Starting phenix.real_space_refine on Fri Aug 7 23:25:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10pm_75375/08_2026/10pm_75375.cif Found real_map, /net/cci-nas-00/data/ceres_data/10pm_75375/08_2026/10pm_75375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10pm_75375/08_2026/10pm_75375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10pm_75375/08_2026/10pm_75375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10pm_75375/08_2026/10pm_75375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10pm_75375/08_2026/10pm_75375.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 198 5.16 5 C 14542 2.51 5 N 4411 2.21 5 O 4719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23870 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "D" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "C" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "B" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "K" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "J" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "I" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "H" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "G" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "F" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Chain: "E" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2170 Classifications: {'peptide': 285} Link IDs: {'TRANS': 284} Time building chain proxies: 5.19, per 1000 atoms: 0.22 Number of scatterers: 23870 At special positions: 0 Unit cell: (149.52, 151.656, 199.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 198 16.00 O 4719 8.00 N 4411 7.00 C 14542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 15 sheets defined 70.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.973A pdb=" N ILE A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 99 removed outlier: 3.610A pdb=" N ALA A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 128 removed outlier: 4.187A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 246 removed outlier: 4.291A pdb=" N GLY A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 276 removed outlier: 3.509A pdb=" N GLU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.554A pdb=" N LEU A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 281 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 33 removed outlier: 3.722A pdb=" N PHE D 11 " --> pdb=" O MET D 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 98 removed outlier: 3.834A pdb=" N LYS D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET D 87 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 91 " --> pdb=" O MET D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 127 removed outlier: 3.533A pdb=" N GLU D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 246 removed outlier: 3.575A pdb=" N ARG D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 226 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 276 Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.899A pdb=" N VAL D 281 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 33 removed outlier: 4.126A pdb=" N SER C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 98 removed outlier: 3.562A pdb=" N ASN C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE C 79 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 90 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 91 " --> pdb=" O MET C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 127 removed outlier: 3.692A pdb=" N GLU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 246 removed outlier: 4.356A pdb=" N GLY C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C 204 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 207 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 278 removed outlier: 3.522A pdb=" N GLU C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'B' and resid 6 through 32 removed outlier: 4.184A pdb=" N MET B 10 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 11 " --> pdb=" O MET B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 98 removed outlier: 3.505A pdb=" N ALA B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 127 removed outlier: 4.006A pdb=" N GLN B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 246 removed outlier: 4.126A pdb=" N GLY B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 277 Processing helix chain 'B' and resid 278 through 284 removed outlier: 3.707A pdb=" N VAL B 281 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 33 removed outlier: 3.618A pdb=" N PHE K 11 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA K 12 " --> pdb=" O SER K 8 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG K 22 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 99 removed outlier: 3.658A pdb=" N LYS K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE K 72 " --> pdb=" O ASN K 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG K 91 " --> pdb=" O MET K 87 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN K 99 " --> pdb=" O VAL K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 128 removed outlier: 3.630A pdb=" N GLN K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 110 " --> pdb=" O ASP K 106 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU K 113 " --> pdb=" O GLN K 109 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA K 119 " --> pdb=" O SER K 115 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU K 120 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL K 121 " --> pdb=" O LEU K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 247 removed outlier: 3.507A pdb=" N ASN K 197 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE K 200 " --> pdb=" O ALA K 196 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY K 201 " --> pdb=" O ASN K 197 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE K 210 " --> pdb=" O GLY K 206 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN K 211 " --> pdb=" O LEU K 207 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG K 223 " --> pdb=" O GLY K 219 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL K 229 " --> pdb=" O GLU K 225 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN K 237 " --> pdb=" O ILE K 233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE K 245 " --> pdb=" O ALA K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 275 Processing helix chain 'K' and resid 276 through 285 removed outlier: 3.602A pdb=" N LEU K 280 " --> pdb=" O ASN K 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 33 removed outlier: 4.279A pdb=" N MET J 10 " --> pdb=" O ASN J 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE J 11 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG J 22 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 98 removed outlier: 3.616A pdb=" N LEU J 46 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 55 " --> pdb=" O LYS J 51 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY J 69 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN J 71 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA J 76 " --> pdb=" O PHE J 72 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU J 77 " --> pdb=" O ILE J 73 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 128 removed outlier: 3.623A pdb=" N GLN J 116 " --> pdb=" O VAL J 112 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA J 119 " --> pdb=" O SER J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 246 removed outlier: 3.561A pdb=" N ILE J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY J 201 " --> pdb=" O ASN J 197 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR J 202 " --> pdb=" O ARG J 198 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 213 " --> pdb=" O LYS J 209 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU J 226 " --> pdb=" O ASN J 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR J 227 " --> pdb=" O ARG J 223 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE J 233 " --> pdb=" O VAL J 229 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG J 244 " --> pdb=" O ALA J 240 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 275 removed outlier: 3.779A pdb=" N GLN J 253 " --> pdb=" O ASP J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 285 Processing helix chain 'I' and resid 6 through 33 removed outlier: 3.583A pdb=" N GLY I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS I 25 " --> pdb=" O VAL I 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU I 30 " --> pdb=" O ASP I 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER I 32 " --> pdb=" O GLU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 99 removed outlier: 3.647A pdb=" N LEU I 46 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS I 51 " --> pdb=" O ALA I 47 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG I 57 " --> pdb=" O ARG I 53 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN I 71 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA I 76 " --> pdb=" O PHE I 72 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN I 99 " --> pdb=" O VAL I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 127 removed outlier: 3.505A pdb=" N GLU I 113 " --> pdb=" O GLN I 109 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN I 116 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU I 120 " --> pdb=" O GLN I 116 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 246 removed outlier: 3.615A pdb=" N ILE I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY I 201 " --> pdb=" O ASN I 197 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR I 202 " --> pdb=" O ARG I 198 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL I 229 " --> pdb=" O GLU I 225 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE I 245 " --> pdb=" O ALA I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 276 removed outlier: 3.764A pdb=" N LYS I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 284 removed outlier: 3.640A pdb=" N LEU I 280 " --> pdb=" O ASN I 277 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL I 281 " --> pdb=" O SER I 278 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET I 282 " --> pdb=" O GLN I 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 33 removed outlier: 3.561A pdb=" N PHE H 11 " --> pdb=" O MET H 7 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 12 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 98 removed outlier: 3.609A pdb=" N LYS H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG H 57 " --> pdb=" O ARG H 53 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE H 79 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 127 removed outlier: 3.874A pdb=" N GLN H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 247 removed outlier: 4.251A pdb=" N GLY H 201 " --> pdb=" O ASN H 197 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL H 229 " --> pdb=" O GLU H 225 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY H 230 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN H 237 " --> pdb=" O ILE H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 278 removed outlier: 3.511A pdb=" N GLN H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN H 276 " --> pdb=" O ALA H 272 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER H 278 " --> pdb=" O ALA H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'G' and resid 6 through 32 removed outlier: 3.567A pdb=" N GLY G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 99 removed outlier: 3.639A pdb=" N LYS G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR G 83 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN G 99 " --> pdb=" O VAL G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 127 removed outlier: 3.760A pdb=" N GLU G 113 " --> pdb=" O GLN G 109 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN G 116 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP G 122 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 178 Processing helix chain 'G' and resid 192 through 247 removed outlier: 4.318A pdb=" N GLY G 201 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR G 202 " --> pdb=" O ARG G 198 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR G 227 " --> pdb=" O ARG G 223 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY G 230 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP G 232 " --> pdb=" O VAL G 228 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 275 Processing helix chain 'F' and resid 6 through 33 removed outlier: 3.578A pdb=" N PHE F 11 " --> pdb=" O MET F 7 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 99 removed outlier: 3.548A pdb=" N ARG F 57 " --> pdb=" O ARG F 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE F 79 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR F 83 " --> pdb=" O PHE F 