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 2fcl-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-1.6-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/2fcl-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-1.6-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/2fcl-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-1.6-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 191 and 0 Target number of residues in the AU: 191 Target solvent content: 0.4102 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 169 Adjusted target solvent content: 0.48 Input MTZ file: 2fcl-1.6-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: 32.560 36.210 39.280 74.110 86.380 79.700 Input sequence file: 2fcl-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1352 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: 29.656 1.600 Wilson plot Bfac: 8.98 20126 reflections ( 89.82 % complete ) and 0 restraints for refining 1497 atoms. Observations/parameters ratio is 3.36 ------------------------------------------------------ Starting model: R = 0.3115 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2523 (Rfree = 0.000) for 1497 atoms. Found 96 (96 requested) and removed 52 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.42 1.46 Round 1: 142 peptides, 6 chains. Longest chain 32 peptides. Score 0.902 Round 2: 152 peptides, 3 chains. Longest chain 80 peptides. Score 0.945 Round 3: 154 peptides, 1 chains. Longest chain 154 peptides. Score 0.963 Round 4: 154 peptides, 1 chains. Longest chain 154 peptides. Score 0.963 Round 5: 154 peptides, 1 chains. Longest chain 154 peptides. Score 0.963 Taking the results from Round 5 Chains 1, Residues 153, Estimated correctness of the model 99.9 % 1 chains (153 residues) have been docked in sequence ------------------------------------------------------ 20126 reflections ( 89.82 % complete ) and 1488 restraints for refining 1489 atoms. 190 conditional restraints added. Observations/parameters ratio is 3.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2619 (Rfree = 0.000) for 1489 atoms. Found 66 (96 requested) and removed 28 (48 requested) atoms. Cycle 2: After refmac, R = 0.2395 (Rfree = 0.000) for 1526 atoms. Found 56 (98 requested) and removed 5 (49 requested) atoms. Cycle 3: After refmac, R = 0.2258 (Rfree = 0.000) for 1576 atoms. Found 43 (102 requested) and removed 5 (51 requested) atoms. Cycle 4: After refmac, R = 0.2045 (Rfree = 0.000) for 1610 atoms. Found 41 (104 requested) and removed 6 (52 requested) atoms. Cycle 5: After refmac, R = 0.1914 (Rfree = 0.000) for 1641 atoms. Found 43 (106 requested) and removed 8 (53 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.39 1.43 Round 1: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Round 2: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Round 3: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Round 4: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Round 5: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Taking the results from Round 5 Chains 1, Residues 154, Estimated correctness of the model 99.9 % 1 chains (154 residues) have been docked in sequence ------------------------------------------------------ 20126 reflections ( 89.82 % complete ) and 1587 restraints for refining 1619 atoms. 281 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1982 (Rfree = 0.000) for 1619 atoms. Found 62 (104 requested) and removed 19 (52 requested) atoms. Cycle 7: After refmac, R = 0.1868 (Rfree = 0.000) for 1662 atoms. Found 43 (107 requested) and removed 15 (53 requested) atoms. Cycle 8: After refmac, R = 0.1789 (Rfree = 0.000) for 1688 atoms. Found 49 (109 requested) and removed 9 (54 requested) atoms. Cycle 9: After refmac, R = 0.1756 (Rfree = 0.000) for 1726 atoms. Found 36 (111 requested) and removed 14 (55 requested) atoms. Cycle 10: After refmac, R = 0.1725 (Rfree = 0.000) for 1745 atoms. Found 54 (113 requested) and removed 19 (56 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.38 1.42 Round 1: 154 peptides, 1 chains. Longest chain 154 peptides. Score 0.963 Round 2: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Round 3: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Round 4: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Round 5: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Taking the results from Round 5 Chains 1, Residues 154, Estimated correctness of the model 99.9 % 1 chains (154 residues) have been docked in sequence ------------------------------------------------------ 20126 reflections ( 89.82 % complete ) and 1657 restraints for refining 1661 atoms. 