null Sun 23 Dec 22:23:10 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 2isb-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2isb-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2isb-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-1.7-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/2isb-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-1.7-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/2isb-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-1.7-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 208 and 0 Target number of residues in the AU: 208 Target solvent content: 0.4653 Checking the provided sequence file Detected sequence length: 192 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 192 Adjusted target solvent content: 0.51 Input MTZ file: 2isb-1.7-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: 96 Cell parameters: 51.664 51.664 157.756 90.000 90.000 90.000 Input sequence file: 2isb-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.30 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: 49.098 1.660 Wilson plot Bfac: 16.86 25906 reflections ( 98.76 % complete ) and 0 restraints for refining 1705 atoms. Observations/parameters ratio is 3.80 ------------------------------------------------------ Starting model: R = 0.3239 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2665 (Rfree = 0.000) for 1705 atoms. Found 99 (99 requested) and removed 51 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.84 1.82 Round 1: 162 peptides, 9 chains. Longest chain 54 peptides. Score 0.868 Round 2: 167 peptides, 6 chains. Longest chain 62 peptides. Score 0.908 Round 3: 174 peptides, 5 chains. Longest chain 73 peptides. Score 0.926 Round 4: 174 peptides, 4 chains. Longest chain 92 peptides. Score 0.934 Round 5: 173 peptides, 4 chains. Longest chain 133 peptides. Score 0.933 Taking the results from Round 4 Chains 5, Residues 170, Estimated correctness of the model 99.7 % 3 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 86 A Built loop between residues 176 A and 180 A 2 chains (175 residues) following loop building 1 chains (169 residues) in sequence following loop building ------------------------------------------------------ 25906 reflections ( 98.76 % complete ) and 1651 restraints for refining 1590 atoms. 301 conditional restraints added. Observations/parameters ratio is 4.07 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2796 (Rfree = 0.000) for 1590 atoms. Found 72 (92 requested) and removed 48 (46 requested) atoms. Cycle 2: After refmac, R = 0.2544 (Rfree = 0.000) for 1609 atoms. Found 61 (92 requested) and removed 18 (47 requested) atoms. Cycle 3: After refmac, R = 0.2205 (Rfree = 0.000) for 1649 atoms. Found 53 (94 requested) and removed 30 (48 requested) atoms. Cycle 4: After refmac, R = 0.2106 (Rfree = 0.000) for 1665 atoms. Found 66 (93 requested) and removed 29 (48 requested) atoms. Cycle 5: After refmac, R = 0.2065 (Rfree = 0.000) for 1699 atoms. Found 73 (95 requested) and removed 37 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.70 1.68 Round 1: 174 peptides, 5 chains. Longest chain 89 peptides. Score 0.926 Round 2: 173 peptides, 5 chains. Longest chain 91 peptides. Score 0.924 Round 3: 174 peptides, 4 chains. Longest chain 91 peptides. Score 0.934 Round 4: 173 peptides, 3 chains. Longest chain 154 peptides. Score 0.940 Round 5: 173 peptides, 5 chains. Longest chain 69 peptides. Score 0.924 Taking the results from Round 4 Chains 3, Residues 170, Estimated correctness of the model 99.8 % 2 chains (164 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 175 A and 181 A 2 chains (175 residues) following loop building 1 chains (169 residues) in sequence following loop building ------------------------------------------------------ 25906 reflections ( 98.76 % complete ) and 1682 restraints for refining 1632 atoms. 