Starting phenix.real_space_refine on Wed Apr 30 02:47:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jz7_36736/04_2025/8jz7_36736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jz7_36736/04_2025/8jz7_36736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jz7_36736/04_2025/8jz7_36736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jz7_36736/04_2025/8jz7_36736.map" model { file = "/net/cci-nas-00/data/ceres_data/8jz7_36736/04_2025/8jz7_36736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jz7_36736/04_2025/8jz7_36736_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 sd= 0.118 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 69 5.16 5 C 5765 2.51 5 N 1542 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9042 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1805 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.61 Number of scatterers: 9042 At special positions: 0 Unit cell: (99.36, 138, 120.52, 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 69 16.00 O 1666 8.00 N 1542 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.06 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 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: 2.74 Conformation dependent library (CDL) restraints added in 1.2 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 33.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'B' and resid 1 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.506A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.695A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 30 removed outlier: 4.018A pdb=" N ALA D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 207 through 211 Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.501A pdb=" N ALA D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 280 removed outlier: 3.953A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.578A pdb=" N ILE D 285 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 330 through 352 removed outlier: 4.080A pdb=" N VAL D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.513A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.814A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 55 removed outlier: 3.868A pdb=" N LEU A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.514A pdb=" N LEU A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.579A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 removed outlier: 4.444A pdb=" N LEU A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.588A pdb=" N PHE A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.943A pdb=" N VAL A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.547A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.776A pdb=" N THR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 4.165A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.781A pdb=" N ARG A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 Processing helix chain 'A' and resid 227 through 239 removed outlier: 3.681A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.559A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.800A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.610A pdb=" N LEU A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.512A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.709A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.967A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.909A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.585A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.542A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.654A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190 removed outlier: 3.630A pdb=" N LEU D 38 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.919A pdb=" N GLY S 16 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER S 85 " --> pdb=" O GLY S 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.985A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.554A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.929A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 12 through 13 373 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2467 1.33 - 1.46: 2674 1.46 - 1.59: 3998 1.59 - 1.72: 0 1.72 - 1.85: 100 Bond restraints: 9239 Sorted by residual: bond pdb=" C GLU S 234 " pdb=" N TYR S 235 " ideal model delta sigma weight residual 1.331 1.234 0.097 2.07e-02 2.33e+03 2.19e+01 bond pdb=" C04 FI7 A 401 " pdb=" C05 FI7 A 401 " ideal model delta sigma weight residual 1.483 1.390 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" N ARG B 22 " pdb=" CA ARG B 22 " ideal model