Sun 23 Dec 22:22:56 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2anu-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2anu-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.8-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 22:23:06 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.8-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 1241 and 0 Target number of residues in the AU: 1241 Target solvent content: 0.6322 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 67.68 17399 reflections ( 99.75 % complete ) and 0 restraints for refining 13528 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.2871 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2852 (Rfree = 0.000) for 13528 atoms. Found 74 (74 requested) and removed 44 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 13767 seeds are put forward NCS extension: 0 residues added, 13767 seeds are put forward Round 1: 632 peptides, 121 chains. Longest chain 11 peptides. Score 0.321 Round 2: 800 peptides, 117 chains. Longest chain 35 peptides. Score 0.484 Round 3: 855 peptides, 107 chains. Longest chain 23 peptides. Score 0.559 Round 4: 881 peptides, 108 chains. Longest chain 31 peptides. Score 0.575 Round 5: 896 peptides, 107 chains. Longest chain 23 peptides. Score 0.588 Taking the results from Round 5 Chains 107, Residues 789, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 25845 restraints for refining 11064 atoms. 22796 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2438 (Rfree = 0.000) for 11064 atoms. Found 60 (60 requested) and removed 83 (30 requested) atoms. Cycle 2: After refmac, R = 0.2290 (Rfree = 0.000) for 10871 atoms. Found 60 (60 requested) and removed 303 (30 requested) atoms. Cycle 3: After refmac, R = 0.2255 (Rfree = 0.000) for 10532 atoms. Found 58 (58 requested) and removed 68 (29 requested) atoms. Cycle 4: After refmac, R = 0.2099 (Rfree = 0.000) for 10447 atoms. Found 57 (57 requested) and removed 55 (28 requested) atoms. Cycle 5: After refmac, R = 0.1825 (Rfree = 0.000) for 10389 atoms. Found 28 (57 requested) and removed 43 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 10713 seeds are put forward NCS extension: 8 residues added (8 deleted due to clashes), 10721 seeds are put forward Round 1: 778 peptides, 128 chains. Longest chain 20 peptides. Score 0.426 Round 2: 828 peptides, 108 chains. Longest chain 21 peptides. Score 0.537 Round 3: 878 peptides, 111 chains. Longest chain 30 peptides. Score 0.563 Round 4: 903 peptides, 113 chains. Longest chain 22 peptides. Score 0.574 Round 5: 887 peptides, 105 chains. Longest chain 21 peptides. Score 0.588 Taking the results from Round 5 Chains 105, Residues 782, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 25975 restraints for refining 11071 atoms. 22952 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2318 (Rfree = 0.000) for 11071 atoms. Found 60 (60 requested) and removed 97 (30 requested) atoms. Cycle 7: After refmac, R = 0.2176 (Rfree = 0.000) for 10939 atoms. Found 60 (60 requested) and removed 83 (30 requested) atoms. Cycle 8: After refmac, R = 0.2102 (Rfree = 0.000) for 10849 atoms. Found 60 (60 requested) and removed 52 (30 requested) atoms. Cycle 9: After refmac, R = 0.2043 (Rfree = 0.000) for 10796 atoms. Found 59 (59 requested) and removed 51 (29 requested) atoms. Cycle 10: After refmac, R = 0.1998 (Rfree = 0.000) for 10767 atoms. Found 59 (59 requested) and removed 41 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 11159 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 11175 seeds are put forward Round 1: 701 peptides, 120 chains. Longest chain 18 peptides. Score 0.389 Round 2: 818 peptides, 110 chains. Longest chain 18 peptides. Score 0.522 Round 3: 816 peptides, 106 chains. Longest chain 33 peptides. Score 0.534 Round 4: 827 peptides, 103 chains. Longest chain 23 peptides. Score 0.552 Round 5: 873 peptides, 111 chains. Longest chain 20 peptides. Score 0.559 Taking the results from Round 5 Chains 111, Residues 762, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 25828 restraints for refining 11069 atoms. 