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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2anu-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2anu-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.6-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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.6-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 1275 and 0 Target number of residues in the AU: 1275 Target solvent content: 0.6221 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 62.51 20479 reflections ( 99.79 % complete ) and 0 restraints for refining 13666 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.2810 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2693 (Rfree = 0.000) for 13666 atoms. Found 87 (87 requested) and removed 61 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.10 Search for helices and strands: 0 residues in 0 chains, 13909 seeds are put forward NCS extension: 0 residues added, 13909 seeds are put forward Round 1: 682 peptides, 118 chains. Longest chain 18 peptides. Score 0.380 Round 2: 848 peptides, 115 chains. Longest chain 18 peptides. Score 0.528 Round 3: 909 peptides, 115 chains. Longest chain 22 peptides. Score 0.572 Round 4: 933 peptides, 113 chains. Longest chain 22 peptides. Score 0.594 Round 5: 962 peptides, 119 chains. Longest chain 22 peptides. Score 0.596 Taking the results from Round 5 Chains 121, Residues 843, Estimated correctness of the model 13.1 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25122 restraints for refining 11094 atoms. 21788 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2350 (Rfree = 0.000) for 11094 atoms. Found 71 (71 requested) and removed 54 (35 requested) atoms. Cycle 2: After refmac, R = 0.2355 (Rfree = 0.000) for 10943 atoms. Found 71 (71 requested) and removed 49 (35 requested) atoms. Cycle 3: After refmac, R = 0.2326 (Rfree = 0.000) for 10884 atoms. Found 70 (70 requested) and removed 52 (35 requested) atoms. Cycle 4: After refmac, R = 0.2243 (Rfree = 0.000) for 10857 atoms. Found 69 (69 requested) and removed 54 (34 requested) atoms. Cycle 5: After refmac, R = 0.2066 (Rfree = 0.000) for 10825 atoms. Found 37 (69 requested) and removed 44 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.10 Search for helices and strands: 0 residues in 0 chains, 11181 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11198 seeds are put forward Round 1: 833 peptides, 120 chains. Longest chain 23 peptides. Score 0.500 Round 2: 923 peptides, 119 chains. Longest chain 22 peptides. Score 0.569 Round 3: 945 peptides, 114 chains. Longest chain 25 peptides. Score 0.599 Round 4: 939 peptides, 109 chains. Longest chain 23 peptides. Score 0.610 Round 5: 945 peptides, 114 chains. Longest chain 23 peptides. Score 0.599 Taking the results from Round 4 Chains 111, Residues 830, Estimated correctness of the model 18.5 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25433 restraints for refining 11096 atoms. 22150 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2283 (Rfree = 0.000) for 11096 atoms. Found 71 (71 requested) and removed 56 (35 requested) atoms. Cycle 7: After refmac, R = 0.2197 (Rfree = 0.000) for 11022 atoms. Found 71 (71 requested) and removed 47 (35 requested) atoms. Cycle 8: After refmac, R = 0.2176 (Rfree = 0.000) for 10993 atoms. Found 27 (70 requested) and removed 39 (35 requested) atoms. Cycle 9: After refmac, R = 0.1905 (Rfree = 0.000) for 10938 atoms. Found 34 (70 requested) and removed 44 (35 requested) atoms. Cycle 10: After refmac, R = 0.1877 (Rfree = 0.000) for 10913 atoms. Found 21 (70 requested) and removed 41 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.11 Search for helices and strands: 0 residues in 0 chains, 11206 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 11220 seeds are put forward Round 1: 836 peptides, 125 chains. Longest chain 19 peptides. Score 0.485 Round 2: 909 peptides, 118 chains. Longest chain 23 peptides. Score 0.563 Round 3: 929 peptides, 114 chains. Longest chain 27 peptides. Score 0.589 Round 4: 937 peptides, 114 chains. Longest chain 21 peptides. Score 0.594 Round 5: 961 peptides, 117 chains. Longest chain 23 peptides. Score 0.601 Taking the results from Round 5 Chains 122, Residues 844, Estimated correctness of the model 15.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25134 restraints for refining 11094 atoms. 