null Sun 23 Dec 22:23:08 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 2hyt-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-1.8-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/2hyt-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-1.8-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 22:23:18 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/2hyt-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-1.8-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 217 and 0 Target number of residues in the AU: 217 Target solvent content: 0.4723 Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 197 Adjusted target solvent content: 0.52 Input MTZ file: 2hyt-1.8-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: 150 Cell parameters: 82.957 82.957 56.010 90.000 90.000 120.000 Input sequence file: 2hyt-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1576 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: 71.843 1.800 Wilson plot Bfac: 18.03 20953 reflections ( 99.91 % complete ) and 0 restraints for refining 1739 atoms. Observations/parameters ratio is 3.01 ------------------------------------------------------ Starting model: R = 0.3187 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2724 (Rfree = 0.000) for 1739 atoms. Found 80 (80 requested) and removed 36 (40 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.81 1.76 Round 1: 164 peptides, 9 chains. Longest chain 35 peptides. Score 0.860 Round 2: 181 peptides, 3 chains. Longest chain 135 peptides. Score 0.940 Round 3: 185 peptides, 3 chains. Longest chain 149 peptides. Score 0.944 Round 4: 186 peptides, 4 chains. Longest chain 106 peptides. Score 0.938 Round 5: 186 peptides, 4 chains. Longest chain 107 peptides. Score 0.938 Taking the results from Round 3 Chains 3, Residues 182, Estimated correctness of the model 99.7 % 2 chains (171 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 173 A 2 chains (185 residues) following loop building 1 chains (174 residues) in sequence following loop building ------------------------------------------------------ 20953 reflections ( 99.91 % complete ) and 1724 restraints for refining 1679 atoms. 324 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2655 (Rfree = 0.000) for 1679 atoms. Found 57 (77 requested) and removed 38 (38 requested) atoms. Cycle 2: After refmac, R = 0.2282 (Rfree = 0.000) for 1693 atoms. Found 59 (76 requested) and removed 12 (39 requested) atoms. Cycle 3: After refmac, R = 0.2112 (Rfree = 0.000) for 1727 atoms. Found 44 (78 requested) and removed 12 (40 requested) atoms. Cycle 4: After refmac, R = 0.1997 (Rfree = 0.000) for 1755 atoms. Found 29 (79 requested) and removed 8 (40 requested) atoms. Cycle 5: After refmac, R = 0.1917 (Rfree = 0.000) for 1771 atoms. Found 39 (80 requested) and removed 4 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.80 1.75 Round 1: 188 peptides, 2 chains. Longest chain 164 peptides. Score 0.953 Round 2: 187 peptides, 5 chains. Longest chain 61 peptides. Score 0.931 Round 3: 190 peptides, 2 chains. Longest chain 122 peptides. Score 0.955 Round 4: 192 peptides, 1 chains. Longest chain 192 peptides. Score 0.962 Round 5: 187 peptides, 5 chains. Longest chain 61 peptides. Score 0.931 Taking the results from Round 4 Chains 1, Residues 191, Estimated correctness of the model 99.9 % 1 chains (191 residues) have been docked in sequence ------------------------------------------------------ 20953 reflections ( 99.91 % complete ) and 1629 restraints for refining 1761 atoms. 