null Sun 23 Dec 22:22:56 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 2gm6-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-2.0-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/2gm6-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-2.0-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 22:23:06 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/2gm6-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-2.0-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 293 and 0 Target number of residues in the AU: 293 Target solvent content: 0.5495 Checking the provided sequence file Detected sequence length: 208 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 208 Adjusted target solvent content: 0.68 Input MTZ file: 2gm6-2.0-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: 57.001 57.001 216.648 90.000 90.000 90.000 Input sequence file: 2gm6-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1664 target number of atoms Had to go as low as 0.90 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: 55.125 2.000 Wilson plot Bfac: 35.05 25220 reflections ( 99.95 % complete ) and 0 restraints for refining 1852 atoms. Observations/parameters ratio is 3.40 ------------------------------------------------------ Starting model: R = 0.3666 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3097 (Rfree = 0.000) for 1852 atoms. Found 63 (63 requested) and removed 32 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.32 1.81 Round 1: 165 peptides, 16 chains. Longest chain 21 peptides. Score 0.635 Round 2: 181 peptides, 8 chains. Longest chain 79 peptides. Score 0.785 Round 3: 183 peptides, 5 chains. Longest chain 93 peptides. Score 0.822 Round 4: 182 peptides, 7 chains. Longest chain 65 peptides. Score 0.798 Round 5: 188 peptides, 6 chains. Longest chain 78 peptides. Score 0.821 Taking the results from Round 3 Chains 8, Residues 178, Estimated correctness of the model 97.0 % 5 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 60 A Built loop between residues 108 A and 110 A Built loop between residues 123 A and 127 A Built loop between residues 157 A and 164 A 3 chains (186 residues) following loop building 1 chains (175 residues) in sequence following loop building ------------------------------------------------------ 25220 reflections ( 99.95 % complete ) and 1849 restraints for refining 1781 atoms. 393 conditional restraints added. Observations/parameters ratio is 3.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2978 (Rfree = 0.000) for 1781 atoms. Found 61 (61 requested) and removed 32 (30 requested) atoms. Cycle 2: After refmac, R = 0.2617 (Rfree = 0.000) for 1787 atoms. Found 60 (60 requested) and removed 26 (30 requested) atoms. Cycle 3: After refmac, R = 0.2411 (Rfree = 0.000) for 1805 atoms. Found 61 (61 requested) and removed 25 (31 requested) atoms. Cycle 4: After refmac, R = 0.2313 (Rfree = 0.000) for 1837 atoms. Found 55 (62 requested) and removed 30 (31 requested) atoms. Cycle 5: After refmac, R = 0.2225 (Rfree = 0.000) for 1857 atoms. Found 54 (60 requested) and removed 31 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.27 1.77 Round 1: 189 peptides, 2 chains. Longest chain 133 peptides. Score 0.862 Round 2: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.872 Round 3: 186 peptides, 2 chains. Longest chain 130 peptides. Score 0.857 Round 4: 189 peptides, 2 chains. Longest chain 130 peptides. Score 0.862 Round 5: 184 peptides, 5 chains. Longest chain 56 peptides. Score 0.824 Taking the results from Round 2 Chains 1, Residues 189, Estimated correctness of the model 98.4 % 1 chains (189 residues) have been docked in sequence ------------------------------------------------------ 25220 reflections ( 99.95 % complete ) and 1728 restraints for refining 1791 atoms. 191 conditional restraints added. Observations/parameters ratio is 3.