Starting phenix.real_space_refine on Fri Mar 6 12:30:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ev9_31325/03_2026/7ev9_31325_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ev9_31325/03_2026/7ev9_31325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ev9_31325/03_2026/7ev9_31325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ev9_31325/03_2026/7ev9_31325.map" model { file = "/net/cci-nas-00/data/ceres_data/7ev9_31325/03_2026/7ev9_31325_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ev9_31325/03_2026/7ev9_31325_neut.cif" } resolution = 2.6 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= 0.001 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17136 atoms to isotropic. 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 Cu 24 5.60 5 S 81 5.16 5 C 11295 2.51 5 N 2835 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 186 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17220 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 357} Chain: "B" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1811 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {'CU1': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'CU1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: E, I, F, J, G, K Time building chain proxies: 3.45, per 1000 atoms: 0.20 Number of scatterers: 17220 At special positions: 0 Unit cell: (107.682, 107.682, 120.834, 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) Cu 24 28.99 S 81 16.00 O 2985 8.00 N 2835 7.00 C 11295 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: 1.25 Conformation dependent library (CDL) restraints added in 613.5 milliseconds 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3942 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 15 sheets defined 47.5% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 184 through 207 removed outlier: 3.881A pdb=" N TRP A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TRP A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.648A pdb=" N ASP A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 258 removed outlier: 3.635A pdb=" N ARG A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 375 through 382 removed outlier: 3.638A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 381 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 34 removed outlier: 4.098A pdb=" N VAL B 15 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B 27 " --> pdb=" O TRP B 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.556A pdb=" N THR B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 69 through 84 removed outlier: 3.736A pdb=" N SER B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 107 removed outlier: 3.790A pdb=" N CYS B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.566A pdb=" N ALA B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.553A pdb=" N THR B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 169 removed outlier: 3.994A pdb=" N VAL B 169 " --> pdb=" O PRO B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 212 through 238 removed outlier: 3.642A pdb=" N ILE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 123 through 150 Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.648A pdb=" N LEU C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.863A pdb=" N VAL C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.995A pdb=" N ASP C 283 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 207 removed outlier: 3.881A pdb=" N TRP E 195 " --> pdb=" O TRP E 191 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TRP E 206 " --> pdb=" O TRP E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 221 removed outlier: 3.648A pdb=" N ASP E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 258 removed outlier: 3.634A pdb=" N ARG E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 375 through 382 removed outlier: 3.638A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR E 381 " --> pdb=" O ASP E 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 34 removed outlier: 4.098A pdb=" N VAL F 15 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR F 20 " --> pdb=" O GLN F 16 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU F 26 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE F 27 " --> pdb=" O TRP F 23 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL F 32 " --> pdb=" O VAL F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 46 Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 58 through 68 removed outlier: 3.556A pdb=" N THR F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 69 through 84 removed outlier: 3.736A pdb=" N SER F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 removed outlier: 3.790A pdb=" N CYS F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 138 removed outlier: 3.564A pdb=" N ALA F 128 " --> pdb=" O LEU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 155 removed outlier: 3.553A pdb=" N THR F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 169 removed outlier: 3.994A pdb=" N VAL F 169 " --> pdb=" O PRO F 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 166 through 169' Processing helix chain 'F' and resid 179 through 188 Processing helix chain 'F' and resid 212 through 238 removed outlier: 3.643A pdb=" N ILE F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU F 226 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 123 through 150 Processing helix chain 'G' and resid 185 through 199 removed outlier: 3.648A pdb=" N LEU G 199 " --> pdb=" O ALA G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 216 removed outlier: 3.863A pdb=" N VAL G 214 " --> pdb=" O TYR G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 270 Processing helix chain 'G' and resid 280 through 284 removed outlier: 3.994A pdb=" N ASP G 283 " --> pdb=" O GLU G 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 184 through 207 removed outlier: 3.881A pdb=" N TRP I 195 " --> pdb=" O TRP I 191 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP I 206 " --> pdb=" O TRP I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 221 removed outlier: 3.648A pdb=" N ASP I 220 " --> pdb=" O LEU I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 258 removed outlier: 3.635A pdb=" N ARG I 233 " --> pdb=" O SER I 229 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE I 244 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE I 246 " --> pdb=" O ALA I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'I' and resid 375 through 382 removed outlier: 3.639A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR I 381 " --> pdb=" O ASP I 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 34 removed outlier: 4.099A pdb=" N VAL