Mon 24 Dec 00:36:07 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-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/2ash-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-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 00:36:12 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-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 1136 and 0 Target number of residues in the AU: 1136 Target solvent content: 0.6503 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-3.4-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-3.4-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 3.400 Wilson plot Bfac: 78.27 23968 reflections ( 99.79 % complete ) and 0 restraints for refining 13606 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3202 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2740 (Rfree = 0.000) for 13606 atoms. Found 102 (102 requested) and removed 88 (51 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 13942 seeds are put forward NCS extension: 0 residues added, 13942 seeds are put forward Round 1: 730 peptides, 128 chains. Longest chain 16 peptides. Score 0.390 Round 2: 905 peptides, 125 chains. Longest chain 26 peptides. Score 0.547 Round 3: 947 peptides, 122 chains. Longest chain 27 peptides. Score 0.587 Round 4: 1003 peptides, 115 chains. Longest chain 28 peptides. Score 0.644 Round 5: 994 peptides, 112 chains. Longest chain 28 peptides. Score 0.647 Taking the results from Round 5 Chains 112, Residues 882, Estimated correctness of the model 43.3 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24443 restraints for refining 11082 atoms. 20989 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2337 (Rfree = 0.000) for 11082 atoms. Found 83 (83 requested) and removed 58 (41 requested) atoms. Cycle 2: After refmac, R = 0.2124 (Rfree = 0.000) for 10923 atoms. Found 43 (83 requested) and removed 54 (41 requested) atoms. Cycle 3: After refmac, R = 0.2023 (Rfree = 0.000) for 10864 atoms. Found 35 (82 requested) and removed 53 (41 requested) atoms. Cycle 4: After refmac, R = 0.1945 (Rfree = 0.000) for 10810 atoms. Found 26 (81 requested) and removed 43 (40 requested) atoms. Cycle 5: After refmac, R = 0.1899 (Rfree = 0.000) for 10765 atoms. Found 26 (81 requested) and removed 47 (40 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 11158 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 11174 seeds are put forward Round 1: 886 peptides, 127 chains. Longest chain 18 peptides. Score 0.526 Round 2: 970 peptides, 116 chains. Longest chain 20 peptides. Score 0.621 Round 3: 964 peptides, 112 chains. Longest chain 31 peptides. Score 0.628 Round 4: 960 peptides, 108 chains. Longest chain 27 peptides. Score 0.638 Round 5: 960 peptides, 104 chains. Longest chain 31 peptides. Score 0.649 Taking the results from Round 5 Chains 109, Residues 856, Estimated correctness of the model 43.8 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24315 restraints for refining 11082 atoms. 20772 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2212 (Rfree = 0.000) for 11082 atoms. Found 70 (83 requested) and removed 57 (41 requested) atoms. Cycle 7: After refmac, R = 0.2038 (Rfree = 0.000) for 11028 atoms. Found 18 (83 requested) and removed 49 (41 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1998 (Rfree = 0.000) for 10961 atoms. Found 28 (83 requested) and removed 45 (41 requested) atoms. Cycle 9: After refmac, R = 0.1940 (Rfree = 0.000) for 10929 atoms. Found 25 (82 requested) and removed 42 (41 requested) atoms. Cycle 10: After refmac, R = 0.1913 (Rfree = 0.000) for 10896 atoms. Found 17 (82 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 11241 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 11256 seeds are put forward Round 1: 876 peptides, 127 chains. Longest chain 22 peptides. Score 0.518 Round 2: 947 peptides, 118 chains. Longest chain 34 peptides. Score 0.599 Round 3: 987 peptides, 125 chains. Longest chain 21 peptides. Score 0.605 Round 4: 972 peptides, 99 chains. Longest chain 32 peptides. Score 0.670 Round 5: 950 peptides, 118 chains. Longest chain 20 peptides. Score 0.601 Taking the results from Round 4 Chains 105, Residues 873, Estimated correctness of the model 49.8 % 9 chains (160 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 22799 restraints for refining 11086 atoms. 