delta sigma weight residual 1.457 1.516 -0.059 1.33e-02 5.65e+03 1.98e+01 bond pdb=" C20 FI7 A 401 " pdb=" N19 FI7 A 401 " ideal model delta sigma weight residual 1.396 1.327 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C22 FI7 A 401 " pdb=" O23 FI7 A 401 " ideal model delta sigma weight residual 1.269 1.203 0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 9234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 11734 1.58 - 3.17: 637 3.17 - 4.75: 92 4.75 - 6.33: 24 6.33 - 7.92: 13 Bond angle restraints: 12500 Sorted by residual: angle pdb=" C ARG B 22 " pdb=" N LYS B 23 " pdb=" CA LYS B 23 " ideal model delta sigma weight residual 120.31 112.73 7.58 1.52e+00 4.33e-01 2.48e+01 angle pdb=" C GLU A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta sigma weight residual 122.09 114.17 7.92 1.79e+00 3.12e-01 1.96e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 112.97 108.32 4.65 1.06e+00 8.90e-01 1.92e+01 angle pdb=" O ALA B 21 " pdb=" C ALA B 21 " pdb=" N ARG B 22 " ideal model delta sigma weight residual 122.27 116.96 5.31 1.23e+00 6.61e-01 1.87e+01 angle pdb=" N ASP D 328 " pdb=" CA ASP D 328 " pdb=" C ASP D 328 " ideal model delta sigma weight residual 108.60 114.57 -5.97 1.46e+00 4.69e-01 1.67e+01 ... (remaining 12495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 4789 15.05 - 30.09: 546 30.09 - 45.14: 121 45.14 - 60.18: 22 60.18 - 75.23: 12 Dihedral angle restraints: 5490 sinusoidal: 2178 harmonic: 3312 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ALA A 174 " pdb=" C ALA A 174 " pdb=" N ASN A 175 " pdb=" CA ASN A 175 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA MET C 21 " pdb=" C MET C 21 " pdb=" N GLU C 22 " pdb=" CA GLU C 22 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 832 0.040 - 0.079: 391 0.079 - 0.119: 139 0.119 - 0.158: 33 0.158 - 0.198: 3 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CA ILE D 303 " pdb=" N ILE D 303 " pdb=" C ILE D 303 " pdb=" CB ILE D 303 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CB ILE A 13 " pdb=" CA ILE A 13 " pdb=" CG1 ILE A 13 " pdb=" CG2 ILE A 13 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1395 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 FI7 A 401 " -0.078 2.00e-02 2.50e+03 6.24e-02 6.82e+01 pdb=" C05 FI7 A 401 " 0.031 2.00e-02 2.50e+03 pdb=" C07 FI7 A 401 " 0.062 2.00e-02 2.50e+03 pdb=" C08 FI7 A 401 " -0.096 2.00e-02 2.50e+03 pdb=" N06 FI7 A 401 " 0.083 2.00e-02 2.50e+03 pdb=" N15 FI7 A 401 " 0.011 2.00e-02 2.50e+03 pdb=" O16 FI7 A 401 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 FI7 A 401 " 0.081 2.00e-02 2.50e+03 4.13e-02 3.41e+01 pdb=" C08 FI7 A 401 " -0.040 2.00e-02 2.50e+03 pdb=" C09 FI7 A 401 " -0.032 2.00e-02 2.50e+03 pdb=" C10 FI7 A 401 " -0.010 2.00e-02 2.50e+03 pdb=" C11 FI7 A 401 " -0.001 2.00e-02 2.50e+03 pdb=" C13 FI7 A 401 " -0.014 2.00e-02 2.50e+03 pdb=" N14 FI7 A 401 " -0.036 2.00e-02 2.50e+03 pdb=" O12 FI7 A 401 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO S 75 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.037 5.00e-02 4.00e+02 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 870 2.74 - 3.28: 8870 3.28 - 3.82: 14248 3.82 - 4.36: 17565 4.36 - 4.90: 30106 Nonbonded interactions: 71659 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.206 3.040 nonbonded pdb=" O TRP A 59 " pdb=" ND2 ASN A 141 " model vdw 2.221 3.120 nonbonded pdb=" O THR D 262 " pdb=" NZ LYS D 317 " model vdw 2.222 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.247 3.040 ... (remaining 71654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.720 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:14.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 0.097 9243 Z= 0.289 Angle : 0.869 17.573 12508 Z= 0.496 Chirality : 0.051 0.198 1398 Planarity : 0.005 0.066 1580 Dihedral : 13.847 75.228 3338 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.61 % Allowed : 0.61 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.24), residues: 1130 helix: -0.99 (0.28), residues: 335 sheet: -0.19 (0.29), residues: 299 loop : -2.56 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 82 HIS 0.012 0.002 HIS B 54 PHE 0.031 0.003 PHE A 52 TYR 0.033 0.003 TYR S 190 ARG 0.007 0.001 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.15859 ( 373) hydrogen bonds : angle 6.90776 ( 1035) SS BOND : bond 0.01584 ( 4) SS BOND : angle 6.77810 ( 8) covalent geometry : bond 0.00612 ( 9239) covalent geometry : angle 0.85241 (12500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: D 315 ASP cc_start: 0.7065 (p0) cc_final: 0.6860 (p0) REVERT: A 295 