351 conditional restraints added. Observations/parameters ratio is 3.03 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1970 (Rfree = 0.000) for 1661 atoms. Found 99 (107 requested) and removed 22 (53 requested) atoms. Cycle 12: After refmac, R = 0.1895 (Rfree = 0.000) for 1737 atoms. Found 49 (112 requested) and removed 16 (56 requested) atoms. Cycle 13: After refmac, R = 0.1801 (Rfree = 0.000) for 1763 atoms. Found 44 (114 requested) and removed 13 (57 requested) atoms. Cycle 14: After refmac, R = 0.1736 (Rfree = 0.000) for 1791 atoms. Found 53 (116 requested) and removed 8 (58 requested) atoms. Cycle 15: After refmac, R = 0.1717 (Rfree = 0.000) for 1833 atoms. Found 40 (118 requested) and removed 13 (59 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.38 1.42 Round 1: 155 peptides, 2 chains. Longest chain 101 peptides. Score 0.956 Round 2: 155 peptides, 2 chains. Longest chain 101 peptides. Score 0.956 Round 3: 155 peptides, 2 chains. Longest chain 101 peptides. Score 0.956 Round 4: 155 peptides, 2 chains. Longest chain 101 peptides. Score 0.956 Round 5: 155 peptides, 2 chains. Longest chain 101 peptides. Score 0.956 Taking the results from Round 5 Chains 2, Residues 153, Estimated correctness of the model 99.9 % 2 chains (153 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 116 A 1 chains (155 residues) following loop building 1 chains (155 residues) in sequence following loop building ------------------------------------------------------ 20126 reflections ( 89.82 % complete ) and 1685 restraints for refining 1711 atoms. 368 conditional restraints added. Observations/parameters ratio is 2.94 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1878 (Rfree = 0.000) for 1711 atoms. Found 79 (110 requested) and removed 26 (55 requested) atoms. Cycle 17: After refmac, R = 0.1824 (Rfree = 0.000) for 1762 atoms. Found 60 (114 requested) and removed 20 (57 requested) atoms. Cycle 18: After refmac, R = 0.1767 (Rfree = 0.000) for 1798 atoms. Found 52 (116 requested) and removed 19 (58 requested) atoms. Cycle 19: After refmac, R = 0.1745 (Rfree = 0.000) for 1828 atoms. Found 48 (118 requested) and removed 33 (59 requested) atoms. Cycle 20: After refmac, R = 0.1718 (Rfree = 0.000) for 1842 atoms. Found 65 (117 requested) and removed 27 (59 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.38 1.42 Round 1: 155 peptides, 2 chains. Longest chain 101 peptides. Score 0.956 Round 2: 155 peptides, 2 chains. Longest chain 101 peptides. Score 0.956 Round 3: 155 peptides, 2 chains. Longest chain 84 peptides. Score 0.956 Round 4: 156 peptides, 1 chains. Longest chain 156 peptides. Score 0.964 Round 5: 156 peptides, 1 chains. Longest chain 156 peptides. Score 0.964 Taking the results from Round 5 Chains 1, Residues 155, Estimated correctness of the model 99.9 % 1 chains (155 residues) have been docked in sequence ------------------------------------------------------ 20126 reflections ( 89.82 % complete ) and 1703 restraints for refining 1710 atoms. 386 conditional restraints added. Observations/parameters ratio is 2.94 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1879 (Rfree = 0.000) for 1710 atoms. Found 108 (108 requested) and removed 25 (55 requested) atoms. Cycle 22: After refmac, R = 0.1838 (Rfree = 0.000) for 1792 atoms. Found 44 (114 requested) and removed 22 (58 requested) atoms. Cycle 23: After refmac, R = 0.1750 (Rfree = 0.000) for 1811 atoms. Found 51 (115 requested) and removed 13 (58 requested) atoms. Cycle 24: After refmac, R = 0.1720 (Rfree = 0.000) for 1846 atoms. Found 45 (117 requested) and removed 24 (59 requested) atoms. Cycle 25: After refmac, R = 0.1678 (Rfree = 0.000) for 1863 atoms. Found 42 (115 requested) and removed 30 (60 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.38 1.42 Round 1: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Round 2: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Round 3: 154 peptides, 2 chains. Longest chain 84 peptides. Score 0.955 Round 4: 153 peptides, 3 chains. Longest chain 88 peptides. Score 0.946 Round 5: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Taking the results from Round 5 Chains 1, Residues 154, Estimated correctness of the model 99.9 % 1 chains (154 residues) have been docked in sequence ------------------------------------------------------ 20126 reflections ( 89.82 % complete ) and 1724 restraints for refining 1719 atoms. 415 conditional restraints added. Observations/parameters ratio is 2.93 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2119 (Rfree = 0.000) for 1719 atoms. Found 88 (104 requested) and removed 21 (55 requested) atoms. Cycle 27: After refmac, R = 0.1886 (Rfree = 0.000) for 1785 atoms. Found 59 (108 requested) and removed 11 (57 requested) atoms. Cycle 28: After refmac, R = 0.1800 (Rfree = 0.000) for 1831 atoms. Found 36 (111 requested) and removed 9 (59 requested) atoms. Cycle 29: After refmac, R = 0.1750 (Rfree = 0.000) for 1849 atoms. Found 45 (113 requested) and removed 15 (60 requested) atoms. Cycle 30: After refmac, R = 0.1693 (Rfree = 0.000) for 1877 atoms. Found 47 (114 requested) and removed 13 (60 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.38 1.42 Round 1: 154 peptides, 2 chains. Longest chain 84 peptides. Score 0.955 Round 2: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Round 3: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Round 4: 153 peptides, 3 chains. Longest chain 88 peptides. Score 0.946 Round 5: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Taking the results from Round 5 Chains 2, Residues 152, Estimated correctness of the model 99.9 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 116 A 1 chains (154 residues) following loop building 1 chains (154 residues) in sequence following loop building ------------------------------------------------------ 20126 reflections ( 89.82 % complete ) and 1760 restraints for refining 1745 atoms. 