Mon 24 Dec 01:11:59 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-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 01:12:04 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-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 1112 and 0 Target number of residues in the AU: 1112 Target solvent content: 0.6577 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 83.27 20233 reflections ( 99.76 % complete ) and 0 restraints for refining 13444 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3272 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2835 (Rfree = 0.000) for 13444 atoms. Found 86 (86 requested) and removed 258 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 13574 seeds are put forward NCS extension: 0 residues added, 13574 seeds are put forward Round 1: 648 peptides, 118 chains. Longest chain 16 peptides. Score 0.353 Round 2: 859 peptides, 129 chains. Longest chain 27 peptides. Score 0.498 Round 3: 942 peptides, 125 chains. Longest chain 21 peptides. Score 0.574 Round 4: 973 peptides, 120 chains. Longest chain 25 peptides. Score 0.611 Round 5: 938 peptides, 110 chains. Longest chain 23 peptides. Score 0.618 Taking the results from Round 5 Chains 112, Residues 828, Estimated correctness of the model 21.6 % 7 chains (63 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 24098 restraints for refining 11046 atoms. 20693 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2395 (Rfree = 0.000) for 11046 atoms. Found 70 (70 requested) and removed 98 (35 requested) atoms. Cycle 2: After refmac, R = 0.2157 (Rfree = 0.000) for 10861 atoms. Found 41 (70 requested) and removed 53 (35 requested) atoms. Cycle 3: After refmac, R = 0.2081 (Rfree = 0.000) for 10791 atoms. Found 32 (69 requested) and removed 37 (34 requested) atoms. Cycle 4: After refmac, R = 0.2045 (Rfree = 0.000) for 10757 atoms. Found 16 (69 requested) and removed 39 (34 requested) atoms. Cycle 5: After refmac, R = 0.2006 (Rfree = 0.000) for 10724 atoms. Found 9 (68 requested) and removed 37 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11051 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 11067 seeds are put forward Round 1: 861 peptides, 133 chains. Longest chain 30 peptides. Score 0.485 Round 2: 923 peptides, 119 chains. Longest chain 36 peptides. Score 0.579 Round 3: 960 peptides, 118 chains. Longest chain 34 peptides. Score 0.608 Round 4: 993 peptides, 127 chains. Longest chain 30 peptides. Score 0.603 Round 5: 987 peptides, 121 chains. Longest chain 19 peptides. Score 0.617 Taking the results from Round 5 Chains 123, Residues 866, Estimated correctness of the model 21.2 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20233 reflections ( 99.76 % complete ) and 24412 restraints for refining 11052 atoms. 20996 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2293 (Rfree = 0.000) for 11052 atoms. Found 69 (70 requested) and removed 72 (35 requested) atoms. Cycle 7: After refmac, R = 0.2086 (Rfree = 0.000) for 10980 atoms. Found 30 (70 requested) and removed 51 (35 requested) atoms. Cycle 8: After refmac, R = 0.2037 (Rfree = 0.000) for 10934 atoms. Found 23 (70 requested) and removed 45 (35 requested) atoms. Cycle 9: After refmac, R = 0.2008 (Rfree = 0.000) for 10903 atoms. Found 13 (70 requested) and removed 35 (35 requested) atoms. Cycle 10: After refmac, R = 0.2000 (Rfree = 0.000) for 10876 atoms. Found 8 (69 requested) and removed 34 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11156 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 11171 seeds are put forward Round 1: 805 peptides, 126 chains. Longest chain 21 peptides. Score 0.464 Round 2: 883 peptides, 115 chains. Longest chain 33 peptides. Score 0.564 Round 3: 914 peptides, 105 chains. Longest chain 33 peptides. Score 0.617 Round 4: 901 peptides, 114 chains. Longest chain 31 peptides. Score 0.580 Round 5: 897 peptides, 107 chains. Longest chain 31 peptides. Score 0.599 Taking the results from Round 3 Chains 107, Residues 809, Estimated correctness of the model 21.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 24863 restraints for refining 11050 atoms. 