Mon 24 Dec 00:21:45 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2owp-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-4.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:21:49 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/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-4.0-parrot-mrncs/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 287 and 0 Target number of residues in the AU: 287 Target solvent content: 0.6431 Checking the provided sequence file Detected sequence length: 129 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 258 Adjusted target solvent content: 0.68 Input MTZ file: 2owp-4.0-parrot-mrncs.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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 1.20 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: 29.899 4.000 Wilson plot Bfac: 73.28 3914 reflections ( 99.09 % complete ) and 0 restraints for refining 2277 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3757 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3632 (Rfree = 0.000) for 2277 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 2.82 Search for helices and strands: 0 residues in 0 chains, 2289 seeds are put forward NCS extension: 0 residues added, 2289 seeds are put forward Round 1: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.291 Round 2: 140 peptides, 23 chains. Longest chain 9 peptides. Score 0.379 Round 3: 164 peptides, 22 chains. Longest chain 12 peptides. Score 0.483 Round 4: 160 peptides, 23 chains. Longest chain 17 peptides. Score 0.453 Round 5: 163 peptides, 24 chains. Longest chain 12 peptides. Score 0.448 Taking the results from Round 3 Chains 22, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3914 reflections ( 99.09 % complete ) and 4052 restraints for refining 1864 atoms. 3506 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3302 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.3284 (Rfree = 0.000) for 1831 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 3: After refmac, R = 0.3160 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 4: After refmac, R = 0.2861 (Rfree = 0.000) for 1778 atoms. Found 7 (8 requested) and removed 11 (4 requested) atoms. Cycle 5: After refmac, R = 0.2998 (Rfree = 0.000) for 1766 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 2.73 Search for helices and strands: 0 residues in 0 chains, 1822 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1835 seeds are put forward Round 1: 149 peptides, 23 chains. Longest chain 13 peptides. Score 0.413 Round 2: 158 peptides, 24 chains. Longest chain 13 peptides. Score 0.430 Round 3: 162 peptides, 23 chains. Longest chain 18 peptides. Score 0.460 Round 4: 166 peptides, 22 chains. Longest chain 15 peptides. Score 0.490 Round 5: 179 peptides, 25 chains. Longest chain 17 peptides. Score 0.488 Taking the results from Round 4 Chains 23, Residues 144, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3914 reflections ( 99.09 % complete ) and 3837 restraints for refining 1863 atoms. 3219 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3555 (Rfree = 0.000) for 1863 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 7: After refmac, R = 0.3306 (Rfree = 0.000) for 1816 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 8: After refmac, R = 0.3267 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 9: After refmac, R = 0.3126 (Rfree = 0.000) for 1772 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 10: After refmac, R = 0.2830 (Rfree = 0.000) for 1757 atoms. Found 7 (8 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 2.59 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1826 seeds are put forward Round 1: 164 peptides, 25 chains. Longest chain 13 peptides. Score 0.436 Round 2: 172 peptides, 23 chains. Longest chain 16 peptides. Score 0.495 Round 3: 186 peptides, 24 chains. Longest chain 21 peptides. Score 0.525 Round 4: 179 peptides, 24 chains. Longest chain 15 peptides. Score 0.503 Round 5: 185 peptides, 20 chains. Longest chain 22 peptides. Score 0.579 Taking the results from Round 5 Chains 20, Residues 165, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3914 reflections ( 99.09 % complete ) and 3710 restraints for refining 1864 atoms. 3044 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3219 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 12: After refmac, R = 0.3397 (Rfree = 0.000) for 1846 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 13: After refmac, R = 0.3074 (Rfree = 0.000) for 1822 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 14: After refmac, R = 0.3285 (Rfree = 0.000) for 1809 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.3183 (Rfree = 0.000) for 1802 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 2.63 Search for helices and strands: 0 residues in 0 chains, 1851 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 1872 seeds are put forward Round 1: 140 peptides, 23 chains. Longest chain 17 peptides. Score 0.379 Round 2: 170 peptides, 27 chains. Longest chain 17 peptides. Score 0.425 Round 3: 172 peptides, 25 chains. Longest chain 22 peptides. Score 0.464 Round 4: 164 peptides, 26 chains. Longest chain 17 peptides. Score 0.420 Round 5: 168 peptides, 23 chains. Longest chain 17 peptides. Score 0.481 Taking the results from Round 5 Chains 23, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3914 reflections ( 99.09 % complete ) and 3928 restraints for refining 1864 atoms. 3371 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3543 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 17: After refmac, R = 0.3472 (Rfree = 0.000) for 1829 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 18: After refmac, R = 0.3169 (Rfree = 0.000) for 1805 atoms. Found 6 (8 requested) and removed 9 (4 requested) atoms. Cycle 19: After refmac, R = 0.3548 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.3463 (Rfree = 0.000) for 1776 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1834 seeds are put forward Round 1: 123 peptides, 24 chains. Longest chain 12 peptides. Score 0.292 Round 2: 150 peptides, 24 chains. Longest chain 12 peptides. Score 0.400 Round 3: 158 peptides, 24 chains. Longest chain 17 peptides. Score 0.430 Round 4: 151 peptides, 23 chains. Longest chain 11 peptides. Score 0.421 Round 5: 163 peptides, 26 chains. Longest chain 15 peptides. Score 0.416 Taking the results from Round 3 Chains 24, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3914 reflections ( 99.09 % complete ) and 4006 restraints for refining 1864 atoms. 