Starting phenix.real_space_refine on Tue Jul 7 03:52:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c96_16503/07_2026/8c96_16503.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c96_16503/07_2026/8c96_16503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c96_16503/07_2026/8c96_16503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c96_16503/07_2026/8c96_16503.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c96_16503/07_2026/8c96_16503.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c96_16503/07_2026/8c96_16503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c96_16503/07_2026/8c96_16503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c96_16503/07_2026/8c96_16503.map" } resolution = 4.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1475 5.49 5 S 35 5.16 5 C 21970 2.51 5 N 8289 2.21 5 O 12445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44214 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 31713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1475, 31713 Classifications: {'RNA': 1475} Modifications used: {'rna2p_pur': 143, 'rna2p_pyr': 75, 'rna3p_pur': 728, 'rna3p_pyr': 529} Link IDs: {'rna2p': 218, 'rna3p': 1256} Chain breaks: 7 Chain: "D" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1306 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Chain: "E" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1438 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 778 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 789 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 312 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "Z" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Time building chain proxies: 8.67, per 1000 atoms: 0.20 Number of scatterers: 44214 At special positions: 0 Unit cell: (148.75, 183.75, 206.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 1475 15.00 O 12445 8.00 N 8289 7.00 C 21970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 864.4 milliseconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2948 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 22 sheets defined 33.5% alpha, 16.9% beta 484 base pairs and 703 stacking pairs defined. Time for finding SS restraints: 6.62 Creating SS restraints... Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.512A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.719A pdb=" N ALA D 102 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.561A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.510A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 162 Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 199 Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 3.902A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.574A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 4.128A pdb=" N MET K 113 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.797A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 33 removed outlier: 4.130A pdb=" N GLY L 31 " --> pdb=" O GLY L 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG L 33 " --> pdb=" O THR L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 33' Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 128 through 138 removed outlier: 3.539A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 37 through 55 removed outlier: 3.845A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.813A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.122A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.754A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 removed outlier: 4.252A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 22 removed outlier: 3.886A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.001A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 62 removed outlier: 3.923A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 8 Processing helix chain 'Y' and resid 9 through 30 removed outlier: 4.482A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 4.136A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 20 removed outlier: 4.183A pdb=" N ALA 0 20 " --> pdb=" O SER 0 17 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 17 through 20' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 3.946A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'D' and resid 108 through 111 removed outlier: 6.733A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.306A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 35 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 32 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 96 " --> pdb=" O ASN D 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 116 through 119 removed outlier: 3.985A pdb=" N MET D 165 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE D 118 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY D 163 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 120 removed outlier: 3.517A pdb=" N ILE E 119 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET E 188 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU E 147 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 170 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.590A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 73 through 74 Processing sheet with id=AA8, first strand: chain 'K' and resid 7 through 10 removed outlier: 7.099A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE K 41 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU K 58 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.584A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG K 78 " --> pdb=" O GLU P 70 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 122 through 123 removed outlier: 5.554A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'N' and resid 33 through 36 removed outlier: 4.588A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.591A pdb=" N VAL R 4 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 20 through 22 removed outlier: 3.752A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA R 61 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE R 101 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 72 through 77 Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 10 removed outlier: 3.723A pdb=" N ILE S 103 " --> pdb=" O HIS S 7 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AB8, first strand: chain 'U' and resid 63 through 65 removed outlier: 6.551A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.992A pdb=" N VAL U 41 " --> pdb=" O LYS U 60 