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2361 (Rfree = 0.000) for 1791 atoms. Found 57 (57 requested) and removed 29 (30 requested) atoms. Cycle 7: After refmac, R = 0.2181 (Rfree = 0.000) for 1814 atoms. Found 44 (57 requested) and removed 21 (31 requested) atoms. Cycle 8: After refmac, R = 0.2088 (Rfree = 0.000) for 1835 atoms. Found 55 (57 requested) and removed 22 (31 requested) atoms. Cycle 9: After refmac, R = 0.2044 (Rfree = 0.000) for 1866 atoms. Found 51 (58 requested) and removed 30 (31 requested) atoms. Cycle 10: After refmac, R = 0.2000 (Rfree = 0.000) for 1887 atoms. Found 47 (58 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.27 1.77 Round 1: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 2: 190 peptides, 2 chains. Longest chain 130 peptides. Score 0.863 Round 3: 187 peptides, 2 chains. Longest chain 130 peptides. Score 0.859 Round 4: 189 peptides, 2 chains. Longest chain 130 peptides. Score 0.862 Round 5: 187 peptides, 2 chains. Longest chain 130 peptides. Score 0.859 Taking the results from Round 2 Chains 2, Residues 188, Estimated correctness of the model 98.1 % 2 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 141 A and 144 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 25220 reflections ( 99.95 % complete ) and 1723 restraints for refining 1797 atoms. 180 conditional restraints added. Observations/parameters ratio is 3.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2256 (Rfree = 0.000) for 1797 atoms. Found 54 (54 requested) and removed 20 (30 requested) atoms. Cycle 12: After refmac, R = 0.2127 (Rfree = 0.000) for 1829 atoms. Found 47 (55 requested) and removed 22 (31 requested) atoms. Cycle 13: After refmac, R = 0.2061 (Rfree = 0.000) for 1852 atoms. Found 54 (55 requested) and removed 22 (31 requested) atoms. Cycle 14: After refmac, R = 0.2030 (Rfree = 0.000) for 1881 atoms. Found 44 (56 requested) and removed 31 (32 requested) atoms. Cycle 15: After refmac, R = 0.2027 (Rfree = 0.000) for 1890 atoms. Found 41 (55 requested) and removed 24 (32 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.27 1.77 Round 1: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 2: 191 peptides, 1 chains. Longest chain 191 peptides. Score 0.874 Round 3: 188 peptides, 2 chains. Longest chain 130 peptides. Score 0.860 Round 4: 191 peptides, 1 chains. Longest chain 191 peptides. Score 0.874 Round 5: 190 peptides, 2 chains. Longest chain 130 peptides. Score 0.863 Taking the results from Round 4 Chains 1, Residues 190, Estimated correctness of the model 98.4 % 1 chains (190 residues) have been docked in sequence ------------------------------------------------------ 25220 reflections ( 99.95 % complete ) and 1729 restraints for refining 1808 atoms. 186 conditional restraints added. Observations/parameters ratio is 3.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2235 (Rfree = 0.000) for 1808 atoms. Found 51 (51 requested) and removed 20 (30 requested) atoms. Cycle 17: After refmac, R = 0.2095 (Rfree = 0.000) for 1834 atoms. Found 52 (52 requested) and removed 20 (31 requested) atoms. Cycle 18: After refmac, R = 0.2044 (Rfree = 0.000) for 1863 atoms. Found 49 (53 requested) and removed 28 (31 requested) atoms. Cycle 19: After refmac, R = 0.1999 (Rfree = 0.000) for 1881 atoms. Found 43 (52 requested) and removed 25 (32 requested) atoms. Cycle 20: After refmac, R = 0.1991 (Rfree = 0.000) for 1898 atoms. Found 46 (52 requested) and removed 34 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.27 1.77 Round 1: 190 peptides, 2 chains. Longest chain 156 peptides. Score 0.863 Round 2: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 3: 191 peptides, 2 chains. Longest chain 136 peptides. Score 0.865 Round 4: 187 peptides, 2 chains. Longest chain 130 peptides. Score 0.859 Round 5: 188 peptides, 3 chains. Longest chain 115 peptides. Score 0.851 Taking the results from Round 3 Chains 3, Residues 189, Estimated correctness of the model 98.2 % 2 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 146 A and 149 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 25220 reflections ( 99.95 % complete ) and 1727 restraints for refining 1819 atoms. 