCS extension: 0 residues added, 7403 seeds are put forward Round 1: 277 peptides, 58 chains. Longest chain 10 peptides. Score 0.270 Round 2: 358 peptides, 63 chains. Longest chain 16 peptides. Score 0.391 Round 3: 407 peptides, 69 chains. Longest chain 22 peptides. Score 0.434 Round 4: 421 peptides, 62 chains. Longest chain 19 peptides. Score 0.510 Round 5: 437 peptides, 67 chains. Longest chain 17 peptides. Score 0.501 Taking the results from Round 4 Chains 62, Residues 359, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13934 restraints for refining 5961 atoms. 12527 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2695 (Rfree = 0.000) for 5961 atoms. Found 32 (32 requested) and removed 53 (16 requested) atoms. Cycle 2: After refmac, R = 0.2604 (Rfree = 0.000) for 5822 atoms. Found 32 (32 requested) and removed 59 (16 requested) atoms. Cycle 3: After refmac, R = 0.2017 (Rfree = 0.000) for 5714 atoms. Found 26 (31 requested) and removed 36 (15 requested) atoms. Cycle 4: After refmac, R = 0.2175 (Rfree = 0.000) for 5654 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 5: After refmac, R = 0.2046 (Rfree = 0.000) for 5623 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 3.34 Search for helices and strands: 0 residues in 0 chains, 5822 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5844 seeds are put forward Round 1: 377 peptides, 70 chains. Longest chain 19 peptides. Score 0.370 Round 2: 440 peptides, 70 chains. Longest chain 25 peptides. Score 0.484 Round 3: 430 peptides, 68 chains. Longest chain 18 peptides. Score 0.482 Round 4: 436 peptides, 63 chains. Longest chain 28 peptides. Score 0.528 Round 5: 433 peptides, 63 chains. Longest chain 23 peptides. Score 0.523 Taking the results from Round 4 Chains 65, Residues 373, Estimated correctness of the model 0.0 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 12676 restraints for refining 5778 atoms. 11060 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2133 (Rfree = 0.000) for 5778 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 7: After refmac, R = 0.1931 (Rfree = 0.000) for 5667 atoms. Found 31 (31 requested) and removed 47 (15 requested) atoms. Cycle 8: After refmac, R = 0.1776 (Rfree = 0.000) for 5618 atoms. Found 23 (31 requested) and removed 30 (15 requested) atoms. Cycle 9: After refmac, R = 0.1748 (Rfree = 0.000) for 5591 atoms. Found 19 (30 requested) and removed 26 (15 requested) atoms. Cycle 10: After refmac, R = 0.1664 (Rfree = 0.000) for 5563 atoms. Found 19 (30 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.34 Search for helices and strands: 0 residues in 0 chains, 5733 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5752 seeds are put forward Round 1: 378 peptides, 70 chains. Longest chain 13 peptides. Score 0.372 Round 2: 433 peptides, 66 chains. Longest chain 19 peptides. Score 0.501 Round 3: 451 peptides, 67 chains. Longest chain 18 peptides. Score 0.523 Round 4: 460 peptides, 67 chains. Longest chain 31 peptides. Score 0.538 Round 5: 447 peptides, 65 chains. Longest chain 17 peptides. Score 0.531 Taking the results from Round 4 Chains 70, Residues 393, Estimated correctness of the model 0.0 % 13 chains (118 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 12208 restraints for refining 5963 atoms. 10274 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2187 (Rfree = 0.000) for 5963 atoms. Found 32 (32 requested) and removed 69 (16 requested) atoms. Cycle 12: After refmac, R = 0.1920 (Rfree = 0.000) for 5829 atoms. Found 29 (32 requested) and removed 41 (16 requested) atoms. Cycle 13: After refmac, R = 0.1820 (Rfree = 0.000) for 5768 atoms. Found 16 (31 requested) and removed 24 (15 requested) atoms. Cycle 14: After refmac, R = 0.1800 (Rfree = 0.000) for 5740 atoms. Found 11 (31 requested) and removed 26 (15 requested) atoms. Cycle 15: After refmac, R = 0.1761 (Rfree = 0.000) for 5710 atoms. Found 11 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.39 Search for helices and strands: 0 residues in 0 chains, 5843 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 5870 seeds are put forward Round 1: 372 peptides, 66 chains. Longest chain 18 peptides. Score 0.393 Round 2: 429 peptides, 70 chains. Longest chain 15 peptides. Score 0.465 Round 3: 434 peptides, 67 chains. Longest chain 17 peptides. Score 0.496 Round 4: 441 peptides, 68 chains. Longest chain 26 peptides. Score 0.500 Round 5: 420 peptides, 60 chains. Longest chain 22 peptides. Score 0.523 Taking the results from Round 5 Chains 63, Residues 360, Estimated correctness of the model 0.0 % 7 chains (67 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13042 restraints for refining 5963 atoms. 