J 15 " --> pdb=" O HIS J 11 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR J 20 " --> pdb=" O GLN J 16 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU J 26 " --> pdb=" O ASP J 22 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE J 27 " --> pdb=" O TRP J 23 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE J 30 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL J 32 " --> pdb=" O VAL J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 51 through 55 Processing helix chain 'J' and resid 58 through 68 removed outlier: 3.555A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) Proline residue: J 65 - end of helix Processing helix chain 'J' and resid 69 through 84 removed outlier: 3.735A pdb=" N SER J 77 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 107 removed outlier: 3.789A pdb=" N CYS J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 138 removed outlier: 3.565A pdb=" N ALA J 128 " --> pdb=" O LEU J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 155 removed outlier: 3.554A pdb=" N THR J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY J 153 " --> pdb=" O ALA J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 165 Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 169 removed outlier: 3.995A pdb=" N VAL J 169 " --> pdb=" O PRO J 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 166 through 169' Processing helix chain 'J' and resid 179 through 188 Processing helix chain 'J' and resid 212 through 238 removed outlier: 3.642A pdb=" N ILE J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU J 226 " --> pdb=" O PHE J 222 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 Processing helix chain 'K' and resid 123 through 150 Processing helix chain 'K' and resid 185 through 199 removed outlier: 3.649A pdb=" N LEU K 199 " --> pdb=" O ALA K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 216 removed outlier: 3.863A pdb=" N VAL K 214 " --> pdb=" O TYR K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 270 Processing helix chain 'K' and resid 280 through 284 removed outlier: 3.993A pdb=" N ASP K 283 " --> pdb=" O GLU K 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.405A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP A 123 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 105 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A 125 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A 103 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 127 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 108 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.944A pdb=" N THR A 140 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A 154 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL A 138 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP A 156 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TRP A 136 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR A 158 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY A 134 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 removed outlier: 5.598A pdb=" N LEU A 314 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE A 394 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 316 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N SER A 283 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N ASP A 406 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LYS A 285 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLU A 287 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AA6, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.405A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP E 123 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE E 105 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG E 125 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER E 103 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL E 127 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 60 removed outlier: 4.946A pdb=" N THR E 140 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY E 154 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL E 138 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP E 156 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TRP E 136 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR E 158 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY E 134 " --> pdb=" O THR E 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AA9, first strand: chain 'E' and resid 341 through 342 removed outlier: 5.598A pdb=" N LEU E 314 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE E 394 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 316 " --> pdb=" O PHE E 392 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N SER E 283 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N ASP E 406 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LYS E 285 " --> pdb=" O ASP E 406 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLU E 287 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 171 through 173 Processing sheet with id=AB2, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.403A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP I 123 " --> pdb=" O ILE I 105 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE I 105 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG I 125 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER I 103 " --> pdb=" O ARG I 125 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL I 127 " --> pdb=" O LYS I 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 58 through 60 removed outlier: 4.944A pdb=" N THR I 140 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY I 154 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL I 138 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP I 156 " --> pdb=" O TRP I 136 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP I 136 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR I 158 " --> pdb=" O GLY I 134 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY I 134 " --> pdb=" O THR I 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AB5, first strand: chain 'I' and resid 341 through 342 removed outlier: 5.599A pdb=" N LEU I 314 " --> pdb=" O PHE I 394 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE I 394 " --> pdb=" O LEU I 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU I 316 " --> pdb=" O PHE I 392 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N SER I 283 " --> pdb=" O GLN I 404 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N ASP I 406 " --> pdb=" O SER I 283 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LYS I 285 " --> pdb=" O ASP I 406 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLU I 287 " --> pdb=" O PRO I 408 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 171 through 173 801 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2640 1.32 - 1.44: 5417 1.44 - 1.56: 9526 1.56 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 17739 Sorted by residual: bond pdb=" C ILE B 102 " pdb=" N ASN B 103 " ideal model delta sigma weight residual 1.335 1.408 -0.073 1.31e-02 5.83e+03 3.13e+01 bond pdb=" C ILE F 102 " pdb=" N ASN F 103 " ideal model delta sigma weight residual 1.335 1.408 -0.073 1.31e-02 5.83e+03 3.13e+01 bond pdb=" C ILE J 102 " pdb=" N ASN J 103 " ideal model delta sigma weight residual 1.335 1.408 -0.073 1.31e-02 5.83e+03 3.10e+01 bond pdb=" C ASN F 103 " pdb=" N ARG F 104 " ideal model delta sigma weight residual 1.335 1.410 -0.075 1.36e-02 5.41e+03 3.08e+01 bond pdb=" C ASN J 103 " pdb=" N ARG J 104 " ideal model delta sigma weight residual 1.335 1.410 -0.075 1.36e-02 5.41e+03 3.08e+01 ... (remaining 17734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 23589 2.49 - 4.99: 537 4.99 - 7.48: 48 7.48 - 9.97: 6 9.97 - 12.47: 6 Bond angle restraints: 24186 Sorted by residual: angle pdb=" C PHE I 212 " pdb=" N ILE I 213 " pdb=" CA ILE I 213 " ideal model delta sigma weight residual 122.13 134.60 -12.47 1.85e+00 2.92e-01 4.54e+01 angle pdb=" C PHE A 212 " pdb=" N ILE A 213 " pdb=" CA ILE A 213 " ideal model delta sigma weight residual 122.13 134.56 -12.43 1.85e+00 2.92e-01 4.51e+01 angle pdb=" C PHE E 212 " pdb=" N ILE E 213 " pdb=" CA ILE E 213 " ideal model delta sigma weight residual 122.13 134.52 -12.39 1.85e+00 2.92e-01 4.49e+01 angle pdb=" N ILE I 213 " pdb=" CA ILE I 213 " pdb=" C ILE I 213 " ideal model delta sigma weight residual 108.88 119.22 -10.34 2.16e+00 2.14e-01 2.29e+01 angle pdb=" N ILE E 213 " pdb=" CA ILE E 213 " pdb=" C ILE E 213 " ideal model delta sigma weight residual 108.88 119.21 -10.33 2.16e+00 2.14e-01 2.29e+01 ... (remaining 24181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.63: 8680 14.63 - 29.25: 1124 29.25 - 43.88: 247 43.88 - 58.51: 53 58.51 - 73.14: 12 Dihedral angle restraints: 10116 sinusoidal: 3954 harmonic: 6162 Sorted by residual: dihedral pdb=" CA ILE I 213 " pdb=" C ILE I 213 " pdb=" N PRO I 214 " pdb=" CA PRO I 214 " ideal model delta harmonic sigma weight residual 180.00 127.61 52.39 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA ILE E 213 " pdb=" C ILE E 213 " pdb=" N PRO E 214 " pdb=" CA PRO E 214 " ideal model delta harmonic sigma weight residual 180.00 127.62 52.38 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA ILE A 213 " pdb=" C ILE A 213 " pdb=" N PRO A 214 " pdb=" CA PRO A 214 " ideal model delta harmonic sigma weight residual 180.00 127.64 52.36 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 10113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1692 0.048 - 0.095: 650 0.095 - 0.143: 224 0.143 - 0.191: 28 0.191 - 0.239: 19 Chirality restraints: 2613 Sorted by residual: chirality pdb=" CB VAL E 59 " pdb=" CA VAL E 59 " pdb=" CG1 VAL E 59 " pdb=" CG2 VAL E 59 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL A 59 " pdb=" CA VAL A 59 " pdb=" CG1 VAL A 59 " pdb=" CG2 VAL A 59 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB VAL I 59 " pdb=" CA VAL I 59 " pdb=" CG1 VAL I 59 " pdb=" CG2 VAL I 59 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2610 not shown) Planarity restraints: 3021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 213 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO I 214 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO I 214 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO I 214 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 213 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO E 214 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO E 214 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO E 214 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 213 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.06e+01 pdb=" N PRO A 214 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " 0.062 5.00e-02 4.00e+02 ... (remaining 3018 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 45 2.25 - 2.92: 6785 2.92 - 3.58: 23355 3.58 - 4.24: 43815 4.24 - 4.90: 74055 Nonbonded interactions: 148055 Sorted by model distance: nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU1 I 502 " model vdw 1.593 3.060 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU1 A 502 " model vdw 1.594 3.060 nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU1 E 502 " model vdw 1.595 3.060 nonbonded pdb=" ND1 HIS E 137 " pdb="CU CU1 E 503 " model vdw 1.611 3.060 nonbonded pdb=" ND1 HIS I 137 " pdb="CU CU1 I 503 " model vdw 1.612 3.060 ... (remaining 148050 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } 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 individual isotropic 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: 7.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.007 0.075 17739 Z= 0.295 Angle : 0.883 12.466 24186 Z= 0.506 Chirality : 0.058 0.239 2613 Planarity : 0.009 0.114 3021 Dihedral : 13.746 73.136 6174 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -3.14 (0.15), residues: 2106 helix: -2.75 (0.12), residues: 930 sheet: -0.38 (0.24), residues: 387 loop : -1.85 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 117 TYR 0.051 0.003 TYR G 210 PHE 0.021 0.002 PHE E 71 TRP 0.018 0.002 TRP J 152 HIS 0.005 0.001 HIS J 232 Details of bonding type rmsd covalent geometry : bond 0.00657 (17739) covalent geometry : angle 0.88316 (24186) hydrogen bonds : bond 0.15944 ( 801) hydrogen bonds : angle 7.95340 ( 2313) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.645 Fit side-chains REVERT: A 208 ARG cc_start: 0.7610 (mtm110) cc_final: 0.5799 (mmp-170) REVERT: A 237 MET cc_start: 0.6876 (ptp) cc_final: 0.6275 (ptt) REVERT: A 343 GLU cc_start: 0.7584 (pm20) cc_final: 0.7368 (pm20) REVERT: C 259 MET cc_start: 0.6332 (mtm) cc_final: 0.5924 (mtm) REVERT: E 163 MET cc_start: 0.7942 (ttt) cc_final: 0.7720 (ttt) REVERT: E 208 ARG cc_start: 0.7441 (mtm110) cc_final: 0.5531 (mmp-170) REVERT: E 237 MET cc_start: 0.6873 (ptp) cc_final: 0.6285 (ptt) REVERT: E 343 GLU cc_start: 0.7602 (pm20) cc_final: 0.7348 (pm20) REVERT: F 24 MET cc_start: 0.7559 (mtm) cc_final: 0.7309 (mtt) REVERT: F 100 GLU cc_start: 0.7519 (pt0) cc_final: 0.7234 (pt0) REVERT: G 259 MET cc_start: 0.6487 (mtm) cc_final: 0.5845 (mtm) REVERT: I 208 ARG cc_start: 0.7519 (mtm110) cc_final: 0.5796 (mmp-170) REVERT: I 237 MET cc_start: 0.6945 (ptp) cc_final: 0.6335 (ptt) REVERT: I 343 GLU cc_start: 0.7545 (pm20) cc_final: 0.7344 (pm20) REVERT: J 100 GLU cc_start: 0.7632 (pt0) cc_final: 