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 3.755A pdb=" N GLN F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 246 removed outlier: 3.527A pdb=" N ARG F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY F 201 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG F 223 " --> pdb=" O GLY F 219 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP F 232 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 277 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'E' and resid 6 through 33 removed outlier: 3.637A pdb=" N ALA E 12 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 31 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 98 removed outlier: 3.632A pdb=" N LYS E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 69 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR E 83 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG E 91 " --> pdb=" O MET E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 127 removed outlier: 3.927A pdb=" N GLU E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 247 removed outlier: 3.518A pdb=" N ILE E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY E 201 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 226 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP E 232 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA E 234 " --> pdb=" O GLY E 230 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 276 removed outlier: 3.577A pdb=" N GLN E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN E 261 " --> pdb=" O TYR E 257 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 285 removed outlier: 4.862A pdb=" N LEU E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 281 " --> pdb=" O SER E 278 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 156 Processing sheet with id=AA2, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'D' and resid 154 through 156 Processing sheet with id=AA4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AA5, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AA6, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.675A pdb=" N MET K 153 " --> pdb=" O VAL K 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 137 through 140 removed outlier: 6.022A pdb=" N GLY J 138 " --> pdb=" O THR J 171 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR J 171 " --> pdb=" O GLY J 138 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE J 140 " --> pdb=" O ILE J 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 153 through 155 removed outlier: 4.754A pdb=" N MET J 153 " --> pdb=" O VAL J 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 180 through 181 removed outlier: 3.799A pdb=" N LYS J 186 " --> pdb=" O ASP J 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 137 through 140 removed outlier: 6.150A pdb=" N GLY I 138 " --> pdb=" O THR I 171 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N THR I 171 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE I 140 " --> pdb=" O ILE I 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AB3, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.656A pdb=" N MET H 153 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'F' and resid 153 through 156 removed outlier: 4.624A pdb=" N MET F 153 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 154 through 156 1731 hydrogen bonds defined for protein. 5070 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: 4.65 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7322 1.33 - 1.46: 4935 1.46 - 1.58: 11358 1.58 - 1.71: 2 1.71 - 1.83: 396 Bond restraints: 24013 Sorted by residual: bond pdb=" CA ASN C 6 " pdb=" CB ASN C 6 " ideal model delta sigma weight residual 1.533 1.652 -0.119 2.29e-02 1.91e+03 2.70e+01 bond pdb=" CA ASN J 6 " pdb=" CB ASN J 6 " ideal model delta sigma weight residual 1.531 1.599 -0.068 1.52e-02 4.33e+03 2.02e+01 bond pdb=" CB ASN H 197 " pdb=" CG ASN H 197 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 5.00e+00 bond pdb=" CB ASN B 277 " pdb=" CG ASN B 277 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.65e+00 bond pdb=" CB ASP C 194 " pdb=" CG ASP C 194 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.28e+00 ... (remaining 24008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 31479 3.42 - 6.84: 614 6.84 - 10.26: 108 10.26 - 13.68: 28 13.68 - 17.10: 12 Bond angle restraints: 32241 Sorted by residual: angle pdb=" N ASN I 131 " pdb=" CA ASN I 131 " pdb=" C ASN I 131 " ideal model delta sigma weight residual 111.52 102.32 9.20 1.40e+00 5.10e-01 4.32e+01 angle pdb=" CB ARG F 223 " pdb=" CG ARG F 223 " pdb=" CD ARG F 223 " ideal model delta sigma weight residual 111.30 96.32 14.98 2.30e+00 1.89e-01 4.24e+01 angle pdb=" C ASN J 6 " pdb=" CA ASN J 6 " pdb=" CB ASN J 6 " ideal model delta sigma weight residual 109.72 119.82 -10.10 1.73e+00 3.34e-01 3.41e+01 angle pdb=" CA GLN D 111 " pdb=" CB GLN D 111 " pdb=" CG GLN D 111 " ideal model delta sigma weight residual 114.10 125.72 -11.62 2.00e+00 2.50e-01 3.38e+01 angle pdb=" CA ARG F 223 " pdb=" CB ARG F 223 " pdb=" CG ARG F 223 " ideal model delta sigma weight residual 114.10 125.52 -11.42 2.00e+00 2.50e-01 3.26e+01 ... (remaining 32236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12437 17.94 - 35.87: 1807 35.87 - 53.81: 524 53.81 - 71.74: 115 71.74 - 89.68: 22 Dihedral angle restraints: 14905 sinusoidal: 5951 harmonic: 8954 Sorted by residual: dihedral pdb=" CA ASN H 4 " pdb=" C ASN H 4 " pdb=" N HIS H 5 " pdb=" CA HIS H 5 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ASN A 134 " pdb=" C ASN A 134 " pdb=" N MET A 135 " pdb=" CA MET A 135 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ILE H 245 " pdb=" C ILE H 245 " pdb=" N ARG H 246 " pdb=" CA ARG H 246 " ideal model delta harmonic sigma weight residual -180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 14902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3535 0.110 - 0.221: 167 0.221 - 0.331: 12 0.331 - 0.441: 2 0.441 - 0.551: 2 Chirality restraints: 3718 Sorted by residual: chirality pdb=" CG LEU E 30 " pdb=" CB LEU E 30 " pdb=" CD1 LEU E 30 " pdb=" CD2 LEU E 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" CB ILE G 36 " pdb=" CA ILE G 36 " pdb=" CG1 ILE G 36 " pdb=" CG2 ILE G 36 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CG LEU D 117 " pdb=" CB LEU D 117 " pdb=" CD1 LEU D 117 " pdb=" CD2 LEU D 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3715 not shown) Planarity restraints: 4301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 6 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C ASN D 6 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN D 6 " 0.021 2.00e-02 2.50e+03 pdb=" N MET D 7 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 131 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C ASN A 131 " -0.052 2.00e-02 2.50e+03 pdb=" O ASN A 131 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 132 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 130 " -0.015 2.00e-02 2.50e+03 2.05e-02 7.32e+00 pdb=" CG PHE I 130 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE I 130 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE I 130 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE I 130 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 130 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 130 " -0.000 2.00e-02 2.50e+03 ... (remaining 4298 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6087 2.78 - 3.31: 23352 3.31 - 3.84: 37997 3.84 - 4.37: 44400 4.37 - 4.90: 72157 Nonbonded interactions: 183993 Sorted by model distance: nonbonded pdb=" O ALA K 195 " pdb=" OG SER K 199 " model vdw 2.253 3.040 nonbonded pdb=" O ILE H 262 " pdb=" OG1 THR H 266 " model vdw 2.255 3.040 nonbonded pdb=" O ALA D 196 " pdb=" OG SER D 199 " model vdw 2.258 3.040 nonbonded pdb=" N ASN I 71 " pdb=" OD1 ASN I 71 " model vdw 2.267 3.120 nonbonded pdb=" O LEU C 80 " pdb=" OG1 THR C 84 " model vdw 2.267 3.040 ... (remaining 183988 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.860 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.006 0.119 24013 Z= 0.257 Angle : 1.224 17.099 32241 Z= 0.654 Chirality : 0.055 0.551 3718 Planarity : 0.007 0.082 4301 Dihedral : 18.611 89.680 9119 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.55 % Allowed : 41.88 % Favored : 56.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.11), residues: 3113 helix: -2.33 (0.08), residues: 2035 sheet: None (None), residues: 0 loop : -1.84 (0.15), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG F 223 TYR 0.037 0.004 TYR J 220 PHE 0.047 0.004 PHE I 130 TRP 0.026 0.005 TRP A 154 HIS 0.010 0.002 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.26 (24013) covalent geometry : angle 1.22434 / 0.65 (32241) hydrogen bonds : bond 0.28157 / 19.11 ( 1731) hydrogen bonds : angle 8.98186 / 6.34 ( 5070) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 701 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9237 (m-10) cc_final: 0.8979 (m-10) REVERT: A 108 MET cc_start: 0.9400 (tpp) cc_final: 0.9170 (tpp) REVERT: A 161 MET cc_start: 0.8084 (ttm) cc_final: 0.7781 (tpt) REVERT: A 252 LYS cc_start: 0.9579 (mmmm) cc_final: 0.9143 (mmtm) REVERT: A 254 MET cc_start: 0.9511 (mmm) cc_final: 0.9241 (tpp) REVERT: A 256 GLU cc_start: 0.9152 (tt0) cc_final: 0.8827 (tp30) REVERT: A 259 LYS cc_start: 0.9161 (tmtp) cc_final: 0.8581 (tttp) REVERT: A 277 ASN cc_start: 0.9482 (OUTLIER) cc_final: 0.9266 (p0) REVERT: D 11 PHE cc_start: 0.9323 (t80) cc_final: 0.8423 (t80) REVERT: D 27 ILE cc_start: 0.9595 (tp) cc_final: 0.9121 (pt) REVERT: D 30 LEU cc_start: 0.9449 (tp) cc_final: 0.9014 (tt) REVERT: D 36 ILE cc_start: 0.9531 (mp) cc_final: 0.9231 (mt) REVERT: D 108 MET cc_start: 0.9393 (tpt) cc_final: 0.9135 (tpp) REVERT: D 172 MET cc_start: 0.9065 (mmm) cc_final: 0.8854 (mmp) REVERT: D 221 GLN cc_start: 0.8808 (tt0) cc_final: 0.8372 (tp40) REVERT: D 256 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8607 (tp30) REVERT: D 257 TYR cc_start: 0.9428 (t80) cc_final: 0.9037 (t80) REVERT: D 275 ASN cc_start: 0.9067 (t0) cc_final: 0.8841 (t0) REVERT: C 26 ASP cc_start: 0.8236 (m-30) cc_final: 0.7337 (m-30) REVERT: C 133 MET cc_start: 0.8829 (ttt) cc_final: 0.8624 (ttp) REVERT: C 139 ARG cc_start: 0.8474 (ttt180) cc_final: 0.7455 (mmt180) REVERT: C 186 LYS cc_start: 0.9240 (mtmt) cc_final: 0.8966 (mtmm) REVERT: C 208 LYS cc_start: 0.9535 (mtpt) cc_final: 0.9085 (mtmm) REVERT: C 256 GLU cc_start: 0.8787 (tp30) cc_final: 0.8261 (tm-30) REVERT: C 259 LYS cc_start: 0.9597 (pptt) cc_final: 0.9325 (tmmt) REVERT: B 26 ASP cc_start: 0.8566 (m-30) cc_final: 0.8251 (t0) REVERT: B 108 MET cc_start: 0.9096 (ttp) cc_final: 0.8765 (tpt) REVERT: B 135 MET cc_start: 0.8465 (ptp) cc_final: 0.7983 (ptp) REVERT: B 186 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8658 (ttmm) REVERT: B 232 ASP cc_start: 0.9202 (m-30) cc_final: 0.8978 (m-30) REVERT: B 242 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8324 (tp30) REVERT: B 252 LYS cc_start: 0.9464 (mmmm) cc_final: 0.8975 (mmpt) REVERT: K 11 PHE cc_start: 0.8645 (t80) cc_final: 0.8065 (t80) REVERT: K 15 THR cc_start: 0.9305 (m) cc_final: 0.9033 (m) REVERT: K 70 ILE cc_start: 0.8866 (mt) cc_final: 0.8637 (tp) REVERT: K 161 MET cc_start: 0.8925 (ptt) cc_final: 0.8161 (tpp) REVERT: K 167 VAL cc_start: 0.9593 (t) cc_final: 0.9165 (p) REVERT: K 252 LYS cc_start: 0.9681 (mmmm) cc_final: 0.9023 (mmtt) REVERT: K 256 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8553 (tp30) REVERT: K 259 LYS cc_start: 0.4557 (tttt) cc_final: 0.4297 (tttt) REVERT: K 268 ILE cc_start: 0.9406 (mm) cc_final: 0.9154 (mt) REVERT: J 16 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8975 (tm-30) REVERT: J 42 ASP cc_start: 0.8531 (t0) cc_final: 0.8255 (t0) REVERT: J 77 GLU cc_start: 0.6525 (tt0) cc_final: 0.5549 (tp30) REVERT: J 155 PHE cc_start: 0.8665 (m-80) cc_final: 0.7938 (m-80) REVERT: J 232 ASP cc_start: 0.9015 (m-30) cc_final: 0.8573 (m-30) REVERT: J 233 ILE cc_start: 0.9096 (tt) cc_final: 0.8399 (mm) REVERT: J 236 GLU cc_start: 0.5813 (tt0) cc_final: 0.5114 (mt-10) REVERT: J 257 TYR cc_start: 0.9520 (t80) cc_final: 0.9279 (t80) REVERT: I 16 GLN cc_start: 0.9145 (tp40) cc_final: 0.8835 (tp-100) REVERT: I 52 MET cc_start: 0.9117 (mtm) cc_final: 0.8825 (mpp) REVERT: I 135 MET cc_start: 0.8796 (ptp) cc_final: 0.8532 (ptt) REVERT: I 204 ASP cc_start: 0.9399 (OUTLIER) cc_final: 0.9171 (m-30) REVERT: I 256 GLU cc_start: 0.8040 (tm-30) cc_final: 0.6720 (tm-30) REVERT: I 260 ASN cc_start: 0.9216 (m-40) cc_final: 0.8738 (m110) REVERT: I 283 SER cc_start: 0.9694 (m) cc_final: 0.9465 (p) REVERT: H 26 ASP cc_start: 0.9033 (m-30) cc_final: 0.6368 (m-30) REVERT: H 29 LYS cc_start: 0.9507 (mttt) cc_final: 0.9128 (mttp) REVERT: H 50 GLU cc_start: 0.9388 (mm-30) cc_final: 0.8914 (pt0) REVERT: H 