21692 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2133 (Rfree = 0.000) for 11094 atoms. Found 71 (71 requested) and removed 60 (35 requested) atoms. Cycle 12: After refmac, R = 0.1990 (Rfree = 0.000) for 11021 atoms. Found 52 (71 requested) and removed 42 (35 requested) atoms. Cycle 13: After refmac, R = 0.1973 (Rfree = 0.000) for 10987 atoms. Found 53 (70 requested) and removed 46 (35 requested) atoms. Cycle 14: After refmac, R = 0.1928 (Rfree = 0.000) for 10963 atoms. Found 55 (70 requested) and removed 41 (35 requested) atoms. Cycle 15: After refmac, R = 0.1910 (Rfree = 0.000) for 10951 atoms. Found 50 (70 requested) and removed 39 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 11283 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 11301 seeds are put forward Round 1: 862 peptides, 131 chains. Longest chain 19 peptides. Score 0.484 Round 2: 907 peptides, 122 chains. Longest chain 20 peptides. Score 0.548 Round 3: 935 peptides, 119 chains. Longest chain 49 peptides. Score 0.578 Round 4: 921 peptides, 113 chains. Longest chain 46 peptides. Score 0.586 Round 5: 939 peptides, 121 chains. Longest chain 21 peptides. Score 0.574 Taking the results from Round 4 Chains 115, Residues 808, Estimated correctness of the model 9.1 % 6 chains (120 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 24262 restraints for refining 11094 atoms. 20577 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2193 (Rfree = 0.000) for 11094 atoms. Found 59 (71 requested) and removed 48 (35 requested) atoms. Cycle 17: After refmac, R = 0.2147 (Rfree = 0.000) for 11049 atoms. Found 36 (71 requested) and removed 50 (35 requested) atoms. Cycle 18: After refmac, R = 0.2136 (Rfree = 0.000) for 11010 atoms. Found 24 (70 requested) and removed 41 (35 requested) atoms. Cycle 19: After refmac, R = 0.2199 (Rfree = 0.000) for 10970 atoms. Found 51 (70 requested) and removed 43 (35 requested) atoms. Cycle 20: After refmac, R = 0.2166 (Rfree = 0.000) for 10966 atoms. Found 46 (70 requested) and removed 42 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 11262 seeds are put forward NCS extension: 26 residues added (13 deleted due to clashes), 11288 seeds are put forward Round 1: 785 peptides, 124 chains. Longest chain 18 peptides. Score 0.447 Round 2: 870 peptides, 119 chains. Longest chain 20 peptides. Score 0.531 Round 3: 877 peptides, 118 chains. Longest chain 24 peptides. Score 0.540 Round 4: 898 peptides, 115 chains. Longest chain 24 peptides. Score 0.564 Round 5: 878 peptides, 120 chains. Longest chain 28 peptides. Score 0.534 Taking the results from Round 4 Chains 115, Residues 783, Estimated correctness of the model 0.1 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25459 restraints for refining 11095 atoms. 22342 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2164 (Rfree = 0.000) for 11095 atoms. Found 67 (71 requested) and removed 53 (35 requested) atoms. Cycle 22: After refmac, R = 0.1976 (Rfree = 0.000) for 11049 atoms. Found 38 (71 requested) and removed 39 (35 requested) atoms. Cycle 23: After refmac, R = 0.1941 (Rfree = 0.000) for 11014 atoms. Found 16 (70 requested) and removed 38 (35 requested) atoms. Cycle 24: After refmac, R = 0.1940 (Rfree = 0.000) for 10977 atoms. Found 14 (70 requested) and removed 41 (35 requested) atoms. Cycle 25: After refmac, R = 0.2023 (Rfree = 0.000) for 10928 atoms. Found 52 (70 requested) and removed 40 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.06 Search for helices and strands: 0 residues in 0 chains, 11255 seeds are put forward NCS extension: 10 residues added (14 deleted due to clashes), 11265 seeds are put forward Round 1: 759 peptides, 125 chains. Longest chain 21 peptides. Score 0.421 Round 2: 809 peptides, 110 chains. Longest chain 20 peptides. Score 0.515 Round 3: 824 peptides, 107 chains. Longest chain 23 peptides. Score 0.537 Round 4: 855 peptides, 114 chains. Longest chain 24 peptides. Score 0.537 Round 5: 862 peptides, 112 chains. Longest chain 32 peptides. Score 0.548 Taking the results from Round 5 Chains 114, Residues 750, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25861 restraints for refining 11094 atoms. 22942 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2192 (Rfree = 0.000) for 11094 atoms. Found 69 (71 requested) and removed 41 (35 requested) atoms. Cycle 27: After refmac, R = 0.1995 (Rfree = 0.000) for 11055 atoms. Found 67 (71 requested) and removed 41 (35 requested) atoms. Cycle 28: After refmac, R = 0.1822 (Rfree = 0.000) for 11038 atoms. Found 27 (71 requested) and removed 36 (35 requested) atoms. Cycle 29: After refmac, R = 0.1845 (Rfree = 0.000) for 11005 atoms. Found 39 (70 requested) and removed 36 (35 requested) atoms. Cycle 30: After refmac, R = 0.1718 (Rfree = 0.000) for 10986 atoms. Found 26 (70 requested) and removed 38 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.11 Search for helices and strands: 0 residues in 0 chains, 11323 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11343 seeds are put forward Round 1: 717 peptides, 127 chains. Longest chain 15 peptides. Score 0.376 Round 2: 823 peptides, 125 chains. Longest chain 21 peptides. Score 0.474 Round 3: 822 peptides, 113 chains. Longest chain 24 peptides. Score 0.515 Round 4: 844 peptides, 120 chains. Longest chain 23 peptides. Score 0.508 Round 5: 840 peptides, 117 chains. Longest chain 20 peptides. Score 0.515 Taking the results from Round 5 Chains 121, Residues 723, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25931 restraints for refining 11093 atoms. 