null 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 2pg3-2.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-2.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-2.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-2.4-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/2pg3-2.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-2.4-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 19:28:07 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/2pg3-2.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-2.4-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 188 and 0 Target number of residues in the AU: 188 Target solvent content: 0.5715 Checking the provided sequence file Detected sequence length: 232 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 232 Adjusted target solvent content: 0.47 Input MTZ file: 2pg3-2.4-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: 92 Cell parameters: 78.154 78.154 77.755 90.000 90.000 90.000 Input sequence file: 2pg3-2.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1856 target number of atoms Had to go as low as 0.50 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 3 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: 27.561 2.400 Wilson plot Bfac: 41.76 9882 reflections ( 99.88 % complete ) and 0 restraints for refining 2065 atoms. Observations/parameters ratio is 1.20 ------------------------------------------------------ Starting model: R = 0.3718 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3183 (Rfree = 0.000) for 2065 atoms. Found 26 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.54 2.64 Round 1: 103 peptides, 19 chains. Longest chain 11 peptides. Score 0.370 Round 2: 123 peptides, 17 chains. Longest chain 18 peptides. Score 0.548 Round 3: 151 peptides, 17 chains. Longest chain 25 peptides. Score 0.682 Round 4: 155 peptides, 14 chains. Longest chain 49 peptides. Score 0.749 Round 5: 157 peptides, 13 chains. Longest chain 47 peptides. Score 0.771 Taking the results from Round 5 Chains 13, Residues 144, Estimated correctness of the model 91.5 % 3 chains (84 residues) have been docked in sequence Building loops using Loopy2018 13 chains (144 residues) following loop building 3 chains (84 residues) in sequence following loop building ------------------------------------------------------ 9882 reflections ( 99.88 % complete ) and 2947 restraints for refining 1749 atoms. 2090 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3165 (Rfree = 0.000) for 1749 atoms. Found 26 (35 requested) and removed 23 (17 requested) atoms. Cycle 2: After refmac, R = 0.2924 (Rfree = 0.000) for 1724 atoms. Found 19 (34 requested) and removed 23 (17 requested) atoms. Cycle 3: After refmac, R = 0.2768 (Rfree = 0.000) for 1708 atoms. Found 16 (34 requested) and removed 19 (17 requested) atoms. Cycle 4: After refmac, R = 0.2720 (Rfree = 0.000) for 1699 atoms. Found 14 (32 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.2648 (Rfree = 0.000) for 1693 atoms. Found 13 (31 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.54 2.64 Round 1: 155 peptides, 13 chains. Longest chain 40 peptides. Score 0.765 Round 2: 173 peptides, 11 chains. Longest chain 48 peptides. Score 0.840 Round 3: 176 peptides, 11 chains. Longest chain 44 peptides. Score 0.846 Round 4: 176 peptides, 11 chains. Longest chain 44 peptides. Score 0.846 Round 5: 170 peptides, 11 chains. Longest chain 44 peptides. Score 0.833 Taking the results from Round 4 Chains 11, Residues 165, Estimated correctness of the model 95.9 % 4 chains (142 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 46 A Built loop between residues 137 A and 147 A 8 chains (180 residues) following loop building 2 chains (160 residues) in sequence following loop building ------------------------------------------------------ 9882 reflections ( 99.88 % complete ) and 2091 restraints for refining 1749 atoms. 