Sun 23 Dec 22:23:08 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 2ash-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ash-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ash-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-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/2ash-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-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 22:23:17 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/2ash-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-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 1084 and 0 Target number of residues in the AU: 1084 Target solvent content: 0.6663 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.85 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: 103.605 3.800 Wilson plot Bfac: 89.48 Failed to save intermediate PDB 17200 reflections ( 99.72 % complete ) and 0 restraints for refining 13444 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3360 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3013 (Rfree = 0.000) for 13444 atoms. Found 73 (73 requested) and removed 76 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.57 Search for helices and strands: 0 residues in 0 chains, 13654 seeds are put forward NCS extension: 0 residues added, 13654 seeds are put forward Round 1: 541 peptides, 108 chains. Longest chain 10 peptides. Score 0.289 Round 2: 708 peptides, 114 chains. Longest chain 17 peptides. Score 0.425 Round 3: 744 peptides, 115 chains. Longest chain 17 peptides. Score 0.453 Round 4: 760 peptides, 111 chains. Longest chain 24 peptides. Score 0.482 Round 5: 777 peptides, 112 chains. Longest chain 26 peptides. Score 0.492 Taking the results from Round 5 Chains 113, Residues 665, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 25863 restraints for refining 11024 atoms. 23212 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2524 (Rfree = 0.000) for 11024 atoms. Found 54 (60 requested) and removed 63 (30 requested) atoms. Cycle 2: After refmac, R = 0.2396 (Rfree = 0.000) for 10817 atoms. Found 58 (60 requested) and removed 54 (30 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2249 (Rfree = 0.000) for 10724 atoms. Found 49 (59 requested) and removed 50 (29 requested) atoms. Cycle 4: After refmac, R = 0.2231 (Rfree = 0.000) for 10637 atoms. Found 58 (58 requested) and removed 40 (29 requested) atoms. Cycle 5: After refmac, R = 0.2112 (Rfree = 0.000) for 10602 atoms. Found 58 (58 requested) and removed 43 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 11046 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 11071 seeds are put forward Round 1: 668 peptides, 128 chains. Longest chain 10 peptides. Score 0.331 Round 2: 775 peptides, 117 chains. Longest chain 27 peptides. Score 0.472 Round 3: 780 peptides, 116 chains. Longest chain 23 peptides. Score 0.480 Round 4: 768 peptides, 106 chains. Longest chain 29 peptides. Score 0.506 Round 5: 816 peptides, 112 chains. Longest chain 22 peptides. Score 0.523 Taking the results from Round 5 Chains 112, Residues 704, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 25020 restraints for refining 10888 atoms. 22298 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2216 (Rfree = 0.000) for 10888 atoms. Found 48 (59 requested) and removed 80 (29 requested) atoms. Cycle 7: After refmac, R = 0.2090 (Rfree = 0.000) for 10753 atoms. Found 59 (59 requested) and removed 47 (29 requested) atoms. Cycle 8: After refmac, R = 0.1927 (Rfree = 0.000) for 10710 atoms. Found 48 (59 requested) and removed 46 (29 requested) atoms. Cycle 9: After refmac, R = 0.1921 (Rfree = 0.000) for 10675 atoms. Found 58 (58 requested) and removed 53 (29 requested) atoms. Cycle 10: After refmac, R = 0.1580 (Rfree = 0.000) for 10655 atoms. Found 18 (58 requested) and removed 37 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.56 Search for helices and strands: 0 residues in 0 chains, 11036 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 11047 seeds are put forward Round 1: 706 peptides, 132 chains. Longest chain 12 peptides. Score 0.352 Round 2: 770 peptides, 117 chains. Longest chain 16 peptides. Score 0.468 Round 3: 757 peptides, 109 chains. Longest chain 27 peptides. Score 0.486 Round 4: 794 peptides, 109 chains. Longest chain 29 peptides. Score 0.516 Round 5: 767 peptides, 110 chains. Longest chain 19 peptides. Score 0.491 Taking the results from Round 4 Chains 109, Residues 685, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 25357 restraints for refining 11025 atoms. 