Sun 23 Dec 22:22:44 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 2pc1-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-1.5-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/2pc1-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-1.5-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 22:22:53 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/2pc1-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-1.5-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 197 and 0 Target number of residues in the AU: 197 Target solvent content: 0.4299 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 201 Adjusted target solvent content: 0.42 Input MTZ file: 2pc1-1.5-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: 1 Cell parameters: 35.480 37.650 41.500 94.220 109.420 113.080 Input sequence file: 2pc1-1.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 1608 target number of atoms Had to go as low as 0.40 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: 25.956 1.500 Wilson plot Bfac: 11.47 27578 reflections ( 95.11 % complete ) and 0 restraints for refining 1781 atoms. Observations/parameters ratio is 3.87 ------------------------------------------------------ Starting model: R = 0.3093 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2550 (Rfree = 0.000) for 1781 atoms. Found 119 (138 requested) and removed 78 (69 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.52 1.69 Round 1: 145 peptides, 10 chains. Longest chain 30 peptides. Score 0.845 Round 2: 154 peptides, 6 chains. Longest chain 45 peptides. Score 0.910 Round 3: 157 peptides, 6 chains. Longest chain 45 peptides. Score 0.915 Round 4: 161 peptides, 5 chains. Longest chain 47 peptides. Score 0.929 Round 5: 160 peptides, 5 chains. Longest chain 61 peptides. Score 0.928 Taking the results from Round 4 Chains 5, Residues 156, Estimated correctness of the model 99.8 % 4 chains (145 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 119 A and 128 A Built loop between residues 141 A and 144 A 3 chains (166 residues) following loop building 2 chains (155 residues) in sequence following loop building ------------------------------------------------------ 27578 reflections ( 95.11 % complete ) and 1777 restraints for refining 1641 atoms. 440 conditional restraints added. Observations/parameters ratio is 4.20 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2743 (Rfree = 0.000) for 1641 atoms. Found 75 (127 requested) and removed 46 (63 requested) atoms. Cycle 2: After refmac, R = 0.2487 (Rfree = 0.000) for 1669 atoms. Found 68 (126 requested) and removed 13 (64 requested) atoms. Cycle 3: After refmac, R = 0.2341 (Rfree = 0.000) for 1722 atoms. Found 46 (131 requested) and removed 6 (67 requested) atoms. Cycle 4: After refmac, R = 0.2112 (Rfree = 0.000) for 1760 atoms. Found 55 (134 requested) and removed 8 (68 requested) atoms. Cycle 5: After refmac, R = 0.2022 (Rfree = 0.000) for 1803 atoms. Found 53 (137 requested) and removed 15 (70 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.49 1.66 Round 1: 159 peptides, 5 chains. Longest chain 60 peptides. Score 0.927 Round 2: 161 peptides, 4 chains. Longest chain 60 peptides. Score 0.938 Round 3: 159 peptides, 6 chains. Longest chain 47 peptides. Score 0.918 Round 4: 161 peptides, 4 chains. Longest chain 60 peptides. Score 0.938 Round 5: 158 peptides, 6 chains. Longest chain 60 peptides. Score 0.916 Taking the results from Round 4 Chains 5, Residues 157, Estimated correctness of the model 99.8 % 4 chains (153 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 A and 65 A Built loop between residues 119 A and 128 A Built loop between residues 172 A and 176 A 1 chains (170 residues) following loop building 1 chains (170 residues) in sequence following loop building ------------------------------------------------------ 27578 reflections ( 95.11 % complete ) and 1779 restraints for refining 1773 atoms. 