null Tue 25 Dec 19:27:58 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 2p4g-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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/2p4g-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 ============================================================ Tue 25 Dec 19:28:06 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/2p4g-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 259 and 0 Target number of residues in the AU: 259 Target solvent content: 0.6812 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 270 Adjusted target solvent content: 0.67 Input MTZ file: 2p4g-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: 172 Cell parameters: 115.650 115.650 56.930 90.000 90.000 120.000 Input sequence file: 2p4g-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2160 target number of atoms Had to go as low as 1.15 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: 28.913 4.001 Wilson plot Bfac: 101.46 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3771 reflections ( 99.58 % complete ) and 0 restraints for refining 2386 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3466 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3057 (Rfree = 0.000) for 2386 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.94 3.11 Search for helices and strands: 0 residues in 0 chains, 2419 seeds are put forward Round 1: 121 peptides, 23 chains. Longest chain 9 peptides. Score 0.301 Round 2: 155 peptides, 19 chains. Longest chain 20 peptides. Score 0.497 Round 3: 162 peptides, 17 chains. Longest chain 22 peptides. Score 0.550 Round 4: 167 peptides, 21 chains. Longest chain 17 peptides. Score 0.506 Round 5: 159 peptides, 15 chains. Longest chain 20 peptides. Score 0.570 Taking the results from Round 5 Chains 15, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3771 reflections ( 99.58 % complete ) and 4452 restraints for refining 1951 atoms. 3891 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2471 (Rfree = 0.000) for 1951 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 2: After refmac, R = 0.2239 (Rfree = 0.000) for 1923 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.2271 (Rfree = 0.000) for 1905 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.2005 (Rfree = 0.000) for 1891 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2000 (Rfree = 0.000) for 1886 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.02 Search for helices and strands: 0 residues in 0 chains, 1927 seeds are put forward Round 1: 153 peptides, 23 chains. Longest chain 15 peptides. Score 0.426 Round 2: 158 peptides, 19 chains. Longest chain 17 peptides. Score 0.507 Round 3: 157 peptides, 19 chains. Longest chain 23 peptides. Score 0.504 Round 4: 158 peptides, 19 chains. Longest chain 17 peptides. Score 0.507 Round 5: 165 peptides, 23 chains. Longest chain 17 peptides. Score 0.469 Taking the results from Round 4 Chains 19, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3771 reflections ( 99.58 % complete ) and 4424 restraints for refining 1950 atoms. 3887 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2216 (Rfree = 0.000) for 1950 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 7: After refmac, R = 0.2049 (Rfree = 0.000) for 1925 atoms. Found 4 (9 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2002 (Rfree = 0.000) for 1909 atoms. Found 3 (9 requested) and removed 11 (4 requested) atoms. Cycle 9: After refmac, R = 0.1944 (Rfree = 0.000) for 1895 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.2380 (Rfree = 0.000) for 1886 atoms. Found 3 (8 requested) and removed 22 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 2.96 Search for helices and strands: 0 residues in 0 chains, 1965 seeds are put forward Round 1: 141 peptides, 21 chains. Longest chain 12 peptides. Score 0.415 Round 2: 152 peptides, 21 chains. Longest chain 15 peptides. Score 0.455 Round 3: 156 peptides, 20 chains. Longest chain 15 peptides. Score 0.485 Round 4: 153 peptides, 19 chains. Longest chain 18 peptides. Score 0.490 Round 5: 158 peptides, 19 chains. Longest chain 21 peptides. Score 0.507 Taking the results from Round 5 Chains 20, Residues 139, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3771 reflections ( 99.58 % complete ) and 4160 restraints for refining 1951 atoms. 