3494 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3651 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 22: After refmac, R = 0.3541 (Rfree = 0.000) for 1832 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 23: After refmac, R = 0.3269 (Rfree = 0.000) for 1807 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 24: After refmac, R = 0.3403 (Rfree = 0.000) for 1793 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 25: After refmac, R = 0.3160 (Rfree = 0.000) for 1779 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 2.56 Search for helices and strands: 0 residues in 0 chains, 1827 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1848 seeds are put forward Round 1: 141 peptides, 25 chains. Longest chain 12 peptides. Score 0.348 Round 2: 153 peptides, 25 chains. Longest chain 13 peptides. Score 0.395 Round 3: 161 peptides, 26 chains. Longest chain 15 peptides. Score 0.409 Round 4: 161 peptides, 27 chains. Longest chain 16 peptides. Score 0.392 Round 5: 156 peptides, 27 chains. Longest chain 12 peptides. Score 0.373 Taking the results from Round 3 Chains 26, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3914 reflections ( 99.09 % complete ) and 4017 restraints for refining 1864 atoms. 3503 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3604 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 27 (4 requested) atoms. Cycle 27: After refmac, R = 0.3525 (Rfree = 0.000) for 1826 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 28: After refmac, R = 0.3494 (Rfree = 0.000) for 1806 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.3545 (Rfree = 0.000) for 1789 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 30: After refmac, R = 0.3466 (Rfree = 0.000) for 1779 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 2.65 Search for helices and strands: 0 residues in 0 chains, 1854 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1876 seeds are put forward Round 1: 126 peptides, 25 chains. Longest chain 9 peptides. Score 0.286 Round 2: 146 peptides, 27 chains. Longest chain 11 peptides. Score 0.334 Round 3: 148 peptides, 26 chains. Longest chain 13 peptides. Score 0.359 Round 4: 137 peptides, 22 chains. Longest chain 14 peptides. Score 0.385 Round 5: 130 peptides, 19 chains. Longest chain 14 peptides. Score 0.410 Taking the results from Round 5 Chains 19, Residues 111, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3914 reflections ( 99.09 % complete ) and 4006 restraints for refining 1864 atoms. 3552 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3479 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 32: After refmac, R = 0.3558 (Rfree = 0.000) for 1833 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 33: After refmac, R = 0.3253 (Rfree = 0.000) for 1813 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 34: After refmac, R = 0.3411 (Rfree = 0.000) for 1801 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.3073 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1852 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 7 peptides. Score 0.260 Round 2: 132 peptides, 23 chains. Longest chain 13 peptides. Score 0.347 Round 3: 130 peptides, 22 chains. Longest chain 9 peptides. Score 0.357 Round 4: 137 peptides, 21 chains. Longest chain 15 peptides. Score 0.402 Round 5: 148 peptides, 25 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 4 Chains 21, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3914 reflections ( 99.09 % complete ) and 4088 restraints for refining 1864 atoms. 3645 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3497 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.3502 (Rfree = 0.000) for 1838 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 38: After refmac, R = 0.3507 (Rfree = 0.000) for 1822 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 39: After refmac, R = 0.3329 (Rfree = 0.000) for 1806 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 40: After refmac, R = 0.2980 (Rfree = 0.000) for 1796 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 2.55 Search for helices and strands: 0 residues in 0 chains, 1839 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 1864 seeds are put forward Round 1: 127 peptides, 26 chains. Longest chain 8 peptides. Score 0.272 Round 2: 136 peptides, 25 chains. Longest chain 11 peptides. Score 0.328 Round 3: 137 peptides, 24 chains. Longest chain 11 peptides. Score 0.350 Round 4: 146 peptides, 25 chains. Longest chain 13 peptides. Score 0.368 Round 5: 148 peptides, 24 chains. Longest chain 14 peptides. Score 0.393 Taking the results from Round 5 Chains 25, Residues 124, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3914 reflections ( 99.09 % complete ) and 3943 restraints for refining 1864 atoms. 3431 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3561 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 42: After refmac, R = 0.3427 (Rfree = 0.000) for 1843 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 43: After refmac, R = 0.2895 (Rfree = 0.000) for 1821 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.3282 (Rfree = 0.000) for 1812 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 45: After refmac, R = 0.3322 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 2.52 Search for helices and strands: 0 residues in 0 chains, 1841 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1858 seeds are put forward Round 1: 117 peptides, 25 chains. Longest chain 9 peptides. Score 0.247 Round 2: 123 peptides, 23 chains. Longest chain 10 peptides. Score 0.310 Round 3: 140 peptides, 27 chains. Longest chain 8 peptides. Score 0.309 Round 4: 133 peptides, 23 chains. Longest chain 12 peptides. Score 0.351 Round 5: 123 peptides, 21 chains. Longest chain 12 peptides. Score 0.346 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 110, 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 2owp-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3914 reflections ( 99.09 % complete ) and 4146 restraints for refining 1864 atoms. 3729 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3490 (Rfree = 0.000) for 1864 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3265 (Rfree = 0.000) for 1838 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3400 (Rfree = 0.000) for 1819 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3231 (Rfree = 0.000) for 1802 atoms. TimeTaking 25.72