363 conditional restraints added. Observations/parameters ratio is 3.89 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2235 (Rfree = 0.000) for 1773 atoms. Found 81 (134 requested) and removed 58 (68 requested) atoms. Cycle 7: After refmac, R = 0.2085 (Rfree = 0.000) for 1793 atoms. Found 59 (133 requested) and removed 20 (69 requested) atoms. Cycle 8: After refmac, R = 0.1985 (Rfree = 0.000) for 1828 atoms. Found 60 (136 requested) and removed 17 (71 requested) atoms. Cycle 9: After refmac, R = 0.1931 (Rfree = 0.000) for 1868 atoms. Found 48 (139 requested) and removed 17 (72 requested) atoms. Cycle 10: After refmac, R = 0.1905 (Rfree = 0.000) for 1887 atoms. Found 53 (141 requested) and removed 21 (73 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.48 1.65 Round 1: 158 peptides, 6 chains. Longest chain 45 peptides. Score 0.916 Round 2: 159 peptides, 6 chains. Longest chain 46 peptides. Score 0.918 Round 3: 160 peptides, 5 chains. Longest chain 60 peptides. Score 0.928 Round 4: 161 peptides, 5 chains. Longest chain 60 peptides. Score 0.929 Round 5: 158 peptides, 6 chains. Longest chain 46 peptides. Score 0.916 Taking the results from Round 4 Chains 5, Residues 156, Estimated correctness of the model 99.8 % 4 chains (148 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 118 A and 128 A Built loop between residues 142 A and 144 A 2 chains (168 residues) following loop building 1 chains (160 residues) in sequence following loop building ------------------------------------------------------ 27578 reflections ( 95.11 % complete ) and 1937 restraints for refining 1792 atoms. 573 conditional restraints added. Observations/parameters ratio is 3.85 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2145 (Rfree = 0.000) for 1792 atoms. Found 92 (133 requested) and removed 46 (69 requested) atoms. Cycle 12: After refmac, R = 0.2041 (Rfree = 0.000) for 1833 atoms. Found 58 (136 requested) and removed 15 (71 requested) atoms. Cycle 13: After refmac, R = 0.1965 (Rfree = 0.000) for 1875 atoms. Found 42 (139 requested) and removed 14 (72 requested) atoms. Cycle 14: After refmac, R = 0.1911 (Rfree = 0.000) for 1899 atoms. Found 41 (142 requested) and removed 23 (74 requested) atoms. Cycle 15: After refmac, R = 0.1857 (Rfree = 0.000) for 1915 atoms. Found 37 (140 requested) and removed 24 (74 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.48 1.65 Round 1: 161 peptides, 5 chains. Longest chain 61 peptides. Score 0.929 Round 2: 160 peptides, 6 chains. Longest chain 47 peptides. Score 0.919 Round 3: 158 peptides, 7 chains. Longest chain 40 peptides. Score 0.907 Round 4: 161 peptides, 5 chains. Longest chain 61 peptides. Score 0.929 Round 5: 160 peptides, 6 chains. Longest chain 61 peptides. Score 0.919 Taking the results from Round 4 Chains 5, Residues 156, Estimated correctness of the model 99.8 % 4 chains (148 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 119 A and 128 A Built loop between residues 141 A and 144 A 2 chains (168 residues) following loop building 1 chains (160 residues) in sequence following loop building ------------------------------------------------------ 27578 reflections ( 95.11 % complete ) and 1914 restraints for refining 1802 atoms. 550 conditional restraints added. Observations/parameters ratio is 3.83 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2096 (Rfree = 0.000) for 1802 atoms. Found 103 (129 requested) and removed 59 (70 requested) atoms. Cycle 17: After refmac, R = 0.2036 (Rfree = 0.000) for 1842 atoms. Found 64 (129 requested) and removed 25 (71 requested) atoms. Cycle 18: After refmac, R = 0.1945 (Rfree = 0.000) for 1875 atoms. Found 56 (131 requested) and removed 11 (73 requested) atoms. Cycle 19: After refmac, R = 0.1875 (Rfree = 0.000) for 1916 atoms. Found 52 (134 requested) and removed 21 (74 requested) atoms. Cycle 20: After refmac, R = 0.1819 (Rfree = 0.000) for 1943 atoms. Found 52 (136 requested) and removed 19 (75 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.48 1.65 Round 1: 159 peptides, 5 chains. Longest chain 61 peptides. Score 0.927 Round 2: 161 peptides, 4 chains. Longest chain 61 peptides. Score 0.938 Round 3: 160 peptides, 6 chains. Longest chain 49 peptides. Score 0.919 Round 4: 160 peptides, 5 chains. Longest chain 61 peptides. Score 0.928 Round 5: 160 peptides, 5 chains. Longest chain 61 peptides. Score 0.928 Taking the results from Round 2 Chains 4, Residues 157, Estimated correctness of the model 99.8 % 4 chains (157 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 119 A and 128 A Built loop between residues 172 A and 176 A 1 chains (170 residues) following loop building 1 chains (170 residues) in sequence following loop building ------------------------------------------------------ 27578 reflections ( 95.11 % complete ) and 1850 restraints for refining 1818 atoms. 