332 conditional restraints added. Observations/parameters ratio is 3.97 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2373 (Rfree = 0.000) for 1632 atoms. Found 77 (89 requested) and removed 52 (47 requested) atoms. Cycle 7: After refmac, R = 0.2136 (Rfree = 0.000) for 1655 atoms. Found 54 (88 requested) and removed 26 (48 requested) atoms. Cycle 8: After refmac, R = 0.2031 (Rfree = 0.000) for 1678 atoms. Found 54 (90 requested) and removed 30 (49 requested) atoms. Cycle 9: After refmac, R = 0.1985 (Rfree = 0.000) for 1698 atoms. Found 57 (89 requested) and removed 41 (49 requested) atoms. Cycle 10: After refmac, R = 0.1958 (Rfree = 0.000) for 1710 atoms. Found 60 (87 requested) and removed 47 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.68 1.66 Round 1: 171 peptides, 7 chains. Longest chain 47 peptides. Score 0.904 Round 2: 173 peptides, 5 chains. Longest chain 92 peptides. Score 0.924 Round 3: 174 peptides, 4 chains. Longest chain 92 peptides. Score 0.934 Round 4: 174 peptides, 4 chains. Longest chain 92 peptides. Score 0.934 Round 5: 174 peptides, 4 chains. Longest chain 92 peptides. Score 0.934 Taking the results from Round 5 Chains 5, Residues 170, Estimated correctness of the model 99.7 % 3 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 86 A Built loop between residues 176 A and 180 A 2 chains (175 residues) following loop building 1 chains (169 residues) in sequence following loop building ------------------------------------------------------ 25906 reflections ( 98.76 % complete ) and 1652 restraints for refining 1642 atoms. 302 conditional restraints added. Observations/parameters ratio is 3.94 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2109 (Rfree = 0.000) for 1642 atoms. Found 82 (82 requested) and removed 47 (47 requested) atoms. Cycle 12: After refmac, R = 0.2014 (Rfree = 0.000) for 1675 atoms. Found 59 (81 requested) and removed 40 (48 requested) atoms. Cycle 13: After refmac, R = 0.1971 (Rfree = 0.000) for 1690 atoms. Found 60 (80 requested) and removed 31 (49 requested) atoms. Cycle 14: After refmac, R = 0.1935 (Rfree = 0.000) for 1717 atoms. Found 57 (80 requested) and removed 37 (50 requested) atoms. Cycle 15: After refmac, R = 0.1949 (Rfree = 0.000) for 1734 atoms. Found 63 (79 requested) and removed 27 (50 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.69 1.67 Round 1: 172 peptides, 7 chains. Longest chain 48 peptides. Score 0.906 Round 2: 174 peptides, 5 chains. Longest chain 94 peptides. Score 0.926 Round 3: 176 peptides, 3 chains. Longest chain 156 peptides. Score 0.943 Round 4: 172 peptides, 5 chains. Longest chain 71 peptides. Score 0.923 Round 5: 175 peptides, 3 chains. Longest chain 153 peptides. Score 0.942 Taking the results from Round 3 Chains 4, Residues 173, Estimated correctness of the model 99.8 % 2 chains (167 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 176 A and 180 A 2 chains (175 residues) following loop building 1 chains (170 residues) in sequence following loop building ------------------------------------------------------ 25906 reflections ( 98.76 % complete ) and 1661 restraints for refining 1658 atoms. 307 conditional restraints added. Observations/parameters ratio is 3.91 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2073 (Rfree = 0.000) for 1658 atoms. Found 75 (75 requested) and removed 52 (48 requested) atoms. Cycle 17: After refmac, R = 0.1999 (Rfree = 0.000) for 1679 atoms. Found 61 (74 requested) and removed 34 (48 requested) atoms. Cycle 18: After refmac, R = 0.1979 (Rfree = 0.000) for 1701 atoms. Found 61 (73 requested) and removed 34 (49 requested) atoms. Cycle 19: After refmac, R = 0.1930 (Rfree = 0.000) for 1723 atoms. Found 56 (72 requested) and removed 36 (50 requested) atoms. Cycle 20: After refmac, R = 0.1923 (Rfree = 0.000) for 1738 atoms. Found 58 (71 requested) and removed 41 (50 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.70 1.68 Round 1: 171 peptides, 6 chains. Longest chain 51 peptides. Score 0.913 Round 2: 173 peptides, 5 chains. Longest chain 94 peptides. Score 0.924 Round 3: 175 peptides, 3 chains. Longest chain 153 peptides. Score 0.942 Round 4: 171 peptides, 6 chains. Longest chain 59 peptides. Score 0.913 Round 5: 172 peptides, 4 chains. Longest chain 94 peptides. Score 0.931 Taking the results from Round 3 Chains 4, Residues 172, Estimated correctness of the model 99.8 % 2 chains (164 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 176 A and 180 A 2 chains (174 residues) following loop building 1 chains (167 residues) in sequence following loop building ------------------------------------------------------ 25906 reflections ( 98.76 % complete ) and 1697 restraints for refining 1654 atoms. 