Starting phenix.real_space_refine on Thu Jun 26 21:17:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ev9_31325/06_2025/7ev9_31325_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ev9_31325/06_2025/7ev9_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_31325/06_2025/7ev9_31325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ev9_31325/06_2025/7ev9_31325.map" model { file = "/net/cci-nas-00/data/ceres_data/7ev9_31325/06_2025/7ev9_31325_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ev9_31325/06_2025/7ev9_31325_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: G, K, F, J, E, I Time building chain proxies: 8.76, per 1000 atoms: 0.51 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: 4.19 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.88 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: 5.32 Time building geometry restraints manager: 5.03 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: 0.12 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } 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: 164.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 40.690 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 220.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP J 152 HIS 0.005 0.001 HIS J 232 PHE 0.021 0.002 PHE E 71 TYR 0.051 0.003 TYR G 210 ARG 0.006 0.001 ARG G 117 Details of bonding type rmsd hydrogen bonds : bond 0.15944 ( 801) hydrogen bonds : angle 7.95340 ( 2313) covalent geometry : bond 0.00657 (17739) covalent geometry : angle 0.88316 (24186) *********************** 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 : 1.978 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: 0.7520 (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: 0.6206 (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: 1.5092 time to fit residues: 429.9356 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 : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 166 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 193 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 187 ASN A 192 HIS A 265 GLN A 401 GLN B 103 ASN B 107 ASN B 187 ASN B 240 ASN C 134 HIS C 264 GLN 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 187 ASN I 192 HIS I 265 GLN I 399 ASN I 401 GLN ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN J 240 ASN K 134 HIS K 264 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106967 restraints weight = 16858.337| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.71 r_work: 0.3269 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17739 Z= 0.120 Angle : 0.566 8.529 24186 Z= 0.299 Chirality : 0.043 0.138 2613 Planarity : 0.006 0.098 3021 Dihedral : 5.568 51.544 2340 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.11 % Allowed : 10.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2106 helix: -0.82 (0.16), residues: 918 sheet: 0.10 (0.25), residues: 399 loop : -1.22 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 152 HIS 0.003 0.001 HIS I 33 PHE 0.013 0.001 PHE B 31 TYR 0.015 0.001 TYR B 188 ARG 0.005 0.000 ARG J 236 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 801) hydrogen bonds : angle 5.37911 ( 2313) covalent geometry : bond 0.00276 (17739) covalent geometry : angle 0.56550 (24186) *********************** 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 274 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 2.229 Fit side-chains REVERT: A 208 ARG cc_start: 0.7525 (mtm110) cc_final: 0.5476 (mmp-170) REVERT: A 237 MET cc_start: 0.7111 (ptp) cc_final: 0.6811 (ttp) REVERT: A 343 GLU cc_start: 0.7947 (pm20) cc_final: 0.7617 (pm20) REVERT: A 404 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8065 (tm-30) REVERT: B 43 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7990 (mp) REVERT: C 198 ARG cc_start: 0.6460 (mpt180) cc_final: 0.5874 (mpp-170) REVERT: E 208 ARG cc_start: 0.7504 (mtm110) cc_final: 0.5467 (mmp-170) REVERT: E 218 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6547 (tpp) REVERT: E 237 MET cc_start: 0.6978 (ptp) cc_final: 0.6686 (ttp) REVERT: E 343 GLU cc_start: 0.7972 (pm20) cc_final: 0.7609 (pm20) REVERT: E 399 ASN cc_start: 0.7637 (m-40) cc_final: 0.7392 (m110) REVERT: F 82 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6190 (mpt90) REVERT: G 198 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6380 (mpt180) REVERT: G 259 MET cc_start: 0.6134 (mtm) cc_final: 0.5827 (mtm) REVERT: I 135 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8258 (t70) REVERT: I 208 ARG cc_start: 0.7577 (mtm110) cc_final: 0.5643 (mmp-170) REVERT: I 218 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6659 (tpp) REVERT: I 237 MET cc_start: 0.7071 (ptp) cc_final: 0.6405 (ptt) REVERT: I 339 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7535 (p0) REVERT: I 343 GLU cc_start: 0.8034 (pm20) cc_final: 0.7669 (pm20) REVERT: I 404 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: J 111 TRP cc_start: 0.6368 (m100) cc_final: 0.5849 (m-10) outliers start: 38 outliers final: 1 residues processed: 255 average time/residue: 1.5820 time to fit residues: 448.4392 Evaluate side-chains 214 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 82 ARG Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain I residue 135 ASP Chi-restraints excluded: chain I residue 218 MET Chi-restraints excluded: chain I residue 339 ASP 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 123 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 209 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN E 72 HIS F 103 ASN F 107 ASN F 240 ASN I 72 HIS I 108 GLN I 399 ASN J 103 ASN J 107 ASN J 240 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103570 restraints weight = 16212.012| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.70 r_work: 0.3201 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1705 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= 0.128 Angle : 0.553 8.580 24186 Z= 0.290 Chirality : 0.043 0.138 2613 Planarity : 0.005 0.095 3021 Dihedral : 5.332 52.199 2340 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.78 % Allowed : 11.89 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2106 helix: -0.18 (0.17), residues: 942 sheet: 0.33 (0.26), residues: 399 loop : -0.96 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 152 HIS 0.004 0.001 HIS E 139 PHE 0.011 0.001 PHE A 71 TYR 0.017 0.001 TYR J 188 ARG 0.006 0.000 ARG J 236 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 801) hydrogen bonds : angle 5.12635 ( 2313) covalent geometry : bond 0.00303 (17739) covalent geometry : angle 0.55272 (24186) *********************** 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 265 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 2.034 Fit side-chains REVERT: A 160 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: A 208 ARG cc_start: 0.7587 (mtm110) cc_final: 0.5516 (mmp-170) REVERT: A 237 MET cc_start: 0.7022 (ptp) cc_final: 0.6756 (ttp) REVERT: A 299 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7581 (ttp-170) REVERT: A 343 GLU cc_start: 0.7934 (pm20) cc_final: 0.7641 (pm20) REVERT: A 404 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: B 43 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7901 (mp) REVERT: C 198 ARG cc_start: 0.6489 (mpt180) cc_final: 0.5611 (mpt180) REVERT: E 208 ARG cc_start: 0.7522 (mtm110) cc_final: 0.5509 (mmp-170) REVERT: E 218 MET cc_start: 0.6854 (tpp) cc_final: 0.6614 (tpp) REVERT: E 237 MET cc_start: 0.7014 (ptp) cc_final: 0.6739 (ttp) REVERT: E 299 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7431 (ttp80) REVERT: E 343 GLU cc_start: 0.7897 (pm20) cc_final: 0.7550 (pm20) REVERT: F 82 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6033 (mpt90) REVERT: G 198 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5556 (mpt180) REVERT: G 259 MET cc_start: 0.6197 (mtm) cc_final: 0.5924 (mtm) REVERT: I 53 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8406 (p) REVERT: I 135 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8268 (t70) REVERT: I 208 ARG cc_start: 0.7612 (mtm110) cc_final: 0.5662 (mmp-170) REVERT: I 237 MET cc_start: 0.6841 (ptp) cc_final: 0.6232 (ptt) REVERT: I 299 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7392 (ttp80) REVERT: I 339 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7478 (p0) REVERT: I 343 GLU cc_start: 0.7939 (pm20) cc_final: 0.7619 (pm20) REVERT: I 404 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: J 111 TRP cc_start: 0.6317 (m100) cc_final: 0.5701 (m-10) outliers start: 50 outliers final: 12 