TYR cc_start: 0.6748 (m-80) cc_final: 0.5974 (m-80) outliers start: 6 outliers final: 1 residues processed: 184 average time/residue: 1.3562 time to fit residues: 264.8543 Evaluate side-chains 148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 195 HIS ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.156753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.135680 restraints weight = 15212.072| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.07 r_work: 0.3984 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9243 Z= 0.145 Angle : 0.681 10.910 12508 Z= 0.353 Chirality : 0.046 0.213 1398 Planarity : 0.004 0.063 1580 Dihedral : 7.053 58.328 1265 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.23 % Allowed : 13.49 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.24), residues: 1130 helix: -0.24 (0.29), residues: 336 sheet: -0.08 (0.30), residues: 295 loop : -2.34 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.009 0.001 HIS A 189 PHE 0.023 0.002 PHE A 117 TYR 0.014 0.002 TYR A 295 ARG 0.004 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 373) hydrogen bonds : angle 5.37232 ( 1035) SS BOND : bond 0.00430 ( 4) SS BOND : angle 1.60473 ( 8) covalent geometry : bond 0.00321 ( 9239) covalent geometry : angle 0.68049 (12500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.047 Fit side-chains REVERT: B 42 ARG cc_start: 0.7644 (tpt-90) cc_final: 0.7438 (tpt90) REVERT: D 53 MET cc_start: 0.6898 (mtt) cc_final: 0.6468 (mmm) REVERT: D 315 ASP cc_start: 0.7466 (p0) cc_final: 0.7167 (p0) REVERT: S 220 GLU cc_start: 0.8295 (tt0) cc_final: 0.7949 (tt0) REVERT: S 230 MET cc_start: 0.7076 (ttp) cc_final: 0.6675 (mtp) REVERT: S 235 TYR cc_start: 0.8101 (m-80) cc_final: 0.7717 (m-80) REVERT: A 26 ILE cc_start: 0.5101 (OUTLIER) cc_final: 0.4696 (mm) REVERT: A 52 PHE cc_start: 0.6271 (m-10) cc_final: 0.6006 (m-10) REVERT: A 95 PHE cc_start: 0.7556 (m-10) cc_final: 0.7257 (m-80) REVERT: A 141 ASN cc_start: 0.7773 (p0) cc_final: 0.7520 (p0) REVERT: A 234 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.7027 (mmt) REVERT: A 295 TYR cc_start: 0.7004 (m-80) cc_final: 0.6513 (m-80) outliers start: 22 outliers final: 5 residues processed: 171 average time/residue: 1.4512 time to fit residues: 263.5161 Evaluate side-chains 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 195 HIS ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.156832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.135550 restraints weight = 15391.510| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.11 r_work: 0.3984 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9243 Z= 0.147 Angle : 0.651 10.412 12508 Z= 0.336 Chirality : 0.045 0.231 1398 Planarity : 0.004 0.063 1580 Dihedral : 6.641 56.669 1263 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.54 % Allowed : 16.84 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.25), residues: 1130 helix: 0.14 (0.30), residues: 336 sheet: -0.06 (0.30), residues: 296 loop : -2.34 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.015 0.002 PHE B 234 TYR 0.009 0.001 TYR D 320 ARG 0.004 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 373) hydrogen bonds : angle 5.14455 ( 1035) SS BOND : bond 0.00496 ( 4) SS BOND : angle 1.64390 ( 8) covalent geometry : bond 0.00331 ( 9239) covalent geometry : angle 0.64997 (12500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: B 76 ASP cc_start: 0.6959 (t0) cc_final: 0.6744 (t0) REVERT: D 53 MET cc_start: 0.6956 (mtt) cc_final: 0.6477 (mmm) REVERT: D 229 ASP cc_start: 0.7215 (t70) cc_final: 0.6648 (t0) REVERT: D 315 ASP cc_start: 0.7431 (p0) cc_final: 0.7102 (p0) REVERT: S 235 TYR cc_start: 0.7980 (m-80) cc_final: 0.7506 (m-80) REVERT: A 92 ASP cc_start: 0.5688 (p0) cc_final: 0.5480 (p0) REVERT: A 141 ASN cc_start: 0.7808 (p0) cc_final: 0.7598 (p0) REVERT: A 234 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.7059 (mmt) REVERT: A 295 TYR cc_start: 0.7046 (m-80) cc_final: 0.6556 (m-80) outliers start: 25 outliers final: 11 residues processed: 168 average time/residue: 1.4530 time to fit residues: 259.8609 Evaluate side-chains 156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 195 HIS A 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.159475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.138226 restraints weight = 15289.670| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.09 r_work: 0.4017 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9243 Z= 0.120 Angle : 0.616 10.938 12508 Z= 0.317 Chirality : 0.044 0.194 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.385 