358 conditional restraints added. Observations/parameters ratio is 3.92 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2062 (Rfree = 0.000) for 1654 atoms. Found 65 (65 requested) and removed 44 (48 requested) atoms. Cycle 22: After refmac, R = 0.1997 (Rfree = 0.000) for 1674 atoms. Found 55 (64 requested) and removed 29 (48 requested) atoms. Cycle 23: After refmac, R = 0.1928 (Rfree = 0.000) for 1697 atoms. Found 63 (63 requested) and removed 27 (49 requested) atoms. Cycle 24: After refmac, R = 0.1919 (Rfree = 0.000) for 1732 atoms. Found 53 (64 requested) and removed 36 (50 requested) atoms. Cycle 25: After refmac, R = 0.1887 (Rfree = 0.000) for 1744 atoms. Found 58 (63 requested) and removed 31 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.70 1.68 Round 1: 173 peptides, 5 chains. Longest chain 59 peptides. Score 0.924 Round 2: 171 peptides, 5 chains. Longest chain 93 peptides. Score 0.922 Round 3: 173 peptides, 4 chains. Longest chain 109 peptides. Score 0.933 Round 4: 173 peptides, 4 chains. Longest chain 93 peptides. Score 0.933 Round 5: 169 peptides, 4 chains. Longest chain 128 peptides. Score 0.928 Taking the results from Round 4 Chains 4, Residues 169, Estimated correctness of the model 99.7 % 3 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 175 A and 178 A 2 chains (173 residues) following loop building 1 chains (167 residues) in sequence following loop building ------------------------------------------------------ 25906 reflections ( 98.76 % complete ) and 1691 restraints for refining 1660 atoms. 356 conditional restraints added. Observations/parameters ratio is 3.90 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2065 (Rfree = 0.000) for 1660 atoms. Found 58 (58 requested) and removed 44 (48 requested) atoms. Cycle 27: After refmac, R = 0.1970 (Rfree = 0.000) for 1669 atoms. Found 56 (56 requested) and removed 16 (48 requested) atoms. Cycle 28: After refmac, R = 0.1927 (Rfree = 0.000) for 1706 atoms. Found 56 (57 requested) and removed 24 (49 requested) atoms. Cycle 29: After refmac, R = 0.1922 (Rfree = 0.000) for 1733 atoms. Found 46 (59 requested) and removed 41 (50 requested) atoms. Cycle 30: After refmac, R = 0.1904 (Rfree = 0.000) for 1734 atoms. Found 57 (57 requested) and removed 31 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.69 1.67 Round 1: 170 peptides, 5 chains. Longest chain 55 peptides. Score 0.921 Round 2: 172 peptides, 5 chains. Longest chain 92 peptides. Score 0.923 Round 3: 173 peptides, 5 chains. Longest chain 92 peptides. Score 0.924 Round 4: 176 peptides, 4 chains. Longest chain 103 peptides. Score 0.936 Round 5: 174 peptides, 5 chains. Longest chain 92 peptides. Score 0.926 Taking the results from Round 4 Chains 5, Residues 172, Estimated correctness of the model 99.7 % 3 chains (165 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 75 A Built loop between residues 176 A and 180 A 2 chains (176 residues) following loop building 1 chains (170 residues) in sequence following loop building ------------------------------------------------------ 25906 reflections ( 98.76 % complete ) and 1694 restraints for refining 1676 atoms. 336 conditional restraints added. Observations/parameters ratio is 3.86 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2275 (Rfree = 0.000) for 1676 atoms. Found 52 (52 requested) and removed 51 (48 requested) atoms. Cycle 32: After refmac, R = 0.1991 (Rfree = 0.000) for 1676 atoms. Found 50 (50 requested) and removed 21 (48 requested) atoms. Cycle 33: After refmac, R = 0.1915 (Rfree = 0.000) for 1700 atoms. Found 51 (51 requested) and removed 23 (49 requested) atoms. Cycle 34: After refmac, R = 0.1883 (Rfree = 0.000) for 1726 atoms. Found 42 (52 requested) and removed 31 (50 requested) atoms. Cycle 35: After refmac, R = 0.1840 (Rfree = 0.000) for 1734 atoms. Found 50 (50 requested) and removed 27 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.69 1.67 Round 1: 174 peptides, 6 chains. Longest chain 48 peptides. Score 0.917 Round 2: 177 peptides, 3 chains. Longest chain 156 peptides. Score 0.944 Round 3: 175 peptides, 4 chains. Longest chain 92 peptides. Score 0.935 Round 4: 176 peptides, 4 chains. Longest chain 102 peptides. Score 0.936 Round 5: 174 peptides, 5 chains. Longest chain 92 peptides. Score 0.926 Taking the results from Round 2 Chains 4, Residues 174, Estimated correctness of the model 99.8 % 2 chains (167 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 175 A and 179 A 3 chains (177 residues) following loop building 1 chains (170 residues) in sequence following loop building ------------------------------------------------------ 25906 reflections ( 98.76 % complete ) and 1658 restraints for refining 1675 atoms. 