742 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2955 (Rfree = 0.000) for 1749 atoms. Found 25 (31 requested) and removed 37 (17 requested) atoms. Cycle 7: After refmac, R = 0.2722 (Rfree = 0.000) for 1730 atoms. Found 17 (31 requested) and removed 19 (17 requested) atoms. Cycle 8: After refmac, R = 0.2609 (Rfree = 0.000) for 1726 atoms. Found 19 (30 requested) and removed 19 (17 requested) atoms. Cycle 9: After refmac, R = 0.2556 (Rfree = 0.000) for 1725 atoms. Found 12 (29 requested) and removed 17 (17 requested) atoms. Cycle 10: After refmac, R = 0.2485 (Rfree = 0.000) for 1720 atoms. Found 17 (29 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.53 2.63 Round 1: 175 peptides, 9 chains. Longest chain 49 peptides. Score 0.866 Round 2: 183 peptides, 13 chains. Longest chain 37 peptides. Score 0.839 Round 3: 185 peptides, 9 chains. Longest chain 73 peptides. Score 0.883 Round 4: 188 peptides, 7 chains. Longest chain 51 peptides. Score 0.905 Round 5: 185 peptides, 8 chains. Longest chain 85 peptides. Score 0.893 Taking the results from Round 4 Chains 9, Residues 181, Estimated correctness of the model 98.3 % 4 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 47 A Built loop between residues 139 A and 143 A 6 chains (192 residues) following loop building 2 chains (176 residues) in sequence following loop building ------------------------------------------------------ 9882 reflections ( 99.88 % complete ) and 1924 restraints for refining 1749 atoms. 456 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2642 (Rfree = 0.000) for 1749 atoms. Found 28 (28 requested) and removed 26 (17 requested) atoms. Cycle 12: After refmac, R = 0.2393 (Rfree = 0.000) for 1750 atoms. Found 27 (27 requested) and removed 19 (17 requested) atoms. Cycle 13: After refmac, R = 0.2266 (Rfree = 0.000) for 1758 atoms. Found 16 (27 requested) and removed 17 (17 requested) atoms. Cycle 14: After refmac, R = 0.2223 (Rfree = 0.000) for 1753 atoms. Found 21 (26 requested) and removed 19 (17 requested) atoms. Cycle 15: After refmac, R = 0.2203 (Rfree = 0.000) for 1755 atoms. Found 20 (25 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.50 2.60 Round 1: 182 peptides, 7 chains. Longest chain 86 peptides. Score 0.897 Round 2: 185 peptides, 9 chains. Longest chain 51 peptides. Score 0.883 Round 3: 192 peptides, 12 chains. Longest chain 40 peptides. Score 0.867 Round 4: 193 peptides, 9 chains. Longest chain 75 peptides. Score 0.895 Round 5: 192 peptides, 8 chains. Longest chain 51 peptides. Score 0.902 Taking the results from Round 5 Chains 8, Residues 184, Estimated correctness of the model 98.2 % 4 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 45 A Built loop between residues 141 A and 144 A 5 chains (191 residues) following loop building 2 chains (172 residues) in sequence following loop building ------------------------------------------------------ 9882 reflections ( 99.88 % complete ) and 2005 restraints for refining 1749 atoms. 560 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2332 (Rfree = 0.000) for 1749 atoms. Found 24 (24 requested) and removed 22 (17 requested) atoms. Cycle 17: After refmac, R = 0.2111 (Rfree = 0.000) for 1750 atoms. Found 24 (24 requested) and removed 19 (17 requested) atoms. Cycle 18: After refmac, R = 0.2008 (Rfree = 0.000) for 1755 atoms. Found 23 (23 requested) and removed 20 (17 requested) atoms. Cycle 19: After refmac, R = 0.1998 (Rfree = 0.000) for 1756 atoms. Found 22 (22 requested) and removed 22 (17 requested) atoms. Cycle 20: After refmac, R = 0.1933 (Rfree = 0.000) for 1756 atoms. Found 22 (22 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.50 2.60 Round 1: 196 peptides, 5 chains. Longest chain 114 peptides. Score 0.930 Round 2: 199 peptides, 5 chains. Longest chain 115 peptides. Score 0.933 Round 3: 198 peptides, 6 chains. Longest chain 67 peptides. Score 0.925 Round 4: 195 peptides, 10 chains. Longest chain 40 peptides. Score 0.890 Round 5: 198 peptides, 7 chains. Longest chain 74 peptides. Score 0.918 Taking the results from Round 2 Chains 5, Residues 194, Estimated correctness of the model 99.1 % 3 chains (184 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A 4 chains (196 residues) following loop building 2 chains (186 residues) in sequence following loop building ------------------------------------------------------ 9882 reflections ( 99.88 % complete ) and 1900 restraints for refining 1749 atoms. 