Starting phenix.real_space_refine on Sat Aug 23 02:20:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jz7_36736/08_2025/8jz7_36736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jz7_36736/08_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_36736/08_2025/8jz7_36736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jz7_36736/08_2025/8jz7_36736.map" model { file = "/net/cci-nas-00/data/ceres_data/8jz7_36736/08_2025/8jz7_36736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jz7_36736/08_2025/8jz7_36736_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.98, per 1000 atoms: 0.22 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: 0.64 Conformation dependent library (CDL) restraints added in 335.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.25 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: 0.99 Time building geometry restraints manager: 0.84 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: 1.040 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- 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 : 15.37 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG S 67 TYR 0.033 0.003 TYR S 190 PHE 0.031 0.003 PHE A 52 TRP 0.035 0.003 TRP B 82 HIS 0.012 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 9239) covalent geometry : angle 0.85241 (12500) SS BOND : bond 0.01584 ( 4) SS BOND : angle 6.77810 ( 8) hydrogen bonds : bond 0.15859 ( 373) hydrogen bonds : angle 6.90776 ( 1035) *********************** 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 : 0.295 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: 0.5043 time to fit residues: 98.2058 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 : 0.189 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 B 340 ASN D 195 HIS A 223 HIS A 286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.156395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.135278 restraints weight = 15312.402| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.08 r_work: 0.3975 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9243 Z= 0.152 Angle : 0.693 11.143 12508 Z= 0.358 Chirality : 0.046 0.220 1398 Planarity : 0.004 0.063 1580 Dihedral : 7.061 58.270 1265 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.33 % Allowed : 13.59 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.24), residues: 1130 helix: -0.24 (0.30), residues: 335 sheet: -0.09 (0.30), residues: 295 loop : -2.35 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.015 0.002 TYR A 295 PHE 0.025 0.002 PHE A 117 TRP 0.025 0.002 TRP B 82 HIS 0.010 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9239) covalent geometry : angle 0.69168 (12500) SS BOND : bond 0.00451 ( 4) SS BOND : angle 1.63713 ( 8) hydrogen bonds : bond 0.04868 ( 373) hydrogen bonds : angle 5.36074 ( 1035) *********************** 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 185 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.205 Fit side-chains REVERT: B 46 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8357 (mpp80) REVERT: D 29 LYS cc_start: 0.8218 (tttp) cc_final: 0.7828 (tptt) REVERT: D 53 MET cc_start: 0.6893 (mtt) cc_final: 0.6451 (mmm) REVERT: D 315 ASP cc_start: 0.7461 (p0) cc_final: 0.7150 (p0) REVERT: S 230 MET cc_start: 0.7085 (ttp) cc_final: 0.6686 (mtp) REVERT: S 235 TYR cc_start: 0.8132 (m-80) cc_final: 0.7747 (m-80) REVERT: A 52 PHE cc_start: 0.6169 (m-10) cc_final: 0.5953 (m-10) REVERT: A 141 ASN cc_start: 0.7773 (p0) cc_final: 0.7515 (p0) REVERT: A 234 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.7050 (mmt) REVERT: A 295 TYR cc_start: 0.7032 (m-80) cc_final: 0.6533 (m-80) outliers start: 23 outliers final: 6 residues processed: 172 average time/residue: 0.4852 time to fit residues: 88.6591 Evaluate side-chains 156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG 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 98 optimal weight: 0.6980 chunk 101 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** 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 = 0.4415 r_free = 0.4415 target = 0.157163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.135661 restraints weight = 15151.059| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.15 r_work: 0.3989 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9243 Z= 0.138 Angle : 0.640 10.613 12508 Z= 0.330 Chirality : 0.045 0.231 1398 Planarity : 0.004 0.063 1580 Dihedral : 6.644 57.662 1263 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.84 % Allowed : 17.24 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.25), residues: 1130 helix: 0.16 (0.30), residues: 336 sheet: -0.07 (0.30), residues: 295 loop : -2.34 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 67 TYR 0.008 0.001 TYR D 320 PHE 0.014 0.002 PHE B 234 TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9239) covalent geometry : angle 0.63932 (12500) SS BOND : bond 0.00487 ( 4) SS BOND : angle 1.56356 ( 8) hydrogen bonds : bond 0.04471 ( 373) hydrogen bonds : angle 5.11273 ( 1035) *********************** 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 189 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8363 (mpp80) REVERT: B 76 ASP cc_start: 0.6880 (t0) cc_final: 0.6625 (t0) REVERT: D 53 MET cc_start: 0.7029 (mtt) cc_final: 0.6550 (mmm) REVERT: D 229 ASP cc_start: 0.7245 (t70) cc_final: 0.6669 (t0) REVERT: D 315 ASP cc_start: 0.7427 (p0) cc_final: 0.7117 (p0) REVERT: S 21 SER cc_start: 0.7434 (p) cc_final: 0.7029 (t) REVERT: S 235 TYR cc_start: 0.7984 (m-80) cc_final: 0.7499 (m-80) REVERT: A 95 PHE cc_start: 0.7538 (m-10) cc_final: 0.7256 (m-80) REVERT: A 141 ASN cc_start: 0.7810 (p0) cc_final: 0.7609 (p0) REVERT: A 295 TYR cc_start: 0.7075 (m-80) cc_final: 0.6549 (m-80) outliers start: 28 outliers final: 11 residues processed: 173 average time/residue: 0.4841 time to fit residues: 89.0794 Evaluate side-chains 163 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 C residue 21 MET Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 203 ILE 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 37 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 74 optimal weight: 0.0020 chunk 102 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 B 340 ASN D 195 HIS A 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.158527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.136684 restraints weight = 15516.910| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.13 r_work: 0.4030 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2141 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= 0.122 Angle : 0.616 10.900 12508 Z= 0.316 Chirality : 0.044 0.194 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.429 57.167 1263 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.35 % Allowed : 18.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.25), residues: 1130 helix: 0.32 (0.30), residues: 340 sheet: -0.06 (0.30), residues: 296 loop : -2.17 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 67 TYR 0.008 0.001 TYR S 102 PHE 0.020 0.002 PHE A 74 TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9239) covalent geometry : angle 0.61493 (12500) SS BOND : bond 0.00475 ( 4) SS BOND : angle 1.45515 ( 8) hydrogen bonds : bond 0.03986 ( 373) hydrogen bonds : angle 4.91056 ( 1035) *********************** 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 186 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8245 (mpp80) REVERT: B 76 ASP cc_start: 0.6587 (t0) cc_final: 0.6314 (t0) REVERT: B 78 LYS cc_start: 0.7331 (mptt) cc_final: 0.7060 (mptt) REVERT: D 53 MET cc_start: 0.6945 (mtt) cc_final: 0.6457 (mmm) REVERT: D 229 ASP cc_start: 0.7156 (t70) cc_final: 0.6555 (t0) REVERT: D 315 ASP cc_start: 0.7400 (p0) cc_final: 0.7075 (p0) REVERT: S 21 SER cc_start: 0.7472 (p) cc_final: 0.7104 (t) REVERT: S 235 TYR cc_start: 0.7906 (m-80) cc_final: 0.7410 (m-80) REVERT: A 295 TYR cc_start: 0.7006 (m-80) cc_final: 0.6560 (m-80) outliers start: 33 outliers final: 13 residues processed: 171 average time/residue: 0.4385 time to fit residues: 80.0763 Evaluate side-chains 156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 C residue 21 MET Chi-restraints excluded: chain S residue 31 SER 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 203 ILE 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 62 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.0040 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 B 340 ASN A 68 ASN A 217 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.158415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.137213 restraints weight = 15282.482| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.11 r_work: 0.4015 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3887 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9243 Z= 0.120 Angle : 0.603 10.318 12508 Z= 0.309 Chirality : 0.043 0.182 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.348 57.029 1263 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.74 % Allowed : 21.81 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.25), residues: 1130 helix: 0.49 (0.30), residues: 341 sheet: -0.02 (0.30), residues: 291 loop : -2.16 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 67 TYR 0.008 0.001 TYR S 102 PHE 0.022 0.001 PHE A 296 TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9239) covalent geometry : angle 0.60167 (12500) SS BOND : bond 0.00464 ( 4) SS BOND : angle 1.55142 ( 8) hydrogen bonds : bond 0.03901 ( 373) hydrogen bonds : angle 4.78322 ( 1035) *********************** 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: 27 poor density : 151 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8303 (mpp80) REVERT: B 76 ASP cc_start: 0.6649 (t0) cc_final: 0.6394 (t0) REVERT: D 53 MET cc_start: 0.6927 (mtt) cc_final: 0.6456 (mmm) REVERT: D 229 ASP cc_start: 0.7207 (t70) cc_final: 0.6583 (t0) REVERT: D 315 ASP cc_start: 0.7376 (p0) cc_final: 0.7054 (p0) REVERT: S 21 SER cc_start: 0.7426 (p) cc_final: 0.7080 (t) REVERT: A 109 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6972 (tmm) REVERT: A 196 GLU cc_start: 0.7983 (pt0) cc_final: 0.7720 (pt0) REVERT: A 198 PHE cc_start: 0.6122 (m-10) cc_final: 0.5915 (m-80) REVERT: A 234 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6939 (mmt) REVERT: A 295 TYR cc_start: 0.7066 (m-80) cc_final: 0.6641 (m-80) REVERT: A 296 PHE cc_start: 0.6640 (m-80) cc_final: 0.6353 (m-80) outliers start: 27 outliers final: 12 residues processed: 168 average time/residue: 0.6172 time to fit residues: 110.2174 Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 B residue 274 THR Chi-restraints excluded: chain C residue 21 MET 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 210 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.157468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.135183 restraints weight = 15448.046| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.15 r_work: 0.3999 