Mon 24 Dec 00:15:44 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2anu-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-parrot-mrncs ############### 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 00:15:49 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/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.4-parrot-mrncs/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-mrncs.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-mrncs.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 13496 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.2789 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2546 (Rfree = 0.000) for 13496 atoms. Found 101 (101 requested) and removed 69 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 2.96 Search for helices and strands: 0 residues in 0 chains, 13787 seeds are put forward NCS extension: 0 residues added, 13787 seeds are put forward Round 1: 809 peptides, 123 chains. Longest chain 18 peptides. Score 0.470 Round 2: 961 peptides, 119 chains. Longest chain 37 peptides. Score 0.595 Round 3: 994 peptides, 115 chains. Longest chain 35 peptides. Score 0.628 Round 4: 1002 peptides, 101 chains. Longest chain 37 peptides. Score 0.671 Round 5: 1007 peptides, 95 chains. Longest chain 49 peptides. Score 0.689 Taking the results from Round 5 Chains 101, Residues 912, Estimated correctness of the model 55.0 % 13 chains (257 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 21703 restraints for refining 11124 atoms. 17017 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2348 (Rfree = 0.000) for 11124 atoms. Found 84 (84 requested) and removed 96 (42 requested) atoms. Cycle 2: After refmac, R = 0.2266 (Rfree = 0.000) for 10938 atoms. Found 72 (83 requested) and removed 61 (41 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2230 (Rfree = 0.000) for 10849 atoms. Found 65 (82 requested) and removed 52 (41 requested) atoms. Cycle 4: After refmac, R = 0.2174 (Rfree = 0.000) for 10818 atoms. Found 53 (82 requested) and removed 51 (41 requested) atoms. Cycle 5: After refmac, R = 0.2116 (Rfree = 0.000) for 10776 atoms. Found 55 (81 requested) and removed 50 (40 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 2.93 Search for helices and strands: 0 residues in 0 chains, 11094 seeds are put forward NCS extension: 19 residues added (32 deleted due to clashes), 11113 seeds are put forward Round 1: 962 peptides, 110 chains. Longest chain 23 peptides. Score 0.622 Round 2: 1050 peptides, 98 chains. Longest chain 39 peptides. Score 0.704 Round 3: 1046 peptides, 96 chains. Longest chain 37 peptides. Score 0.707 Round 4: 1065 peptides, 96 chains. Longest chain 42 peptides. Score 0.717 Round 5: 1066 peptides, 94 chains. Longest chain 50 peptides. Score 0.722 Taking the results from Round 5 Chains 101, Residues 972, Estimated correctness of the model 63.4 % 17 chains (348 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 90 A Built loop between residues 225 A and 231 A Built loop between residues 113 C and 117 C Built loop between residues 104 D and 107 D 96 chains (987 residues) following loop building 13 chains (365 residues) in sequence following loop building ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 20442 restraints for refining 11129 atoms. 15003 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2447 (Rfree = 0.000) for 11129 atoms. Found 84 (84 requested) and removed 87 (42 requested) atoms. Cycle 7: After refmac, R = 0.2323 (Rfree = 0.000) for 10996 atoms. Found 67 (82 requested) and removed 58 (42 requested) atoms. Cycle 8: After refmac, R = 0.2203 (Rfree = 0.000) for 10950 atoms. Found 61 (80 requested) and removed 55 (41 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2109 (Rfree = 0.000) for 10916 atoms. Found 37 (77 requested) and removed 49 (41 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2083 (Rfree = 0.000) for 10886 atoms. Found 46 (75 requested) and removed 52 