Mon 24 Dec 00:27:15 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 2ash-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.2-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/2ash-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.2-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 00:27:20 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/2ash-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.2-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 1160 and 0 Target number of residues in the AU: 1160 Target solvent content: 0.6429 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-3.2-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.85 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: 103.605 3.200 Wilson plot Bfac: 73.62 28706 reflections ( 99.82 % complete ) and 0 restraints for refining 13469 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3200 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2649 (Rfree = 0.000) for 13469 atoms. Found 120 (120 requested) and removed 85 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 13786 seeds are put forward NCS extension: 0 residues added, 13786 seeds are put forward Round 1: 783 peptides, 130 chains. Longest chain 18 peptides. Score 0.430 Round 2: 892 peptides, 128 chains. Longest chain 18 peptides. Score 0.527 Round 3: 991 peptides, 120 chains. Longest chain 19 peptides. Score 0.622 Round 4: 1017 peptides, 119 chains. Longest chain 24 peptides. Score 0.642 Round 5: 1032 peptides, 112 chains. Longest chain 32 peptides. Score 0.670 Taking the results from Round 5 Chains 118, Residues 920, Estimated correctness of the model 58.5 % 16 chains (222 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 22025 restraints for refining 11128 atoms. 17611 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2649 (Rfree = 0.000) for 11128 atoms. Found 99 (99 requested) and removed 84 (49 requested) atoms. Cycle 2: After refmac, R = 0.2473 (Rfree = 0.000) for 10970 atoms. Found 68 (100 requested) and removed 63 (50 requested) atoms. Cycle 3: After refmac, R = 0.2357 (Rfree = 0.000) for 10879 atoms. Found 43 (98 requested) and removed 58 (49 requested) atoms. Cycle 4: After refmac, R = 0.2277 (Rfree = 0.000) for 10818 atoms. Found 34 (97 requested) and removed 66 (48 requested) atoms. Cycle 5: After refmac, R = 0.2242 (Rfree = 0.000) for 10765 atoms. Found 49 (96 requested) and removed 63 (48 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 11122 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 11143 seeds are put forward Round 1: 933 peptides, 120 chains. Longest chain 22 peptides. Score 0.583 Round 2: 1011 peptides, 114 chains. Longest chain 38 peptides. Score 0.652 Round 3: 1022 peptides, 111 chains. Longest chain 30 peptides. Score 0.667 Round 4: 1033 peptides, 109 chains. Longest chain 30 peptides. Score 0.678 Round 5: 1038 peptides, 106 chains. Longest chain 32 peptides. Score 0.689 Taking the results from Round 5 Chains 110, Residues 932, Estimated correctness of the model 62.8 % 9 chains (121 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 23048 restraints for refining 11130 atoms. 18919 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2468 (Rfree = 0.000) for 11130 atoms. Found 80 (99 requested) and removed 79 (49 requested) atoms. Cycle 7: After refmac, R = 0.2252 (Rfree = 0.000) for 11072 atoms. Found 30 (99 requested) and removed 57 (49 requested) atoms. Cycle 8: After refmac, R = 0.2199 (Rfree = 0.000) for 11019 atoms. Found 32 (99 requested) and removed 54 (49 requested) atoms. Cycle 9: After refmac, R = 0.2155 (Rfree = 0.000) for 10986 atoms. Found 31 (98 requested) and removed 51 (49 requested) atoms. Cycle 10: After refmac, R = 0.2120 (Rfree = 0.000) for 10953 atoms. Found 23 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 11318 seeds are put forward NCS extension: 6 residues added (9 deleted due to clashes), 11324 seeds are put forward Round 1: 947 peptides, 127 chains. Longest chain 22 peptides. Score 0.571 Round 2: 1022 peptides, 113 chains. Longest chain 40 peptides. Score 0.661 Round 3: 1042 peptides, 110 chains. Longest chain 30 peptides. Score 0.681 Round 4: 1016 peptides, 108 chains. Longest chain 31 peptides. Score 0.671 Round 5: 1012 peptides, 108 chains. Longest chain 39 peptides. Score 0.669 Taking the results from Round 3 Chains 115, Residues 932, Estimated correctness of the model 61.0 % 10 chains (166 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 28706 reflections ( 99.82 % complete ) and 22327 restraints for refining 11131 atoms. 