Tue 25 Dec 19:27:57 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 2pw4-1.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-1.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-1.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-1.4-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/2pw4-1.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-1.4-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 ============================================================ Tue 25 Dec 19:28:06 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/2pw4-1.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-1.4-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 228 and 0 Target number of residues in the AU: 228 Target solvent content: 0.4098 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 1 Adjusted target number of residues: 188 Adjusted target solvent content: 0.51 Input MTZ file: 2pw4-1.4-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: 5 Cell parameters: 77.750 59.670 57.820 90.000 128.790 90.000 Input sequence file: 2pw4-1.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1504 target number of atoms Had to go as low as 0.45 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 1 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 Loops will be built when appropriate and at the last cycle Resolution range: 25.783 1.450 Wilson plot Bfac: 8.95 36230 reflections ( 99.06 % complete ) and 0 restraints for refining 1661 atoms. Observations/parameters ratio is 5.45 ------------------------------------------------------ Starting model: R = 0.3261 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2729 (Rfree = 0.000) for 1661 atoms. Found 142 (142 requested) and removed 75 (71 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.39 1.37 Round 1: 165 peptides, 8 chains. Longest chain 38 peptides. Score 0.887 Round 2: 176 peptides, 3 chains. Longest chain 86 peptides. Score 0.945 Round 3: 179 peptides, 3 chains. Longest chain 113 peptides. Score 0.948 Round 4: 180 peptides, 2 chains. Longest chain 95 peptides. Score 0.955 Round 5: 180 peptides, 2 chains. Longest chain 158 peptides. Score 0.955 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 36230 reflections ( 99.06 % complete ) and 1650 restraints for refining 1680 atoms. 246 conditional restraints added. Observations/parameters ratio is 5.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2636 (Rfree = 0.000) for 1680 atoms. Found 106 (143 requested) and removed 22 (71 requested) atoms. Cycle 2: After refmac, R = 0.2507 (Rfree = 0.000) for 1764 atoms. Found 50 (151 requested) and removed 7 (75 requested) atoms. Cycle 3: After refmac, R = 0.2381 (Rfree = 0.000) for 1805 atoms. Found 37 (154 requested) and removed 9 (77 requested) atoms. Cycle 4: After refmac, R = 0.2151 (Rfree = 0.000) for 1833 atoms. Found 62 (156 requested) and removed 6 (78 requested) atoms. Cycle 5: After refmac, R = 0.2060 (Rfree = 0.000) for 1885 atoms. Found 57 (161 requested) and removed 11 (80 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.36 1.34 Round 1: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 2: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 3: 178 peptides, 3 chains. Longest chain 149 peptides. Score 0.947 Round 4: 178 peptides, 3 chains. Longest chain 150 peptides. Score 0.947 Round 5: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 36230 reflections ( 99.06 % complete ) and 1803 restraints for refining 1821 atoms. 394 conditional restraints added. Observations/parameters ratio is 4.97 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2051 (Rfree = 0.000) for 1821 atoms. Found 94 (155 requested) and removed 13 (77 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2059 (Rfree = 0.000) for 1898 atoms. Found 41 (162 requested) and removed 13 (81 requested) atoms. Cycle 8: After refmac, R = 0.1944 (Rfree = 0.000) for 1924 atoms. Found 44 (164 requested) and removed 6 (82 requested) atoms. Cycle 9: After refmac, R = 0.1884 (Rfree = 0.000) for 1959 atoms. Found 34 (167 requested) and removed 15 (83 requested) atoms. Cycle 10: After refmac, R = 0.1826 (Rfree = 0.000) for 1973 atoms. Found 52 (169 requested) and removed 11 (84 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.35 1.33 Round 1: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 2: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 3: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 4: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 5: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 36230 reflections ( 99.06 % complete ) and 1825 restraints for refining 1853 atoms. 