18769 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2262 (Rfree = 0.000) for 11086 atoms. Found 64 (83 requested) and removed 67 (41 requested) atoms. Cycle 12: After refmac, R = 0.2055 (Rfree = 0.000) for 11016 atoms. Found 29 (83 requested) and removed 45 (41 requested) atoms. Cycle 13: After refmac, R = 0.1980 (Rfree = 0.000) for 10973 atoms. Found 25 (83 requested) and removed 49 (41 requested) atoms. Cycle 14: After refmac, R = 0.1916 (Rfree = 0.000) for 10933 atoms. Found 15 (82 requested) and removed 43 (41 requested) atoms. Cycle 15: After refmac, R = 0.1870 (Rfree = 0.000) for 10893 atoms. Found 14 (82 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 11233 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 11262 seeds are put forward Round 1: 821 peptides, 116 chains. Longest chain 20 peptides. Score 0.513 Round 2: 878 peptides, 101 chains. Longest chain 34 peptides. Score 0.605 Round 3: 924 peptides, 111 chains. Longest chain 38 peptides. Score 0.605 Round 4: 921 peptides, 111 chains. Longest chain 33 peptides. Score 0.603 Round 5: 901 peptides, 103 chains. Longest chain 25 peptides. Score 0.614 Taking the results from Round 5 Chains 106, Residues 798, Estimated correctness of the model 33.2 % 6 chains (65 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24437 restraints for refining 11083 atoms. 21102 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2191 (Rfree = 0.000) for 11083 atoms. Found 71 (83 requested) and removed 56 (41 requested) atoms. Cycle 17: After refmac, R = 0.1985 (Rfree = 0.000) for 11055 atoms. Found 24 (83 requested) and removed 45 (41 requested) atoms. Cycle 18: After refmac, R = 0.1974 (Rfree = 0.000) for 11012 atoms. Found 26 (83 requested) and removed 43 (41 requested) atoms. Cycle 19: After refmac, R = 0.1928 (Rfree = 0.000) for 10982 atoms. Found 16 (83 requested) and removed 42 (41 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 20: After refmac, R = 0.1871 (Rfree = 0.000) for 10944 atoms. Found 17 (82 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 11247 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 11259 seeds are put forward Round 1: 842 peptides, 132 chains. Longest chain 23 peptides. Score 0.473 Round 2: 889 peptides, 118 chains. Longest chain 27 peptides. Score 0.558 Round 3: 892 peptides, 118 chains. Longest chain 27 peptides. Score 0.560 Round 4: 854 peptides, 118 chains. Longest chain 16 peptides. Score 0.532 Round 5: 883 peptides, 114 chains. Longest chain 29 peptides. Score 0.567 Taking the results from Round 5 Chains 118, Residues 769, Estimated correctness of the model 17.5 % 6 chains (67 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24583 restraints for refining 11085 atoms. 21398 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2169 (Rfree = 0.000) for 11085 atoms. Found 67 (83 requested) and removed 56 (41 requested) atoms. Cycle 22: After refmac, R = 0.1972 (Rfree = 0.000) for 11044 atoms. Found 27 (83 requested) and removed 45 (41 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1900 (Rfree = 0.000) for 11005 atoms. Found 31 (83 requested) and removed 47 (41 requested) atoms. Cycle 24: After refmac, R = 0.1891 (Rfree = 0.000) for 10970 atoms. Found 37 (82 requested) and removed 42 (41 requested) atoms. Cycle 25: After refmac, R = 0.1824 (Rfree = 0.000) for 10956 atoms. Found 22 (82 requested) and removed 43 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 11285 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 11299 seeds are put forward Round 1: 762 peptides, 124 chains. Longest chain 19 peptides. Score 0.434 Round 2: 872 peptides, 127 chains. Longest chain 27 peptides. Score 0.515 Round 3: 875 peptides, 115 chains. Longest chain 24 peptides. Score 0.558 Round 4: 899 peptides, 119 chains. Longest chain 29 peptides. Score 0.562 Round 5: 866 peptides, 112 chains. Longest chain 23 peptides. Score 0.561 Taking the results from Round 4 Chains 123, Residues 780, Estimated correctness of the model 15.8 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24844 restraints for refining 11086 atoms. 21735 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2136 (Rfree = 0.000) for 11086 atoms. Found 49 (83 requested) and removed 47 (41 requested) atoms. Cycle 27: After refmac, R = 0.1944 (Rfree = 0.000) for 11045 atoms. Found 31 (83 requested) and removed 44 (41 requested) atoms. Cycle 28: After refmac, R = 0.1911 (Rfree = 0.000) for 11017 atoms. Found 20 (83 requested) and removed 44 (41 requested) atoms. Cycle 29: After refmac, R = 0.1863 (Rfree = 0.000) for 10984 atoms. Found 18 (83 requested) and removed 44 (41 requested) atoms. Cycle 30: After refmac, R = 0.1884 (Rfree = 0.000) for 10949 atoms. Found 21 (82 requested) and removed 44 (41 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 11308 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 11324 seeds are put forward Round 1: 742 peptides, 134 chains. Longest chain 20 peptides. Score 0.377 Round 2: 805 peptides, 109 chains. Longest chain 27 peptides. Score 0.525 Round 3: 824 peptides, 118 chains. Longest chain 22 peptides. Score 0.508 Round 4: 810 peptides, 113 chains. Longest chain 18 peptides. Score 0.515 Round 5: 811 peptides, 108 chains. Longest chain 23 peptides. Score 0.533 Taking the results from Round 5 Chains 111, Residues 703, Estimated correctness of the model 5.3 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25035 restraints for refining 11084 atoms. 