Mon 24 Dec 00:27:01 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 2oc6-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oc6-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oc6-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-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/2oc6-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-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 00:27:06 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/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6646 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: 2oc6-3.8-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: 2oc6-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1984 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 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 3.802 Wilson plot Bfac: 87.20 2794 reflections ( 99.61 % complete ) and 0 restraints for refining 2211 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3589 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2877 (Rfree = 0.000) for 2211 atoms. Found 8 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 0 residues added, 2248 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.259 Round 2: 101 peptides, 21 chains. Longest chain 7 peptides. Score 0.282 Round 3: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.390 Round 4: 117 peptides, 20 chains. Longest chain 12 peptides. Score 0.405 Round 5: 116 peptides, 20 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 4 Chains 20, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4225 restraints for refining 1794 atoms. 3857 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2343 (Rfree = 0.000) for 1794 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. Cycle 2: After refmac, R = 0.2249 (Rfree = 0.000) for 1768 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.2213 (Rfree = 0.000) for 1759 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 4: After refmac, R = 0.2129 (Rfree = 0.000) for 1758 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.2132 (Rfree = 0.000) for 1757 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 1829 seeds are put forward NCS extension: 0 residues added, 1829 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 10 peptides. Score 0.294 Round 2: 133 peptides, 22 chains. Longest chain 18 peptides. Score 0.447 Round 3: 126 peptides, 20 chains. Longest chain 12 peptides. Score 0.456 Round 4: 123 peptides, 20 chains. Longest chain 14 peptides. Score 0.439 Round 5: 127 peptides, 18 chains. Longest chain 21 peptides. Score 0.507 Taking the results from Round 5 Chains 20, Residues 109, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4026 restraints for refining 1793 atoms. 3565 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2479 (Rfree = 0.000) for 1793 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 7: After refmac, R = 0.2334 (Rfree = 0.000) for 1789 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 8: After refmac, R = 0.2267 (Rfree = 0.000) for 1784 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.2259 (Rfree = 0.000) for 1779 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2154 (Rfree = 0.000) for 1776 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 1829 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 1857 seeds are put forward Round 1: 108 peptides, 21 chains. Longest chain 10 peptides. Score 0.326 Round 2: 114 peptides, 19 chains. Longest chain 14 peptides. Score 0.413 Round 3: 111 peptides, 14 chains. Longest chain 18 peptides. Score 0.517 Round 4: 107 peptides, 17 chains. Longest chain 13 peptides. Score 0.423 Round 5: 107 peptides, 16 chains. Longest chain 18 peptides. Score 0.448 Taking the results from Round 3 Chains 14, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4232 restraints for refining 1794 atoms. 3858 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2340 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 12: After refmac, R = 0.2311 (Rfree = 0.000) for 1790 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. Cycle 13: After refmac, R = 0.2637 (Rfree = 0.000) for 1791 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2130 (Rfree = 0.000) for 1782 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2104 (Rfree = 0.000) for 1780 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 1843 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1861 seeds are put forward Round 1: 108 peptides, 20 chains. Longest chain 13 peptides. Score 0.352 Round 2: 122 peptides, 17 chains. Longest chain 15 peptides. Score 0.504 Round 3: 117 peptides, 20 chains. Longest chain 15 peptides. Score 0.405 Round 4: 119 peptides, 18 chains. Longest chain 17 peptides. Score 0.465 Round 5: 121 peptides, 17 chains. Longest chain 17 peptides. Score 0.499 Taking the results from Round 2 Chains 17, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4149 restraints for refining 1794 atoms. 3746 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2541 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 17: After refmac, R = 0.2177 (Rfree = 0.000) for 1793 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.2164 (Rfree = 0.000) for 1789 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2198 (Rfree = 0.000) for 1786 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2096 (Rfree = 0.000) for 1782 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1842 seeds are put forward NCS extension: 0 residues added, 1842 seeds are put forward Round 1: 105 peptides, 20 chains. Longest chain 11 peptides. Score 0.334 Round 2: 104 peptides, 14 chains. Longest chain 14 peptides. Score 0.481 Round 3: 102 peptides, 15 chains. Longest chain 14 peptides. Score 0.445 Round 4: 112 peptides, 15 chains. Longest chain 14 peptides. Score 0.499 Round 5: 115 peptides, 15 chains. Longest chain 16 peptides. Score 0.515 Taking the results from Round 5 Chains 15, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4209 restraints for refining 1793 atoms. 