390 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2053 (Rfree = 0.000) for 1749 atoms. Found 21 (21 requested) and removed 22 (17 requested) atoms. Cycle 22: After refmac, R = 0.1928 (Rfree = 0.000) for 1746 atoms. Found 20 (20 requested) and removed 17 (17 requested) atoms. Cycle 23: After refmac, R = 0.1868 (Rfree = 0.000) for 1747 atoms. Found 20 (20 requested) and removed 20 (17 requested) atoms. Cycle 24: After refmac, R = 0.1860 (Rfree = 0.000) for 1745 atoms. Found 19 (19 requested) and removed 18 (17 requested) atoms. Cycle 25: After refmac, R = 0.1816 (Rfree = 0.000) for 1745 atoms. Found 18 (18 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.49 2.59 Round 1: 198 peptides, 6 chains. Longest chain 103 peptides. Score 0.925 Round 2: 202 peptides, 3 chains. Longest chain 123 peptides. Score 0.949 Round 3: 198 peptides, 7 chains. Longest chain 62 peptides. Score 0.918 Round 4: 197 peptides, 6 chains. Longest chain 104 peptides. Score 0.924 Round 5: 197 peptides, 9 chains. Longest chain 59 peptides. Score 0.901 Taking the results from Round 2 Chains 3, Residues 199, Estimated correctness of the model 99.5 % 3 chains (199 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 42 A 2 chains (201 residues) following loop building 2 chains (201 residues) in sequence following loop building ------------------------------------------------------ 9882 reflections ( 99.88 % complete ) and 1790 restraints for refining 1749 atoms. 196 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2017 (Rfree = 0.000) for 1749 atoms. Found 17 (17 requested) and removed 18 (17 requested) atoms. Cycle 27: After refmac, R = 0.1861 (Rfree = 0.000) for 1747 atoms. Found 17 (17 requested) and removed 17 (17 requested) atoms. Cycle 28: After refmac, R = 0.1791 (Rfree = 0.000) for 1744 atoms. Found 17 (17 requested) and removed 19 (17 requested) atoms. Cycle 29: After refmac, R = 0.1805 (Rfree = 0.000) for 1741 atoms. Found 17 (17 requested) and removed 18 (17 requested) atoms. Cycle 30: After refmac, R = 0.1799 (Rfree = 0.000) for 1740 atoms. Found 17 (17 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.50 2.60 Round 1: 192 peptides, 5 chains. Longest chain 103 peptides. Score 0.926 Round 2: 200 peptides, 4 chains. Longest chain 75 peptides. Score 0.941 Round 3: 191 peptides, 6 chains. Longest chain 70 peptides. Score 0.917 Round 4: 193 peptides, 6 chains. Longest chain 122 peptides. Score 0.919 Round 5: 194 peptides, 10 chains. Longest chain 44 peptides. Score 0.888 Taking the results from Round 2 Chains 4, Residues 196, Estimated correctness of the model 99.3 % 4 chains (196 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 48 A Built loop between residues 168 A and 171 A 2 chains (202 residues) following loop building 2 chains (202 residues) in sequence following loop building ------------------------------------------------------ 9882 reflections ( 99.88 % complete ) and 1795 restraints for refining 1749 atoms. 194 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2046 (Rfree = 0.000) for 1749 atoms. Found 17 (17 requested) and removed 20 (17 requested) atoms. Cycle 32: After refmac, R = 0.1903 (Rfree = 0.000) for 1745 atoms. Found 17 (17 requested) and removed 17 (17 requested) atoms. Cycle 33: After refmac, R = 0.1843 (Rfree = 0.000) for 1744 atoms. Found 17 (17 requested) and removed 18 (17 requested) atoms. Cycle 34: After refmac, R = 0.1837 (Rfree = 0.000) for 1743 atoms. Found 17 (17 requested) and removed 18 (17 requested) atoms. Cycle 35: After refmac, R = 0.1816 (Rfree = 0.000) for 1742 atoms. Found 17 (17 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.50 2.60 Round 1: 201 peptides, 6 chains. Longest chain 103 peptides. Score 0.928 Round 2: 203 peptides, 7 chains. Longest chain 47 peptides. Score 0.923 Round 3: 202 peptides, 7 chains. Longest chain 48 peptides. Score 0.922 Round 4: 197 peptides, 6 chains. Longest chain 119 peptides. Score 0.924 Round 5: 201 peptides, 8 chains. Longest chain 75 peptides. Score 0.914 Taking the results from Round 1 Chains 6, Residues 195, Estimated correctness of the model 99.0 % 4 chains (189 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 47 A Built loop between residues 196 A and 200 A 4 chains (201 residues) following loop building 2 chains (195 residues) in sequence following loop building ------------------------------------------------------ 9882 reflections ( 99.88 % complete ) and 1841 restraints for refining 1749 atoms. 