residues processed: 242 average time/residue: 1.3461 time to fit residues: 361.9918 Evaluate side-chains 227 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 352 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 43 LEU 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 251 MET 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 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 135 ASP 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 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 161 optimal weight: 0.1980 chunk 90 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 209 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.147553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.106576 restraints weight = 16928.469| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.74 r_work: 0.3263 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17739 Z= 0.115 Angle : 0.531 8.434 24186 Z= 0.278 Chirality : 0.043 0.136 2613 Planarity : 0.005 0.091 3021 Dihedral : 5.152 51.809 2340 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.67 % Allowed : 13.28 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2106 helix: 0.23 (0.17), residues: 945 sheet: 0.46 (0.26), residues: 399 loop : -0.77 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 152 HIS 0.004 0.001 HIS A 139 PHE 0.011 0.001 PHE E 71 TYR 0.015 0.001 TYR B 188 ARG 0.006 0.000 ARG J 236 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 801) hydrogen bonds : angle 4.94412 ( 2313) covalent geometry : bond 0.00270 (17739) covalent geometry : angle 0.53127 (24186) *********************** 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 264 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 1.947 Fit side-chains REVERT: A 160 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: A 208 ARG cc_start: 0.7608 (mtm110) cc_final: 0.5531 (mmp-170) REVERT: A 226 GLU cc_start: 0.7206 (pp20) cc_final: 0.6753 (pp20) REVERT: A 237 MET cc_start: 0.7083 (ptp) cc_final: 0.6839 (ttp) REVERT: A 299 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7619 (ttp-170) REVERT: A 343 GLU cc_start: 0.7885 (pm20) cc_final: 0.7574 (pm20) REVERT: A 404 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: B 42 MET cc_start: 0.7194 (mmp) cc_final: 0.6992 (mmp) REVERT: C 198 ARG cc_start: 0.6550 (mpt180) cc_final: 0.5800 (mmt90) REVERT: E 208 ARG cc_start: 0.7477 (mtm110) cc_final: 0.5507 (mmp-170) REVERT: F 82 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6039 (mpt90) REVERT: F 100 GLU cc_start: 0.7590 (pt0) cc_final: 0.7316 (pt0) REVERT: F 150 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6893 (ptt) REVERT: G 198 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6417 (mpt180) REVERT: G 259 MET cc_start: 0.6324 (mtm) cc_final: 0.6050 (mtm) REVERT: I 53 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8503 (p) REVERT: I 208 ARG cc_start: 0.7519 (mtm110) cc_final: 0.5533 (mmp-170) REVERT: I 233 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5526 (mtm180) REVERT: I 237 MET cc_start: 0.6849 (ptp) cc_final: 0.6407 (ptt) REVERT: I 299 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7422 (ttp80) REVERT: I 339 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7523 (p0) REVERT: I 343 GLU cc_start: 0.7885 (pm20) cc_final: 0.7584 (pm20) REVERT: I 404 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: J 100 GLU cc_start: 0.7479 (pt0) cc_final: 0.6303 (mt-10) REVERT: J 111 TRP cc_start: 0.6464 (m100) cc_final: 0.5855 (m-10) outliers start: 48 outliers final: 13 residues processed: 240 average time/residue: 1.3982 time to fit residues: 372.1511 Evaluate side-chains 222 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 273 LYS 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 191 THR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain F residue 43 LEU 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 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 48 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 88 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 180 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3763 r_free = 0.3763 target = 0.145061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.103884 restraints weight = 17375.891| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.77 