3561 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2176 (Rfree = 0.000) for 1951 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 12: After refmac, R = 0.1963 (Rfree = 0.000) for 1933 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.1955 (Rfree = 0.000) for 1920 atoms. Found 3 (9 requested) and removed 15 (4 requested) atoms. Cycle 14: After refmac, R = 0.1914 (Rfree = 0.000) for 1901 atoms. Found 3 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.1856 (Rfree = 0.000) for 1892 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.88 3.06 Search for helices and strands: 0 residues in 0 chains, 1958 seeds are put forward Round 1: 146 peptides, 22 chains. Longest chain 15 peptides. Score 0.417 Round 2: 154 peptides, 21 chains. Longest chain 15 peptides. Score 0.462 Round 3: 141 peptides, 18 chains. Longest chain 16 peptides. Score 0.465 Round 4: 151 peptides, 19 chains. Longest chain 19 peptides. Score 0.483 Round 5: 153 peptides, 20 chains. Longest chain 15 peptides. Score 0.475 Taking the results from Round 4 Chains 19, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3771 reflections ( 99.58 % complete ) and 4432 restraints for refining 1950 atoms. 3923 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2042 (Rfree = 0.000) for 1950 atoms. Found 8 (9 requested) and removed 10 (4 requested) atoms. Cycle 17: After refmac, R = 0.1884 (Rfree = 0.000) for 1937 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 18: After refmac, R = 0.1807 (Rfree = 0.000) for 1929 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 19: After refmac, R = 0.1835 (Rfree = 0.000) for 1922 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.1782 (Rfree = 0.000) for 1924 atoms. Found 4 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.91 3.09 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward Round 1: 129 peptides, 20 chains. Longest chain 12 peptides. Score 0.387 Round 2: 149 peptides, 21 chains. Longest chain 19 peptides. Score 0.444 Round 3: 160 peptides, 23 chains. Longest chain 13 peptides. Score 0.451 Round 4: 145 peptides, 20 chains. Longest chain 14 peptides. Score 0.446 Round 5: 147 peptides, 19 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 5 Chains 19, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3771 reflections ( 99.58 % complete ) and 4457 restraints for refining 1951 atoms. 3964 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2136 (Rfree = 0.000) for 1951 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 22: After refmac, R = 0.2035 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 23: After refmac, R = 0.1837 (Rfree = 0.000) for 1918 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.1894 (Rfree = 0.000) for 1909 atoms. Found 8 (9 requested) and removed 9 (4 requested) atoms. Cycle 25: After refmac, R = 0.2400 (Rfree = 0.000) for 1900 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.86 3.05 Search for helices and strands: 0 residues in 0 chains, 1991 seeds are put forward Round 1: 132 peptides, 23 chains. Longest chain 9 peptides. Score 0.346 Round 2: 144 peptides, 19 chains. Longest chain 15 peptides. Score 0.459 Round 3: 148 peptides, 20 chains. Longest chain 16 peptides. Score 0.457 Round 4: 149 peptides, 21 chains. Longest chain 15 peptides. Score 0.444 Round 5: 143 peptides, 20 chains. Longest chain 19 peptides. Score 0.439 Taking the results from Round 2 Chains 19, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3771 reflections ( 99.58 % complete ) and 4220 restraints for refining 1950 atoms. 3739 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1868 (Rfree = 0.000) for 1950 atoms. Found 3 (9 requested) and removed 21 (4 requested) atoms. Cycle 27: After refmac, R = 0.1819 (Rfree = 0.000) for 1920 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.1665 (Rfree = 0.000) for 1908 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.1731 (Rfree = 0.000) for 1906 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.1829 (Rfree = 0.000) for 1902 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.91 3.09 Search for helices and strands: 0 residues in 0 chains, 1970 seeds are put forward Round 1: 120 peptides, 23 chains. Longest chain 11 peptides. Score 0.296 Round 2: 135 peptides, 19 chains. Longest chain 13 peptides. Score 0.427 Round 3: 142 peptides, 23 chains. Longest chain 13 peptides. Score 0.385 Round 4: 144 peptides, 19 chains. Longest chain 19 peptides. Score 0.459 Round 5: 143 peptides, 19 chains. Longest chain 14 peptides. Score 0.456 Taking the results from Round 4 Chains 19, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3771 reflections ( 99.58 % complete ) and 4299 restraints for refining 1950 atoms. 