276 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1972 (Rfree = 0.000) for 1749 atoms. Found 17 (17 requested) and removed 20 (17 requested) atoms. Cycle 37: After refmac, R = 0.1873 (Rfree = 0.000) for 1745 atoms. Found 17 (17 requested) and removed 18 (17 requested) atoms. Cycle 38: After refmac, R = 0.1857 (Rfree = 0.000) for 1744 atoms. Found 17 (17 requested) and removed 21 (17 requested) atoms. Cycle 39: After refmac, R = 0.1827 (Rfree = 0.000) for 1740 atoms. Found 17 (17 requested) and removed 20 (17 requested) atoms. Cycle 40: After refmac, R = 0.1822 (Rfree = 0.000) for 1736 atoms. Found 17 (17 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.49 2.59 Round 1: 197 peptides, 6 chains. Longest chain 103 peptides. Score 0.924 Round 2: 203 peptides, 6 chains. Longest chain 69 peptides. Score 0.930 Round 3: 201 peptides, 7 chains. Longest chain 49 peptides. Score 0.921 Round 4: 203 peptides, 6 chains. Longest chain 118 peptides. Score 0.930 Round 5: 207 peptides, 8 chains. Longest chain 51 peptides. Score 0.920 Taking the results from Round 4 Chains 7, Residues 197, Estimated correctness of the model 99.0 % 4 chains (187 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 18 A and 21 A Built loop between residues 39 A and 48 A 4 chains (206 residues) following loop building 2 chains (197 residues) in sequence following loop building ------------------------------------------------------ 9882 reflections ( 99.88 % complete ) and 1843 restraints for refining 1749 atoms. 253 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2093 (Rfree = 0.000) for 1749 atoms. Found 17 (17 requested) and removed 21 (17 requested) atoms. Cycle 42: After refmac, R = 0.1900 (Rfree = 0.000) for 1745 atoms. Found 17 (17 requested) and removed 18 (17 requested) atoms. Cycle 43: After refmac, R = 0.1812 (Rfree = 0.000) for 1744 atoms. Found 17 (17 requested) and removed 21 (17 requested) atoms. Cycle 44: After refmac, R = 0.1780 (Rfree = 0.000) for 1739 atoms. Found 17 (17 requested) and removed 19 (17 requested) atoms. Cycle 45: After refmac, R = 0.1783 (Rfree = 0.000) for 1737 atoms. Found 17 (17 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.49 2.59 Round 1: 196 peptides, 5 chains. Longest chain 103 peptides. Score 0.930 Round 2: 204 peptides, 4 chains. Longest chain 75 peptides. Score 0.944 Round 3: 203 peptides, 5 chains. Longest chain 77 peptides. Score 0.937 Round 4: 198 peptides, 7 chains. Longest chain 74 peptides. Score 0.918 Round 5: 197 peptides, 6 chains. Longest chain 68 peptides. Score 0.924 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 200, Estimated correctness of the model 99.4 % 4 chains (200 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 43 A and 48 A Built loop between residues 83 A and 95 A Built loop between residues 168 A and 171 A 1 chains (217 residues) following loop building 1 chains (217 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 9882 reflections ( 99.88 % complete ) and 1712 restraints for refining 1674 atoms. Observations/parameters ratio is 1.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2558 (Rfree = 0.000) for 1674 atoms. Found 9 (17 requested) and removed 0 (17 requested) atoms. Cycle 47: After refmac, R = 0.2320 (Rfree = 0.000) for 1674 atoms. Found 6 (17 requested) and removed 0 (17 requested) atoms. Cycle 48: After refmac, R = 0.2230 (Rfree = 0.000) for 1674 atoms. Found 2 (17 requested) and removed 0 (17 requested) atoms. Cycle 49: After refmac, R = 0.2194 (Rfree = 0.000) for 1674 atoms. Found 1 (17 requested) and removed 0 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:12:52 GMT 2018 Job finished. TimeTaking 44.92 Used memory is bytes: 14513784