23037 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2169 (Rfree = 0.000) for 11093 atoms. Found 71 (71 requested) and removed 39 (35 requested) atoms. Cycle 32: After refmac, R = 0.2094 (Rfree = 0.000) for 11080 atoms. Found 60 (71 requested) and removed 42 (35 requested) atoms. Cycle 33: After refmac, R = 0.2084 (Rfree = 0.000) for 11063 atoms. Found 70 (71 requested) and removed 40 (35 requested) atoms. Cycle 34: After refmac, R = 0.2018 (Rfree = 0.000) for 11068 atoms. Found 71 (71 requested) and removed 43 (35 requested) atoms. Cycle 35: After refmac, R = 0.1790 (Rfree = 0.000) for 11074 atoms. Found 11 (71 requested) and removed 36 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 11384 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 11409 seeds are put forward Round 1: 669 peptides, 118 chains. Longest chain 15 peptides. Score 0.368 Round 2: 791 peptides, 122 chains. Longest chain 25 peptides. Score 0.459 Round 3: 801 peptides, 114 chains. Longest chain 16 peptides. Score 0.495 Round 4: 797 peptides, 117 chains. Longest chain 17 peptides. Score 0.482 Round 5: 802 peptides, 114 chains. Longest chain 15 peptides. Score 0.496 Taking the results from Round 5 Chains 114, Residues 688, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 26247 restraints for refining 11093 atoms. 23534 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2023 (Rfree = 0.000) for 11093 atoms. Found 69 (71 requested) and removed 44 (35 requested) atoms. Cycle 37: After refmac, R = 0.1994 (Rfree = 0.000) for 11073 atoms. Found 71 (71 requested) and removed 38 (35 requested) atoms. Cycle 38: After refmac, R = 0.2009 (Rfree = 0.000) for 11067 atoms. Found 71 (71 requested) and removed 40 (35 requested) atoms. Cycle 39: After refmac, R = 0.1702 (Rfree = 0.000) for 11066 atoms. Found 20 (71 requested) and removed 37 (35 requested) atoms. Cycle 40: After refmac, R = 0.1660 (Rfree = 0.000) for 11028 atoms. Found 17 (70 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.11 Search for helices and strands: 0 residues in 0 chains, 11343 seeds are put forward NCS extension: 8 residues added (5 deleted due to clashes), 11351 seeds are put forward Round 1: 695 peptides, 132 chains. Longest chain 15 peptides. Score 0.336 Round 2: 764 peptides, 118 chains. Longest chain 20 peptides. Score 0.451 Round 3: 765 peptides, 114 chains. Longest chain 19 peptides. Score 0.466 Round 4: 775 peptides, 115 chains. Longest chain 20 peptides. Score 0.471 Round 5: 763 peptides, 114 chains. Longest chain 21 peptides. Score 0.465 Taking the results from Round 4 Chains 116, Residues 660, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 26441 restraints for refining 11096 atoms. 23838 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1993 (Rfree = 0.000) for 11096 atoms. Found 53 (71 requested) and removed 41 (35 requested) atoms. Cycle 42: After refmac, R = 0.1932 (Rfree = 0.000) for 11073 atoms. Found 51 (71 requested) and removed 39 (35 requested) atoms. Cycle 43: After refmac, R = 0.1989 (Rfree = 0.000) for 11064 atoms. Found 58 (71 requested) and removed 37 (35 requested) atoms. Cycle 44: After refmac, R = 0.1954 (Rfree = 0.000) for 11063 atoms. Found 71 (71 requested) and removed 41 (35 requested) atoms. Cycle 45: After refmac, R = 0.2032 (Rfree = 0.000) for 11070 atoms. Found 71 (71 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 11391 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11409 seeds are put forward Round 1: 593 peptides, 108 chains. Longest chain 15 peptides. Score 0.337 Round 2: 692 peptides, 114 chains. Longest chain 22 peptides. Score 0.404 Round 3: 701 peptides, 111 chains. Longest chain 15 peptides. Score 0.424 Round 4: 691 peptides, 109 chains. Longest chain 15 peptides. Score 0.423 Round 5: 671 peptides, 107 chains. Longest chain 14 peptides. Score 0.413 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 111, Residues 590, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2anu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20479 reflections ( 99.79 % complete ) and 26869 restraints for refining 11096 atoms. 24558 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2141 (Rfree = 0.000) for 11096 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.2086 (Rfree = 0.000) for 11025 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.2118 (Rfree = 0.000) for 10968 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1878 (Rfree = 0.000) for 10906 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:01:36 GMT 2018 Job finished. TimeTaking 158.68 Used memory is bytes: 15808880