Starting phenix.real_space_refine on Mon May 12 16:04:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jz7_36736/05_2025/8jz7_36736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jz7_36736/05_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_36736/05_2025/8jz7_36736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jz7_36736/05_2025/8jz7_36736.map" model { file = "/net/cci-nas-00/data/ceres_data/8jz7_36736/05_2025/8jz7_36736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jz7_36736/05_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-5687/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: 5.85, per 1000 atoms: 0.65 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 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: 1.29 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: 2.64 Time building geometry restraints manager: 2.87 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.480 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.880 ------------------------------------------------------------------------------- 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 : 0.900 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: 1.2396 time to fit residues: 242.5845 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 : 0.887 ------------------------------------------------------------------------------- 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 = 0.135702 restraints weight = 15212.083| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.07 r_work: 0.3985 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.911 Fit side-chains REVERT: B 42 ARG cc_start: 0.7652 (tpt-90) cc_final: 0.7445 (tpt90) REVERT: D 53 MET cc_start: 0.6903 (mtt) cc_final: 0.6471 (mmm) REVERT: D 315 ASP cc_start: 0.7461 (p0) cc_final: 0.7161 (p0) REVERT: S 220 GLU cc_start: 0.8287 (tt0) cc_final: 0.7938 (tt0) REVERT: S 230 MET cc_start: 0.7069 (ttp) cc_final: 0.6661 (mtp) REVERT: S 235 TYR cc_start: 0.8105 (m-80) cc_final: 0.7717 (m-80) REVERT: A 26 ILE cc_start: 0.5079 (OUTLIER) cc_final: 0.4678 (mm) REVERT: A 52 PHE cc_start: 0.6262 (m-10) cc_final: 0.5997 (m-10) REVERT: A 95 PHE cc_start: 0.7550 (m-10) cc_final: 0.7250 (m-80) REVERT: A 141 ASN cc_start: 0.7779 (p0) cc_final: 0.7526 (p0) REVERT: A 234 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7039 (mmt) REVERT: A 295 TYR cc_start: 0.7007 (m-80) cc_final: 0.6509 (m-80) outliers start: 22 outliers final: 5 residues processed: 171 average time/residue: 1.2541 time to fit residues: 227.9688 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 : 0.982 ------------------------------------------------------------------------------- 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: 0.0670 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.158335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.136847 restraints weight = 15367.212| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.15 r_work: 0.4009 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1887 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= 0.127 Angle : 0.627 10.335 12508 Z= 0.323 Chirality : 0.044 0.219 1398 Planarity : 0.004 0.062 1580 Dihedral : 6.513 56.138 1263 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.54 % Allowed : 17.04 % Favored : 80.43 % 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: -1.35 (0.25), residues: 1130 helix: 0.24 (0.30), residues: 336 sheet: -0.03 (0.30), residues: 296 loop : -2.29 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.013 0.002 PHE A 193 TYR 0.008 0.001 TYR D 320 ARG 0.004 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 373) hydrogen bonds : angle 5.05656 ( 1035) SS BOND : bond 0.00435 ( 4) SS BOND : angle 1.46463 ( 8) covalent geometry : bond 0.00279 ( 9239) covalent geometry : angle 0.62591 (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 184 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: B 76 ASP cc_start: 0.6841 (t0) cc_final: 0.6598 (t0) REVERT: D 53 MET cc_start: 0.6968 (mtt) cc_final: 0.6476 (mmm) REVERT: D 229 ASP cc_start: 0.7203 (t70) cc_final: 0.6640 (t0) REVERT: D 315 ASP cc_start: 0.7432 (p0) cc_final: 0.7121 (p0) REVERT: D 331 ASN cc_start: 0.7767 (m110) cc_final: 0.7525 (m-40) REVERT: S 21 SER cc_start: 0.7380 (p) cc_final: 0.7024 (t) REVERT: S 235 TYR cc_start: 0.7959 (m-80) cc_final: 0.7473 (m-80) REVERT: A 95 PHE cc_start: 0.7463 (m-10) cc_final: 0.7137 (m-80) REVERT: A 234 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.7031 (mmt) REVERT: A 295 TYR cc_start: 0.7043 (m-80) cc_final: 0.6539 (m-80) outliers start: 25 outliers final: 8 residues processed: 171 average time/residue: 1.1627 time to fit residues: 212.2506 Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN 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 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: 4.9990 chunk 46 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 57 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.138007 restraints weight = 15261.308| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.07 r_work: 0.4019 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9243 Z= 0.120 Angle : 0.619 11.188 12508 Z= 0.317 Chirality : 0.044 0.195 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.426 57.738 1263 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.25 % Allowed : 18.46 % Favored : 78.30 % 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: 0.38 (0.30), residues: 340 sheet: -0.06 (0.30), residues: 297 loop : -2.15 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.006 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 0.03970 ( 373) hydrogen bonds : angle 4.89252 ( 1035) SS BOND : bond 0.00453 ( 4) SS BOND : angle 1.40622 ( 8) covalent geometry : bond 0.00266 ( 9239) covalent geometry : angle 0.61825 (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 185 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8319 (mpp80) REVERT: B 76 ASP cc_start: 0.6629 (t0) cc_final: 0.6350 (t0) REVERT: C 62 ARG cc_start: 0.6962 (mtm180) cc_final: 0.6761 (mtt180) REVERT: D 53 MET cc_start: 0.6931 (mtt) cc_final: 0.6477 (mmm) REVERT: D 229 ASP cc_start: 0.7153 (t70) cc_final: 0.6569 (t0) REVERT: D 315 ASP cc_start: 0.7418 (p0) cc_final: 0.7087 (p0) REVERT: D 331 ASN cc_start: 0.7712 (m110) cc_final: 0.7380 (m-40) REVERT: S 21 SER cc_start: 0.7450 (p) cc_final: 0.7092 (t) REVERT: S 235 TYR cc_start: 0.7903 (m-80) cc_final: 0.7393 (m-80) REVERT: A 95 PHE cc_start: 0.7428 (m-10) cc_final: 0.7158 (m-80) REVERT: A 196 GLU cc_start: 0.7986 (pt0) cc_final: 0.7705 (pt0) REVERT: A 234 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6957 (mmt) REVERT: A 295 TYR cc_start: 0.7022 (m-80) cc_final: 0.6587 (m-80) outliers start: 32 outliers final: 15 residues processed: 171 average time/residue: 1.1695 time to fit residues: 213.6951 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 141 ASN Chi-restraints excluded: chain A residue 165 LYS 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: 0.8980 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4421 r_free = 0.4421 target = 0.157222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.136307 restraints weight = 15140.686| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.06 r_work: 0.3998 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2251 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= 0.138 Angle : 0.634 10.296 12508 Z= 0.325 Chirality : 0.045 0.203 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.377 56.542 1263 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.14 % Allowed : 20.99 % Favored : 75.86 % 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: 0.39 (0.30), residues: 345 sheet: -0.01 (0.31), residues: 290 loop : -2.17 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.008 0.001 HIS A 189 PHE 0.024 0.002 PHE A 296 TYR 0.008 0.001 TYR S 59 ARG 0.003 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 373) hydrogen bonds : angle 4.86920 ( 1035) SS BOND : bond 0.00612 ( 4) SS BOND : angle 1.73492 ( 8) covalent geometry : bond 0.00312 ( 9239) covalent geometry : angle 0.63308 (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 186 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8297 (mpp80) REVERT: B 76 ASP cc_start: 0.6766 (t0) cc_final: 0.6527 (t0) REVERT: D 53 MET cc_start: 0.6979 (mtt) cc_final: 0.6442 (mmm) REVERT: D 229 ASP cc_start: 0.7201 (t70) cc_final: 0.6583 (t0) REVERT: D 315 ASP cc_start: 0.7368 (p0) cc_final: 0.7049 (p0) REVERT: D 331 ASN cc_start: 0.7762 (m110) cc_final: 0.7523 (m-40) REVERT: S 21 SER cc_start: 0.7607 (p) cc_final: 0.7224 (t) REVERT: S 31 SER cc_start: 0.7370 (OUTLIER) cc_final: 0.7030 (p) REVERT: A 95 PHE cc_start: 0.7531 (m-10) cc_final: 0.7276 (m-80) REVERT: A 109 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6987 (tmm) REVERT: A 141 ASN cc_start: 0.7854 (p0) cc_final: 0.7407 (t0) REVERT: A 196 GLU cc_start: 0.8016 (pt0) cc_final: 0.7757 (pt0) REVERT: A 234 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.7018 (mmt) REVERT: A 295 TYR cc_start: 0.7106 (m-80) cc_final: 0.6636 (m-80) REVERT: A 296 PHE cc_start: 0.6696 (m-80) cc_final: 0.6387 (m-80) outliers start: 31 outliers final: 14 residues processed: 172 average time/residue: 1.2008 time to fit residues: 220.2892 Evaluate side-chains 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 D residue 343 ILE 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 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: 0.4980 chunk 82 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 331 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 = 0.4437 r_free = 0.4437 target = 0.158847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.137910 restraints weight = 15010.329| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.04 r_work: 0.4024 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9243 Z= 0.120 Angle : 0.620 10.141 12508 Z= 0.317 Chirality : 0.044 0.170 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.286 56.271 1263 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.14 % Allowed : 22.01 % 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: -1.10 (0.25), residues: 1130 helix: 0.59 (0.30), residues: 341 sheet: -0.02 (0.31), residues: 290 loop : -2.16 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.023 0.002 PHE A 74 TYR 0.010 0.001 TYR S 102 ARG 0.003 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 373) hydrogen bonds : angle 4.80158 ( 1035) SS BOND : bond 0.00538 ( 4) SS BOND : angle 1.61977 ( 8) covalent geometry : bond 0.00266 ( 9239) covalent geometry : angle 0.61921 (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 188 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8296 (mpp80) REVERT: B 76 ASP cc_start: 0.6693 (t0) cc_final: 0.6451 (t0) REVERT: D 53 MET cc_start: 0.7003 (mtt) cc_final: 0.6533 (mmm) REVERT: D 229 ASP cc_start: 0.7164 (t70) cc_final: 0.6540 (t0) REVERT: D 315 ASP cc_start: 0.7348 (p0) cc_final: 0.7029 (p0) REVERT: D 331 ASN cc_start: 0.7688 (m110) cc_final: 0.7426 (m-40) REVERT: S 21 SER cc_start: 0.7416 (p) cc_final: 0.7099 (t) REVERT: S 31 SER cc_start: 0.7346 (OUTLIER) cc_final: 0.7001 (p) REVERT: A 95 PHE cc_start: 0.7505 (m-10) cc_final: 0.7285 (m-80) REVERT: A 141 ASN cc_start: 0.7812 (p0) cc_final: 0.7484 (t0) REVERT: A 196 GLU cc_start: 0.7963 (pt0) cc_final: 0.7656 (pt0) REVERT: A 295 TYR cc_start: 0.7125 (m-80) cc_final: 0.6642 (m-80) REVERT: A 296 PHE cc_start: 0.6668 (m-80) cc_final: 0.6378 (m-80) outliers start: 31 outliers final: 15 residues processed: 175 average time/residue: 1.1571 time to fit residues: 217.0509 Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 C residue 21 MET Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain S residue 31 SER 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 203 ILE Chi-restraints excluded: chain A residue 226 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: 0.0770 chunk 55 optimal weight: 8.9990 chunk 61 optimal weight: 0.0270 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.0010 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 0.2802 ------------------------------------------------------------------------------- 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 C 18 GLN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.162228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.141567 restraints weight = 15286.033| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.06 r_work: 0.4068 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9243 Z= 0.105 Angle : 0.608 10.469 12508 Z= 0.306 Chirality : 0.043 0.142 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.080 55.319 1263 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.74 % Allowed : 23.23 % 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: -0.98 (0.25), residues: 1130 helix: 0.79 (0.31), residues: 339 sheet: -0.02 (0.30), residues: 289 loop : -2.09 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.023 0.001 PHE B 241 TYR 0.013 0.001 TYR S 102 ARG 0.002 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 373) hydrogen bonds : angle 4.68227 ( 1035) SS BOND : bond 0.00377 ( 4) SS BOND : angle 1.31869 ( 8) covalent geometry : bond 0.00226 ( 9239) covalent geometry : angle 0.60766 (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 185 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8264 (mpp80) REVERT: B 76 ASP cc_start: 0.6315 (t0) cc_final: 0.6049 (t0) REVERT: B 262 MET cc_start: 0.7168 (tpt) cc_final: 