null Sun 23 Dec 22:22:43 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 2p1a-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-4.0-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/2p1a-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-4.0-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 22:22:53 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/2p1a-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-4.0-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 183 and 0 Target number of residues in the AU: 183 Target solvent content: 0.6774 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.46 Input MTZ file: 2p1a-4.0-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: 19 Cell parameters: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.65 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.570 4.001 Wilson plot Bfac: 98.76 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2832 reflections ( 99.33 % complete ) and 0 restraints for refining 2719 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3626 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3594 (Rfree = 0.000) for 2719 atoms. Found 12 (12 requested) and removed 40 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.00 4.22 Search for helices and strands: 0 residues in 0 chains, 2766 seeds are put forward NCS extension: 0 residues added, 2766 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 7 peptides. Score 0.211 Round 2: 95 peptides, 20 chains. Longest chain 7 peptides. Score 0.263 Round 3: 95 peptides, 14 chains. Longest chain 15 peptides. Score 0.413 Round 4: 99 peptides, 15 chains. Longest chain 11 peptides. Score 0.410 Round 5: 92 peptides, 13 chains. Longest chain 14 peptides. Score 0.421 Taking the results from Round 5 Chains 13, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 5754 restraints for refining 2223 atoms. 5451 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2814 (Rfree = 0.000) for 2223 atoms. Found 5 (10 requested) and removed 15 (5 requested) atoms. Cycle 2: After refmac, R = 0.2665 (Rfree = 0.000) for 2172 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 3: After refmac, R = 0.2712 (Rfree = 0.000) for 2149 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 4: After refmac, R = 0.2473 (Rfree = 0.000) for 2125 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 5: After refmac, R = 0.2435 (Rfree = 0.000) for 2102 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.94 4.16 Search for helices and strands: 0 residues in 0 chains, 2209 seeds are put forward NCS extension: 10 residues added (1 deleted due to clashes), 2219 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.254 Round 2: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.312 Round 3: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.322 Round 4: 81 peptides, 13 chains. Longest chain 11 peptides. Score 0.360 Round 5: 86 peptides, 12 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 5 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4279 restraints for refining 1848 atoms. 3995 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2657 (Rfree = 0.000) for 1848 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 7: After refmac, R = 0.2545 (Rfree = 0.000) for 1829 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 8: After refmac, R = 0.2522 (Rfree = 0.000) for 1806 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 9: After refmac, R = 0.2529 (Rfree = 0.000) for 1787 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.2513 (Rfree = 0.000) for 1780 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.92 4.13 Search for helices and strands: 0 residues in 0 chains, 1897 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1914 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 6 peptides. Score 0.235 Round 2: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.335 Round 3: 89 peptides, 14 chains. Longest chain 11 peptides. Score 0.380 Round 4: 96 peptides, 15 chains. Longest chain 11 peptides. Score 0.394 Round 5: 90 peptides, 14 chains. Longest chain 11 peptides. Score 0.385 Taking the results from Round 4 Chains 15, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 3809 restraints for refining 1721 atoms. 3500 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2405 (Rfree = 0.000) for 1721 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 12: After refmac, R = 0.2266 (Rfree = 0.000) for 1699 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2186 (Rfree = 0.000) for 1692 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2135 (Rfree = 0.000) for 1679 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.2192 (Rfree = 0.000) for 1673 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.90 4.11 Search for helices and strands: 0 residues in 0 chains, 1781 seeds are put forward NCS extension: 0 residues added, 1781 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 10 peptides. Score 0.299 Round 2: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.333 Round 3: 99 peptides, 17 chains. Longest chain 14 peptides. Score 0.361 Round 4: 106 peptides, 17 chains. Longest chain 14 peptides. Score 0.400 Round 5: 108 peptides, 17 chains. Longest chain 12 peptides. Score 0.410 Taking the results from Round 5 Chains 17, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 3752 restraints for refining 1751 atoms. 3405 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2251 (Rfree = 0.000) for 1751 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 17: After refmac, R = 0.2275 (Rfree = 0.000) for 1738 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 18: After refmac, R = 0.2255 (Rfree = 0.000) for 1723 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 19: After refmac, R = 0.2162 (Rfree = 0.000) for 1704 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.2180 (Rfree = 0.000) for 1692 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.89 4.10 Search for helices and strands: 0 residues in 0 chains, 1801 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1819 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 8 peptides. Score 0.291 Round 2: 112 peptides, 17 chains. Longest chain 12 peptides. Score 0.431 Round 3: 112 peptides, 18 chains. Longest chain 13 peptides. Score 0.408 Round 4: 118 peptides, 17 chains. Longest chain 19 peptides. Score 0.461 Round 5: 109 peptides, 16 chains. Longest chain 17 peptides. Score 0.439 Taking the results from Round 4 Chains 17, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 3710 restraints for refining 1745 atoms. 