184 conditional restraints added. Observations/parameters ratio is 3.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2203 (Rfree = 0.000) for 1819 atoms. Found 48 (48 requested) and removed 20 (31 requested) atoms. Cycle 22: After refmac, R = 0.2082 (Rfree = 0.000) for 1844 atoms. Found 49 (49 requested) and removed 20 (31 requested) atoms. Cycle 23: After refmac, R = 0.2026 (Rfree = 0.000) for 1873 atoms. Found 50 (50 requested) and removed 28 (32 requested) atoms. Cycle 24: After refmac, R = 0.1995 (Rfree = 0.000) for 1893 atoms. Found 48 (49 requested) and removed 34 (32 requested) atoms. Cycle 25: After refmac, R = 0.1981 (Rfree = 0.000) for 1904 atoms. Found 48 (48 requested) and removed 34 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.29 1.78 Round 1: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 2: 191 peptides, 2 chains. Longest chain 136 peptides. Score 0.865 Round 3: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 4: 190 peptides, 2 chains. Longest chain 130 peptides. Score 0.863 Round 5: 186 peptides, 3 chains. Longest chain 76 peptides. Score 0.847 Taking the results from Round 2 Chains 3, Residues 189, Estimated correctness of the model 98.2 % 2 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 146 A and 149 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 25220 reflections ( 99.95 % complete ) and 1728 restraints for refining 1820 atoms. 185 conditional restraints added. Observations/parameters ratio is 3.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2233 (Rfree = 0.000) for 1820 atoms. Found 45 (45 requested) and removed 21 (31 requested) atoms. Cycle 27: After refmac, R = 0.2090 (Rfree = 0.000) for 1843 atoms. Found 45 (45 requested) and removed 10 (31 requested) atoms. Cycle 28: After refmac, R = 0.2032 (Rfree = 0.000) for 1875 atoms. Found 46 (46 requested) and removed 25 (32 requested) atoms. Cycle 29: After refmac, R = 0.2040 (Rfree = 0.000) for 1893 atoms. Found 45 (45 requested) and removed 33 (32 requested) atoms. Cycle 30: After refmac, R = 0.2016 (Rfree = 0.000) for 1904 atoms. Found 44 (44 requested) and removed 30 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.28 1.77 Round 1: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 2: 191 peptides, 1 chains. Longest chain 191 peptides. Score 0.874 Round 3: 188 peptides, 2 chains. Longest chain 130 peptides. Score 0.860 Round 4: 190 peptides, 2 chains. Longest chain 130 peptides. Score 0.863 Round 5: 188 peptides, 4 chains. Longest chain 76 peptides. Score 0.841 Taking the results from Round 2 Chains 1, Residues 190, Estimated correctness of the model 98.4 % 1 chains (190 residues) have been docked in sequence ------------------------------------------------------ 25220 reflections ( 99.95 % complete ) and 1713 restraints for refining 1819 atoms. 170 conditional restraints added. Observations/parameters ratio is 3.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2221 (Rfree = 0.000) for 1819 atoms. Found 41 (41 requested) and removed 22 (31 requested) atoms. Cycle 32: After refmac, R = 0.2088 (Rfree = 0.000) for 1836 atoms. Found 40 (40 requested) and removed 21 (31 requested) atoms. Cycle 33: After refmac, R = 0.2030 (Rfree = 0.000) for 1855 atoms. Found 39 (39 requested) and removed 20 (31 requested) atoms. Cycle 34: After refmac, R = 0.1995 (Rfree = 0.000) for 1872 atoms. Found 38 (38 requested) and removed 23 (32 requested) atoms. Cycle 35: After refmac, R = 0.1994 (Rfree = 0.000) for 1886 atoms. Found 37 (37 requested) and removed 26 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.27 1.77 Round 1: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 2: 191 peptides, 2 chains. Longest chain 136 peptides. Score 0.865 Round 3: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 4: 188 peptides, 3 chains. Longest chain 107 peptides. Score 0.851 Round 5: 187 peptides, 3 chains. Longest chain 114 peptides. Score 0.849 Taking the results from Round 2 Chains 3, Residues 189, Estimated correctness of the model 98.2 % 2 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 146 A and 149 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 25220 reflections ( 99.95 % complete ) and 1714 restraints for refining 1818 atoms. 