434 conditional restraints added. Observations/parameters ratio is 3.79 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2332 (Rfree = 0.000) for 1818 atoms. Found 75 (127 requested) and removed 46 (70 requested) atoms. Cycle 22: After refmac, R = 0.2041 (Rfree = 0.000) for 1845 atoms. Found 70 (126 requested) and removed 15 (71 requested) atoms. Cycle 23: After refmac, R = 0.1935 (Rfree = 0.000) for 1894 atoms. Found 57 (129 requested) and removed 12 (73 requested) atoms. Cycle 24: After refmac, R = 0.1890 (Rfree = 0.000) for 1930 atoms. Found 48 (132 requested) and removed 16 (75 requested) atoms. Cycle 25: After refmac, R = 0.1830 (Rfree = 0.000) for 1954 atoms. Found 40 (134 requested) and removed 20 (76 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.49 1.66 Round 1: 157 peptides, 6 chains. Longest chain 44 peptides. Score 0.915 Round 2: 161 peptides, 5 chains. Longest chain 61 peptides. Score 0.929 Round 3: 159 peptides, 6 chains. Longest chain 46 peptides. Score 0.918 Round 4: 160 peptides, 5 chains. Longest chain 61 peptides. Score 0.928 Round 5: 160 peptides, 5 chains. Longest chain 60 peptides. Score 0.928 Taking the results from Round 2 Chains 6, Residues 156, Estimated correctness of the model 99.8 % 4 chains (143 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 59 A Built loop between residues 118 A and 128 A Built loop between residues 141 A and 144 A 2 chains (168 residues) following loop building 1 chains (159 residues) in sequence following loop building ------------------------------------------------------ 27578 reflections ( 95.11 % complete ) and 1981 restraints for refining 1836 atoms. 621 conditional restraints added. Observations/parameters ratio is 3.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2395 (Rfree = 0.000) for 1836 atoms. Found 85 (125 requested) and removed 44 (71 requested) atoms. Cycle 27: After refmac, R = 0.2111 (Rfree = 0.000) for 1873 atoms. Found 70 (125 requested) and removed 8 (72 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2007 (Rfree = 0.000) for 1929 atoms. Found 59 (129 requested) and removed 14 (75 requested) atoms. Cycle 29: After refmac, R = 0.1942 (Rfree = 0.000) for 1967 atoms. Found 56 (132 requested) and removed 25 (76 requested) atoms. Cycle 30: After refmac, R = 0.1902 (Rfree = 0.000) for 1993 atoms. Found 50 (133 requested) and removed 23 (77 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.49 1.66 Round 1: 156 peptides, 5 chains. Longest chain 59 peptides. Score 0.923 Round 2: 159 peptides, 5 chains. Longest chain 46 peptides. Score 0.927 Round 3: 160 peptides, 5 chains. Longest chain 61 peptides. Score 0.928 Round 4: 157 peptides, 4 chains. Longest chain 60 peptides. Score 0.933 Round 5: 157 peptides, 6 chains. Longest chain 46 peptides. Score 0.915 Taking the results from Round 4 Chains 4, Residues 153, Estimated correctness of the model 99.8 % 3 chains (147 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 118 A and 128 A 2 chains (164 residues) following loop building 1 chains (158 residues) in sequence following loop building ------------------------------------------------------ 27578 reflections ( 95.11 % complete ) and 2164 restraints for refining 1892 atoms. 824 conditional restraints added. Observations/parameters ratio is 3.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2358 (Rfree = 0.000) for 1892 atoms. Found 83 (126 requested) and removed 50 (73 requested) atoms. Cycle 32: After refmac, R = 0.2151 (Rfree = 0.000) for 1923 atoms. Found 64 (125 requested) and removed 18 (74 requested) atoms. Cycle 33: After refmac, R = 0.2031 (Rfree = 0.000) for 1963 atoms. Found 54 (129 requested) and removed 22 (76 requested) atoms. Cycle 34: After refmac, R = 0.1958 (Rfree = 0.000) for 1989 atoms. Found 56 (130 requested) and removed 15 (77 requested) atoms. Cycle 35: After refmac, R = 0.1924 (Rfree = 0.000) for 2018 atoms. Found 48 (132 requested) and removed 22 (78 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.50 1.67 Round 1: 157 peptides, 6 chains. Longest chain 60 peptides. Score 0.915 Round 2: 160 peptides, 4 chains. Longest chain 60 peptides. Score 0.936 Round 3: 155 peptides, 6 chains. Longest chain 46 peptides. Score 0.912 Round 4: 160 peptides, 4 chains. Longest chain 60 peptides. Score 0.936 Round 5: 160 peptides, 4 chains. Longest chain 60 peptides. Score 0.936 Taking the results from Round 5 Chains 4, Residues 156, Estimated correctness of the model 99.8 % 3 chains (147 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 118 A and 128 A 2 chains (167 residues) following loop building 1 chains (158 residues) in sequence following loop building ------------------------------------------------------ 27578 reflections ( 95.11 % complete ) and 2137 restraints for refining 1896 atoms. 