null 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 2anu-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2anu-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2anu-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-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 22:23:18 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-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 1306 and 0 Target number of residues in the AU: 1306 Target solvent content: 0.6130 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-3.4-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-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 12240 target number of atoms Had to go as low as 0.80 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 3.400 Wilson plot Bfac: 58.11 24325 reflections ( 99.82 % complete ) and 0 restraints for refining 13524 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.2784 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2553 (Rfree = 0.000) for 13524 atoms. Found 102 (102 requested) and removed 67 (51 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 2.94 Search for helices and strands: 0 residues in 0 chains, 13777 seeds are put forward NCS extension: 0 residues added, 13777 seeds are put forward Round 1: 822 peptides, 129 chains. Longest chain 16 peptides. Score 0.459 Round 2: 932 peptides, 122 chains. Longest chain 28 peptides. Score 0.566 Round 3: 985 peptides, 120 chains. Longest chain 21 peptides. Score 0.608 Round 4: 1026 peptides, 98 chains. Longest chain 40 peptides. Score 0.692 Round 5: 1023 peptides, 101 chains. Longest chain 40 peptides. Score 0.683 Taking the results from Round 4 Chains 108, Residues 928, Estimated correctness of the model 55.8 % 12 chains (225 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 21734 restraints for refining 11127 atoms. 17142 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2399 (Rfree = 0.000) for 11127 atoms. Found 84 (84 requested) and removed 70 (42 requested) atoms. Cycle 2: After refmac, R = 0.2321 (Rfree = 0.000) for 10963 atoms. Found 71 (84 requested) and removed 53 (42 requested) atoms. Cycle 3: After refmac, R = 0.2235 (Rfree = 0.000) for 10904 atoms. Found 62 (82 requested) and removed 53 (41 requested) atoms. Cycle 4: After refmac, R = 0.2187 (Rfree = 0.000) for 10867 atoms. Found 51 (82 requested) and removed 52 (41 requested) atoms. Cycle 5: After refmac, R = 0.2152 (Rfree = 0.000) for 10836 atoms. Found 47 (82 requested) and removed 53 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.92 Search for helices and strands: 0 residues in 0 chains, 11190 seeds are put forward NCS extension: 20 residues added (11 deleted due to clashes), 11210 seeds are put forward Round 1: 950 peptides, 113 chains. Longest chain 30 peptides. Score 0.606 Round 2: 1034 peptides, 101 chains. Longest chain 43 peptides. Score 0.688 Round 3: 1021 peptides, 106 chains. Longest chain 32 peptides. Score 0.668 Round 4: 1051 peptides, 93 chains. Longest chain 39 peptides. Score 0.717 Round 5: 1035 peptides, 95 chains. Longest chain 47 peptides. Score 0.704 Taking the results from Round 4 Chains 96, Residues 958, Estimated correctness of the model 62.1 % 9 chains (207 residues) have been docked in sequence Building loops using Loopy2018 96 chains (958 residues) following loop building 9 chains (207 residues) in sequence following loop building ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 22295 restraints for refining 11127 atoms. 