171 conditional restraints added. Observations/parameters ratio is 3.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2251 (Rfree = 0.000) for 1818 atoms. Found 35 (35 requested) and removed 21 (31 requested) atoms. Cycle 37: After refmac, R = 0.2109 (Rfree = 0.000) for 1831 atoms. Found 33 (33 requested) and removed 14 (31 requested) atoms. Cycle 38: After refmac, R = 0.2048 (Rfree = 0.000) for 1847 atoms. Found 34 (34 requested) and removed 16 (31 requested) atoms. Cycle 39: After refmac, R = 0.2013 (Rfree = 0.000) for 1863 atoms. Found 34 (34 requested) and removed 25 (31 requested) atoms. Cycle 40: After refmac, R = 0.1993 (Rfree = 0.000) for 1872 atoms. Found 33 (33 requested) and removed 24 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.27 1.77 Round 1: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 2: 191 peptides, 1 chains. Longest chain 191 peptides. Score 0.874 Round 3: 188 peptides, 2 chains. Longest chain 130 peptides. Score 0.860 Round 4: 191 peptides, 1 chains. Longest chain 191 peptides. Score 0.874 Round 5: 189 peptides, 3 chains. Longest chain 76 peptides. Score 0.852 Taking the results from Round 4 Chains 1, Residues 190, Estimated correctness of the model 98.4 % 1 chains (190 residues) have been docked in sequence ------------------------------------------------------ 25220 reflections ( 99.95 % complete ) and 1718 restraints for refining 1810 atoms. 175 conditional restraints added. Observations/parameters ratio is 3.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2229 (Rfree = 0.000) for 1810 atoms. Found 31 (31 requested) and removed 26 (31 requested) atoms. Cycle 42: After refmac, R = 0.2091 (Rfree = 0.000) for 1813 atoms. Found 31 (31 requested) and removed 15 (31 requested) atoms. Cycle 43: After refmac, R = 0.2027 (Rfree = 0.000) for 1828 atoms. Found 31 (31 requested) and removed 19 (31 requested) atoms. Cycle 44: After refmac, R = 0.2009 (Rfree = 0.000) for 1839 atoms. Found 31 (31 requested) and removed 25 (31 requested) atoms. Cycle 45: After refmac, R = 0.1976 (Rfree = 0.000) for 1843 atoms. Found 31 (31 requested) and removed 24 (31 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.27 1.77 Round 1: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 2: 190 peptides, 2 chains. Longest chain 130 peptides. Score 0.863 Round 3: 190 peptides, 2 chains. Longest chain 133 peptides. Score 0.863 Round 4: 189 peptides, 2 chains. Longest chain 114 peptides. Score 0.862 Round 5: 184 peptides, 3 chains. Longest chain 107 peptides. Score 0.844 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 188, Estimated correctness of the model 98.1 % 2 chains (188 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 144 A and 147 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 25220 reflections ( 99.95 % complete ) and 1543 restraints for refining 1497 atoms. Observations/parameters ratio is 4.21 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2822 (Rfree = 0.000) for 1497 atoms. Found 25 (25 requested) and removed 0 (25 requested) atoms. Cycle 47: After refmac, R = 0.2606 (Rfree = 0.000) for 1497 atoms. Found 26 (26 requested) and removed 0 (26 requested) atoms. Cycle 48: After refmac, R = 0.2412 (Rfree = 0.000) for 1497 atoms. Found 24 (26 requested) and removed 1 (26 requested) atoms. Cycle 49: After refmac, R = 0.2350 (Rfree = 0.000) for 1497 atoms. Found 13 (26 requested) and removed 3 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:12:24 GMT 2018 Job finished. TimeTaking 49.47 Used memory is bytes: 18140592