785 conditional restraints added. Observations/parameters ratio is 3.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2367 (Rfree = 0.000) for 1896 atoms. Found 87 (123 requested) and removed 42 (73 requested) atoms. Cycle 37: After refmac, R = 0.2087 (Rfree = 0.000) for 1941 atoms. Found 61 (126 requested) and removed 15 (75 requested) atoms. Cycle 38: After refmac, R = 0.2006 (Rfree = 0.000) for 1978 atoms. Found 41 (129 requested) and removed 19 (77 requested) atoms. Cycle 39: After refmac, R = 0.1928 (Rfree = 0.000) for 1994 atoms. Found 44 (130 requested) and removed 21 (77 requested) atoms. Cycle 40: After refmac, R = 0.1876 (Rfree = 0.000) for 2009 atoms. Found 41 (131 requested) and removed 31 (78 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.49 1.66 Round 1: 159 peptides, 5 chains. Longest chain 60 peptides. Score 0.927 Round 2: 158 peptides, 5 chains. Longest chain 60 peptides. Score 0.925 Round 3: 158 peptides, 6 chains. Longest chain 46 peptides. Score 0.916 Round 4: 161 peptides, 4 chains. Longest chain 60 peptides. Score 0.938 Round 5: 159 peptides, 6 chains. Longest chain 46 peptides. Score 0.918 Taking the results from Round 4 Chains 4, Residues 157, Estimated correctness of the model 99.8 % 3 chains (148 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 118 A and 128 A 2 chains (168 residues) following loop building 1 chains (159 residues) in sequence following loop building ------------------------------------------------------ 27578 reflections ( 95.11 % complete ) and 2099 restraints for refining 1880 atoms. 739 conditional restraints added. Observations/parameters ratio is 3.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2134 (Rfree = 0.000) for 1880 atoms. Found 94 (120 requested) and removed 66 (73 requested) atoms. Cycle 42: After refmac, R = 0.1996 (Rfree = 0.000) for 1904 atoms. Found 70 (118 requested) and removed 17 (74 requested) atoms. Cycle 43: After refmac, R = 0.1942 (Rfree = 0.000) for 1952 atoms. Found 46 (122 requested) and removed 21 (76 requested) atoms. Cycle 44: After refmac, R = 0.1885 (Rfree = 0.000) for 1972 atoms. Found 41 (122 requested) and removed 13 (76 requested) atoms. Cycle 45: After refmac, R = 0.1837 (Rfree = 0.000) for 1998 atoms. Found 46 (124 requested) and removed 17 (77 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.49 1.66 Round 1: 156 peptides, 6 chains. Longest chain 44 peptides. Score 0.913 Round 2: 156 peptides, 5 chains. Longest chain 58 peptides. Score 0.923 Round 3: 157 peptides, 6 chains. Longest chain 46 peptides. Score 0.915 Round 4: 158 peptides, 5 chains. Longest chain 58 peptides. Score 0.925 Round 5: 157 peptides, 6 chains. Longest chain 58 peptides. Score 0.915 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 153, Estimated correctness of the model 99.8 % 4 chains (144 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 58 A and 62 A Built loop between residues 118 A and 128 A Built loop between residues 140 A and 144 A 2 chains (168 residues) following loop building 1 chains (159 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 27578 reflections ( 95.11 % complete ) and 1360 restraints for refining 1330 atoms. Observations/parameters ratio is 5.18 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2698 (Rfree = 0.000) for 1330 atoms. Found 49 (82 requested) and removed 0 (82 requested) atoms. Cycle 47: After refmac, R = 0.2515 (Rfree = 0.000) for 1330 atoms. Found 20 (86 requested) and removed 0 (53 requested) atoms. Cycle 48: After refmac, R = 0.2349 (Rfree = 0.000) for 1330 atoms. Found 9 (86 requested) and removed 2 (54 requested) atoms. Cycle 49: After refmac, R = 0.2281 (Rfree = 0.000) for 1330 atoms. TimeTaking 48.08