143 conditional restraints added. Observations/parameters ratio is 2.97 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1990 (Rfree = 0.000) for 1761 atoms. Found 70 (79 requested) and removed 34 (40 requested) atoms. Cycle 7: After refmac, R = 0.1866 (Rfree = 0.000) for 1794 atoms. Found 54 (81 requested) and removed 7 (41 requested) atoms. Cycle 8: After refmac, R = 0.1785 (Rfree = 0.000) for 1835 atoms. Found 57 (83 requested) and removed 18 (42 requested) atoms. Cycle 9: After refmac, R = 0.1713 (Rfree = 0.000) for 1873 atoms. Found 55 (84 requested) and removed 15 (43 requested) atoms. Cycle 10: After refmac, R = 0.1686 (Rfree = 0.000) for 1909 atoms. Found 37 (86 requested) and removed 27 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.79 1.74 Round 1: 189 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 2: 188 peptides, 4 chains. Longest chain 61 peptides. Score 0.939 Round 3: 188 peptides, 3 chains. Longest chain 86 peptides. Score 0.946 Round 4: 188 peptides, 3 chains. Longest chain 122 peptides. Score 0.946 Round 5: 189 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Taking the results from Round 5 Chains 2, Residues 187, Estimated correctness of the model 99.8 % 2 chains (187 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 173 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 20953 reflections ( 99.91 % complete ) and 1662 restraints for refining 1828 atoms. 183 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1869 (Rfree = 0.000) for 1828 atoms. Found 74 (81 requested) and removed 29 (42 requested) atoms. Cycle 12: After refmac, R = 0.1789 (Rfree = 0.000) for 1870 atoms. Found 42 (83 requested) and removed 13 (43 requested) atoms. Cycle 13: After refmac, R = 0.1732 (Rfree = 0.000) for 1892 atoms. Found 38 (84 requested) and removed 18 (43 requested) atoms. Cycle 14: After refmac, R = 0.1696 (Rfree = 0.000) for 1912 atoms. Found 46 (84 requested) and removed 14 (44 requested) atoms. Cycle 15: After refmac, R = 0.1662 (Rfree = 0.000) for 1942 atoms. Found 33 (85 requested) and removed 22 (44 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.79 1.74 Round 1: 189 peptides, 3 chains. Longest chain 133 peptides. Score 0.947 Round 2: 190 peptides, 2 chains. Longest chain 165 peptides. Score 0.955 Round 3: 190 peptides, 2 chains. Longest chain 166 peptides. Score 0.955 Round 4: 189 peptides, 3 chains. Longest chain 122 peptides. Score 0.947 Round 5: 190 peptides, 2 chains. Longest chain 165 peptides. Score 0.955 Taking the results from Round 5 Chains 2, Residues 188, Estimated correctness of the model 99.8 % 2 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 170 A and 173 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 20953 reflections ( 99.91 % complete ) and 1688 restraints for refining 1849 atoms. 209 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1838 (Rfree = 0.000) for 1849 atoms. Found 75 (80 requested) and removed 23 (42 requested) atoms. Cycle 17: After refmac, R = 0.1765 (Rfree = 0.000) for 1896 atoms. Found 45 (82 requested) and removed 16 (43 requested) atoms. Cycle 18: After refmac, R = 0.1700 (Rfree = 0.000) for 1922 atoms. Found 41 (84 requested) and removed 16 (44 requested) atoms. Cycle 19: After refmac, R = 0.1664 (Rfree = 0.000) for 1946 atoms. Found 34 (85 requested) and removed 27 (45 requested) atoms. Cycle 20: After refmac, R = 0.1629 (Rfree = 0.000) for 1949 atoms. Found 44 (83 requested) and removed 18 (45 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.79 1.74 Round 1: 189 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 2: 189 peptides, 4 chains. Longest chain 61 peptides. Score 0.940 Round 3: 191 peptides, 1 chains. Longest chain 191 peptides. Score 0.962 Round 4: 189 peptides, 3 chains. Longest chain 122 peptides. Score 0.947 Round 5: 191 peptides, 1 chains. Longest chain 191 peptides. Score 0.962 Taking the results from Round 5 Chains 1, Residues 190, Estimated correctness of the model 99.9 % 1 chains (190 residues) have been docked in sequence ------------------------------------------------------ 20953 reflections ( 99.91 % complete ) and 1685 restraints for refining 1848 atoms. 