18012 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2376 (Rfree = 0.000) for 11131 atoms. Found 64 (99 requested) and removed 74 (49 requested) atoms. Cycle 12: After refmac, R = 0.2199 (Rfree = 0.000) for 11076 atoms. Found 21 (99 requested) and removed 56 (49 requested) atoms. Cycle 13: After refmac, R = 0.2149 (Rfree = 0.000) for 11011 atoms. Found 18 (99 requested) and removed 52 (49 requested) atoms. Cycle 14: After refmac, R = 0.2145 (Rfree = 0.000) for 10963 atoms. Found 24 (98 requested) and removed 49 (49 requested) atoms. Cycle 15: After refmac, R = 0.2074 (Rfree = 0.000) for 10929 atoms. Found 22 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 11293 seeds are put forward NCS extension: 33 residues added (5 deleted due to clashes), 11326 seeds are put forward Round 1: 935 peptides, 129 chains. Longest chain 25 peptides. Score 0.556 Round 2: 995 peptides, 118 chains. Longest chain 45 peptides. Score 0.631 Round 3: 993 peptides, 119 chains. Longest chain 24 peptides. Score 0.627 Round 4: 1008 peptides, 108 chains. Longest chain 30 peptides. Score 0.667 Round 5: 1014 peptides, 111 chains. Longest chain 28 peptides. Score 0.662 Taking the results from Round 4 Chains 115, Residues 900, Estimated correctness of the model 57.9 % 9 chains (146 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 22737 restraints for refining 11130 atoms. 18638 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2333 (Rfree = 0.000) for 11130 atoms. Found 72 (99 requested) and removed 61 (49 requested) atoms. Cycle 17: After refmac, R = 0.2142 (Rfree = 0.000) for 11112 atoms. Found 28 (99 requested) and removed 53 (49 requested) atoms. Cycle 18: After refmac, R = 0.2103 (Rfree = 0.000) for 11066 atoms. Found 33 (99 requested) and removed 50 (49 requested) atoms. Cycle 19: After refmac, R = 0.2255 (Rfree = 0.000) for 11026 atoms. Found 97 (99 requested) and removed 52 (49 requested) atoms. Cycle 20: After refmac, R = 0.1993 (Rfree = 0.000) for 11057 atoms. Found 31 (99 requested) and removed 52 (49 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 11430 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 11450 seeds are put forward Round 1: 856 peptides, 122 chains. Longest chain 30 peptides. Score 0.520 Round 2: 989 peptides, 112 chains. Longest chain 27 peptides. Score 0.644 Round 3: 982 peptides, 112 chains. Longest chain 24 peptides. Score 0.640 Round 4: 977 peptides, 113 chains. Longest chain 26 peptides. Score 0.634 Round 5: 999 peptides, 108 chains. Longest chain 30 peptides. Score 0.661 Taking the results from Round 5 Chains 114, Residues 891, Estimated correctness of the model 56.5 % 10 chains (146 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 22823 restraints for refining 11129 atoms. 18725 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2338 (Rfree = 0.000) for 11129 atoms. Found 92 (99 requested) and removed 73 (49 requested) atoms. Cycle 22: After refmac, R = 0.2177 (Rfree = 0.000) for 11114 atoms. Found 28 (100 requested) and removed 55 (50 requested) atoms. Cycle 23: After refmac, R = 0.2127 (Rfree = 0.000) for 11069 atoms. Found 30 (99 requested) and removed 54 (49 requested) atoms. Cycle 24: After refmac, R = 0.2129 (Rfree = 0.000) for 11034 atoms. Found 25 (99 requested) and removed 49 (49 requested) atoms. Cycle 25: After refmac, R = 0.2094 (Rfree = 0.000) for 10997 atoms. Found 21 (98 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 11347 seeds are put forward NCS extension: 18 residues added (8 deleted due to clashes), 11365 seeds are put forward Round 1: 872 peptides, 125 chains. Longest chain 20 peptides. Score 0.522 Round 2: 932 peptides, 112 chains. Longest chain 24 peptides. Score 0.608 Round 3: 915 peptides, 109 chains. Longest chain 29 peptides. Score 0.605 Round 4: 921 peptides, 112 chains. Longest chain 25 peptides. Score 0.600 Round 5: 931 peptides, 113 chains. Longest chain 22 peptides. Score 0.604 Taking the results from Round 2 Chains 116, Residues 820, Estimated correctness of the model 43.2 % 5 chains (65 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24157 restraints for refining 11129 atoms. 20716 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2204 (Rfree = 0.000) for 11129 atoms. Found 70 (99 requested) and removed 60 (49 requested) atoms. Cycle 27: After refmac, R = 0.2104 (Rfree = 0.000) for 11119 atoms. Found 30 (99 requested) and removed 50 (49 requested) atoms. Cycle 28: After refmac, R = 0.2067 (Rfree = 0.000) for 11076 atoms. Found 35 (99 requested) and removed 49 (49 requested) atoms. Cycle 29: After refmac, R = 0.1946 (Rfree = 0.000) for 11047 atoms. Found 20 (99 requested) and removed 52 (49 requested) atoms. Cycle 30: After refmac, R = 0.1925 (Rfree = 0.000) for 10995 atoms. Found 42 (98 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 11318 seeds are put forward NCS extension: 7 residues added (8 deleted due to clashes), 11325 seeds are put forward Round 1: 823 peptides, 129 chains. Longest chain 20 peptides. Score 0.468 Round 2: 891 peptides, 119 chains. Longest chain 24 peptides. Score 0.556 Round 3: 900 peptides, 120 chains. Longest chain 20 peptides. Score 0.560 Round 4: 887 peptides, 112 chains. Longest chain 27 peptides. Score 0.576 Round 5: 905 peptides, 118 chains. Longest chain 22 peptides. Score 0.570 Taking the results from Round 4 Chains 113, Residues 775, Estimated correctness of the model 34.4 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24686 restraints for refining 11130 atoms. 