416 conditional restraints added. Observations/parameters ratio is 4.89 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1968 (Rfree = 0.000) for 1853 atoms. Found 100 (158 requested) and removed 14 (79 requested) atoms. Cycle 12: After refmac, R = 0.1945 (Rfree = 0.000) for 1935 atoms. Found 56 (165 requested) and removed 16 (82 requested) atoms. Cycle 13: After refmac, R = 0.1886 (Rfree = 0.000) for 1975 atoms. Found 45 (169 requested) and removed 12 (84 requested) atoms. Cycle 14: After refmac, R = 0.1825 (Rfree = 0.000) for 2004 atoms. Found 51 (171 requested) and removed 18 (85 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1804 (Rfree = 0.000) for 2029 atoms. Found 69 (174 requested) and removed 28 (87 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.34 1.32 Round 1: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 2: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 3: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 4: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 5: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 36230 reflections ( 99.06 % complete ) and 1885 restraints for refining 1889 atoms. 476 conditional restraints added. Observations/parameters ratio is 4.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1914 (Rfree = 0.000) for 1889 atoms. Found 111 (161 requested) and removed 15 (80 requested) atoms. Cycle 17: After refmac, R = 0.1890 (Rfree = 0.000) for 1982 atoms. Found 62 (169 requested) and removed 18 (84 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1845 (Rfree = 0.000) for 2023 atoms. Found 47 (173 requested) and removed 24 (86 requested) atoms. Cycle 19: After refmac, R = 0.1801 (Rfree = 0.000) for 2043 atoms. Found 56 (171 requested) and removed 17 (87 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1792 (Rfree = 0.000) for 2074 atoms. Found 62 (174 requested) and removed 23 (89 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.34 1.32 Round 1: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 2: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 3: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 4: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 5: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 36230 reflections ( 99.06 % complete ) and 1930 restraints for refining 1913 atoms. 521 conditional restraints added. Observations/parameters ratio is 4.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1932 (Rfree = 0.000) for 1913 atoms. Found 107 (160 requested) and removed 17 (81 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1890 (Rfree = 0.000) for 2001 atoms. Found 52 (168 requested) and removed 13 (85 requested) atoms. Cycle 23: After refmac, R = 0.1849 (Rfree = 0.000) for 2036 atoms. Found 68 (171 requested) and removed 12 (87 requested) atoms. Cycle 24: After refmac, R = 0.1826 (Rfree = 0.000) for 2088 atoms. Found 51 (174 requested) and removed 11 (89 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1794 (Rfree = 0.000) for 2124 atoms. Found 52 (178 requested) and removed 14 (91 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.34 1.32 Round 1: 180 peptides, 2 chains. Longest chain 159 peptides. Score 0.955 Round 2: 180 peptides, 2 chains. Longest chain 159 peptides. Score 0.955 Round 3: 180 peptides, 2 chains. Longest chain 159 peptides. Score 0.955 Round 4: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.963 Round 5: 180 peptides, 2 chains. Longest chain 159 peptides. Score 0.955 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 36230 reflections ( 99.06 % complete ) and 1952 restraints for refining 1949 atoms. 532 conditional restraints added. Observations/parameters ratio is 4.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1925 (Rfree = 0.000) for 1949 atoms. Found 108 (163 requested) and removed 19 (83 requested) atoms. Cycle 27: After refmac, R = 0.1904 (Rfree = 0.000) for 2036 atoms. Found 67 (171 requested) and removed 15 (87 requested) atoms. Cycle 28: After refmac, R = 0.1858 (Rfree = 0.000) for 2085 atoms. Found 45 (174 requested) and removed 18 (89 requested) atoms. Cycle 29: After refmac, R = 0.1818 (Rfree = 0.000) for 2104 atoms. Found 60 (176 requested) and removed 17 (90 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1806 (Rfree = 0.000) for 2139 atoms. Found 47 (179 requested) and removed 22 (91 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.34 1.32 Round 1: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 2: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 3: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 4: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 5: 180 peptides, 2 chains. Longest chain 158 peptides. Score 0.955 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 36230 reflections ( 99.06 % complete ) and 2029 restraints for refining 1973 atoms. 