22686 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2021 (Rfree = 0.000) for 11025 atoms. Found 38 (60 requested) and removed 54 (30 requested) atoms. Cycle 12: After refmac, R = 0.2054 (Rfree = 0.000) for 10921 atoms. Found 60 (60 requested) and removed 44 (30 requested) atoms. Cycle 13: After refmac, R = 0.1974 (Rfree = 0.000) for 10879 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 14: After refmac, R = 0.1925 (Rfree = 0.000) for 10827 atoms. Found 52 (59 requested) and removed 41 (29 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1879 (Rfree = 0.000) for 10799 atoms. Found 55 (59 requested) and removed 42 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 11175 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 11199 seeds are put forward Round 1: 613 peptides, 123 chains. Longest chain 11 peptides. Score 0.298 Round 2: 709 peptides, 117 chains. Longest chain 18 peptides. Score 0.414 Round 3: 730 peptides, 120 chains. Longest chain 14 peptides. Score 0.421 Round 4: 725 peptides, 113 chains. Longest chain 17 peptides. Score 0.444 Round 5: 728 peptides, 108 chains. Longest chain 22 peptides. Score 0.466 Taking the results from Round 5 Chains 110, Residues 620, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 25416 restraints for refining 11024 atoms. 22945 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2168 (Rfree = 0.000) for 11024 atoms. Found 60 (60 requested) and removed 52 (30 requested) atoms. Cycle 17: After refmac, R = 0.2038 (Rfree = 0.000) for 10957 atoms. Found 60 (60 requested) and removed 47 (30 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1997 (Rfree = 0.000) for 10930 atoms. Found 60 (60 requested) and removed 59 (30 requested) atoms. Cycle 19: After refmac, R = 0.1911 (Rfree = 0.000) for 10905 atoms. Found 43 (60 requested) and removed 40 (30 requested) atoms. Cycle 20: After refmac, R = 0.1579 (Rfree = 0.000) for 10883 atoms. Found 12 (59 requested) and removed 33 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.57 Search for helices and strands: 0 residues in 0 chains, 11216 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 11239 seeds are put forward Round 1: 617 peptides, 120 chains. Longest chain 12 peptides. Score 0.314 Round 2: 707 peptides, 116 chains. Longest chain 17 peptides. Score 0.417 Round 3: 694 peptides, 107 chains. Longest chain 28 peptides. Score 0.440 Round 4: 697 peptides, 111 chains. Longest chain 19 peptides. Score 0.427 Round 5: 709 peptides, 113 chains. Longest chain 19 peptides. Score 0.430 Taking the results from Round 3 Chains 107, Residues 587, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 25655 restraints for refining 11025 atoms. 23277 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1969 (Rfree = 0.000) for 11025 atoms. Found 45 (60 requested) and removed 41 (30 requested) atoms. Cycle 22: After refmac, R = 0.1984 (Rfree = 0.000) for 10977 atoms. Found 60 (60 requested) and removed 35 (30 requested) atoms. Cycle 23: After refmac, R = 0.1941 (Rfree = 0.000) for 10970 atoms. Found 60 (60 requested) and removed 42 (30 requested) atoms. Cycle 24: After refmac, R = 0.1831 (Rfree = 0.000) for 10961 atoms. Found 52 (60 requested) and removed 49 (30 requested) atoms. Cycle 25: After refmac, R = 0.1886 (Rfree = 0.000) for 10939 atoms. Found 60 (60 requested) and removed 41 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.56 Search for helices and strands: 0 residues in 0 chains, 11308 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 11336 seeds are put forward Round 1: 604 peptides, 118 chains. Longest chain 15 peptides. Score 0.310 Round 2: 674 peptides, 110 chains. Longest chain 16 peptides. Score 0.410 Round 3: 706 peptides, 113 chains. Longest chain 15 peptides. Score 0.427 Round 4: 687 peptides, 106 chains. Longest chain 16 peptides. Score 0.438 Round 5: 700 peptides, 110 chains. Longest chain 17 peptides. Score 0.434 Taking the results from Round 4 Chains 106, Residues 581, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 26092 restraints for refining 11026 atoms. 23822 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1962 (Rfree = 0.000) for 11026 atoms. Found 45 (60 requested) and removed 44 (30 requested) atoms. Cycle 27: After refmac, R = 0.1929 (Rfree = 0.000) for 10987 atoms. Found 60 (60 requested) and removed 44 (30 requested) atoms. Cycle 28: After refmac, R = 0.1860 (Rfree = 0.000) for 10964 atoms. Found 60 (60 requested) and removed 37 (30 requested) atoms. Cycle 29: After refmac, R = 0.1852 (Rfree = 0.000) for 10959 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 30: After refmac, R = 0.1417 (Rfree = 0.000) for 10948 atoms. Found 10 (60 requested) and removed 38 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 11336 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 11354 seeds are put forward Round 1: 563 peptides, 115 chains. Longest chain 9 peptides. Score 0.281 Round 2: 648 peptides, 116 chains. Longest chain 13 peptides. Score 0.362 Round 3: 685 peptides, 116 chains. Longest chain 16 peptides. Score 0.396 Round 4: 690 peptides, 115 chains. Longest chain 13 peptides. Score 0.405 Round 5: 664 peptides, 108 chains. Longest chain 17 peptides. Score 0.409 Taking the results from Round 5 Chains 109, Residues 556, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 26100 restraints for refining 11024 atoms. 