17681 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2330 (Rfree = 0.000) for 11127 atoms. Found 84 (84 requested) and removed 118 (42 requested) atoms. Cycle 7: After refmac, R = 0.2164 (Rfree = 0.000) for 11000 atoms. Found 45 (81 requested) and removed 59 (41 requested) atoms. Cycle 8: After refmac, R = 0.2111 (Rfree = 0.000) for 10921 atoms. Found 36 (79 requested) and removed 52 (41 requested) atoms. Cycle 9: After refmac, R = 0.2027 (Rfree = 0.000) for 10866 atoms. Found 35 (77 requested) and removed 46 (41 requested) atoms. Cycle 10: After refmac, R = 0.1988 (Rfree = 0.000) for 10827 atoms. Found 38 (75 requested) and removed 42 (40 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 2.95 Search for helices and strands: 0 residues in 0 chains, 11068 seeds are put forward NCS extension: 33 residues added (18 deleted due to clashes), 11101 seeds are put forward Round 1: 950 peptides, 122 chains. Longest chain 20 peptides. Score 0.578 Round 2: 1004 peptides, 103 chains. Longest chain 29 peptides. Score 0.667 Round 3: 1019 peptides, 105 chains. Longest chain 28 peptides. Score 0.670 Round 4: 1018 peptides, 106 chains. Longest chain 30 peptides. Score 0.667 Round 5: 1002 peptides, 103 chains. Longest chain 33 peptides. Score 0.666 Taking the results from Round 3 Chains 109, Residues 914, Estimated correctness of the model 49.8 % 8 chains (134 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 23610 restraints for refining 11128 atoms. 19479 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2132 (Rfree = 0.000) for 11128 atoms. Found 74 (76 requested) and removed 73 (42 requested) atoms. Cycle 12: After refmac, R = 0.2008 (Rfree = 0.000) for 11088 atoms. Found 39 (76 requested) and removed 53 (42 requested) atoms. Cycle 13: After refmac, R = 0.1928 (Rfree = 0.000) for 11042 atoms. Found 37 (75 requested) and removed 48 (41 requested) atoms. Cycle 14: After refmac, R = 0.1874 (Rfree = 0.000) for 11008 atoms. Found 29 (75 requested) and removed 45 (41 requested) atoms. Cycle 15: After refmac, R = 0.1839 (Rfree = 0.000) for 10977 atoms. Found 30 (74 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.93 Search for helices and strands: 0 residues in 0 chains, 11272 seeds are put forward NCS extension: 14 residues added (18 deleted due to clashes), 11286 seeds are put forward Round 1: 962 peptides, 118 chains. Longest chain 39 peptides. Score 0.599 Round 2: 991 peptides, 97 chains. Longest chain 30 peptides. Score 0.675 Round 3: 1007 peptides, 107 chains. Longest chain 29 peptides. Score 0.658 Round 4: 1024 peptides, 105 chains. Longest chain 27 peptides. Score 0.673 Round 5: 1005 peptides, 105 chains. Longest chain 29 peptides. Score 0.662 Taking the results from Round 2 Chains 101, Residues 894, Estimated correctness of the model 51.2 % 12 chains (195 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 23138 restraints for refining 11128 atoms. 18808 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2034 (Rfree = 0.000) for 11128 atoms. Found 62 (76 requested) and removed 62 (42 requested) atoms. Cycle 17: After refmac, R = 0.1902 (Rfree = 0.000) for 11091 atoms. Found 49 (76 requested) and removed 44 (42 requested) atoms. Cycle 18: After refmac, R = 0.1863 (Rfree = 0.000) for 11065 atoms. Found 46 (75 requested) and removed 42 (41 requested) atoms. Cycle 19: After refmac, R = 0.1806 (Rfree = 0.000) for 11048 atoms. Found 46 (75 requested) and removed 43 (41 requested) atoms. Cycle 20: After refmac, R = 0.1760 (Rfree = 0.000) for 11038 atoms. Found 23 (75 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 2.93 Search for helices and strands: 0 residues in 0 chains, 11310 seeds are put forward NCS extension: 11 residues added (8 deleted due to clashes), 11321 seeds are put forward Round 1: 924 peptides, 124 chains. Longest chain 22 peptides. Score 0.554 Round 2: 996 peptides, 110 chains. Longest chain 23 peptides. Score 0.643 Round 3: 998 peptides, 97 chains. Longest chain 29 peptides. Score 0.679 Round 4: 987 peptides, 112 chains. Longest chain 38 peptides. Score 0.632 Round 5: 1006 peptides, 110 chains. Longest chain 25 peptides. Score 0.649 Taking the results from Round 3 Chains 102, Residues 901, Estimated correctness of the model 52.3 % 8 chains (150 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 23552 restraints for refining 11126 atoms. 