0.7349 (pt0) REVERT: J 111 TRP cc_start: 0.6447 (m100) cc_final: 0.6207 (m-10) REVERT: K 259 MET cc_start: 0.6462 (mtm) cc_final: 0.6244 (mtm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.6977 time to fit residues: 197.3966 Evaluate side-chains 189 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 137 HIS A 187 ASN A 192 HIS A 265 GLN A 399 ASN A 401 GLN B 103 ASN B 107 ASN B 187 ASN B 240 ASN C 134 HIS C 264 GLN E 137 HIS E 187 ASN E 192 HIS E 265 GLN E 399 ASN E 401 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN F 240 ASN G 134 HIS G 264 GLN I 137 HIS I 187 ASN I 192 HIS I 265 GLN I 399 ASN I 401 GLN J 103 ASN J 107 ASN J 187 ASN J 240 ASN K 134 HIS K 264 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105787 restraints weight = 16737.270| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.72 r_work: 0.3256 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17739 Z= 0.135 Angle : 0.579 8.558 24186 Z= 0.306 Chirality : 0.044 0.137 2613 Planarity : 0.006 0.100 3021 Dihedral : 5.648 51.865 2340 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.50 % Allowed : 9.94 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -1.38 (0.17), residues: 2106 helix: -0.98 (0.15), residues: 942 sheet: 0.05 (0.25), residues: 399 loop : -1.11 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 236 TYR 0.017 0.001 TYR B 188 PHE 0.013 0.001 PHE F 27 TRP 0.017 0.001 TRP B 152 HIS 0.003 0.001 HIS I 33 Details of bonding type rmsd covalent geometry : bond 0.00315 (17739) covalent geometry : angle 0.57927 (24186) hydrogen bonds : bond 0.03430 ( 801) hydrogen bonds : angle 5.43111 ( 2313) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.658 Fit side-chains REVERT: A 160 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: A 208 ARG cc_start: 0.7566 (mtm110) cc_final: 0.5518 (mmp-170) REVERT: A 237 MET cc_start: 0.7172 (ptp) cc_final: 0.6443 (ptt) REVERT: A 343 GLU cc_start: 0.7989 (pm20) cc_final: 0.7648 (pm20) REVERT: A 404 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: B 43 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7998 (mp) REVERT: C 198 ARG cc_start: 0.6505 (mpt180) cc_final: 0.5946 (mpp-170) REVERT: C 259 MET cc_start: 0.6272 (mtm) cc_final: 0.5954 (mtm) REVERT: E 208 ARG cc_start: 0.7544 (mtm110) cc_final: 0.5496 (mmp-170) REVERT: E 218 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6598 (tpp) REVERT: E 237 MET cc_start: 0.7017 (ptp) cc_final: 0.6695 (ttp) REVERT: E 343 GLU cc_start: 0.7967 (pm20) cc_final: 0.7637 (pm20) REVERT: E 399 ASN cc_start: 0.7669 (m-40) cc_final: 0.7426 (m110) REVERT: F 43 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8037 (mp) REVERT: F 82 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6205 (mpt90) REVERT: G 198 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6047 (mmt90) REVERT: G 259 MET cc_start: 0.6226 (mtm) cc_final: 0.5917 (mtm) REVERT: I 208 ARG cc_start: 0.7613 (mtm110) cc_final: 0.5686 (mmp-170) REVERT: I 237 MET cc_start: 0.7097 (ptp) cc_final: 0.6426 (ptt) REVERT: I 339 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7556 (p0) REVERT: I 343 GLU cc_start: 0.8063 (pm20) cc_final: 0.7691 (pm20) REVERT: I 404 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: J 111 TRP cc_start: 0.6433 (m100) cc_final: 0.5917 (m-10) outliers start: 45 outliers final: 5 residues processed: 252 average time/residue: 0.6296 time to fit residues: 176.3473 Evaluate side-chains 216 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 404 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 173 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS B 240 ASN E 72 HIS F 103 ASN F 107 ASN F 240 ASN I 72 HIS I 137 HIS I 399 ASN J 240 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102283 restraints weight = 16942.557| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.74 r_work: 0.3182 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17739 Z= 0.150 Angle : 0.571 8.591 24186 Z= 0.299 Chirality : 0.044 0.140 2613 Planarity : 0.006 0.098 3021 Dihedral : 5.433 52.665 2340 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.89 % Allowed : 11.83 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -0.73 (0.18), residues: 2106 helix: -0.23 (0.17), residues: 942 sheet: 0.26 (0.25), residues: 399 loop : -1.03 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 236 TYR 0.019 0.001 TYR J 188 PHE 0.011 0.001 PHE E 71 TRP 0.015 0.001 TRP B 152 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00360 (17739) covalent geometry : angle 0.57115 (24186) hydrogen bonds : bond 0.03312 ( 801) hydrogen bonds : angle 5.16177 ( 2313) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.721 Fit side-chains TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it. REVERT: A 208 ARG cc_start: 0.7563 (mtm110) cc_final: 0.5479 (mmp-170) REVERT: A 237 MET cc_start: 0.7150 (ptp) cc_final: 0.6844 (ttp) REVERT: A 299 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7628 (ttp-170) REVERT: A 343 GLU cc_start: 0.7971 (pm20) cc_final: 0.7653 (pm20) REVERT: A 404 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: C 198 ARG cc_start: 0.6476 (mpt180) cc_final: 0.5727 (mmt90) REVERT: C 259 MET cc_start: 0.6378 (mtm) cc_final: 0.6110 (mtm) REVERT: E 208 ARG cc_start: 0.7546 (mtm110) cc_final: 0.5473 (mmp-170) REVERT: E 218 MET cc_start: 0.6888 (tpp) cc_final: 0.6651 (tpp) REVERT: E 237 MET cc_start: 0.7044 (ptp) cc_final: 0.6746 (ttp) REVERT: E 299 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7447 (ttp80) REVERT: E 343 GLU cc_start: 0.7921 (pm20) cc_final: 0.7560 (pm20) REVERT: F 82 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6073 (mpt90) REVERT: F 100 GLU cc_start: 0.7809 (pt0) cc_final: 0.7561 (pt0) REVERT: G 198 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5566 (mpt180) REVERT: G 259 MET cc_start: 0.6258 (mtm) cc_final: 0.6001 (mtm) REVERT: I 208 ARG cc_start: 0.7620 (mtm110) cc_final: 0.5704 (mmp-170) REVERT: I 237 MET cc_start: 0.6953 (ptp) cc_final: 0.6249 (ptt) REVERT: I 299 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7459 (ttp80) REVERT: I 339 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7483 (p0) REVERT: I 343 GLU cc_start: 0.7950 (pm20) cc_final: 0.7614 (pm20) REVERT: I 404 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: J 111 TRP cc_start: 0.6381 (m100) cc_final: 0.5755 (m-10) REVERT: K 198 ARG cc_start: 0.6686 (mpt180) cc_final: 0.5612 (mpt180) outliers start: 52 outliers final: 15 residues processed: 247 average time/residue: 0.6369 time to fit residues: 174.1112 Evaluate side-chains 232 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 48 TRP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain J residue 48 TRP Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 185 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 111 optimal weight: 0.0000 chunk 51 optimal weight: 4.9990 chunk 176 optimal weight: 0.3980 chunk 200 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN E 399 ASN F 240 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 ASN J 240 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103435 restraints weight = 17694.835| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.77 r_work: 0.3238 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17739 Z= 0.173 Angle : 0.580 8.517 24186 Z= 0.303 Chirality : 0.045 0.141 2613 Planarity : 0.006 0.097 3021 Dihedral : 5.432 52.364 2340 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.39 % Allowed : 12.33 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -0.49 (0.18), residues: 2106 helix: 0.02 (0.17), residues: 945 sheet: 0.32 (0.25), residues: 399 loop : -0.96 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 236 TYR 0.020 0.001 TYR B 188 PHE 0.012 0.001 PHE E 71 TRP 0.014 0.001 TRP B 152 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00419 (17739) covalent geometry : angle 0.57966 (24186) hydrogen bonds : bond 0.03355 ( 801) hydrogen bonds : angle 5.13209 ( 2313) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 0.639 Fit side-chains TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it. REVERT: A 160 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: A 208 ARG cc_start: 0.7636 (mtm110) cc_final: 0.5565 (mmp-170) REVERT: A 237 MET cc_start: 0.7275 (ptp) cc_final: 0.6935 (ttp) REVERT: A 299 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7662 (ttp-170) REVERT: A 339 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7679 (p0) REVERT: A 343 GLU cc_start: 0.8023 (pm20) cc_final: 0.7731 (pm20) REVERT: A 404 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: B 42 MET cc_start: 0.7207 (mmp) cc_final: 0.6988 (mmp) REVERT: B 84 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7422 (mmt90) REVERT: C 198 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.5760 (mmt90) REVERT: E 208 ARG cc_start: 0.7556 (mtm110) cc_final: 0.5534 (mmp-170) REVERT: E 237 MET cc_start: 0.7040 (ptp) cc_final: 0.6724 (ttp) REVERT: E 299 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7458 (ttp80) REVERT: E 343 GLU cc_start: 0.7988 (pm20) cc_final: 0.7641 (pm20) REVERT: F 82 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6123 (mpt90) REVERT: F 84 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7169 (mmt90) REVERT: G 198 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.5631 (mpt180) REVERT: G 259 MET cc_start: 0.6456 (mtm) cc_final: 0.6202 (mtm) REVERT: I 208 ARG cc_start: 0.7614 (mtm110) cc_final: 0.5715 (mmp-170) REVERT: I 233 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5564 (mtm180) REVERT: I 237 MET cc_start: 0.7133 (ptp) cc_final: 0.6439 (ptt) REVERT: I 299 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7512 (ttp80) REVERT: I 339 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7492 (p0) REVERT: I 343 GLU cc_start: 0.7971 (pm20) cc_final: 0.7641 (pm20) REVERT: I 404 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: J 111 TRP cc_start: 0.6618 (m100) cc_final: 0.5927 (m-10) REVERT: J 136 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7642 (ttp) REVERT: K 198 ARG cc_start: 0.6786 (mpt180) cc_final: 0.5943 (mpt180) outliers start: 61 outliers final: 18 residues processed: 241 average time/residue: 0.6591 time to fit residues: 175.1257 Evaluate side-chains 230 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 48 TRP Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain F residue 48 TRP Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain G residue 210 TYR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain J residue 48 TRP Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 148 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN E 399 ASN F 240 ASN I 108 GLN I 399 ASN J 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106098 restraints weight = 17490.494| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.77 r_work: 0.3268 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17739 Z= 0.110 Angle : 0.528 8.372 24186 Z= 0.277 Chirality : 0.043 0.137 2613 Planarity : 0.005 0.092 3021 Dihedral : 5.167 51.934 2340 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.28 % Allowed : 13.83 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -0.13 (0.18), residues: 2106 helix: 0.32 (0.17), residues: 945 sheet: 0.49 (0.26), residues: 399 loop : -0.78 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 236 TYR 0.014 0.001 TYR B 188 PHE 0.012 0.001 PHE I 71 TRP 0.012 0.001 TRP J 152 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00259 (17739) covalent geometry : angle 0.52792 (24186) hydrogen bonds : bond 0.02880 ( 801) hydrogen bonds : angle 4.93057 ( 2313) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.599 Fit side-chains REVERT: A 160 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: A 208 ARG cc_start: 0.7662 (mtm110) cc_final: 0.5617 (mmp-170) REVERT: A 237 MET cc_start: 0.7114 (ptp) cc_final: 0.6872 (ttp) REVERT: A 299 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7654 (ttp-170) REVERT: A 339 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7602 (p0) REVERT: A 343 GLU cc_start: 0.7903 (pm20) cc_final: 0.7591 (pm20) REVERT: A 404 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: B 39 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7810 (mp) REVERT: B 42 MET cc_start: 0.7103 (mmp) cc_final: 0.6878 (mmp) REVERT: B 43 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7914 (mp) REVERT: C 198 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.5754 (mmt90) REVERT: E 208 ARG cc_start: 0.7499 (mtm110) cc_final: 0.5514 (mmp-170) REVERT: E 226 GLU cc_start: 0.7304 (pp20) cc_final: 0.6796 (pp20) REVERT: E 237 MET cc_start: 0.6978 (ptp) cc_final: 0.6766 (ttp) REVERT: F 82 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6036 (mpt90) REVERT: F 100 GLU cc_start: 0.7744 (pt0) cc_final: 0.6667 (mt-10) REVERT: F 150 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6911 (ttp) REVERT: G 198 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6419 (mpt180) REVERT: G 259 MET cc_start: 0.6312 (mtm) cc_final: 0.6077 (mtm) REVERT: I 53 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8513 (p) REVERT: I 208 ARG cc_start: 0.7540 (mtm110) cc_final: 0.5648 (mmp-170) REVERT: I 218 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6353 (tpp) REVERT: I 233 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.5608 (mtm180) REVERT: I 237 MET cc_start: 