Starting phenix.real_space_refine on Thu Aug 6 07:14:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7t_70208/08_2026/9o7t_70208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7t_70208/08_2026/9o7t_70208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o7t_70208/08_2026/9o7t_70208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7t_70208/08_2026/9o7t_70208.map" model { file = "/net/cci-nas-00/data/ceres_data/9o7t_70208/08_2026/9o7t_70208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7t_70208/08_2026/9o7t_70208.cif" } resolution = 3.26 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= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 28 5.49 5 Mg 12 5.21 5 S 58 5.16 5 C 8758 2.51 5 N 2410 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 13958 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "D" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "E" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "F" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "G" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 241 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "H" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 241 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 5} Link IDs: {'rna2p': 5, 'rna3p': 5} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.36, per 1000 atoms: 0.17 Number of scatterers: 13958 At special positions: 0 Unit cell: (117.975, 108.9, 106.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 28 15.00 Mg 12 11.99 O 2692 8.00 N 2410 7.00 C 8758 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: 1.02 Conformation dependent library (CDL) restraints added in 529.4 milliseconds 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 4 sheets defined 54.2% alpha, 11.0% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.636A pdb=" N MET A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.666A pdb=" N GLU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.888A pdb=" N TYR A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 177 removed outlier: 3.622A pdb=" N SER A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.513A pdb=" N SER A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.506A pdb=" N ILE A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 289 removed outlier: 3.530A pdb=" N GLU A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.569A pdb=" N GLU A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.669A pdb=" N HIS B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 157 through 177 removed outlier: 3.741A pdb=" N SER B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 4.307A pdb=" N ALA B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 removed outlier: 4.456A pdb=" N ARG B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 216 through 233 removed outlier: 3.506A pdb=" N VAL B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 263 through 287 removed outlier: 3.539A pdb=" N CYS B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.604A pdb=" N GLU B 302 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.645A pdb=" N GLN C 99 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 4.000A pdb=" N GLU C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 138 removed outlier: 3.573A pdb=" N GLN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.689A pdb=" N TYR C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 177 Processing helix chain 'C' and resid 181 through 191 Processing helix chain 'C' and resid 209 through 232 removed outlier: 7.913A pdb=" N HIS C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N ILE C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.546A pdb=" N ILE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 286 removed outlier: 3.866A pdb=" N GLU C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.594A pdb=" N ILE D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 124 through 138 Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.852A pdb=" N TYR D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 177 removed outlier: 3.533A pdb=" N TYR D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET D 166 " --> pdb=" O HIS D 162 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 209 through 233 removed outlier: 8.087A pdb=" N HIS D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ILE D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 248 removed outlier: 4.272A pdb=" N MET D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 289 removed outlier: 3.874A pdb=" N GLU D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN D 280 " --> pdb=" O ASP D 276 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.559A pdb=" N HIS E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 138 Processing helix chain 'E' and resid 138 through 143 removed outlier: 3.871A pdb=" N TYR E 143 " --> pdb=" O GLN E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 177 removed outlier: 3.706A pdb=" N SER E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 192 Processing helix chain 'E' and resid 193 through 197 removed outlier: 3.669A pdb=" N VAL E 197 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 233 removed outlier: 7.789A pdb=" N HIS E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ILE E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 263 through 287 removed outlier: 