19406 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2012 (Rfree = 0.000) for 11126 atoms. Found 65 (76 requested) and removed 50 (42 requested) atoms. Cycle 22: After refmac, R = 0.1904 (Rfree = 0.000) for 11107 atoms. Found 35 (76 requested) and removed 43 (42 requested) atoms. Cycle 23: After refmac, R = 0.1868 (Rfree = 0.000) for 11069 atoms. Found 35 (75 requested) and removed 44 (41 requested) atoms. Cycle 24: After refmac, R = 0.1799 (Rfree = 0.000) for 11033 atoms. Found 36 (75 requested) and removed 44 (41 requested) atoms. Cycle 25: After refmac, R = 0.1791 (Rfree = 0.000) for 11003 atoms. Found 30 (75 requested) and removed 42 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.92 Search for helices and strands: 0 residues in 0 chains, 11268 seeds are put forward NCS extension: 21 residues added (8 deleted due to clashes), 11289 seeds are put forward Round 1: 892 peptides, 123 chains. Longest chain 19 peptides. Score 0.534 Round 2: 972 peptides, 110 chains. Longest chain 38 peptides. Score 0.628 Round 3: 969 peptides, 106 chains. Longest chain 48 peptides. Score 0.638 Round 4: 960 peptides, 107 chains. Longest chain 34 peptides. Score 0.630 Round 5: 954 peptides, 109 chains. Longest chain 39 peptides. Score 0.620 Taking the results from Round 3 Chains 108, Residues 863, Estimated correctness of the model 40.6 % 5 chains (116 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 24027 restraints for refining 11126 atoms. 20172 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1987 (Rfree = 0.000) for 11126 atoms. Found 60 (76 requested) and removed 62 (42 requested) atoms. Cycle 27: After refmac, R = 0.1851 (Rfree = 0.000) for 11105 atoms. Found 29 (75 requested) and removed 47 (41 requested) atoms. Cycle 28: After refmac, R = 0.1815 (Rfree = 0.000) for 11069 atoms. Found 32 (75 requested) and removed 48 (41 requested) atoms. Cycle 29: After refmac, R = 0.1811 (Rfree = 0.000) for 11040 atoms. Found 32 (75 requested) and removed 41 (41 requested) atoms. Cycle 30: After refmac, R = 0.1783 (Rfree = 0.000) for 11024 atoms. Found 27 (75 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 2.95 Search for helices and strands: 0 residues in 0 chains, 11301 seeds are put forward NCS extension: 28 residues added (18 deleted due to clashes), 11329 seeds are put forward Round 1: 858 peptides, 114 chains. Longest chain 22 peptides. Score 0.539 Round 2: 921 peptides, 105 chains. Longest chain 27 peptides. Score 0.611 Round 3: 981 peptides, 110 chains. Longest chain 25 peptides. Score 0.634 Round 4: 946 peptides, 101 chains. Longest chain 33 peptides. Score 0.638 Round 5: 954 peptides, 112 chains. Longest chain 26 peptides. Score 0.611 Taking the results from Round 4 Chains 105, Residues 845, Estimated correctness of the model 40.6 % 5 chains (105 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 24000 restraints for refining 11128 atoms. 20255 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1976 (Rfree = 0.000) for 11128 atoms. Found 57 (76 requested) and removed 59 (42 requested) atoms. Cycle 32: After refmac, R = 0.1837 (Rfree = 0.000) for 11091 atoms. Found 32 (76 requested) and removed 46 (42 requested) atoms. Cycle 33: After refmac, R = 0.1810 (Rfree = 0.000) for 11060 atoms. Found 38 (75 requested) and removed 44 (41 requested) atoms. Cycle 34: After refmac, R = 0.1763 (Rfree = 0.000) for 11042 atoms. Found 37 (75 requested) and removed 42 (41 requested) atoms. Cycle 35: After refmac, R = 0.1729 (Rfree = 0.000) for 11022 atoms. Found 29 (75 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 2.91 Search for helices and strands: 0 residues in 0 chains, 11292 seeds are put forward NCS extension: 30 residues added (19 deleted due to clashes), 11322 seeds are put forward Round 1: 839 peptides, 119 chains. Longest chain 19 peptides. Score 0.508 Round 2: 912 peptides, 107 chains. Longest chain 32 peptides. Score 0.599 Round 3: 884 peptides, 108 chains. Longest chain 25 peptides. Score 0.577 Round 4: 908 peptides, 105 chains. Longest chain 28 peptides. Score 0.602 Round 5: 894 peptides, 111 chains. Longest chain 22 peptides. Score 0.574 Taking the results from Round 4 Chains 107, Residues 803, Estimated correctness of the model 29.3 % 5 chains (92 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 24496 restraints for refining 11128 atoms. 