null Mon 24 Dec 07:43:19 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 2anu-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2anu-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2anu-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-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/2anu-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-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 07:43:24 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/2anu-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-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 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-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-3.4-parrot-noncs.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 13635 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.2891 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2680 (Rfree = 0.000) for 13635 atoms. Found 102 (102 requested) and removed 100 (51 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 2.96 Search for helices and strands: 0 residues in 0 chains, 13861 seeds are put forward NCS extension: 0 residues added, 13861 seeds are put forward Round 1: 715 peptides, 121 chains. Longest chain 23 peptides. Score 0.398 Round 2: 854 peptides, 123 chains. Longest chain 24 peptides. Score 0.505 Round 3: 876 peptides, 116 chains. Longest chain 24 peptides. Score 0.545 Round 4: 927 peptides, 117 chains. Longest chain 34 peptides. Score 0.578 Round 5: 923 peptides, 106 chains. Longest chain 33 peptides. Score 0.609 Taking the results from Round 5 Chains 109, Residues 817, Estimated correctness of the model 31.6 % 5 chains (80 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 24036 restraints for refining 11124 atoms. 20539 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2306 (Rfree = 0.000) for 11124 atoms. Found 82 (84 requested) and removed 74 (42 requested) atoms. Cycle 2: After refmac, R = 0.2225 (Rfree = 0.000) for 10980 atoms. Found 54 (84 requested) and removed 54 (42 requested) atoms. Cycle 3: After refmac, R = 0.2185 (Rfree = 0.000) for 10917 atoms. Found 80 (82 requested) and removed 51 (41 requested) atoms. Cycle 4: After refmac, R = 0.2174 (Rfree = 0.000) for 10888 atoms. Found 57 (82 requested) and removed 53 (41 requested) atoms. Cycle 5: After refmac, R = 0.2109 (Rfree = 0.000) for 10856 atoms. Found 63 (82 requested) and removed 48 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.92 Search for helices and strands: 0 residues in 0 chains, 11179 seeds are put forward NCS extension: 17 residues added (14 deleted due to clashes), 11196 seeds are put forward Round 1: 875 peptides, 122 chains. Longest chain 34 peptides. Score 0.525 Round 2: 973 peptides, 115 chains. Longest chain 38 peptides. Score 0.615 Round 3: 966 peptides, 105 chains. Longest chain 30 peptides. Score 0.639 Round 4: 988 peptides, 110 chains. Longest chain 39 peptides. Score 0.638 Round 5: 987 peptides, 106 chains. Longest chain 37 peptides. Score 0.649 Taking the results from Round 5 Chains 114, Residues 881, Estimated correctness of the model 43.8 % 8 chains (121 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 23850 restraints for refining 11126 atoms. 19908 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2291 (Rfree = 0.000) for 11126 atoms. Found 84 (84 requested) and removed 67 (42 requested) atoms. Cycle 7: After refmac, R = 0.2104 (Rfree = 0.000) for 11078 atoms. Found 69 (84 requested) and removed 59 (42 requested) atoms. Cycle 8: After refmac, R = 0.2103 (Rfree = 0.000) for 11036 atoms. Found 62 (83 requested) and removed 51 (41 requested) atoms. Cycle 9: After refmac, R = 0.2024 (Rfree = 0.000) for 11013 atoms. Found 54 (83 requested) and removed 51 (41 requested) atoms. Cycle 10: After refmac, R = 0.2018 (Rfree = 0.000) for 10990 atoms. Found 67 (83 requested) and removed 50 