0.6873 (tpp) REVERT: D 25 GLU cc_start: 0.7425 (tp30) cc_final: 0.7220 (tm-30) REVERT: D 29 LYS cc_start: 0.8044 (tttp) cc_final: 0.7758 (tptp) REVERT: D 53 MET cc_start: 0.6993 (mtt) cc_final: 0.6427 (mmm) REVERT: D 229 ASP cc_start: 0.7173 (t70) cc_final: 0.6548 (t0) REVERT: D 315 ASP cc_start: 0.7336 (p0) cc_final: 0.7073 (p0) REVERT: D 331 ASN cc_start: 0.7529 (m110) cc_final: 0.7215 (m-40) REVERT: S 31 SER cc_start: 0.7286 (OUTLIER) cc_final: 0.6954 (p) REVERT: A 56 LEU cc_start: 0.7124 (tp) cc_final: 0.6798 (tt) REVERT: A 165 LYS cc_start: 0.7120 (tppt) cc_final: 0.6864 (mptt) REVERT: A 196 GLU cc_start: 0.7742 (pt0) cc_final: 0.7466 (pt0) outliers start: 27 outliers final: 13 residues processed: 173 average time/residue: 1.1367 time to fit residues: 210.5232 Evaluate side-chains 153 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 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 C residue 21 MET 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 210 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 203 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: 6.9990 chunk 38 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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** ** D 331 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 = 0.4472 r_free = 0.4472 target = 0.160940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.138816 restraints weight = 15638.253| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.22 r_work: 0.4053 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2918 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= 0.109 Angle : 0.624 10.331 12508 Z= 0.313 Chirality : 0.043 0.138 1398 Planarity : 0.004 0.059 1580 Dihedral : 5.975 54.468 1263 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.23 % Allowed : 24.14 % Favored : 73.63 % 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: -0.90 (0.25), residues: 1130 helix: 0.85 (0.31), residues: 338 sheet: -0.02 (0.30), residues: 289 loop : -2.01 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP S 176 HIS 0.007 0.001 HIS A 189 PHE 0.024 0.001 PHE A 74 TYR 0.010 0.001 TYR S 102 ARG 0.006 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 373) hydrogen bonds : angle 4.64838 ( 1035) SS BOND : bond 0.00401 ( 4) SS BOND : angle 1.43265 ( 8) covalent geometry : bond 0.00237 ( 9239) covalent geometry : angle 0.62314 (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 169 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: B 76 ASP cc_start: 0.6278 (t0) cc_final: 0.5993 (t0) REVERT: D 4 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.6392 (p) REVERT: D 25 GLU cc_start: 0.7462 (tp30) cc_final: 0.7261 (tm-30) REVERT: D 29 LYS cc_start: 0.8034 (tttp) cc_final: 0.7740 (tptp) REVERT: D 53 MET cc_start: 0.6999 (mtt) cc_final: 0.6407 (mmm) REVERT: D 229 ASP cc_start: 0.7253 (t70) cc_final: 0.6598 (t0) REVERT: D 315 ASP cc_start: 0.7350 (p0) cc_final: 0.7078 (p0) REVERT: S 31 SER cc_start: 0.7261 (OUTLIER) cc_final: 0.6909 (p) REVERT: A 56 LEU cc_start: 0.7083 (tp) cc_final: 0.6766 (tt) REVERT: A 165 LYS cc_start: 0.7109 (tppt) cc_final: 0.6845 (mptt) REVERT: A 196 GLU cc_start: 0.7687 (pt0) cc_final: 0.7400 (pt0) outliers start: 22 outliers final: 12 residues processed: 161 average time/residue: 1.1596 time to fit residues: 199.9921 Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 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 C residue 21 MET Chi-restraints excluded: chain D residue 4 THR 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 210 THR Chi-restraints excluded: chain A residue 203 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: 8.9990 chunk 27 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.159967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.137724 restraints weight = 15294.743| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.21 r_work: 0.4037 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9243 Z= 0.120 Angle : 0.635 11.062 12508 Z= 0.317 Chirality : 0.044 0.154 1398 Planarity : 0.004 0.058 1580 Dihedral : 5.983 53.739 1263 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.33 % Allowed : 24.75 % Favored : 72.92 % 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: -0.90 (0.25), residues: 1130 helix: 0.91 (0.31), residues: 337 sheet: -0.01 (0.30), residues: 292 loop : -2.07 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP S 176 HIS 0.006 0.001 HIS A 189 PHE 0.029 0.002 PHE B 241 TYR 0.011 0.001 TYR S 102 