11415 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2152 (Rfree = 0.000) for 5963 atoms. Found 28 (32 requested) and removed 53 (16 requested) atoms. Cycle 17: After refmac, R = 0.2038 (Rfree = 0.000) for 5902 atoms. Found 16 (32 requested) and removed 27 (16 requested) atoms. Cycle 18: After refmac, R = 0.1966 (Rfree = 0.000) for 5878 atoms. Found 12 (32 requested) and removed 19 (16 requested) atoms. Cycle 19: After refmac, R = 0.1938 (Rfree = 0.000) for 5862 atoms. Found 7 (32 requested) and removed 19 (16 requested) atoms. Cycle 20: After refmac, R = 0.1922 (Rfree = 0.000) for 5840 atoms. Found 6 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.36 Search for helices and strands: 0 residues in 0 chains, 5967 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5985 seeds are put forward Round 1: 378 peptides, 73 chains. Longest chain 12 peptides. Score 0.348 Round 2: 426 peptides, 68 chains. Longest chain 17 peptides. Score 0.475 Round 3: 424 peptides, 64 chains. Longest chain 16 peptides. Score 0.501 Round 4: 446 peptides, 69 chains. Longest chain 19 peptides. Score 0.501 Round 5: 431 peptides, 63 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 5 Chains 63, Residues 368, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13663 restraints for refining 5961 atoms. 12202 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2187 (Rfree = 0.000) for 5961 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 22: After refmac, R = 0.2132 (Rfree = 0.000) for 5890 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 23: After refmac, R = 0.1980 (Rfree = 0.000) for 5861 atoms. Found 20 (32 requested) and removed 34 (16 requested) atoms. Cycle 24: After refmac, R = 0.1761 (Rfree = 0.000) for 5824 atoms. Found 24 (32 requested) and removed 25 (16 requested) atoms. Cycle 25: After refmac, R = 0.1711 (Rfree = 0.000) for 5805 atoms. Found 18 (32 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.33 Search for helices and strands: 0 residues in 0 chains, 5925 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 5936 seeds are put forward Round 1: 365 peptides, 70 chains. Longest chain 14 peptides. Score 0.347 Round 2: 404 peptides, 65 chains. Longest chain 18 peptides. Score 0.459 Round 3: 398 peptides, 64 chains. Longest chain 18 peptides. Score 0.457 Round 4: 415 peptides, 64 chains. Longest chain 17 peptides. Score 0.486 Round 5: 411 peptides, 61 chains. Longest chain 17 peptides. Score 0.501 Taking the results from Round 5 Chains 61, Residues 350, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13482 restraints for refining 5912 atoms. 12097 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2443 (Rfree = 0.000) for 5912 atoms. Found 32 (32 requested) and removed 71 (16 requested) atoms. Cycle 27: After refmac, R = 0.1820 (Rfree = 0.000) for 5816 atoms. Found 29 (32 requested) and removed 33 (16 requested) atoms. Cycle 28: After refmac, R = 0.1610 (Rfree = 0.000) for 5787 atoms. Found 11 (31 requested) and removed 28 (15 requested) atoms. Cycle 29: After refmac, R = 0.1508 (Rfree = 0.000) for 5753 atoms. Found 9 (31 requested) and removed 23 (15 requested) atoms. Cycle 30: After refmac, R = 0.1463 (Rfree = 0.000) for 5732 atoms. Found 9 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.38 Search for helices and strands: 0 residues in 0 chains, 5840 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5859 seeds are put forward Round 1: 349 peptides, 74 chains. Longest chain 10 peptides. Score 0.281 Round 2: 375 peptides, 67 chains. Longest chain 10 peptides. Score 0.391 Round 3: 368 peptides, 62 chains. Longest chain 14 peptides. Score 0.418 Round 4: 380 peptides, 60 chains. Longest chain 16 peptides. Score 0.455 Round 5: 377 peptides, 58 chains. Longest chain 16 peptides. Score 0.466 Taking the results from Round 5 Chains 60, Residues 319, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13256 restraints for refining 5919 atoms. 