3.523A pdb=" N GLU E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 96 through 101 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.628A pdb=" N TYR F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 138 Processing helix chain 'F' and resid 138 through 143 removed outlier: 3.893A pdb=" N TYR F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 177 removed outlier: 3.656A pdb=" N SER F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'F' and resid 195 through 200 Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'F' and resid 215 through 232 removed outlier: 4.197A pdb=" N SER F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 248 Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 263 through 289 removed outlier: 3.927A pdb=" N ILE F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 283 " --> pdb=" O MET F 279 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS F 288 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.533A pdb=" N GLY A 70 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 65 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 88 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS A 67 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 86 " --> pdb=" O HIS A 67 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 69 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 83 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR A 33 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLN A 24 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A 35 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 22 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS A 37 " --> pdb=" O HIS A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 16 through 25 removed outlier: 5.610A pdb=" N VAL C 19 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN C 39 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS C 21 " --> pdb=" O HIS C 37 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS C 37 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C 34 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 49 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N MET C 81 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU C 46 " --> pdb=" O MET C 81 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL C 83 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LYS C 48 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLN C 85 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS C 69 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE C 86 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS C 67 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU C 88 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE C 65 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 16 through 24 removed outlier: 5.064A pdb=" N VAL D 19 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN D 39 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS D 21 " --> pdb=" O HIS D 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS D 37 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 9.773A pdb=" N MET D 81 " --> pdb=" O GLU D 44 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU D 46 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL D 83 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS D 48 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N GLN D 85 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS D 69 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE D 86 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS D 67 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU D 88 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE D 65 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 12 through 13 removed outlier: 7.840A pdb=" N ILE F 65 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS F 67 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE F 86 " --> pdb=" O HIS F 67 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS F 69 " --> pdb=" O ASN F 84 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N MET F 81 " --> pdb=" O GLU F 44 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU F 46 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL F 83 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS F 48 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN F 85 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR F 27 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS F 21 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN F 39 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL F 19 " --> pdb=" O GLN F 39 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2283 1.31 - 1.43: 3839 1.43 - 1.56: 8009 1.56 - 1.68: 43 1.68 - 1.81: 104 Bond restraints: 14278 Sorted by residual: bond pdb=" CA SER D 160 " pdb=" CB SER D 160 " ideal model delta sigma weight residual 1.528 1.456 0.073 1.56e-02 4.11e+03 2.17e+01 bond pdb=" CA TYR F 208 " pdb=" C TYR F 208 " ideal model delta sigma weight residual 1.527 1.468 0.059 1.35e-02 5.49e+03 1.91e+01 bond pdb=" C ARG F 243 " pdb=" O ARG F 243 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.26e-02 6.30e+03 1.73e+01 bond pdb=" CA ARG F 243 " pdb=" C ARG F 243 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.35e-02 5.49e+03 1.64e+01 bond pdb=" CA ALA A 148 " pdb=" CB ALA