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 2.91 Search for helices and strands: 0 residues in 0 chains, 11319 seeds are put forward NCS extension: 22 residues added (8 deleted due to clashes), 11341 seeds are put forward Round 1: 936 peptides, 130 chains. Longest chain 27 peptides. Score 0.544 Round 2: 958 peptides, 111 chains. Longest chain 37 peptides. Score 0.617 Round 3: 976 peptides, 106 chains. Longest chain 30 peptides. Score 0.642 Round 4: 954 peptides, 107 chains. Longest chain 29 peptides. Score 0.626 Round 5: 992 peptides, 109 chains. Longest chain 36 peptides. Score 0.643 Taking the results from Round 5 Chains 114, Residues 883, Estimated correctness of the model 42.1 % 7 chains (138 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 23548 restraints for refining 11129 atoms. 19540 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2251 (Rfree = 0.000) for 11129 atoms. Found 73 (84 requested) and removed 56 (42 requested) atoms. Cycle 12: After refmac, R = 0.2106 (Rfree = 0.000) for 11083 atoms. Found 37 (84 requested) and removed 50 (42 requested) atoms. Cycle 13: After refmac, R = 0.2023 (Rfree = 0.000) for 11031 atoms. Found 36 (83 requested) and removed 47 (41 requested) atoms. Cycle 14: After refmac, R = 0.1957 (Rfree = 0.000) for 10987 atoms. Found 40 (83 requested) and removed 45 (41 requested) atoms. Cycle 15: After refmac, R = 0.1933 (Rfree = 0.000) for 10953 atoms. Found 50 (82 requested) and removed 46 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 2.92 Search for helices and strands: 0 residues in 0 chains, 11246 seeds are put forward NCS extension: 10 residues added (20 deleted due to clashes), 11256 seeds are put forward Round 1: 899 peptides, 129 chains. Longest chain 31 peptides. Score 0.520 Round 2: 960 peptides, 110 chains. Longest chain 42 peptides. Score 0.621 Round 3: 970 peptides, 109 chains. Longest chain 34 peptides. Score 0.630 Round 4: 975 peptides, 114 chains. Longest chain 22 peptides. Score 0.619 Round 5: 951 peptides, 106 chains. Longest chain 32 peptides. Score 0.627 Taking the results from Round 3 Chains 116, Residues 861, Estimated correctness of the model 38.2 % 12 chains (214 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 22648 restraints for refining 11127 atoms. 18353 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2290 (Rfree = 0.000) for 11127 atoms. Found 84 (84 requested) and removed 78 (42 requested) atoms. Cycle 17: After refmac, R = 0.2118 (Rfree = 0.000) for 11038 atoms. Found 69 (84 requested) and removed 58 (42 requested) atoms. Cycle 18: After refmac, R = 0.2035 (Rfree = 0.000) for 10985 atoms. Found 67 (83 requested) and removed 50 (41 requested) atoms. Cycle 19: After refmac, R = 0.1978 (Rfree = 0.000) for 10955 atoms. Found 43 (83 requested) and removed 45 (41 requested) atoms. Cycle 20: After refmac, R = 0.1948 (Rfree = 0.000) for 10913 atoms. Found 50 (82 requested) and removed 48 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 2.93 Search for helices and strands: 0 residues in 0 chains, 11166 seeds are put forward NCS extension: 17 residues added (6 deleted due to clashes), 11183 seeds are put forward Round 1: 874 peptides, 123 chains. Longest chain 34 peptides. Score 0.521 Round 2: 944 peptides, 109 chains. Longest chain 25 peptides. Score 0.614 Round 3: 935 peptides, 113 chains. Longest chain 27 peptides. Score 0.596 Round 4: 929 peptides, 109 chains. Longest chain 34 peptides. Score 0.604 Round 5: 955 peptides, 105 chains. Longest chain 27 peptides. Score 0.632 Taking the results from Round 5 Chains 111, Residues 850, Estimated correctness of the model 38.8 % 7 chains (118 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 24180 restraints for refining 11129 atoms. 