22872 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2243 (Rfree = 0.000) for 11069 atoms. Found 60 (60 requested) and removed 76 (30 requested) atoms. Cycle 12: After refmac, R = 0.2211 (Rfree = 0.000) for 10988 atoms. Found 60 (60 requested) and removed 50 (30 requested) atoms. Cycle 13: After refmac, R = 0.1918 (Rfree = 0.000) for 10956 atoms. Found 22 (60 requested) and removed 45 (30 requested) atoms. Cycle 14: After refmac, R = 0.2000 (Rfree = 0.000) for 10915 atoms. Found 60 (60 requested) and removed 43 (30 requested) atoms. Cycle 15: After refmac, R = 0.1852 (Rfree = 0.000) for 10906 atoms. Found 17 (60 requested) and removed 42 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 11246 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 11272 seeds are put forward Round 1: 739 peptides, 128 chains. Longest chain 15 peptides. Score 0.392 Round 2: 813 peptides, 115 chains. Longest chain 17 peptides. Score 0.501 Round 3: 826 peptides, 104 chains. Longest chain 23 peptides. Score 0.548 Round 4: 867 peptides, 110 chains. Longest chain 22 peptides. Score 0.558 Round 5: 868 peptides, 109 chains. Longest chain 25 peptides. Score 0.562 Taking the results from Round 5 Chains 109, Residues 759, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 25894 restraints for refining 11069 atoms. 22901 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2169 (Rfree = 0.000) for 11069 atoms. Found 60 (60 requested) and removed 36 (30 requested) atoms. Cycle 17: After refmac, R = 0.2101 (Rfree = 0.000) for 11009 atoms. Found 51 (61 requested) and removed 48 (30 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2065 (Rfree = 0.000) for 10965 atoms. Found 60 (60 requested) and removed 52 (30 requested) atoms. Cycle 19: After refmac, R = 0.2094 (Rfree = 0.000) for 10932 atoms. Found 60 (60 requested) and removed 37 (30 requested) atoms. Cycle 20: After refmac, R = 0.2029 (Rfree = 0.000) for 10913 atoms. Found 60 (60 requested) and removed 36 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 11249 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 11268 seeds are put forward Round 1: 721 peptides, 124 chains. Longest chain 17 peptides. Score 0.391 Round 2: 788 peptides, 113 chains. Longest chain 21 peptides. Score 0.489 Round 3: 795 peptides, 112 chains. Longest chain 21 peptides. Score 0.498 Round 4: 825 peptides, 120 chains. Longest chain 21 peptides. Score 0.493 Round 5: 817 peptides, 111 chains. Longest chain 24 peptides. Score 0.518 Taking the results from Round 5 Chains 111, Residues 706, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 17399 reflections ( 99.75 % complete ) and 26401 restraints for refining 11070 atoms. 23628 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2186 (Rfree = 0.000) for 11070 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 22: After refmac, R = 0.2174 (Rfree = 0.000) for 11016 atoms. Found 60 (60 requested) and removed 38 (30 requested) atoms. Cycle 23: After refmac, R = 0.1884 (Rfree = 0.000) for 10993 atoms. Found 41 (60 requested) and removed 41 (30 requested) atoms. Cycle 24: After refmac, R = 0.1805 (Rfree = 0.000) for 10973 atoms. Found 15 (60 requested) and removed 34 (30 requested) atoms. Cycle 25: After refmac, R = 0.1781 (Rfree = 0.000) for 10936 atoms. Found 19 (60 requested) and removed 35 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 11242 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 11259 seeds are put forward Round 1: 689 peptides, 121 chains. Longest chain 14 peptides. Score 0.374 Round 2: 770 peptides, 112 chains. Longest chain 20 peptides. Score 0.478 Round 3: 768 peptides, 117 chains. Longest chain 21 peptides. Score 0.458 Round 4: 769 peptides, 106 chains. Longest chain 22 peptides. Score 0.498 Round 5: 766 peptides, 107 chains. Longest chain 18 peptides. Score 0.492 Taking the results from Round 4 Chains 106, Residues 663, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26566 restraints for refining 11070 atoms. 24020 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2148 (Rfree = 0.000) for 11070 atoms. Found 60 (60 requested) and removed 44 (30 requested) atoms. Cycle 27: After refmac, R = 0.2097 (Rfree = 0.000) for 11036 atoms. Found 60 (60 requested) and removed 36 (30 requested) atoms. Cycle 28: After refmac, R = 0.1806 (Rfree = 0.000) for 11034 atoms. Found 22 (60 requested) and removed 31 (30 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1885 (Rfree = 0.000) for 10995 atoms. Found 60 (60 requested) and removed 33 (30 requested) atoms. Cycle 30: After refmac, R = 0.1712 (Rfree = 0.000) for 11004 atoms. Found 17 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.25 Search for helices and strands: 0 residues in 0 chains, 11320 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 11344 seeds are put forward Round 1: 657 peptides, 122 chains. Longest chain 14 peptides. Score 0.341 Round 2: 726 peptides, 113 chains. Longest chain 18 peptides. Score 0.438 Round 3: 728 peptides, 110 chains. Longest chain 18 peptides. Score 0.450 Round 4: 757 peptides, 105 chains. Longest chain 21 peptides. Score 0.492 Round 5: 738 peptides, 113 chains. Longest chain 18 peptides. Score 0.448 Taking the results from Round 4 Chains 106, Residues 652, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26366 restraints for refining 11071 atoms. 