23889 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2017 (Rfree = 0.000) for 11024 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 32: After refmac, R = 0.1950 (Rfree = 0.000) for 10983 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1859 (Rfree = 0.000) for 10966 atoms. Found 60 (60 requested) and removed 52 (30 requested) atoms. Cycle 34: After refmac, R = 0.1784 (Rfree = 0.000) for 10948 atoms. Found 57 (60 requested) and removed 40 (30 requested) atoms. Cycle 35: After refmac, R = 0.1414 (Rfree = 0.000) for 10943 atoms. Found 17 (60 requested) and removed 36 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 11315 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 11336 seeds are put forward Round 1: 509 peptides, 106 chains. Longest chain 9 peptides. Score 0.264 Round 2: 597 peptides, 109 chains. Longest chain 14 peptides. Score 0.341 Round 3: 624 peptides, 107 chains. Longest chain 15 peptides. Score 0.376 Round 4: 586 peptides, 101 chains. Longest chain 14 peptides. Score 0.364 Round 5: 613 peptides, 101 chains. Longest chain 14 peptides. Score 0.390 Taking the results from Round 5 Chains 101, Residues 512, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 26420 restraints for refining 11027 atoms. 24464 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1992 (Rfree = 0.000) for 11027 atoms. Found 60 (60 requested) and removed 47 (30 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2065 (Rfree = 0.000) for 10990 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 38: After refmac, R = 0.2009 (Rfree = 0.000) for 10953 atoms. Found 60 (60 requested) and removed 43 (30 requested) atoms. Cycle 39: After refmac, R = 0.1975 (Rfree = 0.000) for 10941 atoms. Found 60 (60 requested) and removed 38 (30 requested) atoms. Cycle 40: After refmac, R = 0.1481 (Rfree = 0.000) for 10917 atoms. Found 19 (60 requested) and removed 36 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.57 Search for helices and strands: 0 residues in 0 chains, 11287 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 11310 seeds are put forward Round 1: 475 peptides, 100 chains. Longest chain 8 peptides. Score 0.254 Round 2: 585 peptides, 106 chains. Longest chain 14 peptides. Score 0.342 Round 3: 593 peptides, 101 chains. Longest chain 15 peptides. Score 0.371 Round 4: 606 peptides, 105 chains. Longest chain 16 peptides. Score 0.367 Round 5: 587 peptides, 96 chains. Longest chain 16 peptides. Score 0.387 Taking the results from Round 5 Chains 96, Residues 491, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 25732 restraints for refining 11024 atoms. 23836 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2039 (Rfree = 0.000) for 11024 atoms. Found 60 (60 requested) and removed 55 (30 requested) atoms. Cycle 42: After refmac, R = 0.1997 (Rfree = 0.000) for 10982 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 43: After refmac, R = 0.1894 (Rfree = 0.000) for 10957 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1842 (Rfree = 0.000) for 10949 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 45: After refmac, R = 0.1355 (Rfree = 0.000) for 10946 atoms. Found 13 (60 requested) and removed 40 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.57 Search for helices and strands: 0 residues in 0 chains, 11360 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 11377 seeds are put forward Round 1: 488 peptides, 107 chains. Longest chain 10 peptides. Score 0.236 Round 2: 560 peptides, 107 chains. Longest chain 15 peptides. Score 0.313 Round 3: 574 peptides, 106 chains. Longest chain 13 peptides. Score 0.331 Round 4: 565 peptides, 100 chains. Longest chain 13 peptides. Score 0.348 Round 5: 583 peptides, 105 chains. Longest chain 15 peptides. Score 0.344 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 100, Residues 465, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2ash-3_warpNtrace.pdb as input Building loops using Loopy2018 100 chains (465 residues) following loop building 3 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17200 reflections ( 99.72 % complete ) and 26294 restraints for refining 11026 atoms. 24505 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1959 (Rfree = 0.000) for 11026 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 47: After refmac, R = 0.1931 (Rfree = 0.000) for 10948 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 48: After refmac, R = 0.1854 (Rfree = 0.000) for 10886 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1772 (Rfree = 0.000) for 10837 atoms. Found 0 (59 requested) and removed 29 (29 requested) atoms. Writing output files ... TimeTaking 134.68