3824 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2334 (Rfree = 0.000) for 1793 atoms. Found 9 (9 requested) and removed 28 (4 requested) atoms. Cycle 22: After refmac, R = 0.3094 (Rfree = 0.000) for 1764 atoms. Found 9 (9 requested) and removed 56 (4 requested) atoms. Cycle 23: After refmac, R = 0.2463 (Rfree = 0.000) for 1713 atoms. Found 9 (9 requested) and removed 27 (4 requested) atoms. Cycle 24: After refmac, R = 0.2107 (Rfree = 0.000) for 1693 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2176 (Rfree = 0.000) for 1692 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 1760 seeds are put forward NCS extension: 0 residues added, 1760 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.299 Round 2: 113 peptides, 17 chains. Longest chain 12 peptides. Score 0.457 Round 3: 117 peptides, 18 chains. Longest chain 15 peptides. Score 0.454 Round 4: 118 peptides, 17 chains. Longest chain 11 peptides. Score 0.483 Round 5: 122 peptides, 17 chains. Longest chain 19 peptides. Score 0.504 Taking the results from Round 5 Chains 17, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4132 restraints for refining 1794 atoms. 3729 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2508 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2478 (Rfree = 0.000) for 1792 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.2516 (Rfree = 0.000) for 1789 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2834 (Rfree = 0.000) for 1788 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2721 (Rfree = 0.000) for 1785 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1842 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 1866 seeds are put forward Round 1: 101 peptides, 19 chains. Longest chain 12 peptides. Score 0.336 Round 2: 110 peptides, 18 chains. Longest chain 10 peptides. Score 0.415 Round 3: 112 peptides, 18 chains. Longest chain 12 peptides. Score 0.427 Round 4: 113 peptides, 17 chains. Longest chain 14 peptides. Score 0.457 Round 5: 113 peptides, 18 chains. Longest chain 12 peptides. Score 0.432 Taking the results from Round 4 Chains 17, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4203 restraints for refining 1794 atoms. 3836 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2466 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2211 (Rfree = 0.000) for 1791 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2146 (Rfree = 0.000) for 1787 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2790 (Rfree = 0.000) for 1779 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2023 (Rfree = 0.000) for 1778 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1839 seeds are put forward Round 1: 99 peptides, 23 chains. Longest chain 6 peptides. Score 0.215 Round 2: 99 peptides, 17 chains. Longest chain 11 peptides. Score 0.376 Round 3: 103 peptides, 17 chains. Longest chain 11 peptides. Score 0.400 Round 4: 97 peptides, 16 chains. Longest chain 12 peptides. Score 0.390 Round 5: 97 peptides, 17 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 3 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4303 restraints for refining 1794 atoms. 3976 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2403 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 37: After refmac, R = 0.2097 (Rfree = 0.000) for 1788 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.1989 (Rfree = 0.000) for 1784 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2008 (Rfree = 0.000) for 1778 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.1885 (Rfree = 0.000) for 1774 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 1820 seeds are put forward NCS extension: 0 residues added, 1820 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 11 peptides. Score 0.281 Round 2: 92 peptides, 16 chains. Longest chain 12 peptides. Score 0.360 Round 3: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.377 Round 4: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.389 Round 5: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 4 Chains 14, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4298 restraints for refining 1794 atoms. 4016 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2249 (Rfree = 0.000) for 1794 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 42: After refmac, R = 0.1992 (Rfree = 0.000) for 1794 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2001 (Rfree = 0.000) for 1790 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.1994 (Rfree = 0.000) for 1786 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1960 (Rfree = 0.000) for 1781 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 1846 seeds are put forward NCS extension: 0 residues added, 1846 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 9 peptides. Score 0.276 Round 2: 90 peptides, 17 chains. Longest chain 9 peptides. Score 0.320 Round 3: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.311 Round 4: 90 peptides, 15 chains. Longest chain 12 peptides. Score 0.375 Round 5: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.337 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 75, 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. 2794 reflections ( 99.61 % complete ) and 4334 restraints for refining 1794 atoms. 4049 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2442 (Rfree = 0.000) for 1794 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2175 (Rfree = 0.000) for 1784 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2044 (Rfree = 0.000) for 1779 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2062 (Rfree = 0.000) for 1775 atoms. TimeTaking 24.67