451 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1859 (Rfree = 0.000) for 1745 atoms. Found 105 (105 requested) and removed 20 (56 requested) atoms. Cycle 32: After refmac, R = 0.1821 (Rfree = 0.000) for 1824 atoms. Found 55 (111 requested) and removed 20 (59 requested) atoms. Cycle 33: After refmac, R = 0.1755 (Rfree = 0.000) for 1856 atoms. Found 61 (113 requested) and removed 19 (60 requested) atoms. Cycle 34: After refmac, R = 0.1726 (Rfree = 0.000) for 1898 atoms. Found 44 (115 requested) and removed 25 (61 requested) atoms. Cycle 35: After refmac, R = 0.1689 (Rfree = 0.000) for 1913 atoms. Found 41 (114 requested) and removed 24 (62 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.38 1.42 Round 1: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Round 2: 154 peptides, 2 chains. Longest chain 84 peptides. Score 0.955 Round 3: 154 peptides, 2 chains. Longest chain 143 peptides. Score 0.955 Round 4: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Round 5: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Taking the results from Round 5 Chains 1, Residues 154, Estimated correctness of the model 99.9 % 1 chains (154 residues) have been docked in sequence ------------------------------------------------------ 20126 reflections ( 89.82 % complete ) and 1811 restraints for refining 1769 atoms. 502 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1853 (Rfree = 0.000) for 1769 atoms. Found 96 (103 requested) and removed 22 (57 requested) atoms. Cycle 37: After refmac, R = 0.1816 (Rfree = 0.000) for 1840 atoms. Found 42 (107 requested) and removed 19 (59 requested) atoms. Cycle 38: After refmac, R = 0.1733 (Rfree = 0.000) for 1863 atoms. Found 43 (108 requested) and removed 19 (60 requested) atoms. Cycle 39: After refmac, R = 0.1706 (Rfree = 0.000) for 1885 atoms. Found 50 (110 requested) and removed 21 (61 requested) atoms. Cycle 40: After refmac, R = 0.1681 (Rfree = 0.000) for 1910 atoms. Found 37 (111 requested) and removed 26 (61 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.39 1.43 Round 1: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Round 2: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Round 3: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Round 4: 153 peptides, 3 chains. Longest chain 88 peptides. Score 0.946 Round 5: 155 peptides, 1 chains. Longest chain 155 peptides. Score 0.964 Taking the results from Round 5 Chains 1, Residues 154, Estimated correctness of the model 99.9 % 1 chains (154 residues) have been docked in sequence ------------------------------------------------------ 20126 reflections ( 89.82 % complete ) and 1867 restraints for refining 1778 atoms. 558 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1850 (Rfree = 0.000) for 1778 atoms. Found 101 (101 requested) and removed 22 (57 requested) atoms. Cycle 42: After refmac, R = 0.1808 (Rfree = 0.000) for 1854 atoms. Found 47 (106 requested) and removed 29 (60 requested) atoms. Cycle 43: After refmac, R = 0.1723 (Rfree = 0.000) for 1869 atoms. Found 54 (104 requested) and removed 17 (60 requested) atoms. Cycle 44: After refmac, R = 0.1694 (Rfree = 0.000) for 1905 atoms. Found 54 (106 requested) and removed 26 (61 requested) atoms. Cycle 45: After refmac, R = 0.1680 (Rfree = 0.000) for 1931 atoms. Found 45 (107 requested) and removed 29 (62 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.37 1.41 Round 1: 153 peptides, 1 chains. Longest chain 153 peptides. Score 0.962 Round 2: 154 peptides, 2 chains. Longest chain 100 peptides. Score 0.955 Round 3: 154 peptides, 3 chains. Longest chain 91 peptides. Score 0.947 Round 4: 152 peptides, 2 chains. Longest chain 104 peptides. Score 0.953 Round 5: 153 peptides, 1 chains. Longest chain 153 peptides. Score 0.962 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 152, Estimated correctness of the model 99.9 % 1 chains (152 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 20126 reflections ( 89.82 % complete ) and 1289 restraints for refining 1264 atoms. Observations/parameters ratio is 3.98 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2508 (Rfree = 0.000) for 1264 atoms. Found 68 (68 requested) and removed 0 (68 requested) atoms. Cycle 47: After refmac, R = 0.2214 (Rfree = 0.000) for 1264 atoms. Found 40 (72 requested) and removed 0 (43 requested) atoms. Cycle 48: After refmac, R = 0.2045 (Rfree = 0.000) for 1264 atoms. Found 18 (74 requested) and removed 1 (44 requested) atoms. Cycle 49: After refmac, R = 0.1940 (Rfree = 0.000) for 1264 atoms. TimeTaking 33.6