77 GLU cc_start: 0.8855 (pp20) cc_final: 0.8473 (pp20) REVERT: H 172 MET cc_start: 0.8842 (tpp) cc_final: 0.8265 (mpp) REVERT: H 211 ASN cc_start: 0.9471 (m110) cc_final: 0.9080 (m-40) REVERT: H 242 GLU cc_start: 0.9028 (tp30) cc_final: 0.8550 (tp30) REVERT: H 252 LYS cc_start: 0.9364 (ttmt) cc_final: 0.9147 (mptt) REVERT: G 10 MET cc_start: 0.9646 (mtp) cc_final: 0.9434 (mtp) REVERT: G 13 GLN cc_start: 0.9402 (OUTLIER) cc_final: 0.8988 (pp30) REVERT: G 22 ARG cc_start: 0.9313 (mtm-85) cc_final: 0.8665 (ttp-110) REVERT: G 26 ASP cc_start: 0.8744 (m-30) cc_final: 0.7256 (m-30) REVERT: G 120 GLU cc_start: 0.9041 (tp30) cc_final: 0.8656 (mm-30) REVERT: G 250 MET cc_start: 0.6616 (pmm) cc_final: 0.6294 (tpp) REVERT: G 256 GLU cc_start: 0.9300 (tt0) cc_final: 0.8924 (tm-30) REVERT: F 79 PHE cc_start: 0.9035 (m-10) cc_final: 0.7460 (m-10) REVERT: F 186 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8226 (pttp) REVERT: F 200 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7884 (mt) REVERT: F 260 ASN cc_start: 0.9091 (m-40) cc_final: 0.8162 (m-40) REVERT: F 277 ASN cc_start: 0.9257 (t0) cc_final: 0.8696 (t0) REVERT: E 77 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8135 (tm-30) REVERT: E 165 MET cc_start: 0.8546 (ttp) cc_final: 0.8344 (ptm) REVERT: E 254 MET cc_start: 0.9141 (tpt) cc_final: 0.8932 (tpp) REVERT: E 259 LYS cc_start: 0.9374 (ttmt) cc_final: 0.9160 (tttp) outliers start: 39 outliers final: 11 residues processed: 723 average time/residue: 0.1685 time to fit residues: 189.1010 Evaluate side-chains 506 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 491 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain I residue 204 ASP Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 203 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 68 ASN ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 131 ASN A 134 ASN A 163 GLN D 4 ASN D 111 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN D 239 GLN C 109 GLN C 131 ASN C 160 ASN C 163 GLN C 197 ASN C 261 GLN B 96 GLN B 109 GLN B 111 GLN B 134 ASN B 279 GLN K 5 HIS K 68 ASN K 81 GLN K 163 GLN ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 276 ASN J 16 GLN ** J 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 ASN ** J 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 ASN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 ASN H 111 GLN H 129 GLN H 160 ASN H 211 ASN G 20 ASN G 71 ASN G 81 GLN G 116 GLN G 129 GLN G 211 ASN G 213 GLN G 237 ASN G 261 GLN F 16 GLN F 37 ASN F 68 ASN F 71 ASN F 88 GLN F 129 GLN F 237 ASN ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 109 GLN E 129 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.057232 restraints weight = 107702.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.058685 restraints weight = 50120.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059639 restraints weight = 28512.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060299 restraints weight = 18077.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060758 restraints weight = 12394.569| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24013 Z= 0.147 Angle : 0.636 10.727 32241 Z= 0.350 Chirality : 0.040 0.204 3718 Planarity : 0.004 0.032 4301 Dihedral : 4.939 58.697 3420 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 6.99 % Allowed : 28.98 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3113 helix: 0.57 (0.10), residues: 2167 sheet: None (None), residues: 0 loop : -1.53 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 223 TYR 0.022 0.002 TYR K 220 PHE 0.021 0.002 PHE E 11 TRP 0.011 0.002 TRP F 154 HIS 0.003 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (24013) covalent geometry : angle 0.63643 / 0.35 (32241) hydrogen bonds : bond 0.05673 / 3.78 ( 1731) hydrogen bonds : angle 4.27021 / 3.03 ( 5070) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 530 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8474 (tp30) REVERT: A 52 MET cc_start: 0.9185 (tpt) cc_final: 0.8962 (tpt) REVERT: A 108 MET cc_start: 0.9481 (tpp) cc_final: 0.9055 (tpp) REVERT: A 155 PHE cc_start: 0.8932 (m-80) cc_final: 0.8675 (m-10) REVERT: A 161 MET cc_start: 0.8103 (ttm) cc_final: 0.7720 (tpt) REVERT: A 252 LYS cc_start: 0.9508 (mmmm) cc_final: 0.9034 (mmtm) REVERT: D 11 PHE cc_start: 0.9083 (t80) cc_final: 0.8838 (t80) REVERT: D 30 LEU cc_start: 0.9367 (tp) cc_final: 0.9117 (tt) REVERT: D 36 ILE cc_start: 0.9450 (mp) cc_final: 0.9138 (mt) REVERT: D 108 MET cc_start: 0.9517 (tpt) cc_final: 0.9113 (tpp) REVERT: D 165 MET cc_start: 0.7564 (ptm) cc_final: 0.7326 (tmm) REVERT: D 208 LYS cc_start: 0.9423 (mtmt) cc_final: 0.9223 (mtmt) REVERT: D 256 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8672 (tp30) REVERT: C 16 GLN cc_start: 0.9519 (tm-30) cc_final: 0.9214 (tm-30) REVERT: C 28 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8560 (mt-10) REVERT: C 67 SER cc_start: 0.9724 (OUTLIER) cc_final: 0.9431 (p) REVERT: C 82 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8194 (tm-30) REVERT: C 86 ILE cc_start: 0.9608 (mm) cc_final: 0.9356 (mm) REVERT: C 186 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8589 (mtmm) REVERT: C 208 LYS cc_start: 0.9404 (mtpt) cc_final: 0.8871 (mtmm) REVERT: C 256 GLU cc_start: 0.8938 (tp30) cc_final: 0.8001 (tm-30) REVERT: C 259 LYS cc_start: 0.9587 (pptt) cc_final: 0.9326 (tmmt) REVERT: B 42 ASP cc_start: 0.8480 (t0) cc_final: 0.8150 (t0) REVERT: B 52 MET cc_start: 0.9261 (mtp) cc_final: 0.9021 (ttp) REVERT: B 108 MET cc_start: 0.9227 (ttp) cc_final: 0.8785 (tpt) REVERT: B 144 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8864 (p) REVERT: B 220 TYR cc_start: 0.9357 (m-80) cc_final: 0.9042 (m-80) REVERT: B 224 MET cc_start: 0.9447 (mmm) cc_final: 0.9213 (mmm) REVERT: B 242 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8308 (tp30) REVERT: B 245 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9262 (mm) REVERT: B 249 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8886 (t0) REVERT: B 252 LYS cc_start: 0.9458 (mmmm) cc_final: 0.8886 (mmtt) REVERT: K 11 PHE cc_start: 0.8465 (t80) cc_final: 0.8100 (t80) REVERT: K 70 ILE cc_start: 0.8893 (mt) cc_final: 0.8658 (tp) REVERT: K 161 MET cc_start: 0.9040 (ptt) cc_final: 0.8029 (tpp) REVERT: K 224 MET cc_start: 0.9454 (mmm) cc_final: 0.9230 (mmp) REVERT: K 232 ASP cc_start: 0.9508 (m-30) cc_final: 0.9167 (m-30) REVERT: K 252 LYS cc_start: 0.9655 (mmmm) cc_final: 0.9091 (mptt) REVERT: K 256 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8670 (tp30) REVERT: J 16 GLN cc_start: 0.9029 (tm130) cc_final: 0.8540 (tm-30) REVERT: J 26 ASP cc_start: 0.8878 (m-30) cc_final: 0.8467 (t0) REVERT: J 77 GLU cc_start: 0.6872 (tt0) cc_final: 0.5735 (tp30) REVERT: J 88 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: J 155 PHE cc_start: 0.8902 (m-80) cc_final: 0.8475 (m-10) REVERT: J 172 MET cc_start: 0.8795 (tpp) cc_final: 0.8419 (mpp) REVERT: J 232 ASP cc_start: 0.9016 (m-30) cc_final: 0.7765 (p0) REVERT: J 233 ILE cc_start: 0.9154 (tt) cc_final: 0.7699 (mm) REVERT: J 236 GLU cc_start: 0.6262 (tt0) cc_final: 0.5737 (mt-10) REVERT: J 250 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7934 (mpp) REVERT: I 14 ARG cc_start: 0.8991 (ttp-170) cc_final: 0.8175 (ttt180) REVERT: I 26 ASP cc_start: 0.7935 (m-30) cc_final: 0.7348 (m-30) REVERT: I 256 GLU cc_start: 0.8072 (tm-30) cc_final: 0.6730 (tm-30) REVERT: I 260 ASN cc_start: 0.9170 (m-40) cc_final: 0.8624 (m110) REVERT: I 283 SER cc_start: 0.9694 (m) cc_final: 0.9415 (t) REVERT: H 13 GLN cc_start: 0.9477 (tm-30) cc_final: 0.8606 (tm-30) REVERT: H 50 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8959 (pt0) REVERT: H 53 ARG cc_start: 0.9541 (OUTLIER) cc_final: 0.9261 (mtt180) REVERT: H 77 GLU cc_start: 0.8558 (pp20) cc_final: 0.8275 (tm-30) REVERT: H 86 ILE cc_start: 0.9511 (mm) cc_final: 0.9307 (tp) REVERT: H 135 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7117 (ptt) REVERT: H 167 VAL cc_start: 0.9712 (t) cc_final: 0.9481 (p) REVERT: H 172 MET cc_start: 0.8811 (tpp) cc_final: 0.8157 (mpp) REVERT: H 186 LYS cc_start: 0.9050 (tptm) cc_final: 0.8753 (tppp) REVERT: H 211 ASN cc_start: 0.9604 (m-40) cc_final: 0.9272 (m-40) REVERT: H 224 MET cc_start: 0.9475 (mmm) cc_final: 0.9270 (mmm) REVERT: H 242 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: H 250 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8007 (mmt) REVERT: H 252 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9140 (mmtt) REVERT: H 262 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9166 (tp) REVERT: H 271 LEU cc_start: 0.9460 (tp) cc_final: 0.9259 (tp) REVERT: G 13 GLN cc_start: 0.9534 (pp30) cc_final: 0.9227 (pp30) REVERT: G 52 MET cc_start: 0.9455 (mmm) cc_final: 0.9059 (tpp) REVERT: G 133 MET cc_start: 0.8549 (mmt) cc_final: 0.8316 (mmm) REVERT: G 172 MET cc_start: 0.8187 (tpp) cc_final: 0.7689 (mpp) REVERT: G 204 ASP cc_start: 0.9546 (OUTLIER) cc_final: 0.9046 (m-30) REVERT: G 205 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8716 (mp0) REVERT: G 208 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8989 (mtmm) REVERT: G 250 MET cc_start: 0.6822 (pmm) cc_final: 0.6399 (tpp) REVERT: G 252 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9432 (mmmm) REVERT: F 50 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8622 (pt0) REVERT: F 207 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9157 (tt) REVERT: F 208 LYS cc_start: 0.9463 (mtpp) cc_final: 0.9152 (mtpp) REVERT: F 256 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7834 (tm-30) REVERT: F 260 ASN cc_start: 0.8673 (m-40) cc_final: 0.8047 (m-40) REVERT: F 277 ASN cc_start: 0.8964 (t0) cc_final: 0.8677 (t0) REVERT: E 15 THR cc_start: 0.9575 (m) cc_final: 0.9345 (p) REVERT: E 28 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8231 (mm-30) REVERT: E 108 MET cc_start: 0.9637 (tpp) cc_final: 0.9363 (tpp) REVERT: E 165 MET cc_start: 0.8727 (ttp) cc_final: 0.7681 (tmm) REVERT: E 186 LYS cc_start: 0.9152 (tptm) cc_final: 0.8948 (tptm) REVERT: E 224 MET cc_start: 0.9588 (mmm) cc_final: 0.9321 (mmt) REVERT: E 244 ARG cc_start: 0.9283 (tpp80) cc_final: 0.8293 (ttp-170) outliers start: 176 outliers final: 53 residues processed: 679 average time/residue: 0.1574 time to fit residues: 169.4135 Evaluate side-chains 527 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 458 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 88 GLN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 250 MET Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 250 MET Chi-restraints excluded: chain H residue 262 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 261 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 251 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 GLN A 147 ASN A 260 ASN D 4 ASN D 213 GLN D 277 ASN B 13 GLN B 20 ASN K 213 GLN J 71 ASN J 116 GLN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN I 20 ASN H 129 GLN H 131 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 237 ASN G 71 ASN G 163 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 131 ASN ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN E 261 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.062285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056975 restraints weight = 109255.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058413 restraints weight = 50964.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059370 restraints weight = 29058.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060014 restraints weight = 18523.