297 conditional restraints added. Observations/parameters ratio is 3.87 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2240 (Rfree = 0.000) for 1675 atoms. Found 48 (48 requested) and removed 52 (48 requested) atoms. Cycle 37: After refmac, R = 0.1944 (Rfree = 0.000) for 1667 atoms. Found 48 (48 requested) and removed 13 (48 requested) atoms. Cycle 38: After refmac, R = 0.1915 (Rfree = 0.000) for 1694 atoms. Found 49 (49 requested) and removed 24 (49 requested) atoms. Cycle 39: After refmac, R = 0.1878 (Rfree = 0.000) for 1716 atoms. Found 50 (50 requested) and removed 24 (50 requested) atoms. Cycle 40: After refmac, R = 0.1889 (Rfree = 0.000) for 1739 atoms. Found 50 (50 requested) and removed 31 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.69 1.67 Round 1: 171 peptides, 6 chains. Longest chain 51 peptides. Score 0.913 Round 2: 173 peptides, 4 chains. Longest chain 91 peptides. Score 0.933 Round 3: 174 peptides, 4 chains. Longest chain 108 peptides. Score 0.934 Round 4: 174 peptides, 4 chains. Longest chain 91 peptides. Score 0.934 Round 5: 174 peptides, 4 chains. Longest chain 91 peptides. Score 0.934 Taking the results from Round 5 Chains 4, Residues 170, Estimated correctness of the model 99.7 % 3 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 86 A Built loop between residues 175 A and 178 A 2 chains (176 residues) following loop building 1 chains (169 residues) in sequence following loop building ------------------------------------------------------ 25906 reflections ( 98.76 % complete ) and 1672 restraints for refining 1669 atoms. 318 conditional restraints added. Observations/parameters ratio is 3.88 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2065 (Rfree = 0.000) for 1669 atoms. Found 48 (48 requested) and removed 47 (48 requested) atoms. Cycle 42: After refmac, R = 0.1967 (Rfree = 0.000) for 1668 atoms. Found 48 (48 requested) and removed 24 (48 requested) atoms. Cycle 43: After refmac, R = 0.1885 (Rfree = 0.000) for 1690 atoms. Found 49 (49 requested) and removed 20 (49 requested) atoms. Cycle 44: After refmac, R = 0.1857 (Rfree = 0.000) for 1715 atoms. Found 50 (50 requested) and removed 25 (50 requested) atoms. Cycle 45: After refmac, R = 0.1852 (Rfree = 0.000) for 1734 atoms. Found 47 (50 requested) and removed 30 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.70 1.68 Round 1: 172 peptides, 5 chains. Longest chain 55 peptides. Score 0.923 Round 2: 174 peptides, 4 chains. Longest chain 103 peptides. Score 0.934 Round 3: 171 peptides, 4 chains. Longest chain 106 peptides. Score 0.930 Round 4: 177 peptides, 3 chains. Longest chain 154 peptides. Score 0.944 Round 5: 174 peptides, 4 chains. Longest chain 130 peptides. Score 0.934 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 174, Estimated correctness of the model 99.8 % 2 chains (167 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 175 A and 178 A 2 chains (176 residues) following loop building 1 chains (169 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 25906 reflections ( 98.76 % complete ) and 1354 restraints for refining 1327 atoms. Observations/parameters ratio is 4.88 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2676 (Rfree = 0.000) for 1327 atoms. Found 38 (38 requested) and removed 0 (38 requested) atoms. Cycle 47: After refmac, R = 0.2468 (Rfree = 0.000) for 1327 atoms. Found 39 (39 requested) and removed 0 (39 requested) atoms. Cycle 48: After refmac, R = 0.2301 (Rfree = 0.000) for 1327 atoms. Found 22 (40 requested) and removed 2 (40 requested) atoms. Cycle 49: After refmac, R = 0.2193 (Rfree = 0.000) for 1327 atoms. Found 9 (41 requested) and removed 2 (41 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:27 GMT 2018 Job finished. TimeTaking 47.29 Used memory is bytes: 4269464