Mon 24 Dec 00:12:32 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 2oc6-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oc6-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oc6-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.2-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/2oc6-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.2-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 00:12:37 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/2oc6-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.2-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 185 and 0 Target number of residues in the AU: 185 Target solvent content: 0.6392 Checking the provided sequence file Detected sequence length: 124 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 248 Adjusted target solvent content: 0.52 Input MTZ file: 2oc6-3.2-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: 3 Cell parameters: 48.794 46.883 64.576 90.000 110.073 90.000 Input sequence file: 2oc6-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.85 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: 60.653 3.200 Wilson plot Bfac: 70.91 4655 reflections ( 99.66 % complete ) and 0 restraints for refining 2222 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3598 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3153 (Rfree = 0.000) for 2222 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward NCS extension: 0 residues added, 2259 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 9 peptides. Score 0.309 Round 2: 131 peptides, 22 chains. Longest chain 18 peptides. Score 0.436 Round 3: 137 peptides, 21 chains. Longest chain 20 peptides. Score 0.491 Round 4: 147 peptides, 21 chains. Longest chain 22 peptides. Score 0.540 Round 5: 145 peptides, 22 chains. Longest chain 19 peptides. Score 0.509 Taking the results from Round 4 Chains 21, Residues 126, Estimated correctness of the model 23.9 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 3860 restraints for refining 1808 atoms. 3363 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2631 (Rfree = 0.000) for 1808 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. Cycle 2: After refmac, R = 0.2497 (Rfree = 0.000) for 1796 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. Cycle 3: After refmac, R = 0.2498 (Rfree = 0.000) for 1793 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2489 (Rfree = 0.000) for 1789 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2404 (Rfree = 0.000) for 1781 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 1864 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1886 seeds are put forward Round 1: 120 peptides, 23 chains. Longest chain 10 peptides. Score 0.348 Round 2: 155 peptides, 24 chains. Longest chain 17 peptides. Score 0.515 Round 3: 153 peptides, 25 chains. Longest chain 17 peptides. Score 0.484 Round 4: 130 peptides, 19 chains. Longest chain 12 peptides. Score 0.500 Round 5: 130 peptides, 22 chains. Longest chain 12 peptides. Score 0.430 Taking the results from Round 2 Chains 24, Residues 131, Estimated correctness of the model 16.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4062 restraints for refining 1811 atoms. 3562 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2595 (Rfree = 0.000) for 1811 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 7: After refmac, R = 0.2468 (Rfree = 0.000) for 1810 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 8: After refmac, R = 0.2404 (Rfree = 0.000) for 1801 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 9: After refmac, R = 0.2301 (Rfree = 0.000) for 1795 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2258 (Rfree = 0.000) for 1788 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 1859 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1879 seeds are put forward Round 1: 121 peptides, 21 chains. Longest chain 12 peptides. Score 0.404 Round 2: 143 peptides, 21 chains. Longest chain 16 peptides. Score 0.521 Round 3: 138 peptides, 20 chains. Longest chain 17 peptides. Score 0.518 Round 4: 136 peptides, 22 chains. Longest chain 11 peptides. Score 0.463 Round 5: 140 peptides, 19 chains. Longest chain 15 peptides. Score 0.549 Taking the results from Round 5 Chains 19, Residues 121, Estimated correctness of the model 26.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4073 restraints for refining 1811 atoms. 3608 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2540 (Rfree = 0.000) for 1811 atoms. Found 14 (16 requested) and removed 8 (8 requested) atoms. Cycle 12: After refmac, R = 0.2296 (Rfree = 0.000) for 1811 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 13: After refmac, R = 0.2236 (Rfree = 0.000) for 1803 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2205 (Rfree = 0.000) for 1799 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.2631 (Rfree = 0.000) for 1791 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 1850 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1872 seeds are put forward Round 1: 125 peptides, 21 chains. Longest chain 13 peptides. Score 0.426 Round 2: 138 peptides, 22 chains. Longest chain 15 peptides. Score 0.473 Round 3: 132 peptides, 21 chains. Longest chain 16 peptides. Score 0.464 Round 4: 132 peptides, 21 chains. Longest chain 16 peptides. Score 0.464 Round 5: 145 peptides, 21 chains. Longest chain 18 peptides. Score 0.530 Taking the results from Round 5 Chains 21, Residues 124, Estimated correctness of the model 20.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 3986 restraints for refining 1811 atoms. 3511 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2411 (Rfree = 0.000) for 1811 atoms. Found 12 (16 requested) and removed 9 (8 requested) atoms. Cycle 17: After refmac, R = 0.2574 (Rfree = 0.000) for 1811 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.2405 (Rfree = 0.000) for 1809 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2211 (Rfree = 0.000) for 1809 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2144 (Rfree = 0.000) for 1803 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 1872 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1889 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 10 peptides. Score 0.297 Round 2: 133 peptides, 22 chains. Longest chain 12 peptides. Score 0.447 Round 3: 133 peptides, 22 chains. Longest chain 13 peptides. Score 0.447 Round 4: 139 peptides, 20 chains. Longest chain 19 peptides. Score 0.523 Round 5: 138 peptides, 20 chains. Longest chain 17 peptides. Score 0.518 Taking the results from Round 4 Chains 20, Residues 119, Estimated correctness of the model 18.