null Sun 23 Dec 22:22:55 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 2anu-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2anu-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2anu-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-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/2anu-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-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 22:23:04 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/2anu-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-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 1242 and 0 Target number of residues in the AU: 1242 Target solvent content: 0.6319 Checking the provided sequence file Detected sequence length: 255 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1530 Adjusted target solvent content: 0.55 Input MTZ file: 2anu-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 12240 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: 127.729 4.001 Wilson plot Bfac: 67.56 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 14900 reflections ( 99.71 % complete ) and 0 restraints for refining 13607 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.2950 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2876 (Rfree = 0.000) for 13607 atoms. Found 64 (64 requested) and removed 63 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 13827 seeds are put forward NCS extension: 0 residues added, 13827 seeds are put forward Round 1: 552 peptides, 106 chains. Longest chain 11 peptides. Score 0.305 Round 2: 721 peptides, 120 chains. Longest chain 15 peptides. Score 0.407 Round 3: 789 peptides, 103 chains. Longest chain 20 peptides. Score 0.524 Round 4: 825 peptides, 102 chains. Longest chain 19 peptides. Score 0.554 Round 5: 797 peptides, 95 chains. Longest chain 21 peptides. Score 0.557 Taking the results from Round 5 Chains 95, Residues 702, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26065 restraints for refining 10960 atoms. 23352 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2334 (Rfree = 0.000) for 10960 atoms. Found 52 (52 requested) and removed 56 (26 requested) atoms. Cycle 2: After refmac, R = 0.2303 (Rfree = 0.000) for 10808 atoms. Found 52 (52 requested) and removed 60 (26 requested) atoms. Cycle 3: After refmac, R = 0.1909 (Rfree = 0.000) for 10727 atoms. Found 20 (51 requested) and removed 39 (25 requested) atoms. Cycle 4: After refmac, R = 0.1889 (Rfree = 0.000) for 10665 atoms. Found 15 (50 requested) and removed 41 (25 requested) atoms. Cycle 5: After refmac, R = 0.1867 (Rfree = 0.000) for 10609 atoms. Found 11 (50 requested) and removed 40 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 10995 seeds are put forward NCS extension: 13 residues added (10 deleted due to clashes), 11008 seeds are put forward Round 1: 719 peptides, 117 chains. Longest chain 18 peptides. Score 0.416 Round 2: 760 peptides, 94 chains. Longest chain 25 peptides. Score 0.533 Round 3: 762 peptides, 100 chains. Longest chain 27 peptides. Score 0.514 Round 4: 796 peptides, 109 chains. Longest chain 20 peptides. Score 0.509 Round 5: 802 peptides, 102 chains. Longest chain 27 peptides. Score 0.537 Taking the results from Round 5 Chains 103, Residues 700, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26240 restraints for refining 11053 atoms. 23456 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2178 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 52 (26 requested) atoms. Cycle 7: After refmac, R = 0.2094 (Rfree = 0.000) for 10988 atoms. Found 52 (52 requested) and removed 52 (26 requested) atoms. Cycle 8: After refmac, R = 0.2150 (Rfree = 0.000) for 10952 atoms. Found 52 (52 requested) and removed 55 (26 requested) atoms. Cycle 9: After refmac, R = 0.1685 (Rfree = 0.000) for 10917 atoms. Found 19 (51 requested) and removed 38 (25 requested) atoms. Cycle 10: After refmac, R = 0.1611 (Rfree = 0.000) for 10877 atoms. Found 13 (51 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 11222 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 11246 seeds are put forward Round 1: 721 peptides, 118 chains. Longest chain 17 peptides. Score 0.414 Round 2: 755 peptides, 104 chains. Longest chain 22 peptides. Score 0.494 Round 3: 771 peptides, 102 chains. Longest chain 21 peptides. Score 0.514 Round 4: 800 peptides, 109 chains. Longest chain 18 peptides. Score 0.512 Round 5: 788 peptides, 99 chains. Longest chain 22 peptides. Score 0.537 Taking the results from Round 5 Chains 101, Residues 689, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26481 restraints for refining 11051 atoms. 