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 82 through 86 Processing sheet with id=AC2, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AC3, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AC4, first strand: chain 'Z' and resid 35 through 37 removed outlier: 3.848A pdb=" N VAL Z 35 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE Z 4 " --> pdb=" O ARG Z 37 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1236 hydrogen bonds 2006 hydrogen bond angles 0 basepair planarities 484 basepair parallelities 703 stacking parallelities Total time for adding SS restraints: 23.10 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7165 1.33 - 1.45: 20009 1.45 - 1.57: 17983 1.57 - 1.69: 2943 1.69 - 1.81: 67 Bond restraints: 48167 Sorted by residual: bond pdb=" C1' U A 827 " pdb=" N1 U A 827 " ideal model delta sigma weight residual 1.480 1.574 -0.094 1.50e-02 4.44e+03 3.90e+01 bond pdb=" N MET R 1 " pdb=" CA MET R 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N MET Y 1 " pdb=" CA MET Y 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N ALA U 1 " pdb=" CA ALA U 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N ALA Q 1 " pdb=" CA ALA Q 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 48162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 71332 1.16 - 2.31: 870 2.31 - 3.47: 113 3.47 - 4.62: 31 4.62 - 5.78: 4 Bond angle restraints: 72350 Sorted by residual: angle pdb=" C3' G A 271 " pdb=" O3' G A 271 " pdb=" P A A 272 " ideal model delta sigma weight residual 120.20 123.80 -3.60 1.50e+00 4.44e-01 5.75e+00 angle pdb=" C4' G A 271 " pdb=" C3' G A 271 " pdb=" O3' G A 271 " ideal model delta sigma weight residual 109.40 112.92 -3.52 1.50e+00 4.44e-01 5.52e+00 angle pdb=" C HIS N 31 " pdb=" N GLU N 32 " pdb=" CA GLU N 32 " ideal model delta sigma weight residual 121.54 125.82 -4.28 1.91e+00 2.74e-01 5.01e+00 angle pdb=" C2' A A1287 " pdb=" C1' A A1287 " pdb=" N9 A A1287 " ideal model delta sigma weight residual 112.00 115.09 -3.09 1.50e+00 4.44e-01 4.23e+00 angle pdb=" N LYS D 62 " pdb=" CA LYS D 62 " pdb=" C LYS D 62 " ideal model delta sigma weight residual 109.81 114.30 -4.49 2.21e+00 2.05e-01 4.13e+00 ... (remaining 72345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 24711 34.99 - 69.98: 716 69.98 - 104.96: 65 104.96 - 139.95: 15 139.95 - 174.94: 4 Dihedral angle restraints: 25511 sinusoidal: 20950 harmonic: 4561 Sorted by residual: dihedral pdb=" O4' U A 828 " pdb=" C1' U A 828 " pdb=" N1 U A 828 " pdb=" C2 U A 828 " ideal model delta sinusoidal sigma weight residual -128.00 45.69 -173.69 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 -12.02 -115.98 1 1.70e+01 3.46e-03 4.78e+01 dihedral pdb=" C4' U A 828 " pdb=" C3' U A 828 " pdb=" O3' U A 828 " pdb=" P A A 829 " ideal model delta sinusoidal sigma weight residual -110.00 64.94 -174.94 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 25508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 7389 0.031 - 0.062: 1624 0.062 - 0.093: 149 0.093 - 0.124: 144 0.124 - 0.154: 12 Chirality restraints: 9318 Sorted by residual: chirality pdb=" C1' U A 827 " pdb=" O4' U A 827 " pdb=" C2' U A 827 " pdb=" N1 U A 827 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ILE N 33 " pdb=" N ILE N 33 " pdb=" C ILE N 33 " pdb=" CB ILE N 33 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE R 74 " pdb=" N ILE R 74 " pdb=" C ILE R 74 " pdb=" CB ILE R 74 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 9315 not shown) Planarity restraints: 3647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.010 2.00e-02 2.50e+03 1.32e-02 5.22e+00 pdb=" N9 G A 259 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 259 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G A 259 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.035 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.026 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 259 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 175 " 0.012 2.00e-02 2.50e+03 1.19e-02 4.28e+00 pdb=" N9 G A 175 " -0.014 2.00e-02 2.50e+03 pdb=" C8 G A 175 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 175 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 175 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 175 " 0.030 2.00e-02 2.50e+03 pdb=" O6 G A 175 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G A 175 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A 175 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G A 175 " -0.008 2.00e-02 2.50e+03 pdb=" N3 G A 175 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 175 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 269 " 0.006 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 C A 269 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C A 269 " 0.028 2.00e-02 2.50e+03 pdb=" O2 C A 269 " -0.018 2.00e-02 2.50e+03 pdb=" N3 C A 269 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A 269 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C A 269 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C A 269 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C A 269 " -0.007 2.00e-02 2.50e+03 ... (remaining 3644 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 392 2.52 - 3.12: 32713 3.12 - 3.71: 84293 3.71 - 4.31: 115317 4.31 - 4.90: 159244 Nonbonded interactions: 391959 Sorted by model distance: nonbonded pdb=" O2' A A1009 " pdb=" O4' A A1010 " model vdw 1.928 3.040 nonbonded pdb=" O2' A A2632 " pdb=" O2' G A2811 " model vdw 1.941 3.040 nonbonded pdb=" O2' G A 214 " pdb=" O4' G A 215 " model vdw 1.949 3.040 nonbonded pdb=" OP2 G A 117 " pdb=" O2' A A 119 " model vdw 1.957 3.040 nonbonded pdb=" O2' G A 261 " pdb=" O2' C A 610 " model vdw 1.972 3.040 ... (remaining 391954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 55.510 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.094 48167 Z= 0.080 Angle : 0.364 5.780 72350 Z= 0.188 Chirality : 0.026 0.154 9318 Planarity : 0.002 0.029 3647 Dihedral : 13.382 174.940 22563 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1569 helix: 2.09 (0.25), residues: 474 sheet: 0.52 (0.33), residues: 241 loop : -0.66 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 0 12 TYR 0.008 0.001 TYR N 112 PHE 0.006 0.001 PHE Z 52 TRP 0.004 0.001 TRP R 92 HIS 0.002 0.000 HIS S 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00147 / 0.08 (48167) covalent geometry : angle 0.36405 / 0.19 (72350) hydrogen bonds : bond 0.09920 / 5.84 ( 1693) hydrogen bonds : angle 4.12062 / 2.34 ( 3296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.6948 (ppp) cc_final: 0.6433 (tmm) REVERT: D 18 ASP cc_start: 0.8531 (m-30) cc_final: 0.8215 (t0) REVERT: E 41 GLN cc_start: 0.8815 (tp40) cc_final: 0.8479 (tm-30) REVERT: E 115 GLN cc_start: 0.9040 (tp40) cc_final: 0.8691 (tm-30) REVERT: J 53 TYR cc_start: 0.8045 (m-10) cc_final: 0.7412 (m-80) REVERT: J 92 MET cc_start: 0.9379 (ttm) cc_final: 0.9092 (tpt) REVERT: J 105 VAL cc_start: 0.9319 (t) cc_final: 0.9010 (p) REVERT: K 58 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6037 (pt) REVERT: K 79 PHE cc_start: 0.9327 (m-80) cc_final: 0.8653 (m-80) REVERT: K 87 LEU cc_start: 0.7049 (mt) cc_final: 0.6364 (mp) REVERT: N 13 ASN cc_start: 0.9175 (m-40) cc_final: 0.8861 (m-40) REVERT: N 107 ASN cc_start: 0.8989 (t0) cc_final: 0.8738 (t0) REVERT: P 2 ASN cc_start: 0.9229 (m-40) cc_final: 0.9025 (m-40) REVERT: P 73 PHE cc_start: 0.7594 (m-80) cc_final: 0.7124 (m-80) REVERT: Q 36 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8419 (tm-30) REVERT: Q 48 ASP cc_start: 0.7633 (t0) cc_final: 0.6993 (t0) REVERT: R 86 GLN cc_start: 0.7765 (pp30) cc_final: 0.7457 (pp30) REVERT: R 87 GLN cc_start: 0.7827 (pp30) cc_final: 0.7146 (pp30) REVERT: S 49 LYS cc_start: 0.9570 (tptt) cc_final: 0.8957 (tptt) REVERT: S 68 ASP cc_start: 0.8130 (p0) cc_final: 0.7548 (p0) REVERT: S 74 ILE cc_start: 0.9276 (tt) cc_final: 0.8851 (pt) REVERT: S 99 ARG cc_start: 0.7696 (mpt180) cc_final: 0.6970 (mpt180) REVERT: Y 1 MET cc_start: 0.7729 (ppp) cc_final: 0.7028 (ppp) REVERT: Y 7 ARG cc_start: 0.8404 (ptt180) cc_final: 0.7890 (ptt180) REVERT: Y 29 ARG cc_start: 0.8063 (ptt-90) cc_final: 0.7586 (ptt-90) REVERT: Y 30 MET cc_start: 0.8790 (mmp) cc_final: 0.8427 (mmm) REVERT: 0 14 MET cc_start: 0.9038 (mpp) cc_final: 0.8833 (mpp) REVERT: Z 20 LYS cc_start: 0.9309 (tptm) cc_final: 0.8834 (tptp) REVERT: Z 24 LEU cc_start: 0.9538 (pp) cc_final: 0.9193 (pp) REVERT: Z 43 ILE cc_start: 0.8565 (mm) cc_final: 0.8129 (mm) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.2901 time to fit residues: 145.3624 Evaluate side-chains 192 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 8.9990 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS D 94 GLN E 9 GLN J 47 HIS J 132 HIS P 65 ASN P 76 HIS ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.052349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.039206 restraints weight = 490016.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040350 restraints weight = 226025.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.040995 restraints weight = 146556.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.041365 restraints weight = 115956.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.041517 restraints weight = 101891.245| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 48167 Z= 0.145 Angle : 0.524 9.921 72350 Z= 0.263 Chirality : 0.029 0.195 9318 Planarity : 0.004 0.070 3647 Dihedral : 14.074 175.855 19449 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1569 helix: 1.21 (0.24), residues: 482 sheet: 0.24 (0.32), residues: 257 loop : -0.90 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 59 TYR 0.011 0.002 TYR N 112 PHE 0.023 0.001 PHE N 21 TRP 0.019 0.003 TRP E 78 HIS 0.004 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (48167) covalent geometry : angle 0.52402 / 0.26 (72350) hydrogen bonds : bond 0.06748 / 3.95 ( 1693) hydrogen bonds : angle 3.58375 / 2.15 ( 3296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 PHE cc_start: 0.7877 (m-80) cc_final: 0.7673 (m-80) REVERT: E 41 GLN cc_start: 0.8930 (tp40) cc_final: 0.8447 (tp40) REVERT: E 115 GLN cc_start: 0.9192 (tp40) cc_final: 0.8868 (tp40) REVERT: J 53 TYR cc_start: 0.8390 (m-10) cc_final: 0.7992 (m-80) REVERT: J 67 ASN cc_start: 0.7414 (t0) cc_final: 0.6891 (t0) REVERT: K 3 GLN cc_start: 0.5963 (pm20) cc_final: 0.5453 (pm20) REVERT: K 7 MET cc_start: 0.7518 (tpt) cc_final: 0.7197 (tmm) REVERT: K 58 LEU cc_start: 0.6814 (tp) cc_final: 0.6400 (tp) REVERT: K 79 PHE cc_start: 0.9272 (m-80) cc_final: 0.8727 (m-80) REVERT: N 13 ASN cc_start: 0.9004 (m-40) cc_final: 0.8667 (m-40) REVERT: N 20 MET cc_start: 0.8963 (ttm) cc_final: 0.8382 (tmm) REVERT: N 21 PHE cc_start: 0.8876 (m-80) cc_final: 0.8646 (m-80) REVERT: N 43 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8886 (mm-30) REVERT: P 37 LYS cc_start: 0.6547 (tppt) cc_final: 0.6308 (tppt) REVERT: P 73 PHE cc_start: 0.7819 (m-80) cc_final: 0.7321 (m-80) REVERT: Q 36 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8501 (tm-30) REVERT: Q 48 ASP cc_start: 0.8007 (t0) cc_final: 0.7291 (t0) REVERT: R 27 ILE cc_start: 0.8308 (mm) cc_final: 0.7872 (mm) REVERT: R 31 GLU cc_start: 0.9366 (tm-30) cc_final: 0.8894 (tm-30) REVERT: R 85 LYS cc_start: 0.9328 (tttp) cc_final: 0.9110 (tttp) REVERT: R 86 GLN cc_start: 0.7711 (pp30) cc_final: 0.7461 (pp30) REVERT: R 87 GLN cc_start: 0.8287 (pp30) cc_final: 0.7480 (pp30) REVERT: S 49 LYS cc_start: 0.9548 (tptt) cc_final: 0.8897 (tptt) REVERT: S 68 ASP cc_start: 0.7990 (p0) cc_final: 0.7615 (p0) REVERT: S 74 ILE cc_start: 0.9127 (tt) cc_final: 0.8714 (pt) REVERT: S 99 ARG cc_start: 0.8254 (mpt180) cc_final: 0.7972 (mpt180) REVERT: S 103 ILE cc_start: 0.9557 (pt) cc_final: 0.9218 (mp) REVERT: Y 1 MET cc_start: 0.8032 (ppp) cc_final: 0.7230 (ppp) REVERT: Y 29 ARG cc_start: 0.8256 (ptt-90) cc_final: 0.7662 (ptt-90) REVERT: Z 20 LYS cc_start: 0.9335 (tptm) cc_final: 0.8897 (tptt) REVERT: Z 53 MET cc_start: 0.7870 (mmt) cc_final: 0.7601 (mmt) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2722 time to fit residues: 118.0348 Evaluate side-chains 184 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 44 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 204 optimal weight: 50.0000 chunk 256 optimal weight: 0.1980 chunk 131 optimal weight: 30.0000 chunk 106 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 238 optimal weight: 30.0000 overall best weight: 6.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 164 GLN J 135 GLN N 107 ASN P 65 ASN ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 82 HIS U 68 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.047371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.034451 restraints weight = 485976.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.035471 restraints weight = 223365.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.036073 restraints weight = 144228.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.036404 restraints weight = 113782.