r_work: 0.3246 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17739 Z= 0.173 Angle : 0.575 8.499 24186 Z= 0.300 Chirality : 0.045 0.146 2613 Planarity : 0.005 0.094 3021 Dihedral : 5.328 52.114 2340 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.11 % Allowed : 13.67 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2106 helix: 0.26 (0.17), residues: 948 sheet: 0.47 (0.26), residues: 399 loop : -0.78 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 152 HIS 0.003 0.001 HIS E 139 PHE 0.015 0.001 PHE J 27 TYR 0.020 0.001 TYR J 188 ARG 0.006 0.000 ARG J 236 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 801) hydrogen bonds : angle 5.06484 ( 2313) covalent geometry : bond 0.00420 (17739) covalent geometry : angle 0.57468 (24186) *********************** 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: 56 poor density : 194 time to evaluate : 1.798 Fit side-chains TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it. REVERT: A 160 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: A 208 ARG cc_start: 0.7662 (mtm110) cc_final: 0.5593 (mmp-170) REVERT: A 218 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7094 (ttp) REVERT: A 237 MET cc_start: 0.7155 (ptp) cc_final: 0.6861 (ttp) REVERT: A 299 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7667 (ttp-170) REVERT: A 339 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7593 (p0) REVERT: A 343 GLU cc_start: 0.7942 (pm20) cc_final: 0.7670 (pm20) REVERT: A 404 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: B 42 MET cc_start: 0.7214 (mmp) cc_final: 0.6999 (mmp) REVERT: C 198 ARG cc_start: 0.6508 (mpt180) cc_final: 0.5724 (mmt90) REVERT: E 208 ARG cc_start: 0.7533 (mtm110) cc_final: 0.5533 (mmp-170) REVERT: E 299 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7490 (ttp80) REVERT: F 82 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6104 (mpt90) REVERT: F 100 GLU cc_start: 0.7683 (pt0) cc_final: 0.7386 (pt0) REVERT: F 150 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6909 (ttp) REVERT: G 198 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5566 (mpt180) REVERT: G 259 MET cc_start: 0.6429 (mtm) cc_final: 0.6159 (mtm) REVERT: I 208 ARG cc_start: 0.7593 (mtm110) cc_final: 0.5674 (mmp-170) REVERT: I 233 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.5588 (mtm180) REVERT: I 237 MET cc_start: 0.6949 (ptp) cc_final: 0.6405 (ptt) REVERT: I 299 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7497 (ttp80) REVERT: I 339 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7612 (p0) REVERT: I 343 GLU cc_start: 0.7940 (pm20) cc_final: 0.7650 (pm20) REVERT: I 404 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: J 111 TRP cc_start: 0.6589 (m100) cc_final: 0.5902 (m-10) REVERT: J 150 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6919 (ttp) REVERT: K 198 ARG cc_start: 0.6835 (mpt180) cc_final: 0.5731 (mpt180) outliers start: 56 outliers final: 20 residues processed: 231 average time/residue: 1.3868 time to fit residues: 355.2014 Evaluate side-chains 227 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 218 MET 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 112 THR Chi-restraints excluded: chain B residue 191 THR 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 E residue 352 SER 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 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 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 112 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 42 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 102 optimal weight: 0.0370 chunk 136 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN E 176 GLN E 399 ASN F 240 ASN I 108 GLN I 399 ASN J 240 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.147297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.106509 restraints weight = 17153.954| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.75 r_work: 0.3277 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17739 Z= 0.110 Angle : 0.524 8.349 24186 Z= 0.275 Chirality : 0.043 0.142 2613 Planarity : 0.005 0.090 3021 Dihedral : 5.105 51.840 2340 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.50 % Allowed : 14.11 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2106 