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060493 restraints weight = 12754.997| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24013 Z= 0.131 Angle : 0.555 9.383 32241 Z= 0.301 Chirality : 0.038 0.187 3718 Planarity : 0.003 0.020 4301 Dihedral : 4.118 41.705 3394 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.29 % Allowed : 28.54 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.14), residues: 3113 helix: 1.54 (0.11), residues: 2233 sheet: None (None), residues: 0 loop : -1.64 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 244 TYR 0.027 0.002 TYR E 257 PHE 0.014 0.001 PHE D 140 TRP 0.010 0.002 TRP J 154 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (24013) covalent geometry : angle 0.55456 / 0.30 (32241) hydrogen bonds : bond 0.04835 / 3.24 ( 1731) hydrogen bonds : angle 3.86358 / 2.75 ( 5070) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 503 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9470 (tt) REVERT: A 77 GLU cc_start: 0.6546 (tt0) cc_final: 0.5911 (tp30) REVERT: A 108 MET cc_start: 0.9529 (tpp) cc_final: 0.9136 (tpp) REVERT: A 133 MET cc_start: 0.7820 (mtt) cc_final: 0.7581 (mtp) REVERT: A 161 MET cc_start: 0.8237 (ttm) cc_final: 0.7874 (tpt) REVERT: A 252 LYS cc_start: 0.9518 (mmmm) cc_final: 0.8722 (mptt) REVERT: D 4 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7872 (m-40) REVERT: D 30 LEU cc_start: 0.9370 (tp) cc_final: 0.9061 (tt) REVERT: D 36 ILE cc_start: 0.9461 (mp) cc_final: 0.9197 (mt) REVERT: D 42 ASP cc_start: 0.8704 (t0) cc_final: 0.8233 (t0) REVERT: D 108 MET cc_start: 0.9457 (tpt) cc_final: 0.9102 (tpp) REVERT: D 165 MET cc_start: 0.7437 (ptm) cc_final: 0.7121 (tmm) REVERT: D 172 MET cc_start: 0.9070 (tpp) cc_final: 0.8496 (mpp) REVERT: D 256 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8675 (tp30) REVERT: D 270 MET cc_start: 0.9097 (mtt) cc_final: 0.8673 (mtt) REVERT: C 16 GLN cc_start: 0.9508 (tm-30) cc_final: 0.9191 (tm-30) REVERT: C 28 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8644 (mt-10) REVERT: C 50 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8815 (pt0) REVERT: C 52 MET cc_start: 0.9492 (tpp) cc_final: 0.8947 (mmm) REVERT: C 67 SER cc_start: 0.9703 (OUTLIER) cc_final: 0.9318 (p) REVERT: C 82 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8378 (tm-30) REVERT: C 86 ILE cc_start: 0.9665 (mm) cc_final: 0.9392 (mm) REVERT: C 172 MET cc_start: 0.9090 (tpp) cc_final: 0.8388 (mpp) REVERT: C 186 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8621 (mtmm) REVERT: C 208 LYS cc_start: 0.9398 (mtpt) cc_final: 0.8799 (mtmm) REVERT: C 211 ASN cc_start: 0.9405 (m-40) cc_final: 0.9038 (m110) REVERT: C 256 GLU cc_start: 0.9197 (tp30) cc_final: 0.7794 (tm-30) REVERT: C 259 LYS cc_start: 0.9603 (pptt) cc_final: 0.9328 (tmmt) REVERT: C 260 ASN cc_start: 0.9416 (m-40) cc_final: 0.8515 (m-40) REVERT: B 42 ASP cc_start: 0.8553 (t0) cc_final: 0.8182 (t0) REVERT: B 93 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9252 (mm) REVERT: B 108 MET cc_start: 0.9254 (ttp) cc_final: 0.8797 (tpt) REVERT: B 144 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.8911 (p) REVERT: B 208 LYS cc_start: 0.9590 (mtmt) cc_final: 0.9045 (mtmm) REVERT: B 242 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8376 (tp30) REVERT: B 252 LYS cc_start: 0.9466 (mmmm) cc_final: 0.8989 (mmtt) REVERT: K 11 PHE cc_start: 0.8606 (t80) cc_final: 0.8162 (t80) REVERT: K 13 GLN cc_start: 0.8759 (pt0) cc_final: 0.8520 (pt0) REVERT: K 36 ILE cc_start: 0.9337 (mp) cc_final: 0.9070 (mm) REVERT: K 52 MET cc_start: 0.9043 (mmp) cc_final: 0.8834 (mmm) REVERT: K 70 ILE cc_start: 0.8987 (mt) cc_final: 0.8414 (tp) REVERT: K 108 MET cc_start: 0.9326 (tpp) cc_final: 0.8951 (tpp) REVERT: K 161 MET cc_start: 0.9074 (ptt) cc_final: 0.7979 (tpp) REVERT: K 186 LYS cc_start: 0.8914 (tppt) cc_final: 0.8708 (tppt) REVERT: K 221 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: K 224 MET cc_start: 0.9436 (mmm) cc_final: 0.9212 (mmp) REVERT: K 252 LYS cc_start: 0.9647 (mmmm) cc_final: 0.9084 (mptt) REVERT: K 256 GLU cc_start: 0.9458 (mm-30) cc_final: 0.8697 (tp30) REVERT: J 16 GLN cc_start: 0.8971 (tm130) cc_final: 0.8719 (tm-30) REVERT: J 26 ASP cc_start: 0.8870 (m-30) cc_final: 0.8485 (t0) REVERT: J 42 ASP cc_start: 0.8470 (t0) cc_final: 0.7940 (t0) REVERT: J 77 GLU cc_start: 0.6489 (tt0) cc_final: 0.5068 (tp30) REVERT: J 88 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: J 155 PHE cc_start: 0.8994 (m-80) cc_final: 0.8601 (m-10) REVERT: J 172 MET cc_start: 0.8885 (tpp) cc_final: 0.8543 (mpp) REVERT: J 232 ASP cc_start: 0.8975 (m-30) cc_final: 0.8648 (m-30) REVERT: J 233 ILE cc_start: 0.9209 (tt) cc_final: 0.8182 (mm) REVERT: J 236 GLU cc_start: 0.6221 (tt0) cc_final: 0.5793 (mt-10) REVERT: J 250 MET cc_start: 0.7894 (mpp) cc_final: 0.7653 (tpp) REVERT: I 52 MET cc_start: 0.9136 (mtp) cc_final: 0.8905 (mmm) REVERT: I 211 ASN cc_start: 0.9487 (m-40) cc_final: 0.9261 (m-40) REVERT: I 283 SER cc_start: 0.9709 (m) cc_final: 0.9447 (t) REVERT: H 13 GLN cc_start: 0.9472 (tm-30) cc_final: 0.8628 (tm-30) REVERT: H 26 ASP cc_start: 0.8350 (m-30) cc_final: 0.7762 (m-30) REVERT: H 50 GLU cc_start: 0.9413 (mm-30) cc_final: 0.8943 (pt0) REVERT: H 77 GLU cc_start: 0.8587 (pp20) cc_final: 0.8275 (tm-30) REVERT: H 87 MET cc_start: 0.9678 (mmm) cc_final: 0.9216 (mmm) REVERT: H 135 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7127 (ptt) REVERT: H 172 MET cc_start: 0.8768 (tpp) cc_final: 0.8083 (mpp) REVERT: H 211 ASN cc_start: 0.9612 (m-40) cc_final: 0.9262 (m110) REVERT: H 252 LYS cc_start: 0.9357 (ttmt) cc_final: 0.9128 (mmtt) REVERT: H 256 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7617 (tm-30) REVERT: H 262 ILE cc_start: 0.9583 (mt) cc_final: 0.9288 (tp) REVERT: H 264 SER cc_start: 0.9804 (OUTLIER) cc_final: 0.9571 (p) REVERT: G 13 GLN cc_start: 0.9543 (pp30) cc_final: 0.9197 (pp30) REVERT: G 52 MET cc_start: 0.9411 (mmm) cc_final: 0.9136 (mmm) REVERT: G 77 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7785 (tm-30) REVERT: G 161 MET cc_start: 0.8325 (ttm) cc_final: 0.7986 (tpt) REVERT: G 172 MET cc_start: 0.8515 (tpp) cc_final: 0.7836 (mpp) REVERT: G 208 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8842 (mtmm) REVERT: G 250 MET cc_start: 0.6640 (pmm) cc_final: 0.6102 (tpp) REVERT: G 252 LYS cc_start: 0.9677 (mmmt) cc_final: 0.9444 (mmmm) REVERT: F 50 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8430 (pt0) REVERT: F 52 MET cc_start: 0.9221 (tpp) cc_final: 0.8903 (tpp) REVERT: F 88 GLN cc_start: 0.9176 (mt0) cc_final: 0.8480 (pp30) REVERT: F 131 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8013 (t0) REVERT: F 165 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7376 (ptm) REVERT: F 186 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7885 (mtmm) REVERT: F 256 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7584 (tm-30) REVERT: F 260 ASN cc_start: 0.8857 (m-40) cc_final: 0.7896 (m110) REVERT: E 10 MET cc_start: 0.9603 (OUTLIER) cc_final: 0.9385 (mtp) REVERT: E 15 THR cc_start: 0.9595 (m) cc_final: 0.9375 (p) REVERT: E 28 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7961 (mm-30) REVERT: E 108 MET cc_start: 0.9596 (tpp) cc_final: 0.9330 (tpp) REVERT: E 186 LYS cc_start: 0.9123 (tptm) cc_final: 0.8882 (tptm) REVERT: E 211 ASN cc_start: 0.9579 (m-40) cc_final: 0.9325 (m-40) REVERT: E 220 TYR cc_start: 0.8620 (m-10) cc_final: 0.8358 (m-80) REVERT: E 244 ARG cc_start: 0.9284 (tpp80) cc_final: 0.8357 (ttp-170) outliers start: 108 outliers final: 56 residues processed: 591 average time/residue: 0.1571 time to fit residues: 147.5035 Evaluate side-chains 519 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 450 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 221 GLN Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 88 GLN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 163 GLN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 203 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 180 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 153 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 116 GLN A 277 ASN D 6 ASN D 163 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 GLN I 20 ASN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN H 213 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN E 261 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056624 restraints weight = 109662.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058023 restraints weight = 51377.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058959 restraints weight = 29339.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059588 restraints weight = 18727.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060051 restraints weight = 12813.777| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24013 Z= 0.140 Angle : 0.538 7.699 32241 Z= 0.293 Chirality : 0.039 0.301 3718 Planarity : 0.003 0.037 4301 Dihedral : 3.910 37.574 3390 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.28 % Allowed : 26.80 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.15), residues: 3113 helix: 2.21 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -0.89 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 223 TYR 0.024 0.002 TYR E 257 PHE 0.018 0.001 PHE F 130 TRP 0.010 0.001 TRP F 154 HIS 0.009 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (24013) covalent geometry : angle 0.53823 / 0.29 (32241) hydrogen bonds : bond 0.04494 / 3.00 ( 1731) hydrogen bonds : angle 3.77713 / 2.69 ( 5070) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 465 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9437 (tt) REVERT: A 77 GLU cc_start: 0.6120 (tt0) cc_final: 0.5493 (tp30) REVERT: A 108 MET cc_start: 0.9530 (tpp) cc_final: 0.9282 (tpp) REVERT: A 133 MET cc_start: 0.7584 (mtt) cc_final: 0.7345 (mtp) REVERT: A 161 MET cc_start: 0.8290 (ttm) cc_final: 0.7915 (tpt) REVERT: A 252 LYS cc_start: 0.9534 (mmmm) cc_final: 0.9317 (mmmm) REVERT: A 259 LYS cc_start: 0.9432 (tmtp) cc_final: 0.9162 (tttm) REVERT: A 263 LEU cc_start: 0.9830 (OUTLIER) cc_final: 0.9595 (tt) REVERT: D 4 ASN cc_start: 0.8129 (t0) cc_final: 0.7893 (m-40) REVERT: D 6 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8369 (t0) REVERT: D 10 MET cc_start: 0.9273 (mtp) cc_final: 0.8723 (mtm) REVERT: D 36 ILE cc_start: 0.9481 (mp) cc_final: 0.9213 (mt) REVERT: D 42 ASP cc_start: 0.8663 (t0) cc_final: 0.7992 (t0) REVERT: D 108 MET cc_start: 0.9445 (tpt) cc_final: 0.9110 (tpp) REVERT: D 163 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: D 256 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8703 (tp30) REVERT: C 16 GLN cc_start: 0.9507 (tm-30) cc_final: 0.9048 (tp40) REVERT: C 28 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8822 (mt-10) REVERT: C 52 MET cc_start: 0.9475 (tpp) cc_final: 0.9007 (mmm) REVERT: C 67 SER cc_start: 0.9698 (OUTLIER) cc_final: 0.9287 (p) REVERT: C 82 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8351 (tm-30) REVERT: C 86 ILE cc_start: 0.9645 (mm) cc_final: 0.9384 (mm) REVERT: C 172 MET cc_start: 0.9012 (tpp) cc_final: 0.8323 (mpp) REVERT: C 186 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8619 (mtmm) REVERT: C 208 LYS cc_start: 0.9432 (mtpt) cc_final: 0.8932 (mtmm) REVERT: C 211 ASN cc_start: 0.9447 (m-40) cc_final: 0.9205 (m-40) REVERT: C 250 MET cc_start: 0.8077 (tpp) cc_final: 0.7770 (tpp) REVERT: B 42 ASP cc_start: 0.8611 (t0) cc_final: 0.8324 (t0) REVERT: B 86 ILE cc_start: 0.9491 (mm) cc_final: 0.9115 (tt) REVERT: B 93 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9249 (mm) REVERT: B 108 MET cc_start: 0.9217 (ttp) cc_final: 0.8832 (tpt) REVERT: B 144 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9006 (p) REVERT: B 208 LYS cc_start: 0.9584 (mtmt) cc_final: 0.9022 (mtmm) REVERT: B 252 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9026 (mmtt) REVERT: K 11 PHE cc_start: 0.8746 (t80) cc_final: 0.8288 (t80) REVERT: K 36 ILE cc_start: 0.9321 (mp) cc_final: 0.9103 (mm) REVERT: K 52 MET cc_start: 0.9044 (mmp) cc_final: 0.8738 (mmp) REVERT: K 70 ILE cc_start: 0.9043 (mt) cc_final: 0.8830 (tp) REVERT: K 82 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7251 (mt-10) REVERT: K 108 MET cc_start: 0.9374 (tpp) cc_final: 0.9106 (tpp) REVERT: K 133 MET cc_start: 0.8582 (ttp) cc_final: 0.8331 (ptm) REVERT: K 161 MET cc_start: 0.9103 (ptt) cc_final: 0.7966 (tpp) REVERT: K 186 LYS cc_start: 0.8950 (tppt) cc_final: 0.8745 (tppt) REVERT: K 224 MET cc_start: 0.9441 (mmm) cc_final: 0.9204 (mmp) REVERT: K 252 LYS cc_start: 0.9647 (OUTLIER) cc_final: 0.9065 (mptt) REVERT: K 256 GLU cc_start: 0.9464 (mm-30) cc_final: 0.8701 (tp30) REVERT: J 16 GLN cc_start: 0.8996 (tm130) cc_final: 0.8783 (tm-30) REVERT: J 26 ASP cc_start: 0.8912 (m-30) cc_final: 0.8390 (t0) REVERT: J 42 ASP cc_start: 0.8486 (t0) cc_final: 0.8018 (t0) REVERT: J 77 GLU cc_start: 0.6356 (tt0) cc_final: 0.4809 (tp30) REVERT: J 172 MET cc_start: 0.8985 (tpp) cc_final: 0.8677 (mpp) REVERT: J 232 ASP cc_start: 0.8976 (m-30) cc_final: 0.8703 (m-30) REVERT: J 233 ILE cc_start: 0.9284 (tt) cc_final: 0.8330 (mm) REVERT: J 236 GLU cc_start: 0.6268 (tt0) cc_final: 0.5933 (mt-10) REVERT: J 250 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7672 (tpp) REVERT: I 108 MET cc_start: 0.9365 (tpp) cc_final: 0.9113 (tpp) REVERT: I 256 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8191 (tp30) REVERT: I 259 LYS cc_start: 0.9583 (ttpp) cc_final: 0.9086 (ttpp) REVERT: I 283 SER cc_start: 0.9718 (m) cc_final: 0.9457 (t) REVERT: H 13 GLN cc_start: 0.9470 (tm-30) cc_final: 0.8605 (tm-30) REVERT: H 26 ASP cc_start: 0.8366 (m-30) cc_final: 0.7655 (m-30) REVERT: H 50 GLU cc_start: 0.9432 (mm-30) cc_final: 0.8921 (pt0) REVERT: H 77 GLU cc_start: 0.8599 (pp20) cc_final: 0.8236 (tm-30) REVERT: H 87 MET cc_start: 0.9664 (mmm) cc_final: 0.9190 (mmm) REVERT: H 135 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7247 (ptt) REVERT: H 172 MET cc_start: 0.8809 (tpp) cc_final: 0.8068 (mpp) REVERT: H 211 ASN cc_start: 