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 2.93 Search for helices and strands: 0 residues in 0 chains, 11167 seeds are put forward NCS extension: 28 residues added (30 deleted due to clashes), 11195 seeds are put forward Round 1: 984 peptides, 113 chains. Longest chain 37 peptides. Score 0.627 Round 2: 1041 peptides, 100 chains. Longest chain 41 peptides. Score 0.695 Round 3: 1037 peptides, 100 chains. Longest chain 36 peptides. Score 0.693 Round 4: 1041 peptides, 90 chains. Longest chain 41 peptides. Score 0.719 Round 5: 997 peptides, 92 chains. Longest chain 34 peptides. Score 0.692 Taking the results from Round 4 Chains 93, Residues 951, Estimated correctness of the model 62.6 % 14 chains (314 residues) have been docked in sequence Building loops using Loopy2018 93 chains (951 residues) following loop building 14 chains (314 residues) in sequence following loop building ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 21492 restraints for refining 11129 atoms. 16380 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2369 (Rfree = 0.000) for 11129 atoms. Found 76 (76 requested) and removed 100 (42 requested) atoms. Cycle 12: After refmac, R = 0.2150 (Rfree = 0.000) for 11038 atoms. Found 40 (73 requested) and removed 62 (41 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2080 (Rfree = 0.000) for 10982 atoms. Found 37 (71 requested) and removed 48 (41 requested) atoms. Cycle 14: After refmac, R = 0.2012 (Rfree = 0.000) for 10942 atoms. Found 21 (69 requested) and removed 46 (41 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1968 (Rfree = 0.000) for 10894 atoms. Found 16 (67 requested) and removed 42 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.94 Search for helices and strands: 0 residues in 0 chains, 11192 seeds are put forward NCS extension: 29 residues added (16 deleted due to clashes), 11221 seeds are put forward Round 1: 951 peptides, 121 chains. Longest chain 27 peptides. Score 0.582 Round 2: 1005 peptides, 94 chains. Longest chain 40 peptides. Score 0.691 Round 3: 1031 peptides, 100 chains. Longest chain 60 peptides. Score 0.689 Round 4: 1009 peptides, 89 chains. Longest chain 40 peptides. Score 0.705 Round 5: 972 peptides, 91 chains. Longest chain 44 peptides. Score 0.681 Taking the results from Round 4 Chains 103, Residues 920, Estimated correctness of the model 59.1 % 12 chains (188 residues) have been docked in sequence Building loops using Loopy2018 103 chains (920 residues) following loop building 12 chains (188 residues) in sequence following loop building ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 22573 restraints for refining 11129 atoms. 18116 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2264 (Rfree = 0.000) for 11129 atoms. Found 67 (67 requested) and removed 62 (42 requested) atoms. Cycle 17: After refmac, R = 0.2133 (Rfree = 0.000) for 11076 atoms. Found 36 (66 requested) and removed 50 (42 requested) atoms. Cycle 18: After refmac, R = 0.2061 (Rfree = 0.000) for 11024 atoms. Found 30 (63 requested) and removed 45 (41 requested) atoms. Cycle 19: After refmac, R = 0.2047 (Rfree = 0.000) for 10980 atoms. Found 27 (61 requested) and removed 46 (41 requested) atoms. Cycle 20: After refmac, R = 0.2054 (Rfree = 0.000) for 10944 atoms. Found 34 (59 requested) and removed 45 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 2.93 Search for helices and strands: 0 residues in 0 chains, 11240 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 11261 seeds are put forward Round 1: 899 peptides, 113 chains. Longest chain 28 peptides. Score 0.571 Round 2: 977 peptides, 101 chains. Longest chain 41 peptides. Score 0.657 Round 3: 985 peptides, 113 chains. Longest chain 29 peptides. Score 0.628 Round 4: 992 peptides, 103 chains. Longest chain 30 peptides. Score 0.660 Round 5: 982 peptides, 113 chains. Longest chain 44 peptides. Score 0.626 Taking the results from Round 4 Chains 105, Residues 889, Estimated correctness of the model 47.0 % 5 chains (100 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 24135 restraints for refining 11128 atoms. 