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4119 restraints for refining 1810 atoms. 3663 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2374 (Rfree = 0.000) for 1810 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.2256 (Rfree = 0.000) for 1800 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.2170 (Rfree = 0.000) for 1801 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2137 (Rfree = 0.000) for 1790 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2140 (Rfree = 0.000) for 1781 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 1858 seeds are put forward Round 1: 133 peptides, 27 chains. Longest chain 9 peptides. Score 0.326 Round 2: 144 peptides, 21 chains. Longest chain 13 peptides. Score 0.526 Round 3: 141 peptides, 19 chains. Longest chain 18 peptides. Score 0.554 Round 4: 121 peptides, 18 chains. Longest chain 13 peptides. Score 0.476 Round 5: 129 peptides, 20 chains. Longest chain 17 peptides. Score 0.472 Taking the results from Round 3 Chains 19, Residues 122, Estimated correctness of the model 28.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 3994 restraints for refining 1811 atoms. 3525 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2424 (Rfree = 0.000) for 1811 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 27: After refmac, R = 0.2255 (Rfree = 0.000) for 1814 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2171 (Rfree = 0.000) for 1807 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.2245 (Rfree = 0.000) for 1797 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2174 (Rfree = 0.000) for 1795 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 1865 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 1888 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 7 peptides. Score 0.281 Round 2: 127 peptides, 21 chains. Longest chain 13 peptides. Score 0.437 Round 3: 114 peptides, 18 chains. Longest chain 16 peptides. Score 0.438 Round 4: 121 peptides, 17 chains. Longest chain 19 peptides. Score 0.499 Round 5: 103 peptides, 15 chains. Longest chain 18 peptides. Score 0.451 Taking the results from Round 4 Chains 17, Residues 104, Estimated correctness of the model 11.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4111 restraints for refining 1811 atoms. 3712 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2327 (Rfree = 0.000) for 1811 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 32: After refmac, R = 0.2079 (Rfree = 0.000) for 1814 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.1973 (Rfree = 0.000) for 1815 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.1867 (Rfree = 0.000) for 1807 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1837 (Rfree = 0.000) for 1801 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 1856 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 1881 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 7 peptides. Score 0.291 Round 2: 103 peptides, 17 chains. Longest chain 13 peptides. Score 0.400 Round 3: 105 peptides, 17 chains. Longest chain 16 peptides. Score 0.412 Round 4: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.406 Round 5: 111 peptides, 17 chains. Longest chain 14 peptides. Score 0.446 Taking the results from Round 5 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 3980 restraints for refining 1811 atoms. 3621 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2201 (Rfree = 0.000) for 1811 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.2141 (Rfree = 0.000) for 1808 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.2111 (Rfree = 0.000) for 1808 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2242 (Rfree = 0.000) for 1803 atoms. Found 14 (16 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2105 (Rfree = 0.000) for 1809 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1873 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1895 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 8 peptides. Score 0.239 Round 2: 103 peptides, 21 chains. Longest chain 8 peptides. Score 0.295 Round 3: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.333 Round 4: 95 peptides, 18 chains. Longest chain 11 peptides. Score 0.325 Round 5: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 5 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4288 restraints for refining 1811 atoms. 3984 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2216 (Rfree = 0.000) for 1811 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.2064 (Rfree = 0.000) for 1809 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1968 (Rfree = 0.000) for 1805 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1884 (Rfree = 0.000) for 1803 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1943 (Rfree = 0.000) for 1795 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1862 seeds are put forward NCS extension: 0 residues added, 1862 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 6 peptides. Score 0.265 Round 2: 86 peptides, 15 chains. Longest chain 8 peptides. Score 0.350 Round 3: 85 peptides, 14 chains. Longest chain 16 peptides. Score 0.371 Round 4: 86 peptides, 14 chains. Longest chain 15 peptides. Score 0.377 Round 5: 94 peptides, 14 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 80, 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 2oc6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4655 reflections ( 99.66 % complete ) and 4272 restraints for refining 1811 atoms. 3966 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2123 (Rfree = 0.000) for 1811 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2146 (Rfree = 0.000) for 1797 atoms. Found 0 (16 requested) and removed 3 (8 requested) atoms. Cycle 48: After refmac, R = 0.2053 (Rfree = 0.000) for 1794 atoms. Found 0 (16 requested) and removed 2 (8 requested) atoms. Cycle 49: After refmac, R = 0.2057 (Rfree = 0.000) for 1790 atoms. Found 0 (16 requested) and removed 2 (8 requested) atoms. Writing output files ... TimeTaking 26.25