0.9602 (m-40) cc_final: 0.9368 (m110) REVERT: H 252 LYS cc_start: 0.9359 (ttmt) cc_final: 0.9150 (mptt) REVERT: H 256 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8013 (tm-30) REVERT: H 262 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9221 (tp) REVERT: H 264 SER cc_start: 0.9800 (OUTLIER) cc_final: 0.9562 (p) REVERT: G 13 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.9114 (pp30) REVERT: G 63 SER cc_start: 0.9744 (OUTLIER) cc_final: 0.9357 (p) REVERT: G 67 SER cc_start: 0.9566 (OUTLIER) cc_final: 0.9345 (p) REVERT: G 77 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7795 (tm-30) REVERT: G 120 GLU cc_start: 0.9065 (tp30) cc_final: 0.8673 (tp30) REVERT: G 161 MET cc_start: 0.8375 (ttm) cc_final: 0.8121 (tpt) REVERT: G 172 MET cc_start: 0.8660 (tpp) cc_final: 0.8114 (mpp) REVERT: G 205 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8724 (mp0) REVERT: G 208 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8884 (mtmm) REVERT: G 249 ASP cc_start: 0.9248 (t0) cc_final: 0.8717 (t70) REVERT: G 250 MET cc_start: 0.6102 (pmm) cc_final: 0.5578 (tpp) REVERT: G 252 LYS cc_start: 0.9670 (mmmt) cc_final: 0.9259 (mmmm) REVERT: F 10 MET cc_start: 0.9191 (mtt) cc_final: 0.8920 (mtm) REVERT: F 50 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8688 (pt0) REVERT: F 52 MET cc_start: 0.9235 (tpp) cc_final: 0.9031 (mmp) REVERT: F 87 MET cc_start: 0.9757 (mmm) cc_final: 0.9552 (mmm) REVERT: F 88 GLN cc_start: 0.9155 (mt0) cc_final: 0.8483 (pp30) REVERT: F 101 ILE cc_start: 0.9340 (pt) cc_final: 0.9135 (tp) REVERT: F 165 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7437 (ptm) REVERT: F 256 GLU cc_start: 0.8659 (tm-30) cc_final: 0.7565 (tm-30) REVERT: F 260 ASN cc_start: 0.9050 (m-40) cc_final: 0.8063 (m110) REVERT: E 10 MET cc_start: 0.9612 (OUTLIER) cc_final: 0.9105 (mtp) REVERT: E 15 THR cc_start: 0.9619 (m) cc_final: 0.9410 (p) REVERT: E 28 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8199 (mm-30) REVERT: E 108 MET cc_start: 0.9622 (tpp) cc_final: 0.9334 (tpp) REVERT: E 186 LYS cc_start: 0.9148 (tptm) cc_final: 0.8933 (tptm) REVERT: E 211 ASN cc_start: 0.9514 (m-40) cc_final: 0.9133 (m-40) outliers start: 133 outliers final: 62 residues processed: 568 average time/residue: 0.1560 time to fit residues: 140.8995 Evaluate side-chains 519 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 437 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 200 ILE Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 250 MET Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 262 ILE Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 150 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 244 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 278 optimal weight: 4.9990 chunk 265 optimal weight: 0.5980 chunk 214 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 297 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 GLN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN G 163 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056914 restraints weight = 109641.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058326 restraints weight = 50927.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059271 restraints weight = 28953.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059908 restraints weight = 18351.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060358 restraints weight = 12573.244| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24013 Z= 0.122 Angle : 0.517 8.289 32241 Z= 0.280 Chirality : 0.038 0.256 3718 Planarity : 0.002 0.021 4301 Dihedral : 3.803 17.444 3388 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 4.72 % Allowed : 27.43 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.15), residues: 3113 helix: 2.25 (0.11), residues: 2222 sheet: None (None), residues: 0 loop : -1.20 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 223 TYR 0.014 0.001 TYR D 220 PHE 0.015 0.001 PHE D 140 TRP 0.009 0.001 TRP A 154 HIS 0.007 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (24013) covalent geometry : angle 0.51658 / 0.28 (32241) hydrogen bonds : bond 0.04266 / 2.85 ( 1731) hydrogen bonds : angle 3.66298 / 2.61 ( 5070) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 476 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.5784 (tt0) cc_final: 0.5154 (tp30) REVERT: A 108 MET cc_start: 0.9538 (tpp) cc_final: 0.9286 (tpp) REVERT: A 133 MET cc_start: 0.7611 (mtt) cc_final: 0.7367 (mtp) REVERT: A 161 MET cc_start: 0.8252 (ttm) cc_final: 0.7896 (tpt) REVERT: A 263 LEU cc_start: 0.9833 (OUTLIER) cc_final: 0.9604 (tt) REVERT: D 4 ASN cc_start: 0.8333 (t0) cc_final: 0.8132 (t0) REVERT: D 10 MET cc_start: 0.9254 (mtp) cc_final: 0.8703 (mtm) REVERT: D 36 ILE cc_start: 0.9478 (mp) cc_final: 0.9219 (mt) REVERT: D 42 ASP cc_start: 0.8647 (t0) cc_final: 0.7970 (t0) REVERT: D 52 MET cc_start: 0.9165 (mtp) cc_final: 0.8868 (ttp) REVERT: D 77 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8077 (tm-30) REVERT: D 108 MET cc_start: 0.9449 (tpt) cc_final: 0.9112 (tpp) REVERT: D 172 MET cc_start: 0.9101 (tpp) cc_final: 0.8352 (mpp) REVERT: D 256 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8704 (tp30) REVERT: C 16 GLN cc_start: 0.9496 (tm-30) cc_final: 0.9203 (tp40) REVERT: C 28 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8787 (mt-10) REVERT: C 50 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8910 (pt0) REVERT: C 52 MET cc_start: 0.9494 (tpp) cc_final: 0.9249 (mmm) REVERT: C 67 SER cc_start: 0.9691 (OUTLIER) cc_final: 0.9264 (p) REVERT: C 82 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 86 ILE cc_start: 0.9633 (mm) cc_final: 0.9345 (mm) REVERT: C 172 MET cc_start: 0.8936 (tpp) cc_final: 0.8227 (mpp) REVERT: C 186 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8328 (mtmm) REVERT: C 208 LYS cc_start: 0.9457 (mtpt) cc_final: 0.9043 (mtmm) REVERT: C 211 ASN cc_start: 0.9441 (m-40) cc_final: 0.9205 (m-40) REVERT: C 250 MET cc_start: 0.8093 (tpp) cc_final: 0.7826 (tpp) REVERT: C 260 ASN cc_start: 0.9438 (m-40) cc_final: 0.9213 (m110) REVERT: B 42 ASP cc_start: 0.8640 (t0) cc_final: 0.8331 (t0) REVERT: B 86 ILE cc_start: 0.9503 (mm) cc_final: 0.9181 (tt) REVERT: B 93 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9222 (mm) REVERT: B 108 MET cc_start: 0.9242 (ttp) cc_final: 0.8802 (tpt) REVERT: B 144 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.9005 (p) REVERT: B 161 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8205 (mmt) REVERT: B 224 MET cc_start: 0.9508 (mmm) cc_final: 0.9278 (mmm) REVERT: B 252 LYS cc_start: 0.9478 (mmmm) cc_final: 0.8998 (mmtt) REVERT: K 11 PHE cc_start: 0.8753 (t80) cc_final: 0.8259 (t80) REVERT: K 52 MET cc_start: 0.9091 (mmp) cc_final: 0.8780 (mmp) REVERT: K 82 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7239 (mt-10) REVERT: K 108 MET cc_start: 0.9384 (tpp) cc_final: 0.8928 (tpp) REVERT: K 161 MET cc_start: 0.9107 (ptt) cc_final: 0.7950 (tpp) REVERT: K 172 MET cc_start: 0.8705 (tpp) cc_final: 0.7985 (mpp) REVERT: K 186 LYS cc_start: 0.8941 (tppt) cc_final: 0.8705 (tptt) REVERT: K 252 LYS cc_start: 0.9635 (OUTLIER) cc_final: 0.9069 (mptt) REVERT: K 256 GLU cc_start: 0.9490 (mm-30) cc_final: 0.8729 (tp30) REVERT: J 26 ASP cc_start: 0.8897 (m-30) cc_final: 0.8505 (t0) REVERT: J 42 ASP cc_start: 0.8451 (t0) cc_final: 0.7984 (t0) REVERT: J 77 GLU cc_start: 0.6368 (tt0) cc_final: 0.4765 (tp30) REVERT: J 82 GLU cc_start: 0.8922 (tp30) cc_final: 0.8611 (tt0) REVERT: J 88 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: J 172 MET cc_start: 0.9042 (tpp) cc_final: 0.8723 (mpp) REVERT: J 186 LYS cc_start: 0.9254 (tppp) cc_final: 0.9033 (tppp) REVERT: J 233 ILE cc_start: 0.9314 (tt) cc_final: 0.8892 (mm) REVERT: J 250 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7682 (tpp) REVERT: I 10 MET cc_start: 0.9379 (mtm) cc_final: 0.8771 (mtm) REVERT: I 26 ASP cc_start: 0.7999 (m-30) cc_final: 0.7630 (m-30) REVERT: I 52 MET cc_start: 0.9326 (mmm) cc_final: 0.8683 (mmm) REVERT: I 108 MET cc_start: 0.9314 (tpp) cc_final: 0.8980 (tpp) REVERT: I 256 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: I 283 SER cc_start: 0.9721 (m) cc_final: 0.9489 (t) REVERT: H 13 GLN cc_start: 0.9452 (tm-30) cc_final: 0.8620 (tm-30) REVERT: H 50 GLU cc_start: 0.9444 (mm-30) cc_final: 0.8935 (pt0) REVERT: H 77 GLU cc_start: 0.8601 (pp20) cc_final: 0.8129 (tm-30) REVERT: H 87 MET cc_start: 0.9677 (mmm) cc_final: 0.9219 (mmm) REVERT: H 172 MET cc_start: 0.8832 (tpp) cc_final: 0.8092 (mpp) REVERT: H 211 ASN cc_start: 0.9597 (m-40) cc_final: 0.9356 (m110) REVERT: H 252 LYS cc_start: 0.9429 (ttmt) cc_final: 0.9062 (mmtt) REVERT: H 256 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8292 (tp30) REVERT: H 262 ILE cc_start: 0.9589 (mt) cc_final: 0.9301 (tp) REVERT: H 264 SER cc_start: 0.9783 (OUTLIER) cc_final: 0.9511 (p) REVERT: G 13 GLN cc_start: 0.9492 (OUTLIER) cc_final: 0.9095 (pp30) REVERT: G 63 SER cc_start: 0.9748 (OUTLIER) cc_final: 0.9361 (p) REVERT: G 67 SER cc_start: 0.9522 (OUTLIER) cc_final: 0.9308 (p) REVERT: G 77 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7834 (tm-30) REVERT: G 161 MET cc_start: 0.8374 (ttm) cc_final: 0.8139 (tpt) REVERT: G 172 MET cc_start: 0.8780 (tpp) cc_final: 0.8191 (mpp) REVERT: G 205 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8739 (mp0) REVERT: G 208 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8839 (mtmm) REVERT: G 224 MET cc_start: 0.9306 (tpp) cc_final: 0.9050 (tpp) REVERT: G 249 ASP cc_start: 0.9254 (t0) cc_final: 0.8723 (t70) REVERT: G 250 MET cc_start: 0.6128 (pmm) cc_final: 0.5535 (tpp) REVERT: G 252 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9376 (mtpp) REVERT: F 10 MET cc_start: 0.9175 (mtt) cc_final: 0.8853 (mtm) REVERT: F 50 GLU cc_start: 0.9377 (mm-30) cc_final: 0.8686 (pt0) REVERT: F 52 MET cc_start: 0.9239 (tpp) cc_final: 0.8955 (mmp) REVERT: F 88 GLN cc_start: 0.9150 (mt0) cc_final: 0.8469 (pp30) REVERT: F 256 GLU cc_start: 0.8666 (tm-30) cc_final: 0.7735 (tm-30) REVERT: F 260 ASN cc_start: 0.9116 (m-40) cc_final: 0.8288 (m110) REVERT: E 10 MET cc_start: 0.9608 (OUTLIER) cc_final: 0.9175 (mtp) REVERT: E 28 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7768 (mm-30) REVERT: E 108 MET cc_start: 0.9567 (tpp) cc_final: 0.9279 (tpp) REVERT: E 211 ASN cc_start: 0.9479 (m-40) cc_final: 0.9028 (m110) REVERT: E 252 LYS cc_start: 0.9493 (mtpp) cc_final: 0.9110 (ttmm) REVERT: E 254 MET cc_start: 0.9322 (tpt) cc_final: 0.9052 (tpp) outliers start: 119 outliers final: 67 residues processed: 567 average time/residue: 0.1610 time to fit residues: 143.8117 Evaluate side-chains 517 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 434 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 200 ILE Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 88 GLN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 250 MET Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 278 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 163 GLN Chi-restraints excluded: chain G residue 188 MET Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 263 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 119 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 220 optimal weight: 0.0060 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN D 163 GLN B 213 GLN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 277 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.061570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056463 restraints weight = 109708.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057842 restraints weight = 51945.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058778 restraints weight = 29792.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059402 restraints weight = 19015.