A 148 " ideal model delta sigma weight residual 1.533 1.463 0.070 1.72e-02 3.38e+03 1.63e+01 ... (remaining 14273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 19186 3.02 - 6.04: 173 6.04 - 9.06: 22 9.06 - 12.08: 2 12.08 - 15.10: 1 Bond angle restraints: 19384 Sorted by residual: angle pdb=" N ILE D 194 " pdb=" CA ILE D 194 " pdb=" C ILE D 194 " ideal model delta sigma weight residual 113.47 98.37 15.10 1.01e+00 9.80e-01 2.23e+02 angle pdb=" N VAL C 197 " pdb=" CA VAL C 197 " pdb=" C VAL C 197 " ideal model delta sigma weight residual 112.96 103.07 9.89 1.00e+00 1.00e+00 9.78e+01 angle pdb=" N VAL D 197 " pdb=" CA VAL D 197 " pdb=" C VAL D 197 " ideal model delta sigma weight residual 111.90 104.94 6.96 8.10e-01 1.52e+00 7.38e+01 angle pdb=" N HIS E 250 " pdb=" CA HIS E 250 " pdb=" C HIS E 250 " ideal model delta sigma weight residual 113.97 106.35 7.62 1.28e+00 6.10e-01 3.54e+01 angle pdb=" C4' A H 15 " pdb=" O4' A H 15 " pdb=" C1' A H 15 " ideal model delta sigma weight residual 109.70 105.67 4.03 7.00e-01 2.04e+00 3.31e+01 ... (remaining 19379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.76: 8097 27.76 - 55.51: 459 55.51 - 83.27: 64 83.27 - 111.02: 6 111.02 - 138.78: 4 Dihedral angle restraints: 8630 sinusoidal: 3728 harmonic: 4902 Sorted by residual: dihedral pdb=" C5' A H 6 " pdb=" C4' A H 6 " pdb=" C3' A H 6 " pdb=" O3' A H 6 " ideal model delta sinusoidal sigma weight residual 147.00 95.12 51.88 1 8.00e+00 1.56e-02 5.74e+01 dihedral pdb=" O4' A H 6 " pdb=" C4' A H 6 " pdb=" C3' A H 6 " pdb=" C2' A H 6 " ideal model delta sinusoidal sigma weight residual 24.00 -21.38 45.38 1 8.00e+00 1.56e-02 4.46e+01 dihedral pdb=" C5' U H 7 " pdb=" C4' U H 7 " pdb=" C3' U H 7 " pdb=" O3' U H 7 " ideal model delta sinusoidal sigma weight residual 147.00 107.42 39.58 1 8.00e+00 1.56e-02 3.44e+01 ... (remaining 8627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2080 0.110 - 0.221: 54 0.221 - 0.331: 7 0.331 - 0.442: 5 0.442 - 0.552: 10 Chirality restraints: 2156 Sorted by residual: chirality pdb=" P U H 5 " pdb=" OP1 U H 5 " pdb=" OP2 U H 5 " pdb=" O5' U H 5 " both_signs ideal model delta sigma weight residual True 2.41 2.96 -0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" P U H 7 " pdb=" OP1 U H 7 " pdb=" OP2 U H 7 " pdb=" O5' U H 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" P U G 5 " pdb=" OP1 U G 5 " pdb=" OP2 U G 5 " pdb=" O5' U G 5 " both_signs ideal model delta sigma weight residual True 2.41 2.94 -0.53 2.00e-01 2.50e+01 7.04e+00 ... (remaining 2153 not shown) Planarity restraints: 2398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 146 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C PRO F 146 " -0.051 2.00e-02 2.50e+03 pdb=" O PRO F 146 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA F 147 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 260 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO D 261 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 152 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.77e+00 pdb=" C HIS C 152 " -0.048 2.00e-02 2.50e+03 pdb=" O HIS C 152 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS C 153 " 0.016 2.00e-02 2.50e+03 ... (remaining 2395 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 63 2.39 - 3.02: 7246 3.02 - 3.65: 20267 3.65 - 4.27: 31307 4.27 - 4.90: 53326 Nonbonded interactions: 112209 Sorted by model distance: nonbonded pdb=" NE2 HIS F 162 " pdb="MG MG F 401 " model vdw 1.767 2.250 nonbonded pdb=" NE2 HIS E 249 " pdb="MG MG E 401 " model vdw 1.816 2.250 nonbonded pdb=" NE2 HIS B 249 " pdb="MG MG B 401 " model vdw 1.877 2.250 nonbonded pdb=" CE1 HIS C 162 " pdb="MG MG C 403 " model vdw 1.882 2.390 nonbonded pdb="MG MG F 401 " pdb=" O1 PO4 F 402 " model vdw 1.898 2.170 ... (remaining 112204 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 'C' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.800 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 : 0.005 0.073 14278 Z= 0.335 Angle : 0.715 15.097 19384 Z= 0.455 Chirality : 0.060 0.552 2156 Planarity : 0.004 0.072 2398 Dihedral : 16.838 138.780 5478 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.74 % Favored : 96.14 % Rotamer: Outliers : 1.16 % Allowed : 1.02 % Favored : 97.81 % 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: -1.86 (0.19), residues: 1658 helix: -1.36 (0.16), residues: 780 sheet: -1.07 (0.33), residues: 238 loop : -0.82 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 243 TYR 0.011 0.001 TYR D 75 PHE 0.023 0.001 PHE E 299 TRP 0.010 0.001 TRP D 50 HIS 0.012 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.33 (14278) covalent geometry : angle 0.71508 / 0.46 (19384) hydrogen bonds : bond 0.29267 / 19.97 ( 607) hydrogen bonds : angle 8.28291 / 5.73 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.413 Fit side-chains REVERT: B 299 PHE cc_start: 0.8359 (t80) cc_final: 0.8155 (t80) REVERT: C 196 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8514 (mtpp) outliers start: 17 outliers final: 7 residues processed: 184 average time/residue: 0.0972 time to fit residues: 26.9128 Evaluate side-chains 153 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain F residue 149 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.7476 > 50:) chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS C 128 GLN C 154 