20945 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2029 (Rfree = 0.000) for 11128 atoms. Found 68 (76 requested) and removed 58 (42 requested) atoms. Cycle 37: After refmac, R = 0.1906 (Rfree = 0.000) for 11096 atoms. Found 54 (76 requested) and removed 43 (42 requested) atoms. Cycle 38: After refmac, R = 0.1832 (Rfree = 0.000) for 11085 atoms. Found 46 (75 requested) and removed 48 (41 requested) atoms. Cycle 39: After refmac, R = 0.1788 (Rfree = 0.000) for 11064 atoms. Found 47 (75 requested) and removed 45 (41 requested) atoms. Cycle 40: After refmac, R = 0.1745 (Rfree = 0.000) for 11056 atoms. Found 34 (75 requested) and removed 43 (41 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 2.96 Search for helices and strands: 0 residues in 0 chains, 11331 seeds are put forward NCS extension: 17 residues added (6 deleted due to clashes), 11348 seeds are put forward Round 1: 818 peptides, 127 chains. Longest chain 21 peptides. Score 0.463 Round 2: 853 peptides, 109 chains. Longest chain 18 peptides. Score 0.552 Round 3: 906 peptides, 114 chains. Longest chain 21 peptides. Score 0.573 Round 4: 909 peptides, 117 chains. Longest chain 19 peptides. Score 0.566 Round 5: 883 peptides, 119 chains. Longest chain 22 peptides. Score 0.541 Taking the results from Round 3 Chains 115, Residues 792, Estimated correctness of the model 19.6 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 25028 restraints for refining 11128 atoms. 21720 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1933 (Rfree = 0.000) for 11128 atoms. Found 56 (76 requested) and removed 45 (42 requested) atoms. Cycle 42: After refmac, R = 0.1871 (Rfree = 0.000) for 11115 atoms. Found 52 (76 requested) and removed 47 (42 requested) atoms. Cycle 43: After refmac, R = 0.1851 (Rfree = 0.000) for 11102 atoms. Found 45 (75 requested) and removed 42 (41 requested) atoms. Cycle 44: After refmac, R = 0.1793 (Rfree = 0.000) for 11096 atoms. Found 48 (75 requested) and removed 41 (41 requested) atoms. Cycle 45: After refmac, R = 0.1755 (Rfree = 0.000) for 11094 atoms. Found 41 (75 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 2.94 Search for helices and strands: 0 residues in 0 chains, 11382 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 11397 seeds are put forward Round 1: 758 peptides, 123 chains. Longest chain 18 peptides. Score 0.427 Round 2: 855 peptides, 118 chains. Longest chain 20 peptides. Score 0.523 Round 3: 855 peptides, 113 chains. Longest chain 20 peptides. Score 0.540 Round 4: 870 peptides, 120 chains. Longest chain 19 peptides. Score 0.528 Round 5: 874 peptides, 116 chains. Longest chain 25 peptides. Score 0.544 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 119, Residues 758, Estimated correctness of the model 9.3 % 5 chains (76 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2anu-3_warpNtrace.pdb as input Building loops using Loopy2018 119 chains (758 residues) following loop building 5 chains (76 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24325 reflections ( 99.82 % complete ) and 24911 restraints for refining 11127 atoms. 21618 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1980 (Rfree = 0.000) for 11127 atoms. Found 0 (76 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.1926 (Rfree = 0.000) for 11049 atoms. Found 0 (75 requested) and removed 41 (41 requested) atoms. Cycle 48: After refmac, R = 0.1873 (Rfree = 0.000) for 11000 atoms. Found 0 (75 requested) and removed 29 (41 requested) atoms. Cycle 49: After refmac, R = 0.1845 (Rfree = 0.000) for 10963 atoms. Found 0 (74 requested) and removed 33 (41 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:04:33 GMT 2018 Job finished. TimeTaking 161.42 Used memory is bytes: 16402256