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036542 restraints weight = 100407.748| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 48167 Z= 0.232 Angle : 0.622 10.497 72350 Z= 0.314 Chirality : 0.033 0.243 9318 Planarity : 0.005 0.073 3647 Dihedral : 15.022 176.333 19449 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1569 helix: 0.69 (0.23), residues: 494 sheet: -0.67 (0.30), residues: 256 loop : -1.16 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 21 TYR 0.014 0.002 TYR S 38 PHE 0.023 0.002 PHE N 21 TRP 0.020 0.004 TRP P 30 HIS 0.009 0.002 HIS N 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.23 (48167) covalent geometry : angle 0.62161 / 0.31 (72350) hydrogen bonds : bond 0.09069 / 5.33 ( 1693) hydrogen bonds : angle 3.88354 / 2.24 ( 3296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 231 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8259 (pmm) cc_final: 0.8034 (pmm) REVERT: E 188 MET cc_start: 0.9036 (ptm) cc_final: 0.8692 (ptm) REVERT: J 53 TYR cc_start: 0.8968 (m-80) cc_final: 0.8211 (m-80) REVERT: J 67 ASN cc_start: 0.8106 (t0) cc_final: 0.7575 (t0) REVERT: J 92 MET cc_start: 0.9594 (ttm) cc_final: 0.9185 (tpp) REVERT: K 1 MET cc_start: 0.6220 (tmm) cc_final: 0.5939 (tpp) REVERT: K 7 MET cc_start: 0.7905 (tpt) cc_final: 0.7636 (tmm) REVERT: K 58 LEU cc_start: 0.6961 (tp) cc_final: 0.6531 (tp) REVERT: K 65 THR cc_start: 0.9058 (p) cc_final: 0.8858 (p) REVERT: K 79 PHE cc_start: 0.9234 (m-80) cc_final: 0.8679 (m-10) REVERT: N 13 ASN cc_start: 0.9072 (m-40) cc_final: 0.8835 (m-40) REVERT: N 20 MET cc_start: 0.9057 (ttm) cc_final: 0.8512 (tmm) REVERT: N 21 PHE cc_start: 0.9155 (m-80) cc_final: 0.8744 (m-80) REVERT: P 58 PHE cc_start: 0.9020 (p90) cc_final: 0.8796 (p90) REVERT: R 70 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7628 (tm-30) REVERT: R 85 LYS cc_start: 0.9374 (tttp) cc_final: 0.9096 (tttp) REVERT: S 49 LYS cc_start: 0.9549 (tptt) cc_final: 0.8893 (tptt) REVERT: S 68 ASP cc_start: 0.8030 (p0) cc_final: 0.7579 (p0) REVERT: S 74 ILE cc_start: 0.9250 (tt) cc_final: 0.8858 (pt) REVERT: S 103 ILE cc_start: 0.9623 (pt) cc_final: 0.9329 (mp) REVERT: Y 1 MET cc_start: 0.8276 (ppp) cc_final: 0.7487 (ppp) REVERT: Y 18 LEU cc_start: 0.8772 (pp) cc_final: 0.8531 (tp) REVERT: Y 29 ARG cc_start: 0.7985 (ptt-90) cc_final: 0.7438 (ptt-90) REVERT: Y 30 MET cc_start: 0.8887 (mmp) cc_final: 0.8626 (mmp) REVERT: 0 6 LYS cc_start: 0.9027 (tttt) cc_final: 0.8187 (tmtt) REVERT: 2 14 ARG cc_start: 0.8383 (mmt-90) cc_final: 0.7231 (mmp80) REVERT: Z 20 LYS cc_start: 0.9369 (tptm) cc_final: 0.8949 (tptp) REVERT: Z 24 LEU cc_start: 0.9618 (pp) cc_final: 0.9417 (pp) outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.2658 time to fit residues: 103.1996 Evaluate side-chains 169 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 140 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 40 optimal weight: 40.0000 chunk 293 optimal weight: 8.9990 chunk 200 optimal weight: 40.0000 chunk 281 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN K 3 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN R 11 GLN R 18 GLN R 66 HIS ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.045755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.033037 restraints weight = 487928.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.034018 restraints weight = 222176.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.034588 restraints weight = 143412.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.034879 restraints weight = 113409.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.035066 restraints weight = 101044.289| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 48167 Z= 0.237 Angle : 0.628 8.755 72350 Z= 0.320 Chirality : 0.034 0.204 9318 Planarity : 0.005 0.060 3647 Dihedral : 15.703 179.898 19449 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.15 % Allowed : 5.12 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.20), residues: 1569 helix: 0.62 (0.23), residues: 482 sheet: -0.77 (0.28), residues: 292 loop : -1.32 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 44 TYR 0.020 0.002 TYR K 32 PHE 0.021 0.002 PHE N 21 TRP 0.018 0.003 TRP R 92 HIS 0.011 0.002 HIS J 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.24 (48167) covalent geometry : angle 0.62791 / 0.32 (72350) hydrogen bonds : bond 0.08856 / 5.16 ( 1693) hydrogen bonds : angle 3.87705 / 2.22 ( 3296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.8082 (ppp) cc_final: 0.7858 (ppp) REVERT: D 45 TYR cc_start: 0.8146 (p90) cc_final: 0.7929 (p90) REVERT: D 118 PHE cc_start: 0.6802 (t80) cc_final: 0.6485 (t80) REVERT: E 1 MET cc_start: 0.8066 (pmm) cc_final: 0.7758 (pmm) REVERT: E 9 GLN cc_start: 0.8883 (mp10) cc_final: 0.8681 (mp10) REVERT: J 53 TYR cc_start: 0.9109 (m-80) cc_final: 0.8136 (m-80) REVERT: J 67 ASN cc_start: 0.8638 (t0) cc_final: 0.8117 (t0) REVERT: J 92 MET cc_start: 0.9582 (ttm) cc_final: 0.9154 (tpp) REVERT: J 93 ILE cc_start: 0.9291 (pt) cc_final: 0.9078 (pt) REVERT: J 108 MET cc_start: 0.8341 (tpt) cc_final: 0.8007 (mmm) REVERT: K 1 MET cc_start: 0.6681 (tmm) cc_final: 0.6466 (tmm) REVERT: K 7 MET cc_start: 0.7955 (tpt) cc_final: 0.7668 (tmm) REVERT: K 58 LEU cc_start: 0.6990 (tp) cc_final: 0.6665 (tp) REVERT: K 79 PHE cc_start: 0.9222 (m-80) cc_final: 0.8554 (m-80) REVERT: N 10 LEU cc_start: 0.9136 (mp) cc_final: 0.8885 (mp) REVERT: N 20 MET cc_start: 0.9111 (ttm) cc_final: 0.8546 (tmm) REVERT: N 102 PHE cc_start: 0.8813 (m-10) cc_final: 0.8545 (m-10) REVERT: P 12 MET cc_start: 0.9072 (mmp) cc_final: 0.7530 (mmp) REVERT: P 58 PHE cc_start: 0.8884 (p90) cc_final: 0.8527 (p90) REVERT: Q 36 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8711 (tm-30) REVERT: Q 48 ASP cc_start: 0.8468 (t0) cc_final: 0.7962 (t0) REVERT: R 70 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7766 (tm-30) REVERT: S 38 TYR cc_start: 0.8782 (m-10) cc_final: 0.8339 (m-10) REVERT: S 49 LYS cc_start: 0.9528 (tptt) cc_final: 0.8763 (tptt) REVERT: S 68 ASP cc_start: 0.8056 (p0) cc_final: 0.7681 (p0) REVERT: S 78 GLU cc_start: 0.8327 (mp0) cc_final: 0.8045 (mp0) REVERT: S 99 ARG cc_start: 0.8662 (mpt180) cc_final: 0.8057 (mpt180) REVERT: S 103 ILE cc_start: 0.9617 (pt) cc_final: 0.9371 (mp) REVERT: Y 1 MET cc_start: 0.8328 (ppp) cc_final: 0.7713 (ppp) REVERT: Y 7 ARG cc_start: 0.8628 (ptt180) cc_final: 0.8082 (ptt180) REVERT: Y 13 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8172 (mp0) REVERT: Y 30 MET cc_start: 0.9016 (mmp) cc_final: 0.8557 (mmp) REVERT: 0 6 LYS cc_start: 0.9097 (tttt) cc_final: 0.8235 (tmtt) REVERT: 0 11 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9113 (mmmm) REVERT: 2 14 ARG cc_start: 0.8432 (mmt-90) cc_final: 0.8078 (mmm160) REVERT: Z 20 LYS cc_start: 0.9416 (tptm) cc_final: 0.8876 (tptp) REVERT: Z 51 SER cc_start: 0.9209 (p) cc_final: 0.8820 (m) outliers start: 2 outliers final: 1 residues processed: 229 average time/residue: 0.2645 time to fit residues: 101.3877 Evaluate side-chains 173 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 147 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 277 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 overall best weight: 6.