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN E 151 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.182762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130458 restraints weight = 15190.346| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.81 r_work: 0.3043 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14278 Z= 0.151 Angle : 0.571 8.351 19384 Z= 0.312 Chirality : 0.043 0.286 2156 Planarity : 0.004 0.049 2398 Dihedral : 12.443 122.665 2146 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.82 % Allowed : 6.97 % Favored : 92.21 % 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: -0.48 (0.20), residues: 1658 helix: 0.50 (0.18), residues: 788 sheet: -1.04 (0.32), residues: 250 loop : -0.93 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.012 0.001 TYR E 145 PHE 0.018 0.001 PHE A 17 TRP 0.006 0.001 TRP D 50 HIS 0.008 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (14278) covalent geometry : angle 0.57100 / 0.31 (19384) hydrogen bonds : bond 0.07488 / 5.08 ( 607) hydrogen bonds : angle 5.14444 / 3.53 ( 1695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.372 Fit side-chains REVERT: C 34 MET cc_start: 0.0161 (pmm) cc_final: -0.0354 (ttm) REVERT: D 276 ASP cc_start: 0.8643 (t0) cc_final: 0.8041 (t0) outliers start: 12 outliers final: 9 residues processed: 174 average time/residue: 0.0931 time to fit residues: 24.9506 Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain F residue 149 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 101 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 133 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 58 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 0.0040 chunk 97 optimal weight: 9.9990 overall best weight: 3.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN C 15 HIS C 128 GLN C 154 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 HIS ** F 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.179764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130122 restraints weight = 15309.530| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.89 r_work: 0.3117 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14278 Z= 0.213 Angle : 0.565 8.395 19384 Z= 0.302 Chirality : 0.043 0.205 2156 Planarity : 0.004 0.044 2398 Dihedral : 12.073 118.784 2140 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 9.70 % Favored : 89.14 % 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: -0.16 (0.20), residues: 1658 helix: 0.92 (0.18), residues: 780 sheet: -0.97 (0.32), residues: 250 loop : -0.95 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 243 TYR 0.020 0.001 TYR E 145 PHE 0.018 0.002 PHE B 155 TRP 0.005 0.001 TRP D 50 HIS 0.008 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.21 (14278) covalent geometry : angle 0.56490 / 0.30 (19384) hydrogen bonds : bond 0.06684 / 4.56 ( 607) hydrogen bonds : angle 4.69230 / 3.20 ( 1695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.577 Fit side-chains REVERT: A 276 ASP cc_start: 0.8696 (t0) cc_final: 0.8295 (t0) REVERT: D 210 VAL cc_start: 0.8674 (t) cc_final: 0.8427 (p) outliers start: 17 outliers final: 11 residues processed: 168 average time/residue: 0.1122 time to fit residues: 29.0343 Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 149 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 70 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN C 128 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.184408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131911 restraints weight = 15218.947| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.78 r_work: 0.3046 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14278 Z= 0.114 Angle : 0.478 8.122 19384 Z= 0.257 Chirality : 0.039 0.161 2156 Planarity : 0.004 0.042 2398 Dihedral : 11.908 117.331 2136 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.96 % Allowed : 11.27 % Favored : 87.77 % 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: 0.25 (0.21), residues: 1658 helix: 1.37 (0.19), residues: 778 sheet: -0.85 (0.33), residues: 250 loop : -0.86 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 243 TYR 0.009 0.001 TYR D 138 PHE 0.010 0.001 PHE E 299 TRP 0.005 0.001 TRP D 50 HIS 0.007 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (14278) covalent geometry : angle 0.47796 / 0.26 (19384) hydrogen bonds : bond 0.04829 / 3.29 ( 607) hydrogen bonds : angle 4.34836 / 2.96 ( 1695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.473 Fit side-chains REVERT: D 276 ASP cc_start: 0.8651 (t0) cc_final: 0.7999 (t0) outliers start: 14 outliers final: 10 residues processed: 160 average time/residue: 0.1109 time to fit residues: 27.1805 Evaluate side-chains 158 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain F residue 270 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 158 optimal weight: 0.0370 chunk 72 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.4860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN C 154 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN D 124 ASN ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 HIS F 39 GLN F 151 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.184323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132312 restraints weight = 15193.784| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.91 r_work: 0.3049 