23784 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2032 (Rfree = 0.000) for 11071 atoms. Found 60 (60 requested) and removed 38 (30 requested) atoms. Cycle 32: After refmac, R = 0.2035 (Rfree = 0.000) for 11036 atoms. Found 61 (61 requested) and removed 35 (30 requested) atoms. Cycle 33: After refmac, R = 0.2034 (Rfree = 0.000) for 11024 atoms. Found 60 (60 requested) and removed 44 (30 requested) atoms. Cycle 34: After refmac, R = 0.1943 (Rfree = 0.000) for 11005 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 35: After refmac, R = 0.1665 (Rfree = 0.000) for 10988 atoms. Found 36 (60 requested) and removed 51 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.25 Search for helices and strands: 0 residues in 0 chains, 11268 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 11282 seeds are put forward Round 1: 579 peptides, 114 chains. Longest chain 13 peptides. Score 0.298 Round 2: 680 peptides, 121 chains. Longest chain 13 peptides. Score 0.366 Round 3: 706 peptides, 116 chains. Longest chain 22 peptides. Score 0.409 Round 4: 711 peptides, 113 chains. Longest chain 22 peptides. Score 0.425 Round 5: 735 peptides, 114 chains. Longest chain 18 peptides. Score 0.441 Taking the results from Round 5 Chains 114, Residues 621, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26862 restraints for refining 11066 atoms. 24492 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2153 (Rfree = 0.000) for 11066 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 37: After refmac, R = 0.2212 (Rfree = 0.000) for 11024 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. Cycle 38: After refmac, R = 0.2161 (Rfree = 0.000) for 10992 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 39: After refmac, R = 0.1799 (Rfree = 0.000) for 10974 atoms. Found 31 (60 requested) and removed 73 (30 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1723 (Rfree = 0.000) for 10906 atoms. Found 21 (60 requested) and removed 35 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.25 Search for helices and strands: 0 residues in 0 chains, 11254 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 11273 seeds are put forward Round 1: 554 peptides, 119 chains. Longest chain 11 peptides. Score 0.251 Round 2: 632 peptides, 113 chains. Longest chain 14 peptides. Score 0.353 Round 3: 663 peptides, 118 chains. Longest chain 15 peptides. Score 0.362 Round 4: 674 peptides, 109 chains. Longest chain 17 peptides. Score 0.408 Round 5: 684 peptides, 105 chains. Longest chain 22 peptides. Score 0.432 Taking the results from Round 5 Chains 105, Residues 579, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26923 restraints for refining 11070 atoms. 24712 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2199 (Rfree = 0.000) for 11070 atoms. Found 60 (60 requested) and removed 38 (30 requested) atoms. Cycle 42: After refmac, R = 0.2154 (Rfree = 0.000) for 11038 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 43: After refmac, R = 0.2155 (Rfree = 0.000) for 11004 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 44: After refmac, R = 0.2055 (Rfree = 0.000) for 10993 atoms. Found 60 (60 requested) and removed 42 (30 requested) atoms. Cycle 45: After refmac, R = 0.1692 (Rfree = 0.000) for 10981 atoms. Found 38 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.27 Search for helices and strands: 0 residues in 0 chains, 11307 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 11326 seeds are put forward Round 1: 510 peptides, 109 chains. Longest chain 10 peptides. Score 0.249 Round 2: 583 peptides, 103 chains. Longest chain 13 peptides. Score 0.348 Round 3: 580 peptides, 105 chains. Longest chain 20 peptides. Score 0.337 Round 4: 616 peptides, 101 chains. Longest chain 16 peptides. Score 0.387 Round 5: 625 peptides, 101 chains. Longest chain 17 peptides. Score 0.395 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 101, Residues 524, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17399 reflections ( 99.75 % complete ) and 27546 restraints for refining 11069 atoms. 25551 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2316 (Rfree = 0.000) for 11069 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 47: After refmac, R = 0.2203 (Rfree = 0.000) for 10992 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 48: After refmac, R = 0.1823 (Rfree = 0.000) for 10916 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 49: After refmac, R = 0.1824 (Rfree = 0.000) for 10843 atoms. TimeTaking 149.02