0.6949 (ptp) cc_final: 0.6387 (ptt) REVERT: I 299 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7435 (ttp80) REVERT: I 339 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7520 (p0) REVERT: I 343 GLU cc_start: 0.7916 (pm20) cc_final: 0.7644 (pm20) REVERT: I 404 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: J 111 TRP cc_start: 0.6590 (m100) cc_final: 0.5899 (m-10) REVERT: J 150 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6984 (ttp) REVERT: K 198 ARG cc_start: 0.6732 (mpt180) cc_final: 0.5645 (mpt180) outliers start: 41 outliers final: 6 residues processed: 228 average time/residue: 0.6573 time to fit residues: 165.3711 Evaluate side-chains 216 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 218 MET Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain J residue 150 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN F 240 ASN I 399 ASN J 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102461 restraints weight = 17157.860| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.77 r_work: 0.3184 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17739 Z= 0.143 Angle : 0.549 8.360 24186 Z= 0.287 Chirality : 0.044 0.143 2613 Planarity : 0.005 0.093 3021 Dihedral : 5.221 52.202 2340 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.94 % Allowed : 14.39 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -0.04 (0.18), residues: 2106 helix: 0.40 (0.17), residues: 948 sheet: 0.52 (0.26), residues: 399 loop : -0.73 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 236 TYR 0.019 0.001 TYR B 188 PHE 0.011 0.001 PHE A 71 TRP 0.013 0.001 TRP F 152 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00344 (17739) covalent geometry : angle 0.54941 (24186) hydrogen bonds : bond 0.03097 ( 801) hydrogen bonds : angle 4.97193 ( 2313) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 0.627 Fit side-chains TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it. REVERT: A 160 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: A 208 ARG cc_start: 0.7601 (mtm110) cc_final: 0.5557 (mmp-170) REVERT: A 237 MET cc_start: 0.7045 (ptp) cc_final: 0.6787 (ttp) REVERT: A 299 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7593 (ttp-170) REVERT: A 339 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7566 (p0) REVERT: A 343 GLU cc_start: 0.7931 (pm20) cc_final: 0.7598 (pm20) REVERT: A 404 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: B 42 MET cc_start: 0.7092 (mmp) cc_final: 0.6826 (mmp) REVERT: C 198 ARG cc_start: 0.6353 (OUTLIER) cc_final: 0.5699 (mmt90) REVERT: E 208 ARG cc_start: 0.7554 (mtm110) cc_final: 0.5522 (mmp-170) REVERT: E 237 MET cc_start: 0.6980 (ptp) cc_final: 0.6737 (ttp) REVERT: E 299 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7397 (ttp80) REVERT: F 82 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.5983 (mpt90) REVERT: F 100 GLU cc_start: 0.7729 (pt0) cc_final: 0.6491 (mt-10) REVERT: F 150 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6851 (ttp) REVERT: G 198 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.5466 (mpt180) REVERT: G 259 MET cc_start: 0.6193 (mtm) cc_final: 0.5976 (mtm) REVERT: I 208 ARG cc_start: 0.7525 (mtm110) cc_final: 0.5555 (mmp-170) REVERT: I 218 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6249 (tpp) REVERT: I 237 MET cc_start: 0.6847 (ptp) cc_final: 0.6265 (ptt) REVERT: I 299 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7429 (ttp80) REVERT: I 339 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7581 (p0) REVERT: I 343 GLU cc_start: 0.7921 (pm20) cc_final: 0.7617 (pm20) REVERT: I 404 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: J 111 TRP cc_start: 0.6497 (m100) cc_final: 0.5745 (m-10) REVERT: J 150 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6968 (ttp) REVERT: K 198 ARG cc_start: 0.6674 (mpt180) cc_final: 0.5592 (mpt180) outliers start: 53 outliers final: 18 residues processed: 230 average time/residue: 0.6282 time to fit residues: 159.8434 Evaluate side-chains 224 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 TRP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain F residue 48 TRP Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 218 MET Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 48 TRP Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 61 optimal weight: 0.0070 chunk 58 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN E 399 ASN F 240 ASN I 108 GLN I 399 ASN J 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104066 restraints weight = 17089.150| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.77 r_work: 0.3206 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17739 Z= 0.111 Angle : 0.525 8.397 24186 Z= 0.275 Chirality : 0.043 0.147 2613 Planarity : 0.005 0.090 3021 Dihedral : 5.075 51.936 2340 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.94 % Allowed : 14.67 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: 0.16 (0.18), residues: 2106 helix: 0.58 (0.17), residues: 945 sheet: 0.62 (0.26), residues: 399 loop : -0.63 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 236 TYR 0.014 0.001 TYR B 188 PHE 0.012 0.001 PHE E 71 TRP 0.012 0.001 TRP J 152 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00262 (17739) covalent geometry : angle 0.52489 (24186) hydrogen bonds : bond 0.02835 ( 801) hydrogen bonds : angle 4.86000 ( 2313) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.619 Fit side-chains REVERT: A 53 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8464 (p) REVERT: A 160 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: A 208 ARG cc_start: 0.7606 (mtm110) cc_final: 0.5602 (mmp-170) REVERT: A 237 MET cc_start: 0.6999 (ptp) cc_final: 0.6746 (ttp) REVERT: A 299 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7583 (ttp-170) REVERT: A 339 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7537 (p0) REVERT: A 343 GLU cc_start: 0.7947 (pm20) cc_final: 0.7654 (pm20) REVERT: A 404 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: C 198 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.5527 (mmt-90) REVERT: E 208 ARG cc_start: 0.7493 (mtm110) cc_final: 0.5498 (mmp-170) REVERT: E 299 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7394 (ttp80) REVERT: F 82 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.5877 (mpt90) REVERT: F 100 GLU cc_start: 0.7672 (pt0) cc_final: 0.7420 (pt0) REVERT: F 150 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6812 (ttp) REVERT: G 198 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5415 (mpt180) REVERT: G 259 MET cc_start: 0.6190 (mtm) cc_final: 0.5941 (mtm) REVERT: I 53 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8424 (p) REVERT: I 208 ARG