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14278 Z= 0.125 Angle : 0.474 7.532 19384 Z= 0.254 Chirality : 0.039 0.157 2156 Planarity : 0.004 0.043 2398 Dihedral : 11.806 116.534 2135 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.23 % Allowed : 12.50 % Favored : 86.27 % 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: 0.42 (0.21), residues: 1658 helix: 1.54 (0.19), residues: 778 sheet: -0.76 (0.33), residues: 250 loop : -0.83 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 243 TYR 0.009 0.001 TYR E 145 PHE 0.014 0.001 PHE F 16 TRP 0.004 0.001 TRP D 50 HIS 0.008 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14278) covalent geometry : angle 0.47450 / 0.25 (19384) hydrogen bonds : bond 0.04719 / 3.22 ( 607) hydrogen bonds : angle 4.18014 / 2.84 ( 1695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.527 Fit side-chains REVERT: D 276 ASP cc_start: 0.8695 (t0) cc_final: 0.8484 (t70) outliers start: 18 outliers final: 14 residues processed: 167 average time/residue: 0.0968 time to fit residues: 25.1233 Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 270 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 42 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 85 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 164 optimal weight: 50.0000 chunk 92 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 154 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.192491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136319 restraints weight = 15532.876| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.98 r_work: 0.3026 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14278 Z= 0.192 Angle : 0.532 11.509 19384 Z= 0.281 Chirality : 0.042 0.158 2156 Planarity : 0.004 0.044 2398 Dihedral : 11.804 116.504 2135 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.50 % Allowed : 13.46 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1658 helix: 1.36 (0.19), residues: 780 sheet: -0.81 (0.33), residues: 250 loop : -0.87 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 243 TYR 0.017 0.001 TYR E 145 PHE 0.018 0.002 PHE B 155 TRP 0.005 0.001 TRP D 50 HIS 0.010 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.19 (14278) covalent geometry : angle 0.53166 / 0.28 (19384) hydrogen bonds : bond 0.05505 / 3.75 ( 607) hydrogen bonds : angle 4.27139 / 2.92 ( 1695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.532 Fit side-chains REVERT: A 276 ASP cc_start: 0.8735 (t0) cc_final: 0.8388 (t0) REVERT: C 34 MET cc_start: 0.0113 (pmm) cc_final: -0.0513 (ttp) REVERT: F 80 GLN cc_start: 0.5908 (tp-100) cc_final: 0.5551 (mm110) outliers start: 22 outliers final: 19 residues processed: 168 average time/residue: 0.0903 time to fit residues: 23.3422 Evaluate side-chains 166 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 240 MET Chi-restraints excluded: chain F residue 270 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 150 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.191613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138564 restraints weight = 15398.985| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.84 r_work: 0.3360 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14278 Z= 0.100 Angle : 0.456 5.919 19384 Z= 0.245 Chirality : 0.039 0.149 2156 Planarity : 0.003 0.045 2398 Dihedral : 11.725 115.389 2134 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.02 % Allowed : 14.41 % Favored : 84.56 % 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: 0.55 (0.21), residues: 1658 helix: 1.66 (0.19), residues: 778 sheet: -0.69 (0.33), residues: 250 loop : -0.78 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 243 TYR 0.010 0.001 TYR D 138 PHE 0.016 0.001 PHE F 16 TRP 0.004 0.001 TRP D 50 HIS 0.009 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (14278) covalent geometry : angle 0.45554 / 0.24 (19384) hydrogen bonds : bond 0.04181 / 2.86 ( 607) hydrogen bonds : angle 4.07064 / 2.79 ( 1695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.519 Fit side-chains REVERT: C 34 MET cc_start: 0.0073 (pmm) cc_final: -0.0526 (ttp) REVERT: D 227 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8026 (tp30) REVERT: D 276 ASP cc_start: 0.8607 (t0) cc_final: 0.7930 (t0) REVERT: F 57 MET cc_start: 0.6836 (mpp) cc_final: 0.6616 (mpp) outliers start: 15 outliers final: 11 residues processed: 165 average time/residue: 0.0991 time to fit residues: 25.1084 Evaluate side-chains 157 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain F residue 270 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 103 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 164 optimal weight: 50.0000 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 151 HIS ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.187720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133458 restraints weight = 15392.776| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.89 r_work: 0.3283 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14278 Z= 0.191 Angle : 0.516 5.975 19384 Z= 0.274 Chirality : 0.041 0.151 2156 Planarity : 0.004 0.045 2398 Dihedral : 11.727 115.739 2134 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.09 % Allowed : 14.69 % Favored : 84.22 % 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: 0.39 (0.21), residues: 1658 helix: 1.47 (0.19), residues: 780 sheet: -0.68 (0.33), residues: 242 loop : -0.83 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 243 TYR 0.014 0.001 TYR E 145 PHE 0.018 0.002 PHE B 155 TRP 0.004 0.001 TRP D 50 HIS 0.010 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.19 (14278) covalent geometry : angle 0.51578 / 0.27 (19384) hydrogen bonds : bond 0.05329 / 3.63 ( 607) hydrogen bonds : angle 4.20458 / 2.88 ( 1695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.536 Fit side-chains REVERT: C 34 MET cc_start: 0.0089 (pmm) cc_final: -0.0615 (ttp) REVERT: F 80 GLN cc_start: 0.5864 (tp-100) cc_final: 0.5506 (mm110) outliers start: 16 outliers final: 14 residues processed: 163 average time/residue: 0.1023 time to fit residues: 25.7915 Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 270 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 55 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 142 optimal weight: 0.0870 chunk 154 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.192810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139706 restraints weight = 15544.915| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.88 r_work: 0.3370 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14278 Z= 0.094 Angle : 0.454 6.339 19384 Z= 0.244 Chirality : 0.038 0.146 2156 Planarity : 0.003 0.046 2398 Dihedral : 11.672 114.953 2134 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.96 % Allowed : 14.89 % Favored : 84.15 % 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: 0.67 (0.21), residues: 1658 helix: 1.74 (0.19), residues: 778 sheet: -0.48 (0.34), residues: 240 loop : -0.76 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 132 TYR 0.010 0.001 TYR D 138 PHE 0.017 0.001 PHE F 16 TRP 0.003 0.001 TRP D 50 HIS 0.011 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (14278) covalent geometry : angle 0.45394 / 0.24 (19384) hydrogen bonds : bond 0.03917 / 2.67 ( 607) hydrogen bonds : angle 3.95027 / 2.71 ( 1695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.517 Fit side-chains REVERT: C 34 MET cc_start: 0.0206 (pmm) cc_final: -0.0556 (ttp) REVERT: D 227 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8048 (tp30) REVERT: D 276 ASP cc_start: 0.8596 (t0) cc_final: 0.7850 (t0) outliers start: 14 outliers final: 13 residues processed: 163 average time/residue: 0.1024 time to fit residues: 25.6226 Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 240 MET Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain F residue 270 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 70 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 128 optimal weight: 0.0970 chunk 123 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.189090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135231 restraints weight = 15524.731| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.99 r_work: 0.3070 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14278 Z= 0.178 Angle : 0.520 13.313 19384 Z= 0.274 Chirality : 0.041 0.148 2156 Planarity : 0.004 0.046 2398 Dihedral : 11.676 115.385 2134 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.02 % Allowed : 15.16 % Favored : 83.81 % 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: 0.53 (0.21), residues: 1658 helix: 1.60 (0.19), residues: 780 sheet: -0.56 (0.34), residues: 240 loop : -0.80 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 243 TYR 0.012 0.001 TYR E 145 PHE 0.016 0.001 PHE B 155 TRP 0.002 0.001 TRP F 50 HIS 0.011 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (14278) covalent geometry : angle 0.52038 / 0.27 (19384) hydrogen bonds : bond 0.04920 / 3.35 ( 607) hydrogen bonds : angle 4.08244 / 2.80 ( 1695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.392 Fit side-chains REVERT: C 34 MET cc_start: 0.0250 (pmm) cc_final: -0.0579 (ttp) REVERT: D 227 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7924 (tm-30) outliers start: 15 outliers final: 15 residues processed: 160 average time/residue: 0.1063 time to fit residues: 25.9047 Evaluate side-chains 159 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 240 MET Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain F residue 270 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 75 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.191406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137779 restraints weight = 15446.694| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.88 r_work: 0.3391 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14278 Z= 0.105 Angle : 0.480 11.458 19384 Z= 0.254 Chirality : 0.039 0.147 2156 Planarity : 0.003 0.046 2398 Dihedral : 11.657 115.229 2134 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.89 % Allowed : 15.51 % Favored : 83.61 % 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: 0.68 (0.21), residues: 1658 helix: 1.75 (0.19), residues: 778 sheet: -0.49 (0.34), residues: 240 loop : -0.76 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 243 TYR 0.009 0.001 TYR D 138 PHE 0.030 0.001 PHE C 155 TRP 0.002 0.001 TRP F 50 HIS 0.011 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (14278) covalent geometry : angle 0.48012 / 0.25 (19384) hydrogen bonds : bond 0.04193 / 2.86 ( 607) hydrogen bonds : angle 3.98748 / 2.73 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3232.76 seconds wall clock time: 56 minutes 0.74 seconds (3360.74 seconds total)