23793 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1968 (Rfree = 0.000) for 11051 atoms. Found 38 (52 requested) and removed 41 (26 requested) atoms. Cycle 12: After refmac, R = 0.1814 (Rfree = 0.000) for 10982 atoms. Found 14 (52 requested) and removed 34 (26 requested) atoms. Cycle 13: After refmac, R = 0.1803 (Rfree = 0.000) for 10946 atoms. Found 10 (52 requested) and removed 28 (26 requested) atoms. Cycle 14: After refmac, R = 0.1774 (Rfree = 0.000) for 10918 atoms. Found 8 (51 requested) and removed 33 (25 requested) atoms. Cycle 15: After refmac, R = 0.1764 (Rfree = 0.000) for 10889 atoms. Found 6 (51 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 11212 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 11235 seeds are put forward Round 1: 713 peptides, 123 chains. Longest chain 17 peptides. Score 0.388 Round 2: 763 peptides, 106 chains. Longest chain 19 peptides. Score 0.494 Round 3: 794 peptides, 114 chains. Longest chain 18 peptides. Score 0.490 Round 4: 785 peptides, 105 chains. Longest chain 21 peptides. Score 0.514 Round 5: 767 peptides, 99 chains. Longest chain 22 peptides. Score 0.521 Taking the results from Round 5 Chains 100, Residues 668, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26794 restraints for refining 11053 atoms. 24164 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2007 (Rfree = 0.000) for 11053 atoms. Found 41 (52 requested) and removed 38 (26 requested) atoms. Cycle 17: After refmac, R = 0.2033 (Rfree = 0.000) for 10969 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 18: After refmac, R = 0.1894 (Rfree = 0.000) for 10954 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 19: After refmac, R = 0.1805 (Rfree = 0.000) for 10920 atoms. Found 52 (52 requested) and removed 37 (26 requested) atoms. Cycle 20: After refmac, R = 0.1477 (Rfree = 0.000) for 10900 atoms. Found 19 (51 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 11244 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11260 seeds are put forward Round 1: 641 peptides, 121 chains. Longest chain 15 peptides. Score 0.329 Round 2: 726 peptides, 109 chains. Longest chain 16 peptides. Score 0.452 Round 3: 751 peptides, 115 chains. Longest chain 17 peptides. Score 0.451 Round 4: 739 peptides, 103 chains. Longest chain 15 peptides. Score 0.485 Round 5: 759 peptides, 106 chains. Longest chain 19 peptides. Score 0.490 Taking the results from Round 5 Chains 106, Residues 653, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26591 restraints for refining 11050 atoms. 24041 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1841 (Rfree = 0.000) for 11050 atoms. Found 38 (52 requested) and removed 39 (26 requested) atoms. Cycle 22: After refmac, R = 0.1865 (Rfree = 0.000) for 10952 atoms. Found 52 (52 requested) and removed 34 (26 requested) atoms. Cycle 23: After refmac, R = 0.1977 (Rfree = 0.000) for 10909 atoms. Found 52 (52 requested) and removed 40 (26 requested) atoms. Cycle 24: After refmac, R = 0.1781 (Rfree = 0.000) for 10860 atoms. Found 51 (51 requested) and removed 41 (25 requested) atoms. Cycle 25: After refmac, R = 0.1861 (Rfree = 0.000) for 10826 atoms. Found 51 (51 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.27 Search for helices and strands: 0 residues in 0 chains, 11194 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 11212 seeds are put forward Round 1: 581 peptides, 112 chains. Longest chain 12 peptides. Score 0.308 Round 2: 659 peptides, 104 chains. Longest chain 22 peptides. Score 0.414 Round 3: 645 peptides, 104 chains. Longest chain 17 peptides. Score 0.401 Round 4: 665 peptides, 103 chains. Longest chain 15 peptides. Score 0.423 Round 5: 709 peptides, 105 chains. Longest chain 17 peptides. Score 0.453 Taking the results from Round 5 Chains 105, Residues 604, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26938 restraints for refining 11053 atoms. 24627 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2072 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 32 (26 requested) atoms. Cycle 27: After refmac, R = 0.2017 (Rfree = 0.000) for 10992 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 28: After refmac, R = 0.1959 (Rfree = 0.000) for 10955 atoms. Found 52 (52 requested) and removed 45 (26 requested) atoms. Cycle 29: After refmac, R = 0.1930 (Rfree = 0.000) for 10936 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 30: After refmac, R = 0.1527 (Rfree = 0.000) for 10928 atoms. Found 36 (51 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 11296 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 11316 seeds are put forward Round 1: 583 peptides, 114 chains. Longest chain 10 peptides. Score 0.302 Round 2: 620 peptides, 104 chains. Longest chain 14 peptides. Score 0.379 Round 3: 661 peptides, 109 chains. Longest chain 12 peptides. Score 0.396 Round 4: 662 peptides, 104 chains. Longest chain 15 peptides. Score 0.417 Round 5: 649 peptides, 99 chains. Longest chain 19 peptides. Score 0.425 Taking the results from Round 5 Chains 99, Residues 550, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 27360 restraints for refining 11051 atoms. 