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059839 restraints weight = 13014.816| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24013 Z= 0.129 Angle : 0.526 8.710 32241 Z= 0.285 Chirality : 0.038 0.208 3718 Planarity : 0.002 0.024 4301 Dihedral : 3.758 16.865 3388 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.80 % Allowed : 27.51 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.15), residues: 3113 helix: 2.33 (0.11), residues: 2222 sheet: None (None), residues: 0 loop : -1.13 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 123 TYR 0.016 0.001 TYR K 257 PHE 0.019 0.001 PHE G 11 TRP 0.007 0.001 TRP F 154 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (24013) covalent geometry : angle 0.52557 / 0.28 (32241) hydrogen bonds : bond 0.04185 / 2.80 ( 1731) hydrogen bonds : angle 3.65735 / 2.60 ( 5070) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 449 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.5840 (tt0) cc_final: 0.5154 (tp30) REVERT: A 108 MET cc_start: 0.9516 (tpp) cc_final: 0.9266 (tpp) REVERT: A 161 MET cc_start: 0.8313 (ttm) cc_final: 0.7978 (tpt) REVERT: A 252 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9221 (mmmm) REVERT: A 263 LEU cc_start: 0.9832 (OUTLIER) cc_final: 0.9618 (tt) REVERT: D 36 ILE cc_start: 0.9488 (mp) cc_final: 0.9241 (mt) REVERT: D 42 ASP cc_start: 0.8647 (t0) cc_final: 0.8033 (t0) REVERT: D 77 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 108 MET cc_start: 0.9416 (tpt) cc_final: 0.9102 (tpp) REVERT: D 163 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: D 256 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8673 (tp30) REVERT: C 16 GLN cc_start: 0.9502 (tm-30) cc_final: 0.9022 (tp40) REVERT: C 28 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8830 (mt-10) REVERT: C 36 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8706 (pp) REVERT: C 42 ASP cc_start: 0.8370 (t0) cc_final: 0.8063 (p0) REVERT: C 52 MET cc_start: 0.9426 (tpp) cc_final: 0.9010 (mmm) REVERT: C 67 SER cc_start: 0.9652 (OUTLIER) cc_final: 0.9275 (p) REVERT: C 82 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8215 (tm-30) REVERT: C 86 ILE cc_start: 0.9610 (mm) cc_final: 0.9339 (mm) REVERT: C 172 MET cc_start: 0.8894 (tpp) cc_final: 0.8207 (mpp) REVERT: C 208 LYS cc_start: 0.9462 (mtpt) cc_final: 0.9131 (mtmm) REVERT: C 211 ASN cc_start: 0.9534 (m-40) cc_final: 0.9274 (m-40) REVERT: B 7 MET cc_start: 0.6706 (mmt) cc_final: 0.6412 (mmm) REVERT: B 42 ASP cc_start: 0.8596 (t0) cc_final: 0.8316 (t0) REVERT: B 86 ILE cc_start: 0.9528 (mm) cc_final: 0.9262 (tt) REVERT: B 93 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9233 (mm) REVERT: B 108 MET cc_start: 0.9220 (ttp) cc_final: 0.8829 (tpt) REVERT: B 144 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9026 (p) REVERT: B 161 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8217 (mmt) REVERT: B 224 MET cc_start: 0.9431 (mmm) cc_final: 0.9167 (mmm) REVERT: B 252 LYS cc_start: 0.9467 (mmmm) cc_final: 0.9005 (mmtt) REVERT: K 11 PHE cc_start: 0.8820 (t80) cc_final: 0.8300 (t80) REVERT: K 13 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8704 (tm-30) REVERT: K 82 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7154 (mt-10) REVERT: K 108 MET cc_start: 0.9337 (tpp) cc_final: 0.9088 (tpp) REVERT: K 133 MET cc_start: 0.8554 (ptm) cc_final: 0.8343 (ptm) REVERT: K 161 MET cc_start: 0.9118 (ptt) cc_final: 0.8002 (tpp) REVERT: K 172 MET cc_start: 0.8723 (tpp) cc_final: 0.8049 (mpp) REVERT: K 186 LYS cc_start: 0.8947 (tppt) cc_final: 0.8724 (tptt) REVERT: K 252 LYS cc_start: 0.9622 (OUTLIER) cc_final: 0.9053 (mptt) REVERT: K 256 GLU cc_start: 0.9450 (mm-30) cc_final: 0.8716 (tp30) REVERT: J 26 ASP cc_start: 0.8864 (m-30) cc_final: 0.8533 (t0) REVERT: J 42 ASP cc_start: 0.8450 (t0) cc_final: 0.7995 (t0) REVERT: J 172 MET cc_start: 0.9087 (tpp) cc_final: 0.8800 (mpp) REVERT: J 186 LYS cc_start: 0.9268 (tppp) cc_final: 0.9043 (tppp) REVERT: J 214 ARG cc_start: 0.9477 (mtp180) cc_final: 0.9244 (tpt-90) REVERT: J 233 ILE cc_start: 0.9324 (tt) cc_final: 0.8909 (mm) REVERT: J 250 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7710 (tpp) REVERT: I 10 MET cc_start: 0.9312 (mtm) cc_final: 0.8653 (mtm) REVERT: I 26 ASP cc_start: 0.7972 (m-30) cc_final: 0.7606 (m-30) REVERT: I 108 MET cc_start: 0.9282 (tpp) cc_final: 0.8919 (tpp) REVERT: I 211 ASN cc_start: 0.9380 (m-40) cc_final: 0.9132 (m-40) REVERT: I 256 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: H 13 GLN cc_start: 0.9443 (tm-30) cc_final: 0.8643 (tm-30) REVERT: H 50 GLU cc_start: 0.9387 (mm-30) cc_final: 0.8971 (pt0) REVERT: H 77 GLU cc_start: 0.8589 (pp20) cc_final: 0.8126 (tm-30) REVERT: H 172 MET cc_start: 0.8801 (tpp) cc_final: 0.8091 (mpp) REVERT: H 211 ASN cc_start: 0.9571 (m-40) cc_final: 0.9336 (m110) REVERT: H 252 LYS cc_start: 0.9411 (ttmt) cc_final: 0.9091 (mmtt) REVERT: H 256 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8052 (tm-30) REVERT: H 259 LYS cc_start: 0.5358 (tttt) cc_final: 0.4996 (tttt) REVERT: H 262 ILE cc_start: 0.9546 (mt) cc_final: 0.9292 (tp) REVERT: G 13 GLN cc_start: 0.9454 (OUTLIER) cc_final: 0.9037 (pp30) REVERT: G 52 MET cc_start: 0.9457 (mmm) cc_final: 0.9179 (tpp) REVERT: G 63 SER cc_start: 0.9762 (OUTLIER) cc_final: 0.9364 (p) REVERT: G 67 SER cc_start: 0.9533 (OUTLIER) cc_final: 0.9324 (p) REVERT: G 163 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: G 172 MET cc_start: 0.8872 (tpp) cc_final: 0.8287 (mpp) REVERT: G 208 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8839 (mtmm) REVERT: G 224 MET cc_start: 0.9324 (tpp) cc_final: 0.9070 (tpp) REVERT: G 249 ASP cc_start: 0.9202 (t0) cc_final: 0.8603 (t70) REVERT: G 250 MET cc_start: 0.6266 (pmm) cc_final: 0.5402 (tpp) REVERT: G 252 LYS cc_start: 0.9659 (mmmt) cc_final: 0.9179 (mtpp) REVERT: G 260 ASN cc_start: 0.9162 (m-40) cc_final: 0.8712 (m110) REVERT: F 10 MET cc_start: 0.9132 (mtt) cc_final: 0.8911 (mtp) REVERT: F 50 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8776 (pt0) REVERT: F 88 GLN cc_start: 0.9117 (mt0) cc_final: 0.8509 (pp30) REVERT: F 256 GLU cc_start: 0.8674 (tm-30) cc_final: 0.7719 (tm-30) REVERT: F 260 ASN cc_start: 0.9144 (m-40) cc_final: 0.8304 (m110) REVERT: E 10 MET cc_start: 0.9582 (OUTLIER) cc_final: 0.9194 (mtp) REVERT: E 28 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8361 (mm-30) REVERT: E 108 MET cc_start: 0.9593 (tpp) cc_final: 0.9326 (tpp) REVERT: E 135 MET cc_start: 0.8603 (ttm) cc_final: 0.8374 (ttp) REVERT: E 211 ASN cc_start: 0.9469 (m-40) cc_final: 0.9035 (m-40) REVERT: E 254 MET cc_start: 0.9278 (tpt) cc_final: 0.9011 (tpp) outliers start: 121 outliers final: 78 residues processed: 544 average time/residue: 0.1561 time to fit residues: 135.7891 Evaluate side-chains 519 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 425 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 200 ILE Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 250 MET Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 278 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 163 GLN Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain G residue 188 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 108 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 4 ASN D 163 GLN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 68 ASN G 163 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 277 ASN E 163 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056894 restraints weight = 109216.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058290 restraints weight = 51305.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059229 restraints weight = 29354.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059861 restraints weight = 18727.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060309 restraints weight = 12815.241| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24013 Z= 0.125 Angle : 0.535 9.913 32241 Z= 0.287 Chirality : 0.038 0.196 3718 Planarity : 0.002 0.023 4301 Dihedral : 3.759 16.452 3388 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 4.57 % Allowed : 27.43 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.15), residues: 3113 helix: 2.38 (0.11), residues: 2222 sheet: None (None), residues: 0 loop : -1.09 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 123 TYR 0.017 0.001 TYR G 257 PHE 0.015 0.001 PHE G 11 TRP 0.007 0.001 TRP I 154 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (24013) covalent geometry : angle 0.53506 / 0.29 (32241) hydrogen bonds : bond 0.04108 / 2.74 ( 1731) hydrogen bonds : angle 3.62554 / 2.57 ( 5070) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 454 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4380 (tpt) cc_final: 0.3965 (tpp) REVERT: A 108 MET cc_start: 0.9542 (tpp) cc_final: 0.9286 (tpp) REVERT: A 161 MET cc_start: 0.8334 (ttm) cc_final: 0.7968 (tpt) REVERT: A 186 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8538 (pttp) REVERT: A 252 LYS cc_start: 0.9503 (mmmm) cc_final: 0.9231 (mmmm) REVERT: D 36 ILE cc_start: 0.9483 (mp) cc_final: 0.9245 (mt) REVERT: D 42 ASP cc_start: 0.8684 (t0) cc_final: 0.8045 (t0) REVERT: D 77 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7992 (tm-30) REVERT: D 108 MET cc_start: 0.9382 (tpt) cc_final: 0.9066 (tpp) REVERT: D 163 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: D 256 GLU cc_start: 0.9333 (mm-30) cc_final: 0.8698 (tp30) REVERT: C 16 GLN cc_start: 0.9533 (tm-30) cc_final: 0.9044 (tp40) REVERT: C 28 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8843 (mt-10) REVERT: C 36 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8691 (pp) REVERT: C 42 ASP cc_start: 0.8401 (t0) cc_final: 0.8029 (p0) REVERT: C 50 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8931 (pt0) REVERT: C 52 MET cc_start: 0.9467 (tpp) cc_final: 0.8956 (mmm) REVERT: C 67 SER cc_start: 0.9638 (OUTLIER) cc_final: 0.9252 (p) REVERT: C 82 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8265 (tm-30) REVERT: C 86 ILE cc_start: 0.9616 (mm) cc_final: 0.9383 (mm) REVERT: C 87 MET cc_start: 0.9480 (mmm) cc_final: 0.9171 (mmm) REVERT: C 172 MET cc_start: 0.8919 (tpp) cc_final: 0.8205 (mpp) REVERT: C 208 LYS cc_start: 0.9459 (mtpt) cc_final: 0.9141 (mtmm) REVERT: C 211 ASN cc_start: 0.9555 (m-40) cc_final: 0.9285 (m-40) REVERT: B 7 MET cc_start: 0.6421 (mmt) cc_final: 0.6151 (mmm) REVERT: B 42 ASP cc_start: 0.8620 (t0) cc_final: 0.8306 (t0) REVERT: B 86 ILE cc_start: 0.9530 (mm) cc_final: 0.9289 (tt) REVERT: B 93 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9179 (mm) REVERT: B 108 MET cc_start: 0.9257 (ttp) cc_final: 0.8814 (tpt) REVERT: B 144 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9017 (p) REVERT: B 161 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8263 (mmt) REVERT: B 192 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8547 (p) REVERT: B 252 LYS cc_start: 0.9485 (mmmm) cc_final: 0.9013 (mmtt) REVERT: K 10 MET cc_start: 0.9349 (mtp) cc_final: 0.8842 (mtm) REVERT: K 11 PHE cc_start: 0.8832 (t80) cc_final: 0.8263 (t80) REVERT: K 13 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8757 (tp40) REVERT: K 26 ASP cc_start: 0.9046 (m-30) cc_final: 0.8745 (m-30) REVERT: K 52 MET cc_start: 0.9363 (mmm) cc_final: 0.9012 (mmm) REVERT: K 108 MET cc_start: 0.9377 (tpp) cc_final: 0.8989 (tpp) REVERT: K 161 MET cc_start: 0.9151 (ptt) cc_final: 0.7956 (tpp) REVERT: K 172 MET cc_start: 0.8701 (tpp) cc_final: 0.7970 (mpp) REVERT: K 186 LYS cc_start: 0.8760 (tppt) cc_final: 0.8510 (tptt) REVERT: K 252 LYS cc_start: 0.9615 (OUTLIER) cc_final: 0.9011 (mptt) REVERT: K 256 GLU cc_start: 0.9505 (mm-30) cc_final: 0.8778 (tp30) REVERT: K 282 MET cc_start: 0.9032 (tmm) cc_final: 0.8793 (tpp) REVERT: J 26 ASP cc_start: 0.8947 (m-30) cc_final: 0.8557 (t0) REVERT: J 42 ASP cc_start: 0.8421 (t0) cc_final: 0.7929 (t0) REVERT: J 172 MET cc_start: 0.9111 (tpp) cc_final: 0.8796 (mpp) REVERT: J 186 LYS cc_start: 0.9271 (tppp) cc_final: 0.9040 (tppp) REVERT: J 214 ARG cc_start: 0.9512 (mtp180) cc_final: 0.9251 (tpt-90) REVERT: J 233 ILE cc_start: 0.9333 (tt) cc_final: 0.8928 (mm) REVERT: J 250 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7686 (tpp) REVERT: I 1 MET cc_start: 0.3130 (tpt) cc_final: 0.2703 (tpt) REVERT: I 10 MET cc_start: 0.9331 (mtm) cc_final: 0.8636 (mtm) REVERT: I 26 ASP cc_start: 0.7995 (m-30) cc_final: 0.7586 (m-30) REVERT: I 52 MET cc_start: 0.9324 (mmm) cc_final: 0.9032 (mtp) REVERT: I 82 GLU cc_start: 0.9083 (tt0) cc_final: 0.8882 (tt0) REVERT: I 108 MET cc_start: 0.9285 (tpp) cc_final: 0.8957 (tpp) REVERT: I 211 ASN cc_start: 0.9410 (m-40) cc_final: 0.9138 (m-40) REVERT: I 242 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8702 (tm-30) REVERT: I 256 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: H 13 GLN cc_start: 0.9462 (tm-30) cc_final: 0.8694 (tm-30) REVERT: H 50 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8975 (pt0) REVERT: H 77 GLU cc_start: 0.8617 (pp20) cc_final: 0.8143 (tm-30) REVERT: H 172 MET cc_start: 0.8825 (tpp) cc_final: 0.8073 (mpp) REVERT: H 211 ASN cc_start: 0.9595 (m-40) cc_final: 0.9365 (m110) REVERT: H 252 LYS cc_start: 0.9436 (ttmt) cc_final: 0.9101 (mmtt) REVERT: H 256 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8209 (tm-30) REVERT: H 259 LYS cc_start: 0.5309 (tttt) cc_final: 0.4977 (tttt) REVERT: H 262 ILE cc_start: 0.9546 (mt) cc_final: 0.9310 (tp) REVERT: G 13 GLN cc_start: 0.9560 (OUTLIER) cc_final: 0.9125 (pp30) REVERT: G 25 LYS cc_start: 0.9238 (tppt) cc_final: 0.8693 (tppp) REVERT: G 52 MET cc_start: 0.9532 (mmm) cc_final: 0.9194 (tpp) REVERT: G 63 SER cc_start: 0.9750 (OUTLIER) cc_final: 0.9343 (p) REVERT: G 163 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: G 172 MET cc_start: 0.8922 (tpp) cc_final: 