21489 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2178 (Rfree = 0.000) for 11130 atoms. Found 60 (99 requested) and removed 56 (49 requested) atoms. Cycle 32: After refmac, R = 0.2040 (Rfree = 0.000) for 11111 atoms. Found 23 (99 requested) and removed 50 (49 requested) atoms. Cycle 33: After refmac, R = 0.2028 (Rfree = 0.000) for 11068 atoms. Found 28 (99 requested) and removed 49 (49 requested) atoms. Cycle 34: After refmac, R = 0.1994 (Rfree = 0.000) for 11035 atoms. Found 24 (99 requested) and removed 49 (49 requested) atoms. Cycle 35: After refmac, R = 0.1900 (Rfree = 0.000) for 11001 atoms. Found 14 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 11297 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 11318 seeds are put forward Round 1: 765 peptides, 127 chains. Longest chain 14 peptides. Score 0.426 Round 2: 811 peptides, 108 chains. Longest chain 23 peptides. Score 0.533 Round 3: 815 peptides, 110 chains. Longest chain 22 peptides. Score 0.529 Round 4: 867 peptides, 113 chains. Longest chain 29 peptides. Score 0.558 Round 5: 855 peptides, 107 chains. Longest chain 36 peptides. Score 0.570 Taking the results from Round 5 Chains 109, Residues 748, Estimated correctness of the model 32.7 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24817 restraints for refining 11130 atoms. 21769 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2206 (Rfree = 0.000) for 11130 atoms. Found 58 (99 requested) and removed 53 (49 requested) atoms. Cycle 37: After refmac, R = 0.2088 (Rfree = 0.000) for 11109 atoms. Found 25 (99 requested) and removed 52 (49 requested) atoms. Cycle 38: After refmac, R = 0.2047 (Rfree = 0.000) for 11072 atoms. Found 21 (99 requested) and removed 49 (49 requested) atoms. Cycle 39: After refmac, R = 0.1994 (Rfree = 0.000) for 11038 atoms. Found 22 (99 requested) and removed 49 (49 requested) atoms. Cycle 40: After refmac, R = 0.1949 (Rfree = 0.000) for 11002 atoms. Found 17 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 11281 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 11298 seeds are put forward Round 1: 728 peptides, 118 chains. Longest chain 20 peptides. Score 0.427 Round 2: 790 peptides, 109 chains. Longest chain 26 peptides. Score 0.513 Round 3: 821 peptides, 108 chains. Longest chain 22 peptides. Score 0.541 Round 4: 832 peptides, 109 chains. Longest chain 27 peptides. Score 0.546 Round 5: 823 peptides, 111 chains. Longest chain 21 peptides. Score 0.532 Taking the results from Round 4 Chains 111, Residues 723, Estimated correctness of the model 25.7 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24984 restraints for refining 11129 atoms. 22050 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2095 (Rfree = 0.000) for 11129 atoms. Found 56 (99 requested) and removed 55 (49 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1979 (Rfree = 0.000) for 11111 atoms. Found 29 (99 requested) and removed 49 (49 requested) atoms. Cycle 43: After refmac, R = 0.1949 (Rfree = 0.000) for 11080 atoms. Found 22 (99 requested) and removed 49 (49 requested) atoms. Cycle 44: After refmac, R = 0.1922 (Rfree = 0.000) for 11042 atoms. Found 26 (99 requested) and removed 49 (49 requested) atoms. Cycle 45: After refmac, R = 0.1889 (Rfree = 0.000) for 11015 atoms. Found 27 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 11307 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 11328 seeds are put forward Round 1: 699 peptides, 114 chains. Longest chain 21 peptides. Score 0.417 Round 2: 790 peptides, 102 chains. Longest chain 27 peptides. Score 0.538 Round 3: 772 peptides, 99 chains. Longest chain 27 peptides. Score 0.534 Round 4: 773 peptides, 98 chains. Longest chain 23 peptides. Score 0.539 Round 5: 770 peptides, 102 chains. Longest chain 21 peptides. Score 0.522 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 99, Residues 675, Estimated correctness of the model 23.6 % 4 chains (29 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2ash-3_warpNtrace.pdb as input Building loops using Loopy2018 99 chains (675 residues) following loop building 4 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 28706 reflections ( 99.82 % complete ) and 25385 restraints for refining 11130 atoms. 22665 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2067 (Rfree = 0.000) for 11130 atoms. Found 0 (99 requested) and removed 41 (49 requested) atoms. Cycle 47: After refmac, R = 0.2019 (Rfree = 0.000) for 11069 atoms. Found 0 (99 requested) and removed 18 (49 requested) atoms. Cycle 48: After refmac, R = 0.1981 (Rfree = 0.000) for 11042 atoms. Found 0 (99 requested) and removed 13 (49 requested) atoms. Cycle 49: After refmac, R = 0.1957 (Rfree = 0.000) for 11020 atoms. TimeTaking 123.13