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 89 ASN N 107 ASN P 65 ASN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.044713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032157 restraints weight = 498807.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.033104 restraints weight = 225109.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.033655 restraints weight = 145667.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.033966 restraints weight = 115616.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034097 restraints weight = 102574.685| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 48167 Z= 0.244 Angle : 0.642 9.092 72350 Z= 0.323 Chirality : 0.035 0.246 9318 Planarity : 0.005 0.090 3647 Dihedral : 15.947 178.767 19449 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.20), residues: 1569 helix: 0.54 (0.23), residues: 474 sheet: -1.05 (0.28), residues: 277 loop : -1.33 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG Z 44 TYR 0.013 0.002 TYR N 112 PHE 0.020 0.002 PHE Q 56 TRP 0.020 0.002 TRP P 30 HIS 0.005 0.001 HIS N 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.24 (48167) covalent geometry : angle 0.64153 / 0.32 (72350) hydrogen bonds : bond 0.09413 / 5.48 ( 1693) hydrogen bonds : angle 3.93734 / 2.27 ( 3296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 53 TYR cc_start: 0.9037 (m-80) cc_final: 0.8345 (m-80) REVERT: J 67 ASN cc_start: 0.8641 (t0) cc_final: 0.8134 (t0) REVERT: J 92 MET cc_start: 0.9627 (ttm) cc_final: 0.9206 (tpt) REVERT: J 93 ILE cc_start: 0.9262 (pt) cc_final: 0.9050 (pt) REVERT: J 108 MET cc_start: 0.8284 (tpt) cc_final: 0.7962 (mmm) REVERT: K 1 MET cc_start: 0.6084 (tmm) cc_final: 0.3951 (pmm) REVERT: K 7 MET cc_start: 0.8229 (tpt) cc_final: 0.7847 (tmm) REVERT: K 65 THR cc_start: 0.9002 (p) cc_final: 0.8759 (p) REVERT: K 79 PHE cc_start: 0.9168 (m-80) cc_final: 0.8778 (m-10) REVERT: N 10 LEU cc_start: 0.9098 (mp) cc_final: 0.8890 (mp) REVERT: N 13 ASN cc_start: 0.8873 (t0) cc_final: 0.8536 (t0) REVERT: N 20 MET cc_start: 0.9124 (ttm) cc_final: 0.8590 (tmm) REVERT: N 21 PHE cc_start: 0.9026 (m-10) cc_final: 0.8723 (m-80) REVERT: P 3 ILE cc_start: 0.8863 (pt) cc_final: 0.8648 (pt) REVERT: P 6 GLN cc_start: 0.9195 (pt0) cc_final: 0.8984 (pt0) REVERT: P 12 MET cc_start: 0.9192 (mmp) cc_final: 0.7278 (mmp) REVERT: P 58 PHE cc_start: 0.8912 (p90) cc_final: 0.8534 (p90) REVERT: R 70 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7778 (tm-30) REVERT: R 71 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8786 (tptm) REVERT: S 38 TYR cc_start: 0.8705 (m-10) cc_final: 0.8199 (m-10) REVERT: S 49 LYS cc_start: 0.9532 (tptt) cc_final: 0.9162 (tptm) REVERT: S 68 ASP cc_start: 0.8016 (p0) cc_final: 0.7570 (p0) REVERT: S 99 ARG cc_start: 0.8564 (mpp-170) cc_final: 0.8013 (mpt180) REVERT: S 103 ILE cc_start: 0.9644 (pt) cc_final: 0.9408 (mp) REVERT: U 9 GLU cc_start: 0.8006 (tt0) cc_final: 0.7761 (tt0) REVERT: Y 13 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8362 (mp0) REVERT: Y 30 MET cc_start: 0.9033 (mmp) cc_final: 0.8674 (mmp) REVERT: 0 6 LYS cc_start: 0.9079 (tttt) cc_final: 0.8216 (tmtt) REVERT: 0 11 LYS cc_start: 0.9510 (mmmm) cc_final: 0.9163 (mmmm) REVERT: 0 14 MET cc_start: 0.9201 (mpp) cc_final: 0.8934 (mpp) REVERT: 2 14 ARG cc_start: 0.8864 (mmt-90) cc_final: 0.8232 (mmp80) REVERT: Z 20 LYS cc_start: 0.9408 (tptm) cc_final: 0.8984 (tptt) outliers start: 1 outliers final: 1 residues processed: 212 average time/residue: 0.2637 time to fit residues: 93.3707 Evaluate side-chains 163 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 156 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 226 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 285 optimal weight: 2.9990 chunk 75 optimal weight: 40.0000 chunk 255 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN J 128 ASN J 136 GLN N 31 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN U 52 ASN ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.042451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.029967 restraints weight = 516850.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.030864 restraints weight = 233693.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.031396 restraints weight = 152049.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.031685 restraints weight = 120754.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.031803 restraints weight = 107122.878| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 48167 Z= 0.370 Angle : 0.832 12.335 72350 Z= 0.417 Chirality : 0.044 0.261 9318 Planarity : 0.006 0.061 3647 Dihedral : 17.205 178.970 19449 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 36.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1569 helix: -0.19 (0.22), residues: 471 sheet: -1.50 (0.28), residues: 265 loop : -1.64 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 49 TYR 0.015 0.002 TYR R 2 PHE 0.023 0.003 PHE R 77 TRP 0.044 0.004 TRP P 30 HIS 0.011 0.002 HIS U 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.37 (48167) covalent geometry : angle 0.83203 / 0.42 (72350) hydrogen bonds : bond 0.13260 / 7.74 ( 1693) hydrogen bonds : angle 4.44059 / 2.52 ( 3296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.8205 (ppp) cc_final: 0.7950 (ppp) REVERT: E 9 GLN cc_start: 0.8979 (mp10) cc_final: 0.8731 (mp10) REVERT: E 188 MET cc_start: 0.8794 (ptm) cc_final: 0.8374 (ptm) REVERT: J 53 TYR cc_start: 0.9043 (m-80) cc_final: 0.8182 (m-80) REVERT: J 67 ASN cc_start: 0.8756 (t0) cc_final: 0.8375 (t0) REVERT: J 92 MET cc_start: 0.9610 (ttm) cc_final: 0.9114 (tpt) REVERT: J 108 MET cc_start: 0.8183 (tpt) cc_final: 0.7876 (mmm) REVERT: K 65 THR cc_start: 0.9069 (p) cc_final: 0.8850 (p) REVERT: K 79 PHE cc_start: 0.9300 (m-80) cc_final: 0.8785 (m-10) REVERT: L 81 ASP cc_start: 0.8106 (t70) cc_final: 0.6859 (m-30) REVERT: N 10 LEU cc_start: 0.9199 (mp) cc_final: 0.8939 (mp) REVERT: N 13 ASN cc_start: 0.8871 (t0) cc_final: 0.8557 (t0) REVERT: N 20 MET cc_start: 0.9160 (ttm) cc_final: 0.8690 (tmm) REVERT: N 21 PHE cc_start: 0.9169 (m-10) cc_final: 0.8678 (m-80) REVERT: N 110 MET cc_start: 0.8591 (mpp) cc_final: 0.8336 (mpp) REVERT: P 12 MET cc_start: 0.9189 (mmp) cc_final: 0.7541 (mmm) REVERT: P 58 PHE cc_start: 0.8871 (p90) cc_final: 0.8452 (p90) REVERT: Q 21 LYS cc_start: 0.9513 (mmtt) cc_final: 0.9093 (tptp) REVERT: Q 55 GLN cc_start: 0.9083 (mp10) cc_final: 0.8843 (mp10) REVERT: R 26 ASP cc_start: 0.9246 (p0) cc_final: 0.9039 (p0) REVERT: R 70 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7963 (tm-30) REVERT: R 85 LYS cc_start: 0.9533 (tmtt) cc_final: 0.9296 (tptp) REVERT: S 1 MET cc_start: 0.6039 (ptt) cc_final: 0.5690 (ptt) REVERT: S 38 TYR cc_start: 0.8780 (m-10) cc_final: 0.8125 (m-10) REVERT: S 49 LYS cc_start: 0.9494 (tptt) cc_final: 0.8667 (tptt) REVERT: S 65 ASP cc_start: 0.8513 (t0) cc_final: 0.8270 (t0) REVERT: S 82 MET cc_start: 0.7429 (tpp) cc_final: 0.7172 (tpp) REVERT: S 99 ARG cc_start: 0.8747 (mpp-170) cc_final: 0.7797 (mpt180) REVERT: S 103 ILE cc_start: 0.9699 (pt) cc_final: 0.9443 (mp) REVERT: S 109 ASP cc_start: 0.7979 (m-30) cc_final: 0.7561 (m-30) REVERT: U 9 GLU cc_start: 0.8099 (tt0) cc_final: 0.7859 (tt0) REVERT: Y 30 MET cc_start: 0.9074 (mmp) cc_final: 0.8754 (mmp) REVERT: 0 6 LYS cc_start: 0.9021 (tttt) cc_final: 0.8298 (tmtt) REVERT: 0 11 LYS cc_start: 0.9521 (mmmm) cc_final: 0.8894 (mmmm) REVERT: 0 14 MET cc_start: 0.9216 (mpp) cc_final: 0.8798 (mpp) REVERT: 0 19 ASP cc_start: 0.8922 (m-30) cc_final: 0.8683 (m-30) REVERT: 2 14 ARG cc_start: 0.8957 (mmt-90) cc_final: 0.8216 (mmp80) REVERT: Z 20 LYS cc_start: 0.9435 (tptm) cc_final: 0.8993 (tptt) REVERT: Z 24 LEU cc_start: 0.9616 (pp) cc_final: 0.9406 (pp) REVERT: Z 46 MET cc_start: 0.8774 (mmp) cc_final: 0.8358 (mmp) REVERT: Z 53 MET cc_start: 0.8575 (mmt) cc_final: 0.8167 (mmt) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.2675 time to fit residues: 91.4210 Evaluate side-chains 164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 12 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 286 optimal weight: 7.9990 chunk 37 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN Q 80 ASN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.045381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.033273 restraints weight = 531437.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.034289 restraints weight = 233283.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034888 restraints weight = 148778.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035192 restraints weight = 117426.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.035298 restraints weight = 103866.952| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 48167 Z= 0.218 Angle : 0.634 9.221 72350 Z= 0.320 Chirality : 0.035 0.226 9318 Planarity : 0.005 0.063 3647 Dihedral : 16.549 177.969 19449 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.20), residues: 1569 helix: 0.22 (0.23), residues: 476 sheet: -1.73 (0.29), residues: 272 loop : -1.51 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Z 44 TYR 0.011 0.001 TYR N 112 PHE 0.014 0.002 PHE S 75 TRP 0.017 0.002 TRP P 30 HIS 0.006 0.001 HIS N 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.22 (48167) covalent geometry : angle 0.63379 / 0.32 (72350) hydrogen bonds : bond 0.09105 / 5.28 ( 1693) hydrogen bonds : angle 4.01885 / 2.29 ( 3296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.8148 (ppp) cc_final: 0.7837 (ppp) REVERT: E 9 GLN cc_start: 0.9022 (mp10) cc_final: 0.8712 (mp10) REVERT: E 188 MET cc_start: 0.8780 (ptm) cc_final: 0.8342 (ptm) REVERT: J 53 TYR cc_start: 0.9081 (m-80) cc_final: 0.8119 (m-80) REVERT: J 67 ASN cc_start: 0.8754 (t0) cc_final: 0.8357 (t0) REVERT: J 92 MET cc_start: 0.9670 (ttm) cc_final: 0.9176 (tpt) REVERT: J 108 MET cc_start: 0.8037 (tpt) cc_final: 0.7743 (mmm) REVERT: K 1 MET cc_start: 0.4954 (tmm) cc_final: 0.3433 (pmm) REVERT: K 65 THR cc_start: 0.9022 (p) cc_final: 0.8810 (p) REVERT: K 79 PHE cc_start: 0.9276 (m-80) cc_final: 0.8869 (m-10) REVERT: L 81 ASP cc_start: 0.8132 (t70) cc_final: 0.6887 (m-30) REVERT: N 10 LEU cc_start: 0.9135 (mp) cc_final: 0.8893 (mp) REVERT: N 13 ASN cc_start: 0.8901 (t0) cc_final: 0.8585 (t0) REVERT: N 20 MET cc_start: 0.9226 (ttm) cc_final: 0.8771 (tmm) REVERT: N 21 PHE cc_start: 0.9189 (m-10) cc_final: 0.8639 (m-80) REVERT: N 102 PHE cc_start: 0.8940 (m-10) cc_final: 0.8635 (m-10) REVERT: N 110 MET cc_start: 0.8669 (mpp) cc_final: 0.8339 (mpp) REVERT: P 12 MET cc_start: 0.9153 (mmp) cc_final: 0.7527 (mmm) REVERT: P 58 PHE cc_start: 0.8956 (p90) cc_final: 0.8509 (p90) REVERT: Q 21 LYS cc_start: 0.9482 (mmtt) cc_final: 0.9281 (pttt) REVERT: R 26 ASP cc_start: 0.9209 (p0) cc_final: 0.8994 (p0) REVERT: R 85 LYS cc_start: 0.9564 (tmtt) cc_final: 0.9302 (tptt) REVERT: R 87 GLN cc_start: 0.8936 (pp30) cc_final: 0.8418 (pm20) REVERT: S 49 LYS cc_start: 0.9520 (tptt) cc_final: 0.9135 (tptm) REVERT: S 65 ASP cc_start: 0.8571 (t0) cc_final: 0.8364 (t0) REVERT: S 99 ARG cc_start: 0.8731 (mpp-170) cc_final: 0.7684 (mpt180) REVERT: S 103 ILE cc_start: 0.9688 (pt) cc_final: 0.9458 (mp) REVERT: S 109 ASP cc_start: 0.8209 (m-30) cc_final: 0.7774 (m-30) REVERT: U 9 GLU cc_start: 0.8140 (tt0) cc_final: 0.7883 (tt0) REVERT: Y 30 MET cc_start: 0.9179 (mmp) cc_final: 0.8806 (mmp) REVERT: 0 6 LYS cc_start: 0.9004 (tttt) cc_final: 0.8564 (tttm) REVERT: 0 11 LYS cc_start: 0.9492 (mmmm) cc_final: 0.8852 (mmmm) REVERT: 0 14 MET cc_start: 0.9243 (mpp) cc_final: 0.8776 (mpp) REVERT: 0 19 ASP cc_start: 0.8933 (m-30) cc_final: 0.8671 (m-30) REVERT: 2 14 ARG cc_start: 0.8970 (mmt-90) cc_final: 0.8284 (mmp80) REVERT: Z 20 LYS cc_start: 0.9387 (tptm) cc_final: 0.8969 (tptt) REVERT: Z 46 MET cc_start: 0.8864 (mmp) cc_final: 0.8463 (mmp) REVERT: Z 53 MET cc_start: 0.8758 (mmt) cc_final: 0.8332 (mmt) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2709 time to fit residues: 99.9647 Evaluate side-chains 167 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 120 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 chunk 231 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.044063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.032217 restraints weight = 547829.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.033150 restraints weight = 239944.