helix: 0.51 (0.17), residues: 945 sheet: 0.59 (0.26), residues: 399 loop : -0.62 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 152 HIS 0.004 0.001 HIS A 139 PHE 0.014 0.001 PHE J 27 TYR 0.014 0.001 TYR B 188 ARG 0.006 0.000 ARG J 236 Details of bonding type rmsd hydrogen bonds : bond 0.02847 ( 801) hydrogen bonds : angle 4.88286 ( 2313) covalent geometry : bond 0.00258 (17739) covalent geometry : angle 0.52402 (24186) *********************** 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 249 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 1.971 Fit side-chains REVERT: A 160 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: A 208 ARG cc_start: 0.7669 (mtm110) cc_final: 0.5656 (mmp-170) REVERT: A 226 GLU cc_start: 0.7215 (pp20) cc_final: 0.6757 (pp20) REVERT: A 237 MET cc_start: 0.7101 (ptp) cc_final: 0.6847 (ttp) REVERT: A 339 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7577 (p0) REVERT: A 343 GLU cc_start: 0.7945 (pm20) cc_final: 0.7675 (pm20) REVERT: A 404 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: B 42 MET cc_start: 0.7162 (mmp) cc_final: 0.6941 (mmp) REVERT: C 198 ARG cc_start: 0.6531 (mpt180) cc_final: 0.5792 (mmt90) REVERT: E 208 ARG cc_start: 0.7514 (mtm110) cc_final: 0.5578 (mmp-170) REVERT: E 226 GLU cc_start: 0.7257 (pp20) cc_final: 0.6841 (pp20) REVERT: E 299 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7487 (ttp80) REVERT: F 82 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6010 (mpt90) REVERT: F 84 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7153 (mmt90) REVERT: F 100 GLU cc_start: 0.7604 (pt0) cc_final: 0.7331 (pt0) REVERT: F 150 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6895 (ttp) REVERT: G 198 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.5788 (mmt-90) REVERT: G 259 MET cc_start: 0.6351 (mtm) cc_final: 0.6110 (mtm) REVERT: I 53 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8531 (p) REVERT: I 208 ARG cc_start: 0.7539 (mtm110) cc_final: 0.5595 (mmp-170) REVERT: I 233 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5594 (mtm180) REVERT: I 237 MET cc_start: 0.6871 (ptp) cc_final: 0.6333 (ptt) REVERT: I 299 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7425 (ttp80) REVERT: I 339 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7528 (p0) REVERT: I 343 GLU cc_start: 0.7910 (pm20) cc_final: 0.7625 (pm20) REVERT: I 404 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: J 111 TRP cc_start: 0.6608 (m100) cc_final: 0.5909 (m-10) REVERT: J 150 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7040 (ttp) REVERT: K 198 ARG cc_start: 0.6685 (mpt180) cc_final: 0.5895 (mmt-90) outliers start: 45 outliers final: 15 residues processed: 230 average time/residue: 1.4897 time to fit residues: 378.0136 Evaluate side-chains 224 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 273 LYS 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 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 251 MET Chi-restraints excluded: chain E residue 299 ARG 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 I residue 53 SER Chi-restraints excluded: chain I residue 170 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 121 optimal weight: 2.9990 chunk 160 optimal weight: 0.0670 chunk 162 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 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 = 0.3742 r_free = 0.3742 target = 0.144434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104232 restraints weight = 16864.862| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.76 r_work: 0.3206 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17739 Z= 0.114 Angle : 0.526 8.263 24186 Z= 0.275 Chirality : 0.043 0.140 2613 Planarity : 0.005 0.091 3021 Dihedral : 5.059 52.116 2340 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.67 % Allowed : 14.50 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2106 helix: 0.63 (0.17), residues: 945 sheet: 0.51 (0.26), residues: 393 loop : -0.54 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 152 HIS 0.003 0.001 HIS A 139 PHE 0.013 0.001 PHE J 27 TYR 0.015 0.001 TYR B 188 ARG 0.006 0.000 ARG J 236 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 801) hydrogen bonds : angle 4.85415 ( 2313) covalent geometry : bond 0.00269 (17739) covalent geometry : angle 0.52566 (24186) *********************** 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: 48 poor density : 200 time to evaluate : 2.028 Fit side-chains TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it. REVERT: A 160 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: A 208 ARG cc_start: 0.7660 (mtm110) cc_final: 0.5659 (mmp-170) REVERT: A 237 MET cc_start: 0.7021 (ptp) cc_final: 0.6775 (ttp) REVERT: A 299 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7627 (ttp-170) REVERT: A 339 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7545 (p0) REVERT: A 343 GLU cc_start: 0.7961 (pm20) cc_final: 0.7670 (pm20) REVERT: A 404 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: B 43 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7842 (mp) REVERT: C 198 ARG cc_start: 0.6440 (mpt180) cc_final: 0.5696 (mmt90) REVERT: E 208 ARG cc_start: 0.7497 (mtm110) cc_final: 0.5486 (mmp-170) REVERT: E 226 GLU cc_start: 0.7165 (pp20) cc_final: 0.6823 (pp20) REVERT: E 237 MET cc_start: 0.7094 (ttp) cc_final: 0.6584 (mtm) REVERT: E 299 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7434 (ttp80) REVERT: F 82 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.5879 (mpt90) REVERT: F 84 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7132 (mmt90) REVERT: F 100 GLU cc_start: 0.7547 (pt0) cc_final: 0.7303 (pt0) REVERT: F 150 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6843 (ttp) REVERT: G 198 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.5519 (mpt180) REVERT: G 259 MET cc_start: 0.6269 (mtm) cc_final: 0.6011 (mtm) REVERT: I 53 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8459 (p) REVERT: I 208 ARG cc_start: 0.7572 (mtm110) cc_final: 0.5630 (mmp-170) REVERT: I 233 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.5447 (mtm180) REVERT: I 237 MET cc_start: 0.6788 (ptp) cc_final: 0.6234 (ptt) REVERT: I 299 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7436 (ttp80) REVERT: I 339 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7531 (p0) REVERT: I 343 GLU cc_start: 0.7920 (pm20) cc_final: 0.7596 (pm20) REVERT: I 404 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: J 100 GLU cc_start: 0.7563 (pt0) cc_final: 0.6781 (mt-10) REVERT: J 111 TRP cc_start: 0.6500 (m100) cc_final: 0.5790 (m-10) REVERT: J 150 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6914 (ttp) REVERT: K 198 ARG cc_start: 0.6547 (mpt180) cc_final: 0.5755 (mmt-90) outliers start: 48 outliers final: 18 residues processed: 229 average time/residue: 1.4388 time to fit residues: 364.6194 Evaluate side-chains 229 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 273 LYS 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 43 LEU 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 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 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 170 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 180 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.141230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100834 restraints weight = 17028.093| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.76 r_work: 0.3167 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17739 Z= 0.219 Angle : 0.606 8.632 24186 Z= 0.316 Chirality : 0.046 0.173 2613 Planarity : 0.006 0.095 3021 Dihedral : 5.421 52.795 2340 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.94 % Allowed : 14.83 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP J 152 HIS 0.004 0.001 HIS A 139 PHE 0.013 0.002 PHE J 27 TYR 0.021 0.002 TYR J 188 ARG 0.007 0.000 ARG J 236 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 801) hydrogen bonds : angle 5.15145 ( 2313) covalent geometry : bond 0.00534 (17739) covalent geometry : angle 0.60601 (24186) *********************** 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 247 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 1.788 Fit side-chains TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it. REVERT: A 160 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: A 208 ARG cc_start: 0.7690 (mtm110) cc_final: 0.5662 (mmp-170) REVERT: A 237 MET cc_start: 0.7255 (ptp) cc_final: 0.6484 (ptt) REVERT: A 299 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7598 (ttp-170) REVERT: A 339 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7494 (p0) REVERT: A 343 GLU cc_start: 0.8062 (pm20) cc_final: 0.7729 (pm20) REVERT: A 404 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: B 42 MET cc_start: 0.7225 (mmp) cc_final: 0.6957 (mmp) REVERT: B 150 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7252 (tpp) REVERT: C 198 ARG cc_start: 0.6443 (mpt180) cc_final: 0.5308 (mpt180) REVERT: E 208 ARG cc_start: 0.7584 (mtm110) cc_final: 0.5531 (mmp-170) REVERT: E 237 MET cc_start: 0.7158 (ttp) cc_final: 0.6656 (mtm) REVERT: F 82 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6013 (mpt90) REVERT: F 84 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7162 (mmt90) REVERT: F 100 GLU cc_start: 0.7721 (pt0) cc_final: 0.7331 (pt0) REVERT: F 150 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6817 (ttp) REVERT: G 198 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.6111 (mpt180) REVERT: G 259 MET cc_start: 0.6346 (mtm) cc_final: 0.6123 (mtm) REVERT: I 208 ARG cc_start: 0.7617 (mtm110) cc_final: 0.5677 (mmp-170) REVERT: I 237 MET cc_start: 0.7020 (ptp) cc_final: 0.6301 (ptt) REVERT: I 299 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7458 (ttp80) REVERT: I 339 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7581 (p0) REVERT: I 343 GLU cc_start: 0.8007 (pm20) cc_final: 0.7687 (pm20) REVERT: I 404 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: J 111 TRP cc_start: 0.6519 (m100) cc_final: 0.5777 (m-10) REVERT: J 150 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6985 (ttp) REVERT: K 198 ARG cc_start: 0.6520 (mpt180) cc_final: 0.5611 (mpt180) outliers start: 53 outliers final: 21 residues processed: 227 average time/residue: 1.4140 time to fit residues: 357.3243 Evaluate side-chains 224 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 29 VAL 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 B residue 191 THR 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 352 SER 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7381 > 50: distance: 18 - 23: 11.384 distance: 23 - 24: 13.307 distance: 23 - 178: 13.347 distance: 24 - 25: 39.129 distance: 25 - 26: 24.086 distance: 25 - 27: 15.983 distance: 26 - 175: 10.177 distance: 27 - 28: 30.248 distance: 28 - 29: 62.991 distance: 28 - 31: 30.633 distance: 29 - 30: 26.225 distance: 29 - 35: 69.738 distance: 31 - 32: 24.081 distance: 32 - 33: 38.661 distance: 33 - 34: 39.293 distance: 35 - 36: 68.466 distance: 35 - 41: 31.826 distance: 36 - 37: 56.650 distance: 36 - 39: 15.291 distance: 37 - 38: 37.097 distance: 37 - 42: 41.629 distance: 39 - 40: 37.912 distance: 40 - 41: 18.779 distance: 42 - 43: 57.494 distance: 43 - 44: 43.562 distance: 44 - 45: 45.994 distance: 44 - 46: 43.600 distance: 46 - 47: 21.269 distance: 46 - 52: 36.827 distance: 47 - 48: 13.673 distance: 47 - 50: 29.334 distance: 48 - 49: 33.978 distance: 48 - 53: 40.385 distance: 50 - 51: 27.447 distance: 51 - 52: 22.171 distance: 53 - 54: 33.634 distance: 54 - 55: 59.169 distance: 54 - 57: 15.590 distance: 55 - 56: 25.606 distance: 55 - 60: 52.011 distance: 57 - 58: 49.900 distance: 57 - 59: 54.575 distance: 60 - 61: 16.037 distance: 61 - 62: 43.413 distance: 61 - 64: 13.588 distance: 62 - 63: 36.561 distance: 62 - 71: 40.857 distance: 64 - 65: 39.030 distance: 65 - 66: 22.603 distance: 65 - 67: 36.359 distance: 66 - 68: 30.086 distance: 67 - 69: 11.389 distance: 68 - 70: 20.827 distance: 69 - 70: 14.208 distance: 71 - 72: 34.039 distance: 71 - 126: 18.815 distance: 72 - 73: 42.956 distance: 72 - 75: 46.180 distance: 73 - 74: 42.897 distance: 73 - 79: 55.190 distance: 74 - 123: 23.680 distance: 75 - 76: 30.833 distance: 75 - 77: 23.676 distance: 76 - 78: 28.914 distance: 79 - 80: 15.028 distance: 80 - 81: 12.944 distance: 80 - 83: 25.803 distance: 81 - 82: 14.232 distance: 81 - 90: 16.812 distance: 83 - 84: 27.952 distance: 84 - 85: 14.894 distance: 85 - 86: 12.075 distance: 86 - 87: 9.690 distance: 87 - 88: 9.066 distance: 87 - 89: 10.811 distance: 90 - 91: 12.767 distance: 90 - 112: 14.752 distance: 91 - 92: 23.714 distance: 91 - 94: 10.338 distance: 92 - 93: 25.195 distance: 92 - 99: 20.886 distance: 94 - 95: 25.257 distance: 95 - 96: 25.243 distance: 96 - 97: 14.117 distance: 97 - 98: 6.602