21702 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2137 (Rfree = 0.000) for 11050 atoms. Found 56 (70 requested) and removed 56 (35 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2021 (Rfree = 0.000) for 11004 atoms. Found 30 (70 requested) and removed 47 (35 requested) atoms. Cycle 13: After refmac, R = 0.1982 (Rfree = 0.000) for 10973 atoms. Found 16 (70 requested) and removed 36 (35 requested) atoms. Cycle 14: After refmac, R = 0.1964 (Rfree = 0.000) for 10944 atoms. Found 17 (70 requested) and removed 35 (35 requested) atoms. Cycle 15: After refmac, R = 0.1946 (Rfree = 0.000) for 10922 atoms. Found 9 (70 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11228 seeds are put forward NCS extension: 27 residues added (8 deleted due to clashes), 11255 seeds are put forward Round 1: 754 peptides, 121 chains. Longest chain 28 peptides. Score 0.439 Round 2: 875 peptides, 125 chains. Longest chain 23 peptides. Score 0.524 Round 3: 890 peptides, 115 chains. Longest chain 28 peptides. Score 0.569 Round 4: 892 peptides, 108 chains. Longest chain 27 peptides. Score 0.593 Round 5: 897 peptides, 117 chains. Longest chain 22 peptides. Score 0.567 Taking the results from Round 4 Chains 112, Residues 784, Estimated correctness of the model 11.9 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20233 reflections ( 99.76 % complete ) and 24831 restraints for refining 11052 atoms. 21670 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2201 (Rfree = 0.000) for 11052 atoms. Found 47 (70 requested) and removed 52 (35 requested) atoms. Cycle 17: After refmac, R = 0.2056 (Rfree = 0.000) for 11006 atoms. Found 27 (70 requested) and removed 35 (35 requested) atoms. Cycle 18: After refmac, R = 0.2036 (Rfree = 0.000) for 10986 atoms. Found 20 (70 requested) and removed 37 (35 requested) atoms. Cycle 19: After refmac, R = 0.1975 (Rfree = 0.000) for 10962 atoms. Found 9 (70 requested) and removed 38 (35 requested) atoms. Cycle 20: After refmac, R = 0.1961 (Rfree = 0.000) for 10926 atoms. Found 10 (70 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11230 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11246 seeds are put forward Round 1: 786 peptides, 129 chains. Longest chain 15 peptides. Score 0.436 Round 2: 855 peptides, 112 chains. Longest chain 27 peptides. Score 0.553 Round 3: 834 peptides, 119 chains. Longest chain 33 peptides. Score 0.513 Round 4: 833 peptides, 109 chains. Longest chain 27 peptides. Score 0.547 Round 5: 868 peptides, 112 chains. Longest chain 40 peptides. Score 0.563 Taking the results from Round 5 Chains 114, Residues 756, Estimated correctness of the model 0.0 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20233 reflections ( 99.76 % complete ) and 24815 restraints for refining 11049 atoms. 21759 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2208 (Rfree = 0.000) for 11049 atoms. Found 45 (70 requested) and removed 46 (35 requested) atoms. Cycle 22: After refmac, R = 0.2091 (Rfree = 0.000) for 10981 atoms. Found 18 (70 requested) and removed 48 (35 requested) atoms. Cycle 23: After refmac, R = 0.2044 (Rfree = 0.000) for 10937 atoms. Found 21 (70 requested) and removed 39 (35 requested) atoms. Cycle 24: After refmac, R = 0.2011 (Rfree = 0.000) for 10912 atoms. Found 11 (70 requested) and removed 36 (35 requested) atoms. Cycle 25: After refmac, R = 0.1990 (Rfree = 0.000) for 10878 atoms. Found 8 (69 requested) and removed 34 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 11212 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 11230 seeds are put forward Round 1: 691 peptides, 112 chains. Longest chain 24 peptides. Score 0.418 Round 2: 801 peptides, 113 chains. Longest chain 27 peptides. Score 0.508 Round 3: 837 peptides, 114 chains. Longest chain 27 peptides. Score 0.533 Round 4: 839 peptides, 112 chains. Longest chain 25 peptides. Score 0.541 Round 5: 856 peptides, 113 chains. Longest chain 27 peptides. Score 0.550 Taking the results from Round 5 Chains 117, Residues 743, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25279 restraints for refining 11052 atoms. 22302 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2175 (Rfree = 0.000) for 11052 atoms. Found 51 (70 requested) and removed 40 (35 requested) atoms. Cycle 27: After refmac, R = 0.1977 (Rfree = 0.000) for 11027 atoms. Found 11 (70 requested) and removed 42 (35 requested) atoms. Cycle 28: After refmac, R = 0.1917 (Rfree = 0.000) for 10976 atoms. Found 8 (70 requested) and removed 36 (35 requested) atoms. Cycle 29: After refmac, R = 0.1888 (Rfree = 0.000) for 10941 atoms. Found 8 (70 requested) and removed 35 (35 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1910 (Rfree = 0.000) for 10908 atoms. Found 8 (70 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 11289 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 11304 seeds are put forward Round 1: 724 peptides, 130 chains. Longest chain 19 peptides. Score 0.377 Round 2: 804 peptides, 123 chains. Longest chain 18 peptides. Score 0.474 Round 3: 806 peptides, 116 chains. Longest chain 23 peptides. Score 0.501 Round 4: 807 peptides, 121 chains. Longest chain 22 peptides. Score 0.484 Round 5: 816 peptides, 117 chains. Longest chain 21 peptides. Score 0.506 Taking the results from Round 5 Chains 121, Residues 699, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25413 restraints for refining 11051 atoms. 