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033705 restraints weight = 153291.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.034011 restraints weight = 121467.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034112 restraints weight = 107779.170| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 48167 Z= 0.312 Angle : 0.741 12.099 72350 Z= 0.372 Chirality : 0.039 0.270 9318 Planarity : 0.006 0.170 3647 Dihedral : 17.025 178.761 19449 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 32.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.20), residues: 1569 helix: -0.02 (0.23), residues: 474 sheet: -1.98 (0.28), residues: 270 loop : -1.69 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Y 29 TYR 0.012 0.002 TYR R 2 PHE 0.015 0.002 PHE S 75 TRP 0.027 0.003 TRP R 92 HIS 0.010 0.002 HIS R 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.31 (48167) covalent geometry : angle 0.74090 / 0.37 (72350) hydrogen bonds : bond 0.11636 / 6.81 ( 1693) hydrogen bonds : angle 4.22003 / 2.41 ( 3296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.8261 (ppp) cc_final: 0.7956 (ppp) REVERT: D 118 PHE cc_start: 0.6355 (t80) cc_final: 0.6092 (t80) REVERT: E 9 GLN cc_start: 0.9037 (mp10) cc_final: 0.8717 (mp10) REVERT: E 124 PHE cc_start: 0.7471 (t80) cc_final: 0.7138 (t80) REVERT: E 188 MET cc_start: 0.8798 (ptm) cc_final: 0.8246 (ptm) REVERT: J 53 TYR cc_start: 0.9077 (m-80) cc_final: 0.8151 (m-80) REVERT: J 67 ASN cc_start: 0.8682 (t0) cc_final: 0.8330 (t0) REVERT: J 92 MET cc_start: 0.9648 (ttm) cc_final: 0.9145 (tpt) REVERT: J 108 MET cc_start: 0.8082 (tpt) cc_final: 0.7805 (mmm) REVERT: K 79 PHE cc_start: 0.9211 (m-80) cc_final: 0.8815 (m-10) REVERT: N 10 LEU cc_start: 0.9373 (mp) cc_final: 0.9144 (mp) REVERT: N 13 ASN cc_start: 0.8879 (t0) cc_final: 0.8549 (t0) REVERT: N 20 MET cc_start: 0.9144 (ttm) cc_final: 0.8703 (tmm) REVERT: N 21 PHE cc_start: 0.9186 (m-10) cc_final: 0.8699 (m-80) REVERT: N 28 LEU cc_start: 0.9284 (tt) cc_final: 0.9026 (tp) REVERT: N 110 MET cc_start: 0.8706 (mpp) cc_final: 0.8381 (mpp) REVERT: P 12 MET cc_start: 0.9137 (mmp) cc_final: 0.7651 (mmm) REVERT: P 58 PHE cc_start: 0.8858 (p90) cc_final: 0.8365 (p90) REVERT: Q 21 LYS cc_start: 0.9473 (mmtt) cc_final: 0.9206 (pttt) REVERT: Q 55 GLN cc_start: 0.9123 (mp10) cc_final: 0.8914 (mp10) REVERT: R 26 ASP cc_start: 0.9285 (p0) cc_final: 0.9007 (p0) REVERT: R 85 LYS cc_start: 0.9576 (tmtt) cc_final: 0.9372 (tptp) REVERT: R 87 GLN cc_start: 0.8997 (pp30) cc_final: 0.8441 (pp30) REVERT: R 91 GLN cc_start: 0.8696 (tp40) cc_final: 0.8298 (tp40) REVERT: S 49 LYS cc_start: 0.9499 (tptt) cc_final: 0.9167 (tptm) REVERT: S 65 ASP cc_start: 0.8688 (t0) cc_final: 0.8393 (t0) REVERT: S 82 MET cc_start: 0.8621 (mpp) cc_final: 0.8298 (mpp) REVERT: S 103 ILE cc_start: 0.9716 (pt) cc_final: 0.9478 (mp) REVERT: S 109 ASP cc_start: 0.8041 (m-30) cc_final: 0.7546 (m-30) REVERT: U 9 GLU cc_start: 0.8179 (tt0) cc_final: 0.7900 (tt0) REVERT: Y 7 ARG cc_start: 0.8818 (ptt180) cc_final: 0.8311 (ptt180) REVERT: Y 29 ARG cc_start: 0.8329 (ptt-90) cc_final: 0.7642 (ptt-90) REVERT: Y 30 MET cc_start: 0.9148 (mmp) cc_final: 0.8683 (mmp) REVERT: 0 6 LYS cc_start: 0.9010 (tttt) cc_final: 0.8635 (tttm) REVERT: 0 11 LYS cc_start: 0.9505 (mmmm) cc_final: 0.8916 (mmmm) REVERT: 0 14 MET cc_start: 0.9237 (mpp) cc_final: 0.8763 (mpp) REVERT: 0 19 ASP cc_start: 0.8956 (m-30) cc_final: 0.8700 (m-30) REVERT: 2 14 ARG cc_start: 0.8927 (mmt-90) cc_final: 0.8676 (mmt-90) REVERT: Z 20 LYS cc_start: 0.9419 (tptm) cc_final: 0.8986 (tptt) REVERT: Z 24 LEU cc_start: 0.9632 (pp) cc_final: 0.9416 (pp) REVERT: Z 46 MET cc_start: 0.8864 (mmp) cc_final: 0.8653 (mmp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2692 time to fit residues: 91.6226 Evaluate side-chains 157 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 116 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 289 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.043566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.031073 restraints weight = 499186.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.032015 restraints weight = 224984.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.032553 restraints weight = 145116.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.032848 restraints weight = 115135.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.032992 restraints weight = 102174.444| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 48167 Z= 0.231 Angle : 0.644 8.702 72350 Z= 0.325 Chirality : 0.035 0.236 9318 Planarity : 0.005 0.086 3647 Dihedral : 16.704 177.823 19449 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.20), residues: 1569 helix: 0.13 (0.23), residues: 473 sheet: -1.97 (0.28), residues: 297 loop : -1.63 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG L 2 TYR 0.011 0.002 TYR S 38 PHE 0.015 0.002 PHE S 75 TRP 0.010 0.002 TRP R 92 HIS 0.006 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.23 (48167) covalent geometry : angle 0.64398 / 0.33 (72350) hydrogen bonds : bond 0.09267 / 5.40 ( 1693) hydrogen bonds : angle 4.01333 / 2.29 ( 3296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.8280 (ppp) cc_final: 0.8008 (ppp) REVERT: D 118 PHE cc_start: 0.6192 (t80) cc_final: 0.5877 (t80) REVERT: E 124 PHE cc_start: 0.7407 (t80) cc_final: 0.7071 (t80) REVERT: E 188 MET cc_start: 0.8701 (ptm) cc_final: 0.8130 (ptm) REVERT: J 53 TYR cc_start: 0.9106 (m-80) cc_final: 0.8254 (m-80) REVERT: J 67 ASN cc_start: 0.8827 (t0) cc_final: 0.8466 (t0) REVERT: J 92 MET cc_start: 0.9637 (ttm) cc_final: 0.9104 (tpp) REVERT: J 108 MET cc_start: 0.8067 (tpt) cc_final: 0.7770 (mmm) REVERT: K 65 THR cc_start: 0.9067 (p) cc_final: 0.8843 (p) REVERT: K 79 PHE cc_start: 0.9294 (m-80) cc_final: 0.8652 (m-10) REVERT: K 87 LEU cc_start: 0.6883 (mp) cc_final: 0.6674 (mp) REVERT: N 10 LEU cc_start: 0.9358 (mp) cc_final: 0.9122 (mp) REVERT: N 13 ASN cc_start: 0.8991 (t0) cc_final: 0.8694 (t0) REVERT: N 20 MET cc_start: 0.9137 (ttm) cc_final: 0.8714 (tmm) REVERT: N 21 PHE cc_start: 0.9158 (m-10) cc_final: 0.8555 (m-80) REVERT: P 12 MET cc_start: 0.9095 (mmp) cc_final: 0.7747 (mmp) REVERT: R 87 GLN cc_start: 0.8939 (pp30) cc_final: 0.8375 (pp30) REVERT: R 91 GLN cc_start: 0.8802 (tp40) cc_final: 0.8427 (tp40) REVERT: S 49 LYS cc_start: 0.9525 (tptt) cc_final: 0.8673 (tptm) REVERT: S 65 ASP cc_start: 0.8699 (t0) cc_final: 0.8413 (t0) REVERT: S 82 MET cc_start: 0.8355 (mpp) cc_final: 0.6892 (tpp) REVERT: S 103 ILE cc_start: 0.9708 (pt) cc_final: 0.9485 (mp) REVERT: S 109 