206 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1807 (Rfree = 0.000) for 1848 atoms. Found 75 (78 requested) and removed 28 (42 requested) atoms. Cycle 22: After refmac, R = 0.1729 (Rfree = 0.000) for 1891 atoms. Found 53 (80 requested) and removed 26 (43 requested) atoms. Cycle 23: After refmac, R = 0.1683 (Rfree = 0.000) for 1917 atoms. Found 49 (81 requested) and removed 18 (44 requested) atoms. Cycle 24: After refmac, R = 0.1646 (Rfree = 0.000) for 1945 atoms. Found 37 (83 requested) and removed 31 (45 requested) atoms. Cycle 25: After refmac, R = 0.1619 (Rfree = 0.000) for 1947 atoms. Found 52 (81 requested) and removed 26 (45 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.79 1.74 Round 1: 189 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 2: 187 peptides, 5 chains. Longest chain 61 peptides. Score 0.931 Round 3: 189 peptides, 3 chains. Longest chain 122 peptides. Score 0.947 Round 4: 191 peptides, 2 chains. Longest chain 167 peptides. Score 0.955 Round 5: 188 peptides, 4 chains. Longest chain 115 peptides. Score 0.939 Taking the results from Round 4 Chains 2, Residues 189, Estimated correctness of the model 99.8 % 2 chains (189 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 171 A and 174 A 1 chains (191 residues) following loop building 1 chains (191 residues) in sequence following loop building ------------------------------------------------------ 20953 reflections ( 99.91 % complete ) and 1655 restraints for refining 1842 atoms. 169 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1800 (Rfree = 0.000) for 1842 atoms. Found 74 (76 requested) and removed 23 (42 requested) atoms. Cycle 27: After refmac, R = 0.1725 (Rfree = 0.000) for 1890 atoms. Found 41 (78 requested) and removed 21 (43 requested) atoms. Cycle 28: After refmac, R = 0.1667 (Rfree = 0.000) for 1906 atoms. Found 49 (77 requested) and removed 17 (44 requested) atoms. Cycle 29: After refmac, R = 0.1641 (Rfree = 0.000) for 1933 atoms. Found 49 (78 requested) and removed 23 (44 requested) atoms. Cycle 30: After refmac, R = 0.1614 (Rfree = 0.000) for 1955 atoms. Found 40 (79 requested) and removed 24 (45 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.80 1.75 Round 1: 188 peptides, 3 chains. Longest chain 86 peptides. Score 0.946 Round 2: 188 peptides, 4 chains. Longest chain 61 peptides. Score 0.939 Round 3: 190 peptides, 2 chains. Longest chain 166 peptides. Score 0.955 Round 4: 188 peptides, 4 chains. Longest chain 122 peptides. Score 0.939 Round 5: 188 peptides, 4 chains. Longest chain 86 peptides. Score 0.939 Taking the results from Round 3 Chains 3, Residues 188, Estimated correctness of the model 99.8 % 2 chains (187 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 170 A and 174 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 20953 reflections ( 99.91 % complete ) and 1672 restraints for refining 1845 atoms. 193 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1827 (Rfree = 0.000) for 1845 atoms. Found 73 (73 requested) and removed 20 (42 requested) atoms. Cycle 32: After refmac, R = 0.1735 (Rfree = 0.000) for 1894 atoms. Found 50 (75 requested) and removed 17 (43 requested) atoms. Cycle 33: After refmac, R = 0.1690 (Rfree = 0.000) for 1924 atoms. Found 47 (77 requested) and removed 21 (44 requested) atoms. Cycle 34: After refmac, R = 0.1655 (Rfree = 0.000) for 1946 atoms. Found 42 (77 requested) and removed 29 (45 requested) atoms. Cycle 35: After refmac, R = 0.1638 (Rfree = 0.000) for 1958 atoms. Found 43 (76 requested) and removed 28 (45 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.80 1.75 Round 1: 188 peptides, 2 chains. Longest chain 164 peptides. Score 0.953 Round 2: 185 peptides, 5 chains. Longest chain 61 peptides. Score 0.929 Round 3: 188 peptides, 2 chains. Longest chain 164 peptides. Score 0.953 Round 4: 188 peptides, 4 chains. Longest chain 106 peptides. Score 0.939 Round 5: 188 peptides, 4 chains. Longest chain 86 peptides. Score 0.939 Taking the results from Round 3 Chains 2, Residues 186, Estimated correctness of the model 99.8 % 2 chains (186 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 174 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 20953 reflections ( 99.91 % complete ) and 1720 restraints for refining 1856 atoms. 