55.899 1263 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.25 % Allowed : 18.97 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1130 helix: 0.34 (0.30), residues: 340 sheet: -0.09 (0.30), residues: 297 loop : -2.17 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS A 189 PHE 0.018 0.002 PHE A 74 TYR 0.008 0.001 TYR S 102 ARG 0.003 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 373) hydrogen bonds : angle 4.91000 ( 1035) SS BOND : bond 0.00440 ( 4) SS BOND : angle 1.38274 ( 8) covalent geometry : bond 0.00262 ( 9239) covalent geometry : angle 0.61549 (12500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8307 (mpp80) REVERT: B 76 ASP cc_start: 0.6616 (t0) cc_final: 0.6342 (t0) REVERT: D 53 MET cc_start: 0.6941 (mtt) cc_final: 0.6473 (mmm) REVERT: D 229 ASP cc_start: 0.7155 (t70) cc_final: 0.6562 (t0) REVERT: D 315 ASP cc_start: 0.7415 (p0) cc_final: 0.7085 (p0) REVERT: S 21 SER cc_start: 0.7529 (p) cc_final: 0.7169 (t) REVERT: S 235 TYR cc_start: 0.7934 (m-80) cc_final: 0.7409 (m-80) REVERT: A 234 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6995 (mmt) REVERT: A 295 TYR cc_start: 0.7025 (m-80) cc_final: 0.6577 (m-80) outliers start: 32 outliers final: 13 residues processed: 175 average time/residue: 1.2328 time to fit residues: 230.6973 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 265 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN A 68 ASN A 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.156795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.135375 restraints weight = 15090.257| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.10 r_work: 0.3983 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9243 Z= 0.150 Angle : 0.645 10.712 12508 Z= 0.333 Chirality : 0.045 0.218 1398 Planarity : 0.004 0.062 1580 Dihedral : 6.451 56.293 1263 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.94 % Allowed : 21.50 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.25), residues: 1130 helix: 0.32 (0.30), residues: 345 sheet: -0.05 (0.30), residues: 290 loop : -2.20 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.007 0.001 HIS A 189 PHE 0.024 0.002 PHE A 296 TYR 0.009 0.001 TYR D 320 ARG 0.003 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 373) hydrogen bonds : angle 4.90077 ( 1035) SS BOND : bond 0.00577 ( 4) SS BOND : angle 1.72982 ( 8) covalent geometry : bond 0.00340 ( 9239) covalent geometry : angle 0.64371 (12500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8297 (mpp80) REVERT: B 76 ASP cc_start: 0.6823 (t0) cc_final: 0.6597 (t0) REVERT: D 53 MET cc_start: 0.7036 (mtt) cc_final: 0.6529 (mmm) REVERT: D 229 ASP cc_start: 0.7215 (t70) cc_final: 0.6590 (t0) REVERT: D 315 ASP cc_start: 0.7371 (p0) cc_final: 0.7052 (p0) REVERT: A 109 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7012 (tmm) REVERT: A 234 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.7028 (mmt) REVERT: A 295 TYR cc_start: 0.7091 (m-80) cc_final: 0.6619 (m-80) REVERT: A 296 PHE cc_start: 0.6684 (m-80) cc_final: 0.6375 (m-80) outliers start: 29 outliers final: 15 residues processed: 168 average time/residue: 1.2699 time to fit residues: 227.2925 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 265 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 2 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.155325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.134281 restraints weight = 15001.117| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.02 r_work: 0.3985 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9243 Z= 0.150 Angle : 0.649 10.414 12508 Z= 0.334 Chirality : 0.045 0.204 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.435 56.051 1263 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.25 % Allowed : 21.91 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1130 helix: 0.38 (0.30), residues: 344 sheet: -0.07 (0.30), residues: 289 loop : -2.20 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.021 0.002 PHE A 74 TYR 0.009 0.001 TYR D 320 ARG 0.003 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 373) hydrogen bonds : angle 4.89976 ( 1035) SS BOND : bond 0.00619 ( 4) SS BOND : angle 1.80512 ( 8) covalent geometry : bond 0.00342 ( 9239) covalent geometry : angle 0.64713 (12500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8219 (mpp80) REVERT: B 76 ASP cc_start: 0.6786 (t0) cc_final: 0.6584 (t0) REVERT: D 53 MET cc_start: 0.6953 (mtt) cc_final: 0.6486 (mmm) REVERT: D 229 ASP cc_start: 0.7204 (t70) cc_final: 0.6563 (t0) REVERT: D 315 ASP cc_start: 0.7349 (p0) cc_final: 