20252 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2259 (Rfree = 0.000) for 11128 atoms. Found 59 (59 requested) and removed 61 (42 requested) atoms. Cycle 22: After refmac, R = 0.2116 (Rfree = 0.000) for 11083 atoms. Found 59 (59 requested) and removed 49 (42 requested) atoms. Cycle 23: After refmac, R = 0.2033 (Rfree = 0.000) for 11056 atoms. Found 50 (58 requested) and removed 45 (41 requested) atoms. Cycle 24: After refmac, R = 0.1992 (Rfree = 0.000) for 11033 atoms. Found 58 (58 requested) and removed 45 (41 requested) atoms. Cycle 25: After refmac, R = 0.1938 (Rfree = 0.000) for 11020 atoms. Found 37 (58 requested) and removed 44 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 2.94 Search for helices and strands: 0 residues in 0 chains, 11297 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 11334 seeds are put forward Round 1: 890 peptides, 128 chains. Longest chain 24 peptides. Score 0.516 Round 2: 971 peptides, 112 chains. Longest chain 30 peptides. Score 0.622 Round 3: 915 peptides, 107 chains. Longest chain 24 peptides. Score 0.601 Round 4: 960 peptides, 111 chains. Longest chain 27 peptides. Score 0.618 Round 5: 928 peptides, 104 chains. Longest chain 26 peptides. Score 0.618 Taking the results from Round 2 Chains 115, Residues 859, Estimated correctness of the model 35.7 % 7 chains (110 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 23960 restraints for refining 11127 atoms. 20173 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2163 (Rfree = 0.000) for 11127 atoms. Found 59 (59 requested) and removed 50 (42 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2073 (Rfree = 0.000) for 11096 atoms. Found 59 (59 requested) and removed 47 (42 requested) atoms. Cycle 28: After refmac, R = 0.1997 (Rfree = 0.000) for 11084 atoms. Found 52 (58 requested) and removed 42 (41 requested) atoms. Cycle 29: After refmac, R = 0.1963 (Rfree = 0.000) for 11076 atoms. Found 56 (58 requested) and removed 47 (41 requested) atoms. Cycle 30: After refmac, R = 0.1946 (Rfree = 0.000) for 11064 atoms. Found 39 (58 requested) and removed 45 (41 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 2.95 Search for helices and strands: 0 residues in 0 chains, 11330 seeds are put forward NCS extension: 29 residues added (21 deleted due to clashes), 11359 seeds are put forward Round 1: 862 peptides, 126 chains. Longest chain 18 peptides. Score 0.501 Round 2: 935 peptides, 106 chains. Longest chain 31 peptides. Score 0.617 Round 3: 914 peptides, 113 chains. Longest chain 23 peptides. Score 0.582 Round 4: 935 peptides, 103 chains. Longest chain 46 peptides. Score 0.626 Round 5: 917 peptides, 109 chains. Longest chain 32 peptides. Score 0.596 Taking the results from Round 4 Chains 105, Residues 832, Estimated correctness of the model 36.9 % 4 chains (101 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 24324 restraints for refining 11129 atoms. 20662 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2211 (Rfree = 0.000) for 11129 atoms. Found 59 (59 requested) and removed 61 (42 requested) atoms. Cycle 32: After refmac, R = 0.2033 (Rfree = 0.000) for 11085 atoms. Found 55 (59 requested) and removed 47 (42 requested) atoms. Cycle 33: After refmac, R = 0.1976 (Rfree = 0.000) for 11060 atoms. Found 36 (58 requested) and removed 46 (41 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1958 (Rfree = 0.000) for 11033 atoms. Found 30 (58 requested) and removed 46 (41 requested) atoms. Cycle 35: After refmac, R = 0.1935 (Rfree = 0.000) for 11006 atoms. Found 31 (58 requested) and removed 47 (41 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 2.89 Search for helices and strands: 0 residues in 0 chains, 11291 seeds are put forward NCS extension: 31 residues added (16 deleted due to clashes), 11322 seeds are put forward Round 1: 758 peptides, 116 chains. Longest chain 34 peptides. Score 0.453 Round 2: 839 peptides, 109 chains. Longest chain 19 peptides. Score 0.541 Round 3: 879 peptides, 112 chains. Longest chain 38 peptides. Score 0.560 Round 4: 893 peptides, 113 chains. Longest chain 27 peptides. Score 0.567 Round 5: 888 peptides, 102 chains. Longest chain 23 peptides. Score 0.598 Taking the results from Round 5 Chains 103, Residues 786, Estimated correctness of the model 28.