3818 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1939 (Rfree = 0.000) for 1950 atoms. Found 7 (9 requested) and removed 16 (4 requested) atoms. Cycle 32: After refmac, R = 0.1895 (Rfree = 0.000) for 1931 atoms. Found 6 (9 requested) and removed 11 (4 requested) atoms. Cycle 33: After refmac, R = 0.1810 (Rfree = 0.000) for 1922 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.1833 (Rfree = 0.000) for 1917 atoms. Found 2 (9 requested) and removed 11 (4 requested) atoms. Cycle 35: After refmac, R = 0.1798 (Rfree = 0.000) for 1906 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.92 3.10 Search for helices and strands: 0 residues in 0 chains, 1969 seeds are put forward Round 1: 120 peptides, 19 chains. Longest chain 14 peptides. Score 0.369 Round 2: 127 peptides, 16 chains. Longest chain 15 peptides. Score 0.448 Round 3: 134 peptides, 18 chains. Longest chain 15 peptides. Score 0.440 Round 4: 146 peptides, 19 chains. Longest chain 17 peptides. Score 0.466 Round 5: 144 peptides, 20 chains. Longest chain 16 peptides. Score 0.443 Taking the results from Round 4 Chains 19, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3771 reflections ( 99.58 % complete ) and 4327 restraints for refining 1951 atoms. 3838 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1971 (Rfree = 0.000) for 1951 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 37: After refmac, R = 0.1789 (Rfree = 0.000) for 1941 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.1797 (Rfree = 0.000) for 1933 atoms. Found 2 (9 requested) and removed 14 (4 requested) atoms. Cycle 39: After refmac, R = 0.1802 (Rfree = 0.000) for 1917 atoms. Found 5 (9 requested) and removed 13 (4 requested) atoms. Cycle 40: After refmac, R = 0.2080 (Rfree = 0.000) for 1908 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.84 3.03 Search for helices and strands: 0 residues in 0 chains, 1965 seeds are put forward Round 1: 120 peptides, 22 chains. Longest chain 8 peptides. Score 0.315 Round 2: 122 peptides, 19 chains. Longest chain 15 peptides. Score 0.377 Round 3: 139 peptides, 22 chains. Longest chain 13 peptides. Score 0.391 Round 4: 126 peptides, 18 chains. Longest chain 18 peptides. Score 0.410 Round 5: 138 peptides, 20 chains. Longest chain 11 peptides. Score 0.421 Taking the results from Round 5 Chains 20, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3771 reflections ( 99.58 % complete ) and 4442 restraints for refining 1951 atoms. 3990 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1966 (Rfree = 0.000) for 1951 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 42: After refmac, R = 0.1798 (Rfree = 0.000) for 1942 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.1723 (Rfree = 0.000) for 1939 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1689 (Rfree = 0.000) for 1929 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1654 (Rfree = 0.000) for 1925 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.93 3.10 Search for helices and strands: 0 residues in 0 chains, 1989 seeds are put forward Round 1: 108 peptides, 19 chains. Longest chain 12 peptides. Score 0.320 Round 2: 129 peptides, 20 chains. Longest chain 13 peptides. Score 0.387 Round 3: 138 peptides, 23 chains. Longest chain 11 peptides. Score 0.370 Round 4: 136 peptides, 22 chains. Longest chain 11 peptides. Score 0.379 Round 5: 129 peptides, 21 chains. Longest chain 13 peptides. Score 0.369 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 109, 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 2p4g-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3771 reflections ( 99.58 % complete ) and 4544 restraints for refining 1951 atoms. 4128 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1840 (Rfree = 0.000) for 1951 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1786 (Rfree = 0.000) for 1937 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1783 (Rfree = 0.000) for 1933 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1741 (Rfree = 0.000) for 1927 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:21:34 GMT 2018 Job finished. TimeTaking 53.61 Used memory is bytes: 3957936