620 conditional restraints added. Observations/parameters ratio is 4.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1952 (Rfree = 0.000) for 1973 atoms. Found 103 (166 requested) and removed 12 (84 requested) atoms. Cycle 32: After refmac, R = 0.1895 (Rfree = 0.000) for 2059 atoms. Found 64 (172 requested) and removed 13 (88 requested) atoms. Cycle 33: After refmac, R = 0.1875 (Rfree = 0.000) for 2105 atoms. Found 55 (176 requested) and removed 22 (90 requested) atoms. Cycle 34: After refmac, R = 0.1837 (Rfree = 0.000) for 2131 atoms. Found 70 (178 requested) and removed 15 (91 requested) atoms. Cycle 35: After refmac, R = 0.1828 (Rfree = 0.000) for 2183 atoms. Found 61 (182 requested) and removed 24 (93 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.34 1.32 Round 1: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 2: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 3: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 4: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 5: 180 peptides, 2 chains. Longest chain 158 peptides. Score 0.955 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 36230 reflections ( 99.06 % complete ) and 2071 restraints for refining 2010 atoms. 662 conditional restraints added. Observations/parameters ratio is 4.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1956 (Rfree = 0.000) for 2010 atoms. Found 125 (169 requested) and removed 20 (86 requested) atoms. Cycle 37: After refmac, R = 0.1940 (Rfree = 0.000) for 2112 atoms. Found 68 (176 requested) and removed 16 (90 requested) atoms. Cycle 38: After refmac, R = 0.1901 (Rfree = 0.000) for 2152 atoms. Found 57 (181 requested) and removed 16 (92 requested) atoms. Cycle 39: After refmac, R = 0.1870 (Rfree = 0.000) for 2183 atoms. Found 65 (183 requested) and removed 18 (93 requested) atoms. Cycle 40: After refmac, R = 0.1843 (Rfree = 0.000) for 2220 atoms. Found 57 (186 requested) and removed 26 (95 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.34 1.32 Round 1: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 2: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 3: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 4: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 5: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 36230 reflections ( 99.06 % complete ) and 2127 restraints for refining 2043 atoms. 718 conditional restraints added. Observations/parameters ratio is 4.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1936 (Rfree = 0.000) for 2043 atoms. Found 122 (171 requested) and removed 12 (87 requested) atoms. Cycle 42: After refmac, R = 0.1902 (Rfree = 0.000) for 2149 atoms. Found 63 (180 requested) and removed 21 (92 requested) atoms. Cycle 43: After refmac, R = 0.1861 (Rfree = 0.000) for 2185 atoms. Found 65 (183 requested) and removed 14 (93 requested) atoms. Cycle 44: After refmac, R = 0.1855 (Rfree = 0.000) for 2230 atoms. Found 57 (187 requested) and removed 25 (95 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1839 (Rfree = 0.000) for 2252 atoms. Found 64 (189 requested) and removed 28 (96 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.34 1.32 Round 1: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 2: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 3: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Round 4: 180 peptides, 1 chains. Longest chain 180 peptides. Score 0.962 Round 5: 179 peptides, 2 chains. Longest chain 158 peptides. Score 0.954 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pw4-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 36230 reflections ( 99.06 % complete ) and 2125 restraints for refining 2043 atoms. 716 conditional restraints added. Observations/parameters ratio is 4.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1965 (Rfree = 0.000) for 2043 atoms. Found 0 (171 requested) and removed 6 (87 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1887 (Rfree = 0.000) for 2033 atoms. Found 0 (167 requested) and removed 1 (87 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1802 (Rfree = 0.000) for 2030 atoms. Found 0 (164 requested) and removed 1 (87 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1804 (Rfree = 0.000) for 2027 atoms. Found 0 (159 requested) and removed 1 (86 requested) atoms. Writing output files ... TimeTaking 43.95