11916 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1973 (Rfree = 0.000) for 5919 atoms. Found 30 (32 requested) and removed 45 (16 requested) atoms. Cycle 32: After refmac, R = 0.1803 (Rfree = 0.000) for 5860 atoms. Found 22 (32 requested) and removed 26 (16 requested) atoms. Cycle 33: After refmac, R = 0.1696 (Rfree = 0.000) for 5851 atoms. Found 9 (32 requested) and removed 20 (16 requested) atoms. Cycle 34: After refmac, R = 0.1665 (Rfree = 0.000) for 5830 atoms. Found 10 (32 requested) and removed 25 (16 requested) atoms. Cycle 35: After refmac, R = 0.1627 (Rfree = 0.000) for 5806 atoms. Found 9 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.35 Search for helices and strands: 0 residues in 0 chains, 5914 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5931 seeds are put forward Round 1: 340 peptides, 69 chains. Longest chain 10 peptides. Score 0.305 Round 2: 354 peptides, 61 chains. Longest chain 12 peptides. Score 0.400 Round 3: 360 peptides, 58 chains. Longest chain 15 peptides. Score 0.435 Round 4: 341 peptides, 54 chains. Longest chain 13 peptides. Score 0.432 Round 5: 355 peptides, 53 chains. Longest chain 17 peptides. Score 0.466 Taking the results from Round 5 Chains 56, Residues 302, Estimated correctness of the model 0.0 % 8 chains (69 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13180 restraints for refining 5963 atoms. 11791 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1882 (Rfree = 0.000) for 5963 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. Cycle 37: After refmac, R = 0.1693 (Rfree = 0.000) for 5912 atoms. Found 11 (32 requested) and removed 24 (16 requested) atoms. Cycle 38: After refmac, R = 0.1621 (Rfree = 0.000) for 5882 atoms. Found 17 (32 requested) and removed 25 (16 requested) atoms. Cycle 39: After refmac, R = 0.1634 (Rfree = 0.000) for 5864 atoms. Found 12 (32 requested) and removed 20 (16 requested) atoms. Cycle 40: After refmac, R = 0.1584 (Rfree = 0.000) for 5846 atoms. Found 10 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.34 Search for helices and strands: 0 residues in 0 chains, 5940 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 5965 seeds are put forward Round 1: 309 peptides, 60 chains. Longest chain 14 peptides. Score 0.320 Round 2: 324 peptides, 55 chains. Longest chain 15 peptides. Score 0.392 Round 3: 329 peptides, 53 chains. Longest chain 19 peptides. Score 0.418 Round 4: 351 peptides, 53 chains. Longest chain 17 peptides. Score 0.459 Round 5: 335 peptides, 56 chains. Longest chain 17 peptides. Score 0.405 Taking the results from Round 4 Chains 56, Residues 298, Estimated correctness of the model 0.0 % 9 chains (70 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 12888 restraints for refining 5963 atoms. 11470 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1884 (Rfree = 0.000) for 5963 atoms. Found 26 (32 requested) and removed 36 (16 requested) atoms. Cycle 42: After refmac, R = 0.1727 (Rfree = 0.000) for 5914 atoms. Found 21 (32 requested) and removed 25 (16 requested) atoms. Cycle 43: After refmac, R = 0.1658 (Rfree = 0.000) for 5895 atoms. Found 15 (32 requested) and removed 22 (16 requested) atoms. Cycle 44: After refmac, R = 0.1628 (Rfree = 0.000) for 5871 atoms. Found 8 (32 requested) and removed 22 (16 requested) atoms. Cycle 45: After refmac, R = 0.1597 (Rfree = 0.000) for 5851 atoms. Found 7 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.39 Search for helices and strands: 0 residues in 0 chains, 5911 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5923 seeds are put forward Round 1: 273 peptides, 58 chains. Longest chain 10 peptides. Score 0.261 Round 2: 307 peptides, 56 chains. Longest chain 14 peptides. Score 0.350 Round 3: 310 peptides, 52 chains. Longest chain 14 peptides. Score 0.390 Round 4: 311 peptides, 54 chains. Longest chain 19 peptides. Score 0.375 Round 5: 321 peptides, 56 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 258, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 53 chains (258 residues) following loop building 6 chains (36 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8080 reflections ( 96.28 % complete ) and 13279 restraints for refining 5914 atoms. 12189 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1776 (Rfree = 0.000) for 5914 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1642 (Rfree = 0.000) for 5867 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1598 (Rfree = 0.000) for 5838 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1631 (Rfree = 0.000) for 5818 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:38:46 GMT 2018 Job finished. TimeTaking 67.3 Used memory is bytes: 15505296