20400 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2240 (Rfree = 0.000) for 11129 atoms. Found 76 (84 requested) and removed 59 (42 requested) atoms. Cycle 22: After refmac, R = 0.2104 (Rfree = 0.000) for 11098 atoms. Found 54 (84 requested) and removed 45 (42 requested) atoms. Cycle 23: After refmac, R = 0.2062 (Rfree = 0.000) for 11072 atoms. Found 51 (83 requested) and removed 47 (41 requested) atoms. Cycle 24: After refmac, R = 0.2049 (Rfree = 0.000) for 11045 atoms. Found 36 (83 requested) and removed 51 (41 requested) atoms. Cycle 25: After refmac, R = 0.2034 (Rfree = 0.000) for 11002 atoms. Found 37 (83 requested) and removed 47 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 2.91 Search for helices and strands: 0 residues in 0 chains, 11285 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 11301 seeds are put forward Round 1: 797 peptides, 115 chains. Longest chain 20 peptides. Score 0.489 Round 2: 861 peptides, 111 chains. Longest chain 27 peptides. Score 0.551 Round 3: 859 peptides, 108 chains. Longest chain 35 peptides. Score 0.559 Round 4: 882 peptides, 104 chains. Longest chain 32 peptides. Score 0.588 Round 5: 876 peptides, 107 chains. Longest chain 29 peptides. Score 0.574 Taking the results from Round 4 Chains 104, Residues 778, Estimated correctness of the model 24.7 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 25688 restraints for refining 11129 atoms. 22592 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2122 (Rfree = 0.000) for 11129 atoms. Found 68 (84 requested) and removed 49 (42 requested) atoms. Cycle 27: After refmac, R = 0.2064 (Rfree = 0.000) for 11120 atoms. Found 46 (84 requested) and removed 46 (42 requested) atoms. Cycle 28: After refmac, R = 0.2006 (Rfree = 0.000) for 11102 atoms. Found 51 (83 requested) and removed 43 (41 requested) atoms. Cycle 29: After refmac, R = 0.1954 (Rfree = 0.000) for 11087 atoms. Found 43 (83 requested) and removed 45 (41 requested) atoms. Cycle 30: After refmac, R = 0.1950 (Rfree = 0.000) for 11073 atoms. Found 53 (83 requested) and removed 49 (41 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.94 Search for helices and strands: 0 residues in 0 chains, 11375 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 11402 seeds are put forward Round 1: 773 peptides, 123 chains. Longest chain 29 peptides. Score 0.440 Round 2: 869 peptides, 117 chains. Longest chain 22 peptides. Score 0.537 Round 3: 854 peptides, 114 chains. Longest chain 28 peptides. Score 0.536 Round 4: 881 peptides, 116 chains. Longest chain 39 peptides. Score 0.549 Round 5: 855 peptides, 110 chains. Longest chain 41 peptides. Score 0.550 Taking the results from Round 5 Chains 112, Residues 745, Estimated correctness of the model 11.5 % 3 chains (63 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 25376 restraints for refining 11129 atoms. 22247 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2090 (Rfree = 0.000) for 11129 atoms. Found 70 (84 requested) and removed 49 (42 requested) atoms. Cycle 32: After refmac, R = 0.2010 (Rfree = 0.000) for 11119 atoms. Found 55 (84 requested) and removed 49 (42 requested) atoms. Cycle 33: After refmac, R = 0.2007 (Rfree = 0.000) for 11085 atoms. Found 52 (84 requested) and removed 47 (42 requested) atoms. Cycle 34: After refmac, R = 0.1984 (Rfree = 0.000) for 11056 atoms. Found 54 (83 requested) and removed 47 (41 requested) atoms. Cycle 35: After refmac, R = 0.2010 (Rfree = 0.000) for 11037 atoms. Found 72 (83 requested) and removed 48 (41 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 2.91 Search for helices and strands: 0 residues in 0 chains, 11351 seeds are put forward NCS extension: 26 residues added (25 deleted due to clashes), 11377 seeds are put forward Round 1: 720 peptides, 121 chains. Longest chain 16 peptides. Score 0.402 Round 2: 787 peptides, 120 chains. Longest chain 21 peptides. Score 0.463 Round 3: 828 peptides, 113 chains. Longest chain 27 peptides. Score 0.520 Round 4: 836 peptides, 110 chains. Longest chain 27 peptides. Score 0.536 Round 5: 803 peptides, 107 chains. Longest chain 22 peptides. Score 0.521 Taking the results from Round 4 Chains 112, Residues 726, Estimated correctness of the model 6.4 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 25258 restraints for refining 11129 atoms. 