3323 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2216 (Rfree = 0.000) for 1745 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 22: After refmac, R = 0.2205 (Rfree = 0.000) for 1724 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2107 (Rfree = 0.000) for 1723 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 24: After refmac, R = 0.2051 (Rfree = 0.000) for 1718 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.1974 (Rfree = 0.000) for 1706 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 4.05 Search for helices and strands: 0 residues in 0 chains, 1813 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1838 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 7 peptides. Score 0.265 Round 2: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.297 Round 3: 108 peptides, 18 chains. Longest chain 13 peptides. Score 0.387 Round 4: 113 peptides, 19 chains. Longest chain 15 peptides. Score 0.390 Round 5: 99 peptides, 15 chains. Longest chain 16 peptides. Score 0.410 Taking the results from Round 5 Chains 15, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 3989 restraints for refining 1805 atoms. 3668 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2375 (Rfree = 0.000) for 1805 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.2416 (Rfree = 0.000) for 1786 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2244 (Rfree = 0.000) for 1775 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.2365 (Rfree = 0.000) for 1765 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 30: After refmac, R = 0.2271 (Rfree = 0.000) for 1758 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 4.04 Search for helices and strands: 0 residues in 0 chains, 1853 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 1877 seeds are put forward Round 1: 85 peptides, 19 chains. Longest chain 9 peptides. Score 0.226 Round 2: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.354 Round 3: 103 peptides, 18 chains. Longest chain 12 peptides. Score 0.359 Round 4: 106 peptides, 18 chains. Longest chain 14 peptides. Score 0.376 Round 5: 99 peptides, 17 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 4 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4295 restraints for refining 1891 atoms. 3961 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2292 (Rfree = 0.000) for 1891 atoms. Found 8 (8 requested) and removed 25 (4 requested) atoms. Cycle 32: After refmac, R = 0.2288 (Rfree = 0.000) for 1863 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 33: After refmac, R = 0.2254 (Rfree = 0.000) for 1852 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 34: After refmac, R = 0.2247 (Rfree = 0.000) for 1842 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.2231 (Rfree = 0.000) for 1840 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.84 4.05 Search for helices and strands: 0 residues in 0 chains, 1947 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1967 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 8 peptides. Score 0.233 Round 2: 108 peptides, 19 chains. Longest chain 13 peptides. Score 0.363 Round 3: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.340 Round 4: 106 peptides, 21 chains. Longest chain 9 peptides. Score 0.303 Round 5: 109 peptides, 19 chains. Longest chain 9 peptides. Score 0.368 Taking the results from Round 5 Chains 19, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4505 restraints for refining 1962 atoms. 4164 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2113 (Rfree = 0.000) for 1962 atoms. Found 6 (9 requested) and removed 15 (4 requested) atoms. Cycle 37: After refmac, R = 0.2158 (Rfree = 0.000) for 1933 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 38: After refmac, R = 0.2115 (Rfree = 0.000) for 1920 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 39: After refmac, R = 0.2215 (Rfree = 0.000) for 1907 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 40: After refmac, R = 0.2061 (Rfree = 0.000) for 1899 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.88 4.09 Search for helices and strands: 0 residues in 0 chains, 1989 seeds are put forward NCS extension: 0 residues added, 1989 seeds are put forward Round 1: 66 peptides, 16 chains. Longest chain 5 peptides. Score 0.181 Round 2: 71 peptides, 16 chains. Longest chain 6 peptides. Score 0.216 Round 3: 75 peptides, 16 chains. Longest chain 8 peptides. Score 0.242 Round 4: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.255 Round 5: 91 peptides, 18 chains. Longest chain 7 peptides. Score 0.290 Taking the results from Round 5 Chains 18, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4490 restraints for refining 1935 atoms. 4216 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2162 (Rfree = 0.000) for 1935 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 42: After refmac, R = 0.2101 (Rfree = 0.000) for 1914 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 43: After refmac, R = 0.2110 (Rfree = 0.000) for 1904 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.2114 (Rfree = 0.000) for 1896 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 45: After refmac, R = 0.2033 (Rfree = 0.000) for 1888 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.89 4.10 Search for helices and strands: 0 residues in 0 chains, 1990 seeds are put forward NCS extension: 0 residues added, 1990 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.203 Round 2: 81 peptides, 17 chains. Longest chain 7 peptides. Score 0.254 Round 3: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.282 Round 4: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.268 Round 5: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.319 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2p1a-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2832 reflections ( 99.33 % complete ) and 4138 restraints for refining 1856 atoms. 3881 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2283 (Rfree = 0.000) for 1856 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2182 (Rfree = 0.000) for 1842 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2379 (Rfree = 0.000) for 1831 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2252 (Rfree = 0.000) for 1818 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:41 GMT 2018 Job finished. TimeTaking 31.96 Used memory is bytes: 18804864