25259 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1851 (Rfree = 0.000) for 11051 atoms. Found 31 (52 requested) and removed 35 (26 requested) atoms. Cycle 32: After refmac, R = 0.1988 (Rfree = 0.000) for 10983 atoms. Found 52 (52 requested) and removed 45 (26 requested) atoms. Cycle 33: After refmac, R = 0.1884 (Rfree = 0.000) for 10936 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 34: After refmac, R = 0.1870 (Rfree = 0.000) for 10913 atoms. Found 51 (51 requested) and removed 32 (25 requested) atoms. Cycle 35: After refmac, R = 0.1437 (Rfree = 0.000) for 10915 atoms. Found 24 (51 requested) and removed 62 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 11213 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 11244 seeds are put forward Round 1: 489 peptides, 103 chains. Longest chain 8 peptides. Score 0.253 Round 2: 580 peptides, 106 chains. Longest chain 15 peptides. Score 0.333 Round 3: 549 peptides, 95 chains. Longest chain 18 peptides. Score 0.349 Round 4: 560 peptides, 96 chains. Longest chain 12 peptides. Score 0.355 Round 5: 556 peptides, 89 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 5 Chains 89, Residues 467, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 28186 restraints for refining 11053 atoms. 26407 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2170 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 43 (26 requested) atoms. Cycle 37: After refmac, R = 0.2035 (Rfree = 0.000) for 10992 atoms. Found 52 (52 requested) and removed 46 (26 requested) atoms. Cycle 38: After refmac, R = 0.1946 (Rfree = 0.000) for 10931 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 39: After refmac, R = 0.1902 (Rfree = 0.000) for 10891 atoms. Found 51 (51 requested) and removed 32 (25 requested) atoms. Cycle 40: After refmac, R = 0.1878 (Rfree = 0.000) for 10880 atoms. Found 51 (51 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 11176 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11191 seeds are put forward Round 1: 463 peptides, 96 chains. Longest chain 11 peptides. Score 0.257 Round 2: 553 peptides, 98 chains. Longest chain 13 peptides. Score 0.340 Round 3: 565 peptides, 99 chains. Longest chain 14 peptides. Score 0.348 Round 4: 561 peptides, 97 chains. Longest chain 14 peptides. Score 0.352 Round 5: 562 peptides, 92 chains. Longest chain 17 peptides. Score 0.374 Taking the results from Round 5 Chains 92, Residues 470, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 27720 restraints for refining 11051 atoms. 25932 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1893 (Rfree = 0.000) for 11051 atoms. Found 52 (52 requested) and removed 48 (26 requested) atoms. Cycle 42: After refmac, R = 0.1939 (Rfree = 0.000) for 10980 atoms. Found 52 (52 requested) and removed 40 (26 requested) atoms. Cycle 43: After refmac, R = 0.1927 (Rfree = 0.000) for 10950 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 44: After refmac, R = 0.1873 (Rfree = 0.000) for 10924 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 45: After refmac, R = 0.1929 (Rfree = 0.000) for 10892 atoms. Found 51 (51 requested) and removed 37 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 11235 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 11253 seeds are put forward Round 1: 456 peptides, 98 chains. Longest chain 10 peptides. Score 0.240 Round 2: 524 peptides, 97 chains. Longest chain 17 peptides. Score 0.316 Round 3: 541 peptides, 96 chains. Longest chain 13 peptides. Score 0.337 Round 4: 547 peptides, 90 chains. Longest chain 17 peptides. Score 0.368 Round 5: 569 peptides, 93 chains. Longest chain 14 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 93, Residues 476, 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 2anu-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14900 reflections ( 99.71 % complete ) and 27387 restraints for refining 11050 atoms. 25576 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1909 (Rfree = 0.000) for 11050 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.1815 (Rfree = 0.000) for 10964 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.1842 (Rfree = 0.000) for 10898 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.1800 (Rfree = 0.000) for 10846 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:59:14 GMT 2018 Job finished. TimeTaking 156.32 Used memory is bytes: 27565552