0.7030 (p0) REVERT: S 74 ASP cc_start: 0.7772 (m-30) cc_final: 0.7559 (m-30) REVERT: A 95 PHE cc_start: 0.7433 (m-80) cc_final: 0.7223 (m-80) REVERT: A 109 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6966 (tmm) REVERT: A 198 PHE cc_start: 0.6098 (m-10) cc_final: 0.5871 (m-80) REVERT: A 296 PHE cc_start: 0.6624 (m-80) cc_final: 0.6361 (m-80) outliers start: 32 outliers final: 15 residues processed: 161 average time/residue: 1.3211 time to fit residues: 227.3513 Evaluate side-chains 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN A 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.157686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.136611 restraints weight = 15353.540| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.08 r_work: 0.4002 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9243 Z= 0.131 Angle : 0.626 10.651 12508 Z= 0.322 Chirality : 0.044 0.179 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.393 55.754 1263 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.45 % Allowed : 22.52 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1130 helix: 0.48 (0.30), residues: 341 sheet: -0.08 (0.31), residues: 289 loop : -2.18 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.017 0.002 PHE A 117 TYR 0.010 0.001 TYR S 102 ARG 0.003 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 373) hydrogen bonds : angle 4.84511 ( 1035) SS BOND : bond 0.00558 ( 4) SS BOND : angle 1.65916 ( 8) covalent geometry : bond 0.00293 ( 9239) covalent geometry : angle 0.62482 (12500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8237 (mpp80) REVERT: D 53 MET cc_start: 0.6976 (mtt) cc_final: 0.6468 (mmm) REVERT: D 229 ASP cc_start: 0.7220 (t70) cc_final: 0.6573 (t0) REVERT: D 315 ASP cc_start: 0.7343 (p0) cc_final: 0.7075 (p0) REVERT: S 21 SER cc_start: 0.7452 (p) cc_final: 0.7114 (t) REVERT: S 74 ASP cc_start: 0.7781 (m-30) cc_final: 0.7573 (m-30) REVERT: A 95 PHE cc_start: 0.7405 (m-80) cc_final: 0.7140 (m-80) REVERT: A 196 GLU cc_start: 0.8021 (pt0) cc_final: 0.7715 (pt0) outliers start: 34 outliers final: 21 residues processed: 170 average time/residue: 1.1991 time to fit residues: 217.6761 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 71 optimal weight: 0.0670 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.155169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.133493 restraints weight = 15410.919| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.18 r_work: 0.3990 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9243 Z= 0.144 Angle : 0.649 10.759 12508 Z= 0.332 Chirality : 0.045 0.182 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.404 56.163 1263 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.94 % Allowed : 23.73 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.25), residues: 1130 helix: 0.46 (0.30), residues: 344 sheet: -0.12 (0.30), residues: 289 loop : -2.18 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.020 0.002 PHE A 296 TYR 0.011 0.001 TYR S 102 ARG 0.004 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 373) hydrogen bonds : angle 4.91733 ( 1035) SS BOND : bond 0.00590 ( 4) SS BOND : angle 1.72532 ( 8) covalent geometry : bond 0.00330 ( 9239) covalent geometry : angle 0.64757 (12500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8306 (mpp80) REVERT: D 4 THR cc_start: 0.6633 (OUTLIER) cc_final: 0.6428 (p) REVERT: D 53 MET cc_start: 0.7012 (mtt) cc_final: 0.6525 (mmm) REVERT: D 229 ASP cc_start: 0.7256 (t70) cc_final: 0.6582 (t0) REVERT: D 315 ASP cc_start: 0.7332 (p0) cc_final: 0.7064 (p0) REVERT: S 21 SER cc_start: 0.7430 (p) cc_final: 0.7056 (t) REVERT: S 31 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.7094 (p) REVERT: A 109 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6992 (tmm) REVERT: A 196 GLU cc_start: 0.8041 (pt0) cc_final: 0.7717 (pt0) outliers start: 29 outliers final: 20 residues processed: 167 average time/residue: 1.2715 time to fit residues: 226.1598 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** A 223 HIS ** 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 = 0.4425 r_free = 0.4425 target = 0.156907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.135495 restraints weight = 15056.155| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.12 r_work: 0.3985 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9243 Z= 0.146 Angle : 0.654 10.946 12508 Z= 0.334 Chirality : 0.045 0.186 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.428 56.490 1263 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.94 % Allowed : 24.24 