0.8301 (mpp) REVERT: G 208 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8814 (mtmm) REVERT: G 224 MET cc_start: 0.9412 (tpp) cc_final: 0.9157 (tpp) REVERT: G 249 ASP cc_start: 0.9214 (t0) cc_final: 0.8540 (t70) REVERT: G 250 MET cc_start: 0.6071 (pmm) cc_final: 0.5144 (tpp) REVERT: G 252 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9186 (mtpp) REVERT: G 256 GLU cc_start: 0.9330 (tp30) cc_final: 0.9115 (tp30) REVERT: G 260 ASN cc_start: 0.9319 (m-40) cc_final: 0.8758 (m110) REVERT: F 50 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8665 (pt0) REVERT: F 52 MET cc_start: 0.9239 (mmp) cc_final: 0.8969 (tpp) REVERT: F 88 GLN cc_start: 0.9190 (mt0) cc_final: 0.8520 (pp30) REVERT: F 186 LYS cc_start: 0.8208 (tptp) cc_final: 0.7934 (tptp) REVERT: F 256 GLU cc_start: 0.8721 (tm-30) cc_final: 0.7760 (tm-30) REVERT: F 260 ASN cc_start: 0.9171 (m-40) cc_final: 0.8361 (m110) REVERT: E 10 MET cc_start: 0.9632 (OUTLIER) cc_final: 0.9226 (mtp) REVERT: E 28 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8406 (mm-30) REVERT: E 108 MET cc_start: 0.9610 (tpp) cc_final: 0.9339 (tpp) REVERT: E 163 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8428 (mt0) REVERT: E 172 MET cc_start: 0.8647 (tpp) cc_final: 0.7654 (mpp) REVERT: E 211 ASN cc_start: 0.9465 (m-40) cc_final: 0.9008 (m110) REVERT: E 252 LYS cc_start: 0.9504 (mtpp) cc_final: 0.9107 (ttmm) REVERT: E 259 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8918 (ttmt) outliers start: 115 outliers final: 75 residues processed: 544 average time/residue: 0.1536 time to fit residues: 132.1296 Evaluate side-chains 525 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 432 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 250 MET Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 278 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 163 GLN Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 263 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 98 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 154 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 ASN D 163 GLN C 68 ASN C 279 GLN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 163 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 277 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054992 restraints weight = 111213.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.056339 restraints weight = 51804.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.057238 restraints weight = 29526.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057819 restraints weight = 18835.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058284 restraints weight = 13265.164| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24013 Z= 0.194 Angle : 0.591 10.171 32241 Z= 0.321 Chirality : 0.040 0.216 3718 Planarity : 0.003 0.026 4301 Dihedral : 3.853 18.489 3388 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.80 % Allowed : 27.19 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.15), residues: 3113 helix: 2.34 (0.11), residues: 2211 sheet: None (None), residues: 0 loop : -1.08 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 164 TYR 0.024 0.002 TYR K 257 PHE 0.013 0.001 PHE D 140 TRP 0.011 0.002 TRP F 154 HIS 0.008 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (24013) covalent geometry : angle 0.59091 / 0.32 (32241) hydrogen bonds : bond 0.04464 / 2.98 ( 1731) hydrogen bonds : angle 3.84582 / 2.73 ( 5070) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 413 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9544 (tpp) cc_final: 0.9270 (tpp) REVERT: A 161 MET cc_start: 0.8494 (ttm) cc_final: 0.8044 (tpt) REVERT: A 252 LYS cc_start: 0.9505 (mmmm) cc_final: 0.9172 (mmmm) REVERT: D 42 ASP cc_start: 0.8741 (t0) cc_final: 0.8157 (t0) REVERT: D 108 MET cc_start: 0.9410 (tpt) cc_final: 0.9102 (tpp) REVERT: D 163 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: D 256 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8728 (tp30) REVERT: C 1 MET cc_start: 0.3364 (tpt) cc_final: 0.3116 (tpp) REVERT: C 16 GLN cc_start: 0.9563 (tm-30) cc_final: 0.9080 (tp40) REVERT: C 28 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8878 (mt-10) REVERT: C 52 MET cc_start: 0.9462 (tpp) cc_final: 0.8996 (mmm) REVERT: C 67 SER cc_start: 0.9653 (OUTLIER) cc_final: 0.9266 (p) REVERT: C 82 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 86 ILE cc_start: 0.9620 (mm) cc_final: 0.9359 (mm) REVERT: C 87 MET cc_start: 0.9551 (mmm) cc_final: 0.9313 (mmm) REVERT: C 172 MET cc_start: 0.8974 (tpp) cc_final: 0.8263 (mpp) REVERT: C 208 LYS cc_start: 0.9486 (mtpt) cc_final: 0.9165 (mtmm) REVERT: C 211 ASN cc_start: 0.9581 (m-40) cc_final: 0.9277 (m-40) REVERT: B 1 MET cc_start: 0.3044 (tpt) cc_final: 0.2575 (tpp) REVERT: B 42 ASP cc_start: 0.8628 (t0) cc_final: 0.8307 (t0) REVERT: B 86 ILE cc_start: 0.9555 (mm) cc_final: 0.9336 (tt) REVERT: B 93 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9204 (mm) REVERT: B 108 MET cc_start: 0.9292 (ttp) cc_final: 0.8941 (tpt) REVERT: B 144 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9012 (p) REVERT: B 161 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8377 (mmt) REVERT: B 211 ASN cc_start: 0.9343 (m-40) cc_final: 0.8888 (m110) REVERT: B 220 TYR cc_start: 0.9471 (m-80) cc_final: 0.9112 (m-80) REVERT: B 252 LYS cc_start: 0.9534 (mmmm) cc_final: 0.9031 (mmtt) REVERT: K 10 MET cc_start: 0.9402 (mtp) cc_final: 0.8955 (mtm) REVERT: K 11 PHE cc_start: 0.9002 (t80) cc_final: 0.8585 (t80) REVERT: K 13 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8817 (tm-30) REVERT: K 52 MET cc_start: 0.9349 (mmm) cc_final: 0.9003 (mmm) REVERT: K 108 MET cc_start: 0.9419 (tpp) cc_final: 0.9060 (tpp) REVERT: K 161 MET cc_start: 0.9158 (ptt) cc_final: 0.7950 (tpp) REVERT: K 186 LYS cc_start: 0.8902 (tppt) cc_final: 0.8680 (tptt) REVERT: K 252 LYS cc_start: 0.9647 (OUTLIER) cc_final: 0.9042 (mptt) REVERT: K 256 GLU cc_start: 0.9503 (mm-30) cc_final: 0.8761 (tp30) REVERT: K 282 MET cc_start: 0.9051 (mmm) cc_final: 0.8793 (tpp) REVERT: J 26 ASP cc_start: 0.8966 (m-30) cc_final: 0.8581 (t0) REVERT: J 42 ASP cc_start: 0.8457 (t0) cc_final: 0.8053 (t0) REVERT: J 172 MET cc_start: 0.9125 (tpp) cc_final: 0.8789 (mpp) REVERT: J 186 LYS cc_start: 0.9288 (tppp) cc_final: 0.9051 (tppp) REVERT: J 233 ILE cc_start: 0.9432 (tt) cc_final: 0.9016 (mm) REVERT: J 250 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7632 (mmt) REVERT: I 1 MET cc_start: 0.3123 (tpt) cc_final: 0.2899 (tpt) REVERT: I 10 MET cc_start: 0.9356 (mtm) cc_final: 0.8504 (mtm) REVERT: I 108 MET cc_start: 0.9310 (tpp) cc_final: 0.8906 (tpp) REVERT: I 256 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8414 (tp30) REVERT: H 50 GLU cc_start: 0.9426 (mm-30) cc_final: 0.8958 (pt0) REVERT: H 77 GLU cc_start: 0.8747 (pp20) cc_final: 0.8315 (tm-30) REVERT: H 135 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7608 (ptt) REVERT: H 161 MET cc_start: 0.8781 (ttm) cc_final: 0.7869 (mmt) REVERT: H 172 MET cc_start: 0.8804 (tpp) cc_final: 0.8117 (mpp) REVERT: H 211 ASN cc_start: 0.9589 (m-40) cc_final: 0.9289 (m110) REVERT: H 252 LYS cc_start: 0.9463 (ttmt) cc_final: 0.9164 (mmtt) REVERT: H 256 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8497 (tp30) REVERT: H 259 LYS cc_start: 0.5129 (tttt) cc_final: 0.4783 (tttt) REVERT: G 13 GLN cc_start: 0.9545 (OUTLIER) cc_final: 0.9109 (pp30) REVERT: G 25 LYS cc_start: 0.9122 (tppt) cc_final: 0.8914 (tppt) REVERT: G 52 MET cc_start: 0.9568 (mmm) cc_final: 0.9330 (tpp) REVERT: G 63 SER cc_start: 0.9749 (OUTLIER) cc_final: 0.9375 (p) REVERT: G 172 MET cc_start: 0.8936 (tpp) cc_final: 0.8274 (mpp) REVERT: G 205 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8799 (mp0) REVERT: G 208 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8847 (mtmm) REVERT: G 224 MET cc_start: 0.9464 (tpp) cc_final: 0.9209 (tpp) REVERT: G 249 ASP cc_start: 0.9259 (t0) cc_final: 0.8925 (t70) REVERT: G 252 LYS cc_start: 0.9647 (mmmt) cc_final: 0.9199 (mtpp) REVERT: F 50 GLU cc_start: 0.9387 (mm-30) cc_final: 0.8873 (pt0) REVERT: F 161 MET cc_start: 0.2761 (mmt) cc_final: 0.2171 (mmt) REVERT: F 163 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: F 186 LYS cc_start: 0.8402 (tptp) cc_final: 0.8166 (tptp) REVERT: E 87 MET cc_start: 0.9507 (mmm) cc_final: 0.9144 (mmm) REVERT: E 108 MET cc_start: 0.9605 (tpp) cc_final: 0.9324 (tpp) REVERT: E 172 MET cc_start: 0.8926 (tpp) cc_final: 0.8027 (mpp) REVERT: E 211 ASN cc_start: 0.9550 (m-40) cc_final: 0.9129 (m110) REVERT: E 250 MET cc_start: 0.8347 (mmt) cc_final: 0.7114 (pmm) REVERT: E 257 TYR cc_start: 0.9668 (t80) cc_final: 0.9411 (t80) REVERT: E 259 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8846 (ttmt) REVERT: E 261 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8361 (mp10) outliers start: 121 outliers final: 78 residues processed: 504 average time/residue: 0.1545 time to fit residues: 124.1411 Evaluate side-chains 488 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 395 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 188 MET Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 250 MET Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 278 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain F residue 163 GLN Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 263 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 114 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN E 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.055183 restraints weight = 111486.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.056537 restraints weight = 51895.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057445 restraints weight = 29594.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058059 restraints weight = 18765.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058508 restraints weight = 12859.168| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24013 Z= 0.180 Angle : 0.592 10.941 32241 Z= 0.319 Chirality : 0.040 0.236 3718 Planarity : 0.003 0.024 4301 Dihedral : 3.909 19.361 3388 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 4.21 % Allowed : 27.47 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.15), residues: 3113 helix: 2.34 (0.11), residues: 2211 sheet: None (None), residues: 0 loop : -1.03 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 123 TYR 0.015 0.002 TYR J 257 PHE 0.012 0.001 PHE D 140 TRP 0.009 0.002 TRP D 154 HIS 0.007 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (24013) covalent geometry : angle 0.59177 / 0.32 (32241) hydrogen bonds : bond 0.04419 / 2.95 ( 1731) hydrogen bonds : angle 3.83886 / 2.72 ( 5070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 414 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9567 (tpp) cc_final: 0.9288 (tpp) REVERT: A 161 MET cc_start: 0.8499 (ttm) cc_final: 0.8034 (tpt) REVERT: D 42 ASP cc_start: 0.8899 (t0) cc_final: 0.8696 (t0) REVERT: D 108 MET cc_start: 0.9399 (tpt) cc_final: 0.9073 (tpp) REVERT: D 256 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8738 (tp30) REVERT: C 16 GLN cc_start: 0.9565 (tm-30) cc_final: 0.9069 (tp40) REVERT: C 28 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8864 (mt-10) REVERT: C 36 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8658 (pp) REVERT: C 42 ASP cc_start: 0.8459 (t0) cc_final: 0.8141 (p0) REVERT: C 52 MET cc_start: 0.9455 (tpp) cc_final: 0.8881 (mmm) REVERT: C 67 SER cc_start: 0.9647 (OUTLIER) cc_final: 0.9261 (p) REVERT: C 82 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8243 (tm-30) REVERT: C 86 ILE cc_start: 0.9628 (mm) cc_final: 0.9389 (mm) REVERT: C 172 MET cc_start: 0.8986 (tpp) cc_final: 0.8266 (mpp) REVERT: C 208 LYS cc_start: 0.9484 (mtpt) cc_final: 0.9157 (mtmm) REVERT: C 211 ASN cc_start: 0.9590 (m-40) cc_final: 0.9272 (m-40) REVERT: B 1 MET cc_start: 0.3229 (tpt) cc_final: 0.2721 (tpp) REVERT: B 42 ASP cc_start: 0.8626 (t0) cc_final: 0.8304 (t0) REVERT: B 86 ILE cc_start: 0.9559 (mm) cc_final: 0.9347 (tt) REVERT: B 93 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9196 (mm) REVERT: B 108 MET cc_start: 0.9282 (ttp) cc_final: 0.8920 (tpt) REVERT: B 144 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8983 (p) REVERT: B 161 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8346 (mmt) REVERT: B 211 ASN cc_start: 0.9342 (m-40) cc_final: 0.8891 (m110) REVERT: B 220 TYR cc_start: 0.9473 (m-80) cc_final: 0.9106 (m-80) REVERT: B 252 LYS cc_start: 0.9549 (mmmm) cc_final: 0.9026 (mmtt) REVERT: K 10 MET cc_start: 0.9396 (mtp) cc_final: 0.8925 (mtm) REVERT: K 11 PHE cc_start: 0.9031 (t80) cc_final: 0.8619 (t80) REVERT: K 26 ASP cc_start: 0.9048 (m-30) cc_final: 0.8769 (m-30) REVERT: K 52 MET cc_start: 0.9378 (mmm) cc_final: 0.9045 (mmm) REVERT: K 108 MET cc_start: 0.9425 (tpp) cc_final: 0.9084 (tpp) REVERT: K 186 LYS cc_start: 0.8844 (tppt) cc_final: 0.8622 (tptt) REVERT: K 252 LYS cc_start: 0.9642 (OUTLIER) cc_final: 0.9039 (mptt) REVERT: K 256 GLU cc_start: 0.9481 (mm-30) cc_final: 0.8764 (tp30) REVERT: K 282 MET cc_start: 0.9062 (mmm) cc_final: 0.8804 (tpp) REVERT: J 26 ASP cc_start: 0.8950 (m-30) cc_final: 0.8577 (t0) REVERT: J 42 ASP cc_start: 0.8434 (t0) cc_final: 0.8086 (t0) REVERT: J 172 MET cc_start: 0.9130 (tpp) cc_final: 0.8797 (mpp) REVERT: J 186 LYS cc_start: 0.9291 (tppp) cc_final: 0.9054 (tppp) REVERT: J 233 ILE cc_start: 0.9432 (tt) cc_final: 0.9014 (mm) REVERT: J 250 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7677 (tpp) REVERT: I 1 MET cc_start: 0.3509 (tpt) cc_final: 0.3261 (tpt) REVERT: I 10 MET cc_start: 0.9354 (mtm) cc_final: 0.9026 (mtm) REVERT: I 30 LEU cc_start: 0.9366 (tp) cc_final: 0.9056 (tt) REVERT: I 52 MET cc_start: 0.9282 (mmm) cc_final: 0.8894 (mtp) REVERT: I 108 MET cc_start: 0.9272 (tpp) cc_final: 0.8880 (tpp) REVERT: I 161 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.7926 (tpp) REVERT: I 242 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8658 (tm-30) REVERT: I 256 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: H 50 GLU cc_start: 0.9412 (mm-30) cc_final: 0.8967 (pt0) REVERT: H 77 GLU cc_start: 0.8773 (pp20) cc_final: 0.8340 (tm-30) REVERT: H 135 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7641 (ptt) REVERT: H 211 ASN cc_start: 0.9578 (m-40) cc_final: 0.9271 (m110) REVERT: H 252 LYS cc_start: 0.9442 (ttmt) cc_final: 0.9186 (mptt) REVERT: H 256 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8449 (tp30) REVERT: G 13 GLN cc_start: 0.9563 (OUTLIER) cc_final: 0.9108 (pp30) REVERT: G 25 LYS cc_start: 0.9153 (tppt) cc_final: 0.8619 (tppp) REVERT: G 52 MET cc_start: 0.9582 (mmm) cc_final: 0.9253 (tpp) REVERT: G 63 SER cc_start: 0.9740 (OUTLIER) cc_final: 0.9370 (p) REVERT: G 172 MET cc_start: 0.8930 (tpp) cc_final: 0.8285 (mpp) REVERT: G 208 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8869 (mtmm) REVERT: G 224 MET cc_start: 0.9454 (tpp) cc_final: 0.9201 (tpp) REVERT: G 249 ASP cc_start: 0.9220 (t0) cc_final: 0.8806 (t70) REVERT: G 252 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9172 (mtpp) REVERT: F 50 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8856 (pt0) REVERT: F 161 MET cc_start: 0.2774 (mmt) cc_final: 0.1942 (mmt) REVERT: F 163 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: F 172 MET cc_start: 0.8491 (mmm) cc_final: 0.8282 (ttm) REVERT: F 256 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8554 (tm-30) REVERT: E 10 MET cc_start: 0.9508 (mtp) cc_final: 0.9283 (mtm) REVERT: E 87 MET cc_start: 0.9518 (mmm) cc_final: 0.9212 (mmm) REVERT: E 163 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: E 172 MET cc_start: 0.9023 (tpp) cc_final: 0.8211 (mpp) REVERT: E 211 ASN cc_start: 0.9559 (m-40) cc_final: 0.9142 (m110) REVERT: E 252 LYS cc_start: 0.9406 (ttmm) cc_final: 0.9080 (ttmm) REVERT: E 257 TYR cc_start: 0.9689 (t80) cc_final: 0.9425 (t80) REVERT: E 259 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8876 (ttmt) REVERT: E 261 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8534 (mt0) outliers start: 106 outliers final: 76 residues processed: 498 average time/residue: 0.1596 time to fit residues: 126.0215 Evaluate side-chains 488 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 395 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 188 MET Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 250 MET Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain I residue 282 MET Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 163 GLN Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 255 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 163 GLN I 111 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 277 ASN E 163 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057362 restraints weight = 109526.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058757 restraints weight = 51954.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059705 restraints weight = 29865.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060350 restraints weight = 19002.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060760 restraints weight = 13034.130| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24013 Z= 0.118 Angle : 0.572 10.609 32241 Z= 0.301 Chirality : 0.039 0.219 3718 Planarity : 0.002 0.051 4301 Dihedral : 3.925 19.860 3388 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.06 % Allowed : 29.02 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.15), residues: 3113 helix: 2.38 (0.11), residues: 2222 sheet: None (None), residues: 0 loop : -1.03 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 223 TYR 0.018 0.001 TYR A 102 PHE 0.019 0.001 PHE J 11 TRP 0.007 0.001 TRP J 154 HIS 0.003 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (24013) covalent geometry : angle 0.57230 / 0.30 (32241) hydrogen bonds : bond 0.04092 / 2.74 ( 1731) hydrogen bonds : angle 3.63169 / 2.58 ( 5070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 452 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9536 (tpp) cc_final: 0.9129 (tpp) REVERT: A 161 MET cc_start: 0.8407 (ttm) cc_final: 0.8047 (tpt) REVERT: A 231 ILE cc_start: 0.9715 (mm) cc_final: 0.9485 (mt) REVERT: A 252 LYS cc_start: 0.9557 (mmmm) cc_final: 0.8963 (mmmt) REVERT: D 77 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D 108 MET cc_start: 0.9368 (tpt) cc_final: 0.9037 (tpp) REVERT: D 163 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: D 256 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8698 (tp30) REVERT: C 16 GLN cc_start: 0.9516 (tm-30) cc_final: 0.9089 (tp40) REVERT: C 28 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8304 (mp0) REVERT: C 36 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8422 (pp) REVERT: C 42 ASP cc_start: 0.8396 (t0) cc_final: 0.8147 (p0) REVERT: C 52 MET cc_start: 0.9401 (tpp) cc_final: 0.8797 (mmm) REVERT: C 67 SER cc_start: 0.9627 (OUTLIER) cc_final: 0.9229 (p) REVERT: C 82 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 86 ILE cc_start: 0.9620 (mm) cc_final: 0.9391 (mm) REVERT: C 172 MET cc_start: 0.8883 (tpp) cc_final: 0.8169 (mpp) REVERT: C 208 LYS cc_start: 0.9470 (mtpt) cc_final: 0.9112 (mtmm) REVERT: C 211 ASN cc_start: 0.9565 (m-40) cc_final: 0.9251 (m-40) REVERT: B 7 MET cc_start: 0.6486 (mmt) cc_final: 0.6061 (mmm) REVERT: B 42 ASP cc_start: 0.8626 (t0) cc_final: 0.8300 (t0) REVERT: B 93 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9126 (mm) REVERT: B 108 MET cc_start: 0.9245 (ttp) cc_final: 0.8864 (tpt) REVERT: B 144 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8997 (p) REVERT: B 161 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8283 (mmt) REVERT: B 192 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8447 (p) REVERT: B 220 TYR cc_start: 0.9416 (m-80) cc_final: 0.9054 (m-80) REVERT: B 221 GLN cc_start: 0.8954 (tt0) cc_final: 0.8278 (tp40) REVERT: B 252 LYS cc_start: 0.9505 (mmmm) cc_final: 0.8994 (mmtt) REVERT: B 282 MET cc_start: 0.9097 (tpp) cc_final: 0.8757 (tpp) REVERT: K 10 MET cc_start: 0.9473 (mtp) cc_final: 0.8916 (mtm) REVERT: K 11 PHE cc_start: 0.8851 (t80) cc_final: 0.8206 (t80) REVERT: K 26 ASP cc_start: 0.9002 (m-30) cc_final: 0.8696 (m-30) REVERT: K 52 MET cc_start: 0.9375 (mmm) cc_final: 0.9029 (mmm) REVERT: K 82 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6975 (tt0) REVERT: K 108 MET cc_start: 0.9399 (tpp) cc_final: 0.9057 (tpp) REVERT: K 161 MET cc_start: 0.9163 (ptt) cc_final: 0.7965 (tpp) REVERT: K 252 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.8993 (mptt) REVERT: K 256 GLU cc_start: 0.9490 (mm-30) cc_final: 0.8802 (tp30) REVERT: K 282 MET cc_start: 0.9016 (mmm) cc_final: 0.8747 (tpp) REVERT: J 26 ASP cc_start: 0.8925 (m-30) cc_final: 0.8536 (t0) REVERT: J 42 ASP cc_start: 0.8345 (t0) cc_final: 0.7922 (t0) REVERT: J 172 MET cc_start: 0.9141 (tpp) cc_final: 0.8831 (mpp) REVERT: J 186 LYS cc_start: 0.9253 (tppp) cc_final: 0.9045 (tppp) REVERT: J 192 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8943 (p) REVERT: J 214 ARG cc_start: 0.9500 (mtp180) cc_final: 0.9292 (tpt-90) REVERT: J 233 ILE cc_start: 0.9344 (tt) cc_final: 0.8918 (mm) REVERT: J 250 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7668 (tpp) REVERT: I 1 MET cc_start: 0.3135 (tpt) cc_final: 0.2870 (tpt) REVERT: I 10 MET cc_start: 0.9336 (mtm) cc_final: 0.8486 (mtm) REVERT: I 52 MET cc_start: 0.9284 (mmm) cc_final: 0.8872 (mtp) REVERT: I 108 MET cc_start: 0.9245 (tpp) cc_final: 0.8843 (tpp) REVERT: I 161 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.7781 (tpp) REVERT: I 207 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9371 (mt) REVERT: I 211 ASN cc_start: 0.9438 (m-40) cc_final: 0.9189 (m-40) REVERT: I 242 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8671 (tm-30) REVERT: I 256 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: H 13 GLN cc_start: 0.9476 (tm-30) cc_final: 0.8651 (tm-30) REVERT: H 50 GLU cc_start: 0.9403 (mm-30) cc_final: 0.8984 (pt0) REVERT: H 77 GLU cc_start: 0.8687 (pp20) cc_final: 0.8181 (tm-30) REVERT: H 211 ASN cc_start: 0.9577 (m-40) cc_final: 0.9344 (m110) REVERT: H 252 LYS cc_start: 0.9355 (ttmt) cc_final: 0.9016 (mmtt) REVERT: H 256 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8401 (tp30) REVERT: G 25 LYS cc_start: 0.9120 (tppt) cc_final: 0.8612 (tppp) REVERT: G 28 GLU cc_start: 0.8730 (mt-10) cc_final: 0.7963 (mm-30) REVERT: G 52 MET cc_start: 0.9543 (mmm) cc_final: 0.9247 (tpp) REVERT: G 63 SER cc_start: 0.9703 (OUTLIER) cc_final: 0.9338 (p) REVERT: G 172 MET cc_start: 0.8853 (tpp) cc_final: 0.8253 (mpp) REVERT: G 186 LYS cc_start: 0.8600 (tptp) cc_final: 0.8289 (tptp) REVERT: G 208 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8840 (mtmm) REVERT: G 249 ASP cc_start: 0.9169 (t0) cc_final: 0.8722 (t70) REVERT: G 252 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9150 (mtpp) REVERT: F 50 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8620 (pt0) REVERT: F 52 MET cc_start: 0.9277 (mmm) cc_final: 0.8688 (mmm) REVERT: F 161 MET cc_start: 0.2551 (mmt) cc_final: 0.1812 (mmt) REVERT: F 256 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8476 (tm-30) REVERT: E 10 MET cc_start: 0.9494 (mtp) cc_final: 0.9236 (mtm) REVERT: E 163 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: E 172 MET cc_start: 0.9024 (tpp) cc_final: 0.8291 (mpp) REVERT: E 211 ASN cc_start: 0.9526 (m-40) cc_final: 0.9073 (m110) REVERT: E 250 MET cc_start: 0.8284 (mmt) cc_final: 0.7087 (pmm) REVERT: E 257 TYR cc_start: 0.9691 (t80) cc_final: 0.9143 (t80) REVERT: E 259 LYS cc_start: 0.9134 (ttmt) cc_final: 0.8871 (ttmt) REVERT: E 261 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8190 (mp10) outliers start: 77 outliers final: 49 residues processed: 510 average time/residue: 0.1562 time to fit residues: 125.8245 Evaluate side-chains 490 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 423 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 188 MET Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 250 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 210 optimal weight: 0.0670 chunk 206 optimal weight: 0.9980 chunk 269 optimal weight: 0.0050 chunk 143 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 261 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.057425 restraints weight = 108848.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058803 restraints weight = 52193.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059733 restraints weight = 30117.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060368 restraints weight = 19323.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060822 restraints weight = 13292.305| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 24013 Z= 0.219 Angle : 0.982 59.186 32241 Z= 0.582 Chirality : 0.040 0.333 3718 Planarity : 0.004 0.131 4301 Dihedral : 3.947 22.280 3388 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.32 % Favored : 98.65 % Rotamer: Outliers : 2.86 % Allowed : 29.30 % Favored : 67.84 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.15), residues: 3113 helix: 2.36 (0.11), residues: 2222 sheet: None (None), residues: 0 loop : -1.03 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 223 TYR 0.014 0.001 TYR B 257 PHE 0.028 0.001 PHE D 155 TRP 0.007 0.001 TRP J 154 HIS 0.003 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (24013) covalent geometry : angle 0.98211 / 0.58 (32241) hydrogen bonds : bond 0.04142 / 2.78 ( 1731) hydrogen bonds : angle 3.66599 / 2.60 ( 5070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4001.01 seconds wall clock time: 70 minutes 2.92 seconds (4202.92 seconds total)