241 conditional restraints added. Observations/parameters ratio is 2.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1823 (Rfree = 0.000) for 1856 atoms. Found 70 (70 requested) and removed 25 (42 requested) atoms. Cycle 37: After refmac, R = 0.1743 (Rfree = 0.000) for 1899 atoms. Found 52 (71 requested) and removed 20 (43 requested) atoms. Cycle 38: After refmac, R = 0.1682 (Rfree = 0.000) for 1930 atoms. Found 43 (73 requested) and removed 19 (44 requested) atoms. Cycle 39: After refmac, R = 0.1657 (Rfree = 0.000) for 1951 atoms. Found 34 (74 requested) and removed 26 (45 requested) atoms. Cycle 40: After refmac, R = 0.1633 (Rfree = 0.000) for 1955 atoms. Found 47 (72 requested) and removed 18 (45 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.79 1.74 Round 1: 187 peptides, 3 chains. Longest chain 86 peptides. Score 0.946 Round 2: 185 peptides, 5 chains. Longest chain 61 peptides. Score 0.929 Round 3: 186 peptides, 3 chains. Longest chain 86 peptides. Score 0.945 Round 4: 188 peptides, 3 chains. Longest chain 122 peptides. Score 0.946 Round 5: 186 peptides, 4 chains. Longest chain 86 peptides. Score 0.938 Taking the results from Round 4 Chains 3, Residues 185, Estimated correctness of the model 99.8 % 3 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 A and 130 A Built loop between residues 170 A and 174 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 20953 reflections ( 99.91 % complete ) and 1735 restraints for refining 1865 atoms. 256 conditional restraints added. Observations/parameters ratio is 2.81 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1807 (Rfree = 0.000) for 1865 atoms. Found 69 (69 requested) and removed 27 (43 requested) atoms. Cycle 42: After refmac, R = 0.1732 (Rfree = 0.000) for 1901 atoms. Found 52 (70 requested) and removed 17 (44 requested) atoms. Cycle 43: After refmac, R = 0.1695 (Rfree = 0.000) for 1932 atoms. Found 50 (71 requested) and removed 24 (44 requested) atoms. Cycle 44: After refmac, R = 0.1674 (Rfree = 0.000) for 1956 atoms. Found 41 (72 requested) and removed 28 (45 requested) atoms. Cycle 45: After refmac, R = 0.1640 (Rfree = 0.000) for 1965 atoms. Found 40 (71 requested) and removed 29 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.80 1.75 Round 1: 189 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 2: 186 peptides, 5 chains. Longest chain 61 peptides. Score 0.930 Round 3: 189 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 4: 189 peptides, 3 chains. Longest chain 122 peptides. Score 0.947 Round 5: 186 peptides, 5 chains. Longest chain 61 peptides. Score 0.930 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 187, Estimated correctness of the model 99.8 % 2 chains (187 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 169 A and 173 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 20953 reflections ( 99.91 % complete ) and 1479 restraints for refining 1461 atoms. Observations/parameters ratio is 3.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2530 (Rfree = 0.000) for 1461 atoms. Found 51 (51 requested) and removed 0 (51 requested) atoms. Cycle 47: After refmac, R = 0.2321 (Rfree = 0.000) for 1461 atoms. Found 49 (52 requested) and removed 0 (34 requested) atoms. Cycle 48: After refmac, R = 0.2139 (Rfree = 0.000) for 1461 atoms. Found 35 (55 requested) and removed 0 (36 requested) atoms. Cycle 49: After refmac, R = 0.2030 (Rfree = 0.000) for 1461 atoms. Found 21 (55 requested) and removed 0 (36 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:14:07 GMT 2018 Job finished. TimeTaking 50.99 Used memory is bytes: 18017024