ASP cc_start: 0.8242 (m-30) cc_final: 0.7816 (m-30) REVERT: U 9 GLU cc_start: 0.8151 (tt0) cc_final: 0.7908 (tt0) REVERT: Y 7 ARG cc_start: 0.8809 (ptt180) cc_final: 0.8249 (ptt180) REVERT: 0 6 LYS cc_start: 0.8936 (tttt) cc_final: 0.8562 (tttm) REVERT: 0 11 LYS cc_start: 0.9502 (mmmm) cc_final: 0.8897 (mmmm) REVERT: 0 14 MET cc_start: 0.9248 (mpp) cc_final: 0.8766 (mpp) REVERT: 0 19 ASP cc_start: 0.8970 (m-30) cc_final: 0.8686 (m-30) REVERT: 2 14 ARG cc_start: 0.8927 (mmt-90) cc_final: 0.8688 (mmt-90) REVERT: Z 20 LYS cc_start: 0.9400 (tptm) cc_final: 0.8976 (tptt) REVERT: Z 53 MET cc_start: 0.8762 (mmt) cc_final: 0.8186 (mmt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2756 time to fit residues: 94.7254 Evaluate side-chains 161 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 42 optimal weight: 30.0000 chunk 153 optimal weight: 7.9990 chunk 270 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 274 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN N 18 GLN P 65 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.043954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.031444 restraints weight = 499626.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.032372 restraints weight = 224853.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.032913 restraints weight = 144696.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.033234 restraints weight = 114713.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.033346 restraints weight = 101319.721| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.7463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 48167 Z= 0.210 Angle : 0.620 8.411 72350 Z= 0.313 Chirality : 0.034 0.227 9318 Planarity : 0.005 0.089 3647 Dihedral : 16.528 177.827 19449 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.58 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.20), residues: 1569 helix: 0.28 (0.24), residues: 473 sheet: -1.95 (0.28), residues: 304 loop : -1.57 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 2 TYR 0.011 0.002 TYR N 112 PHE 0.016 0.002 PHE Q 56 TRP 0.013 0.002 TRP Q 60 HIS 0.005 0.001 HIS 0 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 (48167) covalent geometry : angle 0.61955 / 0.31 (72350) hydrogen bonds : bond 0.08895 / 5.19 ( 1693) hydrogen bonds : angle 3.93581 / 2.25 ( 3296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 PHE cc_start: 0.8461 (m-80) cc_final: 0.8251 (m-80) REVERT: D 118 PHE cc_start: 0.6147 (t80) cc_final: 0.5848 (t80) REVERT: E 124 PHE cc_start: 0.7378 (t80) cc_final: 0.7057 (t80) REVERT: E 188 MET cc_start: 0.8707 (ptm) cc_final: 0.8127 (ptm) REVERT: J 53 TYR cc_start: 0.9078 (m-80) cc_final: 0.8197 (m-80) REVERT: J 67 ASN cc_start: 0.8840 (t0) cc_final: 0.8472 (t0) REVERT: J 92 MET cc_start: 0.9612 (ttm) cc_final: 0.9059 (tpp) REVERT: J 108 MET cc_start: 0.8024 (tpt) cc_final: 0.7711 (mmm) REVERT: K 65 THR cc_start: 0.8998 (p) cc_final: 0.8784 (p) REVERT: K 79 PHE cc_start: 0.9262 (m-80) cc_final: 0.8810 (m-10) REVERT: K 87 LEU cc_start: 0.7152 (mp) cc_final: 0.6946 (mp) REVERT: N 10 LEU cc_start: 0.9363 (mp) cc_final: 0.9134 (mp) REVERT: N 13 ASN cc_start: 0.9002 (t0) cc_final: 0.8675 (t0) REVERT: N 20 MET cc_start: 0.9045 (ttm) cc_final: 0.8651 (tmm) REVERT: N 21 PHE cc_start: 0.9228 (m-10) cc_final: 0.8681 (m-80) REVERT: P 12 MET cc_start: 0.9100 (mmp) cc_final: 0.7752 (mmp) REVERT: P 58 PHE cc_start: 0.8889 (p90) cc_final: 0.8288 (p90) REVERT: R 45 GLU cc_start: 0.8875 (mp0) cc_final: 0.8498 (mp0) REVERT: R 91 GLN cc_start: 0.8957 (tp40) cc_final: 0.8542 (tp40) REVERT: S 49 LYS cc_start: 0.9498 (tptt) cc_final: 0.8697 (tptm) REVERT: S 65 ASP cc_start: 0.8614 (t0) cc_final: 0.8280 (t0) REVERT: S 66 ILE cc_start: 0.8284 (mm) cc_final: 0.8069 (mm) REVERT: S 82 MET cc_start: 0.8435 (mpp) cc_final: 0.6856 (tpt) REVERT: S 99 ARG cc_start: 0.8800 (mtt180) cc_final: 0.8598 (mtm180) REVERT: S 103 ILE cc_start: 0.9705 (pt) cc_final: 0.9497 (mp) REVERT: S 109 ASP cc_start: 0.8203 (m-30) cc_final: 0.7791 (m-30) REVERT: U 9 GLU cc_start: 0.8090 (tt0) cc_final: 0.7837 (tt0) REVERT: Y 7 ARG cc_start: 0.8852 (ptt180) cc_final: 0.8309 (ptt180) REVERT: Y 29 ARG cc_start: 0.8563 (ptt-90) cc_final: 0.7891 (ptt-90) REVERT: 0 6 LYS cc_start: 0.8987 (tttt) cc_final: 0.8591 (tttm) REVERT: 0 11 LYS cc_start: 0.9487 (mmmm) cc_final: 0.8899 (mmmm) REVERT: 0 14 MET cc_start: 0.9248 (mpp) cc_final: 0.8773 (mpp) REVERT: 0 19 ASP cc_start: 0.8981 (m-30) cc_final: 0.8715 (m-30) REVERT: 2 14 ARG cc_start: 0.8923 (mmt-90) cc_final: 0.8260 (mmp80) REVERT: Z 20 LYS cc_start: 0.9417 (tptm) cc_final: 0.8992 (tptt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2681 time to fit residues: 91.8002 Evaluate side-chains 161 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 46 optimal weight: 10.0000 chunk 217 optimal weight: 0.6980 chunk 201 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 180 optimal weight: 0.0000 chunk 229 optimal weight: 0.1980 chunk 131 optimal weight: 40.0000 chunk 181 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 overall best weight: 3.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN K 29 HIS L 4 ASN P 65 ASN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.045193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.032536 restraints weight = 500072.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.033521 restraints weight = 224684.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.034095 restraints weight = 144254.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.034425 restraints weight = 114656.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.034574 restraints weight = 100782.085| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 48167 Z= 0.151 Angle : 0.563 10.998 72350 Z= 0.284 Chirality : 0.031 0.214 9318 Planarity : 0.005 0.064 3647 Dihedral : 16.167 178.105 19449 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.20), residues: 1569 helix: 0.42 (0.24), residues: 475 sheet: -1.97 (0.29), residues: 278 loop : -1.44 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 2 TYR 0.010 0.001 TYR N 112 PHE 0.015 0.001 PHE S 75 TRP 0.028 0.002 TRP P 30 HIS 0.009 0.001 HIS K 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (48167) covalent geometry : angle 0.56275 / 0.28 (72350) hydrogen bonds : bond 0.07478 / 4.36 ( 1693) hydrogen bonds : angle 3.76409 / 2.17 ( 3296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7137.81 seconds wall clock time: 125 minutes 44.75 seconds (7544.75 seconds total)