cc_start: 0.7555 (mtm110) cc_final: 0.5615 (mmp-170) REVERT: I 218 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6264 (tpp) REVERT: I 233 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.5428 (mtm180) REVERT: I 237 MET cc_start: 0.6701 (ptp) cc_final: 0.6158 (ptt) REVERT: I 299 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7425 (ttp80) REVERT: I 339 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7513 (p0) REVERT: I 343 GLU cc_start: 0.7886 (pm20) cc_final: 0.7578 (pm20) REVERT: I 404 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: J 100 GLU cc_start: 0.7543 (pt0) cc_final: 0.6660 (mt-10) REVERT: J 111 TRP cc_start: 0.6480 (m100) cc_final: 0.5726 (m-10) REVERT: J 150 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6952 (ttp) REVERT: K 198 ARG cc_start: 0.6519 (mpt180) cc_final: 0.5699 (mmt-90) outliers start: 53 outliers final: 18 residues processed: 230 average time/residue: 0.6640 time to fit residues: 168.5504 Evaluate side-chains 225 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 TRP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 TRP Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 218 MET Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 48 TRP Chi-restraints excluded: chain J residue 150 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 146 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN F 240 ASN I 108 GLN I 399 ASN J 240 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101879 restraints weight = 17121.733| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.78 r_work: 0.3180 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17739 Z= 0.162 Angle : 0.562 8.493 24186 Z= 0.293 Chirality : 0.044 0.153 2613 Planarity : 0.005 0.094 3021 Dihedral : 5.251 52.371 2340 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.83 % Allowed : 15.06 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: 0.09 (0.18), residues: 2106 helix: 0.51 (0.17), residues: 948 sheet: 0.59 (0.26), residues: 399 loop : -0.67 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 236 TYR 0.020 0.001 TYR B 188 PHE 0.013 0.001 PHE A 98 TRP 0.013 0.001 TRP F 152 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00394 (17739) covalent geometry : angle 0.56185 (24186) hydrogen bonds : bond 0.03207 ( 801) hydrogen bonds : angle 5.00393 ( 2313) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 0.691 Fit side-chains TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it. REVERT: A 160 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: A 208 ARG cc_start: 0.7632 (mtm110) cc_final: 0.5624 (mmp-170) REVERT: A 237 MET cc_start: 0.7065 (ptp) cc_final: 0.6793 (ttp) REVERT: A 299 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: A 339 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7550 (p0) REVERT: A 343 GLU cc_start: 0.7918 (pm20) cc_final: 0.7597 (pm20) REVERT: A 404 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: B 42 MET cc_start: 0.7217 (mmp) cc_final: 0.6971 (mmp) REVERT: C 198 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.5733 (mmt90) REVERT: E 208 ARG cc_start: 0.7565 (mtm110) cc_final: 0.5541 (mmp-170) REVERT: F 82 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.5999 (mpt90) REVERT: F 100 GLU cc_start: 0.7757 (pt0) cc_final: 0.7452 (pt0) REVERT: F 150 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6845 (ttp) REVERT: G 126 GLU cc_start: 0.4765 (OUTLIER) cc_final: 0.4514 (tm-30) REVERT: G 198 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5365 (mpt180) REVERT: G 259 MET cc_start: 0.6288 (mtm) cc_final: 0.6066 (mtm) REVERT: I 208 ARG cc_start: 0.7613 (mtm110) cc_final: 0.5656 (mmp-170) REVERT: I 218 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6327 (tpp) REVERT: I 237 MET cc_start: 0.6856 (ptp) cc_final: 0.6258 (ptt) REVERT: I 299 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7498 (ttp80) REVERT: I 339 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7608 (p0) REVERT: I 343 GLU cc_start: 0.7927 (pm20) cc_final: 0.7637 (pm20) REVERT: I 404 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: J 100 GLU cc_start: 0.7570 (pt0) cc_final: 0.6650 (mt-10) REVERT: J 111 TRP cc_start: 0.6523 (m100) cc_final: 0.5751 (m-10) REVERT: J 150 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.6934 (ttp) REVERT: K 198 ARG cc_start: 0.6505 (mpt180) cc_final: 0.5669 (mmt-90) outliers start: 51 outliers final: 25 residues processed: 224 average time/residue: 0.6462 time to fit residues: 159.8958 Evaluate side-chains 226 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 TRP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 TRP Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain G residue 210 TYR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 218 MET Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 48 TRP Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 154 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 41 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN E 399 ASN F 240 ASN I 108 GLN I 399 ASN J 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102604 restraints weight = 17152.841| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.77 r_work: 0.3190 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17739 Z= 0.138 Angle : 0.548 8.420 24186 Z= 0.286 Chirality : 0.044 0.150 2613 Planarity : 0.005 0.092 3021 Dihedral : 5.197 52.283 2340 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.11 % Allowed : 15.00 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: 0.16 (0.18), residues: 2106 helix: 0.56 (0.17), residues: 948 sheet: 0.63 (0.26), residues: 399 loop : -0.62 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 236 TYR 0.018 0.001 TYR B 188 PHE 0.012 0.001 PHE A 98 TRP 0.012 0.001 TRP F 152 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00331 (17739) covalent geometry : angle 0.54798 (24186) hydrogen bonds : bond 0.03063 ( 801) hydrogen bonds : angle 4.96450 ( 2313) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.620 Fit side-chains TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it. REVERT: A 160 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: A 208 ARG cc_start: 0.7642 (mtm110) cc_final: 0.5622 (mmp-170) REVERT: A 237 MET cc_start: 0.7030 (ptp) cc_final: 0.6766 (ttp) REVERT: A 299 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7591 (ttp-170) REVERT: A 339 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7522 (p0) REVERT: A 343 GLU cc_start: 0.7896 (pm20) cc_final: 0.7602 (pm20) REVERT: A 404 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: B 42 MET cc_start: 0.7170 (mmp) cc_final: 0.6952 (mmp) REVERT: B 150 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7228 (tpp) REVERT: C 198 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.5655 (mmt90) REVERT: E 208 ARG cc_start: 0.7534 (mtm110) cc_final: 0.5543 (mmp-170) REVERT: E 299 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7397 (ttp80) REVERT: F 82 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.5905 (mpt90) REVERT: F 100 GLU cc_start: 0.7744 (pt0) cc_final: 0.7448 (pt0) REVERT: F 150 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6769 (ttp) REVERT: G 126 GLU cc_start: 0.4711 (OUTLIER) cc_final: 0.4465 (tm-30) REVERT: G 198 ARG cc_start: 0.6458 (mpt180) cc_final: 0.5333 (mpt180) REVERT: G 259 MET cc_start: 0.6200 (mtm) cc_final: 0.5990 (mtm) REVERT: I 208 ARG cc_start: 0.7591 (mtm110) cc_final: 0.5633 (mmp-170) REVERT: I 218 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6326 (tpp) REVERT: I 233 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.5474 (mtm180) REVERT: I 237 MET cc_start: 0.6840 (ptp) cc_final: 0.6264 (ptt) REVERT: I 299 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7428 (ttp80) REVERT: I 339 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7502 (p0) REVERT: I 343 GLU cc_start: 0.7892 (pm20) cc_final: 0.7600 (pm20) REVERT: I 404 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: J 100 GLU cc_start: 0.7538 (pt0) cc_final: 0.6634 (mt-10) REVERT: J 111 TRP cc_start: 0.6508 (m100) cc_final: 0.5731 (m-10) REVERT: J 150 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6852 (ttp) REVERT: K 198 ARG cc_start: 0.6396 (mpt180) cc_final: 0.5559 (mmt-90) outliers start: 56 outliers final: 25 residues processed: 225 average time/residue: 0.6745 time to fit residues: 167.2865 Evaluate side-chains 228 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 210 TYR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 218 MET Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 48 TRP Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 76 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN F 240 ASN I 108 GLN I 399 ASN J 240 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100773 restraints weight = 17064.967| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.76 r_work: 0.3168 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17739 Z= 0.209 Angle : 0.598 8.566 24186 Z= 0.312 Chirality : 0.046 0.163 2613 Planarity : 0.005 0.095 3021 Dihedral : 5.386 52.640 2340 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.83 % Allowed : 15.39 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -0.01 (0.18), residues: 2106 helix: 0.44 (0.17), residues: 945 sheet: 0.55 (0.26), residues: 399 loop : -0.74 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 236 TYR 0.021 0.002 TYR F 188 PHE 0.013 0.002 PHE A 98 TRP 0.014 0.002 TRP J 152 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00512 (17739) covalent geometry : angle 0.59846 (24186) hydrogen bonds : bond 0.03493 ( 801) hydrogen bonds : angle 5.12599 ( 2313) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.500 Fit side-chains TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it. REVERT: A 160 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: A 208 ARG cc_start: 0.7649 (mtm110) cc_final: 0.5641 (mmp-170) REVERT: A 237 MET cc_start: 0.7234 (ptp) cc_final: 0.6468 (ptt) REVERT: A 299 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7618 (ttp-170) REVERT: A 339 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7497 (p0) REVERT: A 343 GLU cc_start: 0.8087 (pm20) cc_final: 0.7761 (pm20) REVERT: A 404 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: B 150 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7292 (tpp) REVERT: C 198 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5859 (mpt180) REVERT: E 208 ARG cc_start: 0.7577 (mtm110) cc_final: 0.5538 (mmp-170) REVERT: E 299 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7444 (ttp80) REVERT: F 82 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6020 (mpt90) REVERT: F 100 GLU cc_start: 0.7840 (pt0) cc_final: 0.7487 (pt0) REVERT: F 150 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6888 (ttp) REVERT: G 126 GLU cc_start: 0.4773 (OUTLIER) cc_final: 0.4515 (tm-30) REVERT: G 198 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.5375 (mpt180) REVERT: I 208 ARG cc_start: 0.7652 (mtm110) cc_final: 0.5694 (mmp-170) REVERT: I 218 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6385 (tpp) REVERT: I 237 MET cc_start: 0.7066 (ptp) cc_final: 0.6338 (ptt) REVERT: I 299 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7516 (ttp80) REVERT: I 339 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7518 (p0) REVERT: I 343 GLU cc_start: 0.7992 (pm20) cc_final: 0.7678 (pm20) REVERT: I 404 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: J 111 TRP cc_start: 0.6564 (m100) cc_final: 0.5760 (m-10) REVERT: J 150 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6984 (ttp) REVERT: K 198 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.5393 (mpt180) outliers start: 51 outliers final: 25 residues processed: 227 average time/residue: 0.6666 time to fit residues: 166.9072 Evaluate side-chains 230 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain G residue 210 TYR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 218 MET Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 299 ARG Chi-restraints excluded: chain I residue 339 ASP Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 48 TRP Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 198 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 104 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN E 399 ASN F 240 ASN I 108 GLN I 399 ASN J 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103686 restraints weight = 17024.007| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.76 r_work: 0.3202 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17739 Z= 0.117 Angle : 0.533 8.342 24186 Z= 0.279 Chirality : 0.043 0.150 2613 Planarity : 0.005 0.091 3021 Dihedral : 5.134 52.106 2340 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.72 % Allowed : 15.61 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: 0.28 (0.18), residues: 2106 helix: 0.71 (0.18), residues: 927 sheet: 0.67 (0.26), residues: 399 loop : -0.60 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 236 TYR 0.015 0.001 TYR B 188 PHE 0.012 0.001 PHE I 71 TRP 0.011 0.001 TRP J 23 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00276 (17739) covalent geometry : angle 0.53325 (24186) hydrogen bonds : bond 0.02896 ( 801) hydrogen bonds : angle 4.92012 ( 2313) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5973.43 seconds wall clock time: 102 minutes 16.01 seconds (6136.01 seconds total)