22234 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2066 (Rfree = 0.000) for 11129 atoms. Found 66 (84 requested) and removed 46 (42 requested) atoms. Cycle 37: After refmac, R = 0.2008 (Rfree = 0.000) for 11113 atoms. Found 51 (84 requested) and removed 44 (42 requested) atoms. Cycle 38: After refmac, R = 0.1932 (Rfree = 0.000) for 11097 atoms. Found 41 (83 requested) and removed 43 (41 requested) atoms. Cycle 39: After refmac, R = 0.1936 (Rfree = 0.000) for 11071 atoms. Found 45 (83 requested) and removed 44 (41 requested) atoms. Cycle 40: After refmac, R = 0.1896 (Rfree = 0.000) for 11044 atoms. Found 33 (83 requested) and removed 48 (41 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.91 Search for helices and strands: 0 residues in 0 chains, 11301 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 11341 seeds are put forward Round 1: 686 peptides, 115 chains. Longest chain 20 peptides. Score 0.395 Round 2: 785 peptides, 114 chains. Longest chain 26 peptides. Score 0.483 Round 3: 759 peptides, 105 chains. Longest chain 28 peptides. Score 0.494 Round 4: 772 peptides, 106 chains. Longest chain 28 peptides. Score 0.501 Round 5: 745 peptides, 101 chains. Longest chain 18 peptides. Score 0.497 Taking the results from Round 4 Chains 109, Residues 666, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 26016 restraints for refining 11128 atoms. 23327 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2081 (Rfree = 0.000) for 11128 atoms. Found 74 (84 requested) and removed 46 (42 requested) atoms. Cycle 42: After refmac, R = 0.1952 (Rfree = 0.000) for 11118 atoms. Found 49 (84 requested) and removed 43 (42 requested) atoms. Cycle 43: After refmac, R = 0.1930 (Rfree = 0.000) for 11091 atoms. Found 38 (83 requested) and removed 45 (41 requested) atoms. Cycle 44: After refmac, R = 0.1896 (Rfree = 0.000) for 11057 atoms. Found 49 (83 requested) and removed 43 (41 requested) atoms. Cycle 45: After refmac, R = 0.1908 (Rfree = 0.000) for 11044 atoms. Found 51 (83 requested) and removed 48 (41 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.89 Search for helices and strands: 0 residues in 0 chains, 11272 seeds are put forward NCS extension: 25 residues added (13 deleted due to clashes), 11297 seeds are put forward Round 1: 640 peptides, 118 chains. Longest chain 15 peptides. Score 0.341 Round 2: 689 peptides, 111 chains. Longest chain 31 peptides. Score 0.413 Round 3: 730 peptides, 109 chains. Longest chain 38 peptides. Score 0.456 Round 4: 709 peptides, 107 chains. Longest chain 17 peptides. Score 0.446 Round 5: 703 peptides, 110 chains. Longest chain 31 peptides. Score 0.429 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 110, Residues 621, Estimated correctness of the model 0.0 % 2 chains (41 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2anu-3_warpNtrace.pdb as input Building loops using Loopy2018 110 chains (621 residues) following loop building 2 chains (41 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24325 reflections ( 99.82 % complete ) and 25999 restraints for refining 11128 atoms. 23444 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2025 (Rfree = 0.000) for 11128 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.2006 (Rfree = 0.000) for 11044 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Cycle 48: After refmac, R = 0.1907 (Rfree = 0.000) for 10980 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Cycle 49: After refmac, R = 0.1901 (Rfree = 0.000) for 10925 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:01:25 GMT 2018 Job finished. TimeTaking 138.09 Used memory is bytes: 25967312