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 25252 restraints for refining 11128 atoms. 22076 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2508 (Rfree = 0.000) for 11128 atoms. Found 59 (59 requested) and removed 82 (42 requested) atoms. Cycle 37: After refmac, R = 0.2161 (Rfree = 0.000) for 11064 atoms. Found 58 (58 requested) and removed 51 (41 requested) atoms. Cycle 38: After refmac, R = 0.2043 (Rfree = 0.000) for 11042 atoms. Found 48 (58 requested) and removed 48 (41 requested) atoms. Cycle 39: After refmac, R = 0.1997 (Rfree = 0.000) for 11019 atoms. Found 50 (58 requested) and removed 43 (41 requested) atoms. Cycle 40: After refmac, R = 0.1988 (Rfree = 0.000) for 11011 atoms. Found 58 (58 requested) and removed 50 (41 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 2.90 Search for helices and strands: 0 residues in 0 chains, 11292 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 11306 seeds are put forward Round 1: 711 peptides, 116 chains. Longest chain 18 peptides. Score 0.413 Round 2: 830 peptides, 114 chains. Longest chain 20 peptides. Score 0.518 Round 3: 826 peptides, 105 chains. Longest chain 23 peptides. Score 0.545 Round 4: 830 peptides, 106 chains. Longest chain 28 peptides. Score 0.545 Round 5: 816 peptides, 101 chains. Longest chain 28 peptides. Score 0.551 Taking the results from Round 5 Chains 102, Residues 715, Estimated correctness of the model 11.9 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 24325 reflections ( 99.82 % complete ) and 25833 restraints for refining 11129 atoms. 22959 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2223 (Rfree = 0.000) for 11129 atoms. Found 59 (59 requested) and removed 70 (42 requested) atoms. Cycle 42: After refmac, R = 0.2109 (Rfree = 0.000) for 11088 atoms. Found 58 (58 requested) and removed 48 (41 requested) atoms. Cycle 43: After refmac, R = 0.2055 (Rfree = 0.000) for 11064 atoms. Found 58 (58 requested) and removed 45 (41 requested) atoms. Cycle 44: After refmac, R = 0.2039 (Rfree = 0.000) for 11061 atoms. Found 54 (58 requested) and removed 51 (41 requested) atoms. Cycle 45: After refmac, R = 0.1999 (Rfree = 0.000) for 11049 atoms. Found 58 (58 requested) and removed 42 (41 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.89 Search for helices and strands: 0 residues in 0 chains, 11307 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11322 seeds are put forward Round 1: 685 peptides, 121 chains. Longest chain 20 peptides. Score 0.370 Round 2: 776 peptides, 115 chains. Longest chain 23 peptides. Score 0.472 Round 3: 793 peptides, 111 chains. Longest chain 23 peptides. Score 0.500 Round 4: 794 peptides, 109 chains. Longest chain 24 peptides. Score 0.507 Round 5: 813 peptides, 111 chains. Longest chain 20 peptides. Score 0.515 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 111, Residues 702, Estimated correctness of the model 0.0 % 1 chains (19 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. 24325 reflections ( 99.82 % complete ) and 25749 restraints for refining 11129 atoms. 22958 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2068 (Rfree = 0.000) for 11129 atoms. Found 0 (59 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.2010 (Rfree = 0.000) for 11046 atoms. Found 0 (58 requested) and removed 41 (41 requested) atoms. Cycle 48: After refmac, R = 0.1964 (Rfree = 0.000) for 10990 atoms. Found 0 (58 requested) and removed 41 (41 requested) atoms. Cycle 49: After refmac, R = 0.1940 (Rfree = 0.000) for 10939 atoms. TimeTaking 146.53