ARG 0.004 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 373) hydrogen bonds : angle 4.71514 ( 1035) SS BOND : bond 0.00510 ( 4) SS BOND : angle 1.60554 ( 8) covalent geometry : bond 0.00269 ( 9239) covalent geometry : angle 0.63425 (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 164 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: D 4 THR cc_start: 0.6677 (OUTLIER) cc_final: 0.6411 (p) REVERT: D 53 MET cc_start: 0.6977 (mtt) cc_final: 0.6402 (mmm) REVERT: D 229 ASP cc_start: 0.7239 (t70) cc_final: 0.6588 (t0) REVERT: D 315 ASP cc_start: 0.7344 (p0) cc_final: 0.7085 (p0) REVERT: A 56 LEU cc_start: 0.7116 (tp) cc_final: 0.6826 (tt) REVERT: A 92 ASP cc_start: 0.5408 (p0) cc_final: 0.5199 (p0) REVERT: A 107 LEU cc_start: 0.8040 (tp) cc_final: 0.7814 (mp) REVERT: A 165 LYS cc_start: 0.7096 (tppt) cc_final: 0.6821 (mptt) REVERT: A 196 GLU cc_start: 0.7739 (pt0) cc_final: 0.7451 (pt0) outliers start: 23 outliers final: 14 residues processed: 155 average time/residue: 1.1654 time to fit residues: 193.4044 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 203 ILE 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: 0.9990 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 57 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.161427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.138691 restraints weight = 15386.352| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.22 r_work: 0.4037 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9243 Z= 0.123 Angle : 0.658 11.447 12508 Z= 0.328 Chirality : 0.045 0.176 1398 Planarity : 0.004 0.058 1580 Dihedral : 5.949 52.594 1263 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.13 % Allowed : 25.56 % Favored : 72.31 % 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: -0.90 (0.25), residues: 1130 helix: 0.93 (0.30), residues: 337 sheet: 0.01 (0.30), residues: 292 loop : -2.09 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP S 176 HIS 0.007 0.001 HIS A 189 PHE 0.030 0.002 PHE B 241 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 373) hydrogen bonds : angle 4.74197 ( 1035) SS BOND : bond 0.00482 ( 4) SS BOND : angle 1.66946 ( 8) covalent geometry : bond 0.00278 ( 9239) covalent geometry : angle 0.65660 (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 161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: D 4 THR cc_start: 0.6616 (OUTLIER) cc_final: 0.6398 (p) REVERT: D 53 MET cc_start: 0.6925 (mtt) cc_final: 0.6400 (mmm) REVERT: D 229 ASP cc_start: 0.7238 (t70) cc_final: 0.6581 (t0) REVERT: D 315 ASP cc_start: 0.7330 (p0) cc_final: 0.7065 (p0) REVERT: S 94 TYR cc_start: 0.7479 (m-80) cc_final: 0.7272 (m-80) REVERT: A 56 LEU cc_start: 0.7106 (tp) cc_final: 0.6835 (tt) REVERT: A 92 ASP cc_start: 0.5364 (p0) cc_final: 0.5141 (p0) REVERT: A 107 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 196 GLU cc_start: 0.7749 (pt0) cc_final: 0.7467 (pt0) outliers start: 21 outliers final: 16 residues processed: 155 average time/residue: 1.1467 time to fit residues: 190.0966 Evaluate side-chains 160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 203 ILE 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: 3.9990 chunk 105 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.0070 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 217 GLN ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.157544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.136051 restraints weight = 15148.397| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.10 r_work: 0.4006 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9243 Z= 0.148 Angle : 0.678 11.608 12508 Z= 0.339 Chirality : 0.046 0.199 1398 Planarity : 0.004 0.058 1580 Dihedral : 6.106 52.536 1263 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.03 % Allowed : 25.86 % Favored : 72.11 % 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: -0.98 (0.25), residues: 1130 helix: 0.82 (0.30), residues: 339 sheet: -0.04 (0.30), residues: 292 loop : -2.12 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.007 0.001 HIS A 189 PHE 0.033 0.002 PHE S 239 TYR 0.012 0.002 TYR B 59 ARG 0.004 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 373) hydrogen bonds : angle 4.87220 ( 1035) SS BOND : bond 0.00565 ( 4) SS BOND : angle 1.85491 ( 8) covalent geometry : bond 0.00339 ( 9239) covalent geometry : angle 0.67641 (12500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11215.11 seconds wall clock time: 192 minutes 53.61 seconds (11573.61 seconds total)