22613 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2109 (Rfree = 0.000) for 11051 atoms. Found 50 (70 requested) and removed 40 (35 requested) atoms. Cycle 32: After refmac, R = 0.1972 (Rfree = 0.000) for 11012 atoms. Found 24 (70 requested) and removed 39 (35 requested) atoms. Cycle 33: After refmac, R = 0.1951 (Rfree = 0.000) for 10988 atoms. Found 9 (70 requested) and removed 37 (35 requested) atoms. Cycle 34: After refmac, R = 0.1940 (Rfree = 0.000) for 10955 atoms. Found 8 (70 requested) and removed 35 (35 requested) atoms. Cycle 35: After refmac, R = 0.1925 (Rfree = 0.000) for 10925 atoms. Found 8 (70 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 11224 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 11246 seeds are put forward Round 1: 675 peptides, 121 chains. Longest chain 18 peptides. Score 0.367 Round 2: 788 peptides, 121 chains. Longest chain 18 peptides. Score 0.468 Round 3: 743 peptides, 113 chains. Longest chain 20 peptides. Score 0.460 Round 4: 748 peptides, 108 chains. Longest chain 18 peptides. Score 0.483 Round 5: 765 peptides, 122 chains. Longest chain 21 peptides. Score 0.445 Taking the results from Round 4 Chains 109, Residues 640, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 26037 restraints for refining 11051 atoms. 23512 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2041 (Rfree = 0.000) for 11051 atoms. Found 36 (70 requested) and removed 38 (35 requested) atoms. Cycle 37: After refmac, R = 0.2072 (Rfree = 0.000) for 11018 atoms. Found 38 (70 requested) and removed 39 (35 requested) atoms. Cycle 38: After refmac, R = 0.2024 (Rfree = 0.000) for 10996 atoms. Found 39 (70 requested) and removed 41 (35 requested) atoms. Cycle 39: After refmac, R = 0.1980 (Rfree = 0.000) for 10964 atoms. Found 35 (70 requested) and removed 41 (35 requested) atoms. Cycle 40: After refmac, R = 0.1942 (Rfree = 0.000) for 10944 atoms. Found 33 (70 requested) and removed 40 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11348 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 11370 seeds are put forward Round 1: 561 peptides, 108 chains. Longest chain 13 peptides. Score 0.309 Round 2: 664 peptides, 109 chains. Longest chain 17 peptides. Score 0.405 Round 3: 693 peptides, 109 chains. Longest chain 18 peptides. Score 0.431 Round 4: 680 peptides, 109 chains. Longest chain 16 peptides. Score 0.420 Round 5: 703 peptides, 105 chains. Longest chain 21 peptides. Score 0.456 Taking the results from Round 5 Chains 108, Residues 598, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25953 restraints for refining 11051 atoms. 23569 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1994 (Rfree = 0.000) for 11051 atoms. Found 35 (70 requested) and removed 41 (35 requested) atoms. Cycle 42: After refmac, R = 0.1912 (Rfree = 0.000) for 11002 atoms. Found 30 (70 requested) and removed 41 (35 requested) atoms. Cycle 43: After refmac, R = 0.2038 (Rfree = 0.000) for 10969 atoms. Found 57 (70 requested) and removed 40 (35 requested) atoms. Cycle 44: After refmac, R = 0.1924 (Rfree = 0.000) for 10972 atoms. Found 41 (70 requested) and removed 37 (35 requested) atoms. Cycle 45: After refmac, R = 0.1943 (Rfree = 0.000) for 10959 atoms. Found 54 (70 requested) and removed 40 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 11312 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 11335 seeds are put forward Round 1: 570 peptides, 115 chains. Longest chain 10 peptides. Score 0.288 Round 2: 652 peptides, 112 chains. Longest chain 16 peptides. Score 0.382 Round 3: 672 peptides, 114 chains. Longest chain 18 peptides. Score 0.392 Round 4: 679 peptides, 112 chains. Longest chain 14 peptides. Score 0.407 Round 5: 677 peptides, 111 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 111, Residues 566, 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 2ash-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20233 reflections ( 99.76 % complete ) and 26544 restraints for refining 11051 atoms. 24391 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2043 (Rfree = 0.000) for 11051 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.2031 (Rfree = 0.000) for 10978 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.1995 (Rfree = 0.000) for 10912 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1700 (Rfree = 0.000) for 10858 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Writing output files ... TimeTaking 115.48