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1130 helix: 0.47 (0.30), residues: 344 sheet: -0.12 (0.30), residues: 288 loop : -2.17 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.019 0.002 PHE A 296 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 373) hydrogen bonds : angle 4.93432 ( 1035) SS BOND : bond 0.00545 ( 4) SS BOND : angle 1.73767 ( 8) covalent geometry : bond 0.00332 ( 9239) covalent geometry : angle 0.65261 (12500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8284 (mpp80) REVERT: D 4 THR cc_start: 0.6659 (OUTLIER) cc_final: 0.6442 (p) REVERT: D 53 MET cc_start: 0.7030 (mtt) cc_final: 0.6504 (mmm) REVERT: D 229 ASP cc_start: 0.7273 (t70) cc_final: 0.6572 (t0) REVERT: D 315 ASP cc_start: 0.7321 (p0) cc_final: 0.7059 (p0) REVERT: S 21 SER cc_start: 0.7450 (p) cc_final: 0.7083 (t) REVERT: S 31 SER cc_start: 0.7430 (OUTLIER) cc_final: 0.7113 (p) REVERT: A 109 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6973 (tmm) REVERT: A 196 GLU cc_start: 0.8055 (pt0) cc_final: 0.7735 (pt0) REVERT: A 198 PHE cc_start: 0.6149 (m-10) cc_final: 0.5937 (m-80) REVERT: A 234 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7047 (mmt) outliers start: 29 outliers final: 21 residues processed: 165 average time/residue: 1.2283 time to fit residues: 216.0864 Evaluate side-chains 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN B 155 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.155285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.133733 restraints weight = 15196.630| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.12 r_work: 0.3968 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9243 Z= 0.167 Angle : 0.683 11.007 12508 Z= 0.350 Chirality : 0.046 0.212 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.576 57.659 1263 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.74 % Allowed : 25.05 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.25), residues: 1130 helix: 0.45 (0.30), residues: 343 sheet: -0.17 (0.30), residues: 288 loop : -2.24 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.025 0.002 PHE A 74 TYR 0.015 0.002 TYR B 59 ARG 0.007 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 373) hydrogen bonds : angle 4.99397 ( 1035) SS BOND : bond 0.00733 ( 4) SS BOND : angle 2.12193 ( 8) covalent geometry : bond 0.00388 ( 9239) covalent geometry : angle 0.68061 (12500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8291 (mpp80) REVERT: D 4 THR cc_start: 0.6668 (OUTLIER) cc_final: 0.6460 (p) REVERT: D 53 MET cc_start: 0.7085 (mtt) cc_final: 0.6567 (mmm) REVERT: D 315 ASP cc_start: 0.7297 (p0) cc_final: 0.7036 (p0) REVERT: S 21 SER cc_start: 0.7488 (p) cc_final: 0.7092 (t) REVERT: A 107 LEU cc_start: 0.8128 (tp) cc_final: 0.7884 (mp) REVERT: A 109 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7011 (tmm) REVERT: A 198 PHE cc_start: 0.6171 (m-10) cc_final: 0.5952 (m-80) REVERT: A 234 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7160 (mmt) outliers start: 27 outliers final: 20 residues processed: 168 average time/residue: 1.3294 time to fit residues: 239.5184 Evaluate side-chains 170 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.0870 chunk 25 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 49 optimal weight: 0.0270 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 HIS ** A 223 HIS ** 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 = 0.4459 r_free = 0.4459 target = 0.160196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.137969 restraints weight = 15152.685| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.20 r_work: 0.4040 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9243 Z= 0.112 Angle : 0.619 10.669 12508 Z= 0.316 Chirality : 0.044 0.142 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.316 57.285 1263 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.33 % Allowed : 26.06 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.25), residues: 1130 helix: 0.73 (0.30), residues: 338 sheet: -0.16 (0.30), residues: 291 loop : -2.13 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 176 HIS 0.005 0.001 HIS A 189 PHE 0.035 0.001 PHE S 239 TYR 0.012 0.001 TYR S 102 ARG 0.002 0.000 ARG D 242 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 373) hydrogen bonds : angle 4.87120 ( 1035) SS BOND : bond 0.00373 ( 4) SS BOND : angle 1.44145 ( 8) covalent geometry : bond 0.00242 ( 9239) covalent geometry : angle 0.61812 (12500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12176.47 seconds wall clock time: 213 minutes 11.44 seconds (12791.44 seconds total)