22181 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2065 (Rfree = 0.000) for 11084 atoms. Found 51 (83 requested) and removed 45 (41 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1940 (Rfree = 0.000) for 11063 atoms. Found 26 (83 requested) and removed 41 (41 requested) atoms. Cycle 33: After refmac, R = 0.1867 (Rfree = 0.000) for 11035 atoms. Found 19 (83 requested) and removed 41 (41 requested) atoms. Cycle 34: After refmac, R = 0.1832 (Rfree = 0.000) for 10999 atoms. Found 19 (83 requested) and removed 41 (41 requested) atoms. Cycle 35: After refmac, R = 0.1796 (Rfree = 0.000) for 10968 atoms. Found 14 (82 requested) and removed 42 (41 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 11295 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 11316 seeds are put forward Round 1: 695 peptides, 125 chains. Longest chain 16 peptides. Score 0.369 Round 2: 787 peptides, 122 chains. Longest chain 22 peptides. Score 0.464 Round 3: 824 peptides, 116 chains. Longest chain 19 peptides. Score 0.515 Round 4: 819 peptides, 118 chains. Longest chain 23 peptides. Score 0.504 Round 5: 804 peptides, 121 chains. Longest chain 21 peptides. Score 0.481 Taking the results from Round 3 Chains 120, Residues 708, Estimated correctness of the model 0.0 % 6 chains (55 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25089 restraints for refining 11085 atoms. 22192 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1988 (Rfree = 0.000) for 11085 atoms. Found 48 (83 requested) and removed 47 (41 requested) atoms. Cycle 37: After refmac, R = 0.1852 (Rfree = 0.000) for 11057 atoms. Found 26 (83 requested) and removed 42 (41 requested) atoms. Cycle 38: After refmac, R = 0.1824 (Rfree = 0.000) for 11032 atoms. Found 20 (83 requested) and removed 41 (41 requested) atoms. Cycle 39: After refmac, R = 0.1777 (Rfree = 0.000) for 11001 atoms. Found 16 (83 requested) and removed 41 (41 requested) atoms. Cycle 40: After refmac, R = 0.1739 (Rfree = 0.000) for 10966 atoms. Found 14 (82 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 11299 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 11326 seeds are put forward Round 1: 703 peptides, 126 chains. Longest chain 13 peptides. Score 0.373 Round 2: 785 peptides, 122 chains. Longest chain 18 peptides. Score 0.462 Round 3: 758 peptides, 106 chains. Longest chain 23 peptides. Score 0.498 Round 4: 786 peptides, 116 chains. Longest chain 21 peptides. Score 0.485 Round 5: 825 peptides, 117 chains. Longest chain 20 peptides. Score 0.513 Taking the results from Round 5 Chains 118, Residues 708, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25369 restraints for refining 11086 atoms. 22550 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1980 (Rfree = 0.000) for 11086 atoms. Found 57 (83 requested) and removed 45 (41 requested) atoms. Cycle 42: After refmac, R = 0.1843 (Rfree = 0.000) for 11078 atoms. Found 30 (83 requested) and removed 42 (41 requested) atoms. Cycle 43: After refmac, R = 0.1829 (Rfree = 0.000) for 11052 atoms. Found 34 (83 requested) and removed 42 (41 requested) atoms. Cycle 44: After refmac, R = 0.1752 (Rfree = 0.000) for 11033 atoms. Found 26 (83 requested) and removed 41 (41 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1722 (Rfree = 0.000) for 11009 atoms. Found 24 (83 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 11399 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 11418 seeds are put forward Round 1: 657 peptides, 118 chains. Longest chain 16 peptides. Score 0.362 Round 2: 717 peptides, 107 chains. Longest chain 20 peptides. Score 0.460 Round 3: 723 peptides, 109 chains. Longest chain 16 peptides. Score 0.458 Round 4: 741 peptides, 108 chains. Longest chain 22 peptides. Score 0.477 Round 5: 733 peptides, 106 chains. Longest chain 23 peptides. Score 0.478 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 106, Residues 627, 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. 23968 reflections ( 99.79 % complete ) and 25881 restraints for refining 11086 atoms. 23479 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1904 (Rfree = 0.000) for 11086 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Cycle 47: After refmac, R = 0.1857 (Rfree = 0.000) for 11019 atoms. Found 0 (83 requested) and removed 40 (41 requested) atoms. Cycle 48: After refmac, R = 0.1837 (Rfree = 0.000) for 10969 atoms. Found 0 (82 requested) and removed 34 (41 requested) atoms. Cycle 49: After refmac, R = 0.1822 (Rfree = 0.000) for 10930 atoms. TimeTaking 115.1