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2314 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= 0.151 Angle : 0.639 9.968 12508 Z= 0.328 Chirality : 0.045 0.207 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.434 57.344 1263 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.94 % Allowed : 22.52 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.25), residues: 1130 helix: 0.49 (0.30), residues: 344 sheet: -0.03 (0.31), residues: 289 loop : -2.18 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 67 TYR 0.009 0.001 TYR B 59 PHE 0.023 0.002 PHE A 74 TRP 0.022 0.002 TRP B 82 HIS 0.007 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9239) covalent geometry : angle 0.63788 (12500) SS BOND : bond 0.00559 ( 4) SS BOND : angle 1.82544 ( 8) hydrogen bonds : bond 0.04409 ( 373) hydrogen bonds : angle 4.83243 ( 1035) *********************** 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 183 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8234 (mpp80) REVERT: B 76 ASP cc_start: 0.6771 (t0) cc_final: 0.6537 (t0) REVERT: D 53 MET cc_start: 0.7005 (mtt) cc_final: 0.6476 (mmm) REVERT: D 229 ASP cc_start: 0.7206 (t70) cc_final: 0.6564 (t0) REVERT: D 315 ASP cc_start: 0.7349 (p0) cc_final: 0.7032 (p0) REVERT: S 21 SER cc_start: 0.7500 (p) cc_final: 0.7135 (t) REVERT: A 109 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7014 (tmm) REVERT: A 234 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7003 (mmt) REVERT: A 295 TYR cc_start: 0.7147 (m-80) cc_final: 0.6714 (m-80) REVERT: A 296 PHE cc_start: 0.6621 (m-80) cc_final: 0.6361 (m-80) outliers start: 29 outliers final: 16 residues processed: 169 average time/residue: 0.5897 time to fit residues: 106.0526 Evaluate side-chains 163 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 295 THR 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 25 PHE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 62 optimal weight: 0.0170 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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 B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.155436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.134327 restraints weight = 15253.864| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.08 r_work: 0.3996 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9243 Z= 0.139 Angle : 0.627 10.265 12508 Z= 0.322 Chirality : 0.044 0.195 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.412 57.140 1263 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.55 % Allowed : 22.92 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.25), residues: 1130 helix: 0.52 (0.30), residues: 344 sheet: -0.05 (0.31), residues: 289 loop : -2.16 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 208 TYR 0.009 0.001 TYR S 102 PHE 0.023 0.002 PHE A 25 TRP 0.022 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9239) covalent geometry : angle 0.62596 (12500) SS BOND : bond 0.00556 ( 4) SS BOND : angle 1.75731 ( 8) hydrogen bonds : bond 0.04222 ( 373) hydrogen bonds : angle 4.81902 ( 1035) *********************** 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 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8240 (mpp80) REVERT: B 76 ASP cc_start: 0.6724 (t0) cc_final: 0.6500 (t0) REVERT: D 4 THR cc_start: 0.6604 (OUTLIER) cc_final: 0.6375 (p) REVERT: D 53 MET cc_start: 0.6936 (mtt) cc_final: 0.6455 (mmm) REVERT: D 229 ASP cc_start: 0.7225 (t70) cc_final: 0.6575 (t0) REVERT: D 315 ASP cc_start: 0.7326 (p0) cc_final: 0.7055 (p0) REVERT: S 21 SER cc_start: 0.7471 (p) cc_final: 0.7112 (t) REVERT: S 230 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6853 (mtm) REVERT: A 95 PHE cc_start: 0.7366 (m-80) cc_final: 0.7103 (m-80) REVERT: A 109 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6975 (tmm) REVERT: A 196 GLU cc_start: 0.8029 (pt0) cc_final: 0.7781 (pt0) REVERT: A 234 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6972 (mmt) outliers start: 35 outliers final: 21 residues processed: 169 average time/residue: 0.5239 time to fit residues: 94.5644 Evaluate side-chains 168 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 176 GLN 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 B residue 340 ASN 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 343 ILE 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 S residue 230 MET Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 234 MET 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 104 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN A 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.157360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.134902 restraints weight = 15355.621| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.24 r_work: 0.3996 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2543 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= 0.130 Angle : 0.632 10.485 12508 Z= 0.322 Chirality : 0.044 0.174 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.406 57.218 1263 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.45 % Allowed : 23.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.25), residues: 1130 helix: 0.63 (0.30), residues: 341 sheet: -0.06 (0.31), residues: 289 loop : -2.13 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 208 TYR 0.011 0.001 TYR S 102 PHE 0.041 0.002 PHE S 239 TRP 0.022 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9239) covalent geometry : angle 0.63119 (12500) SS BOND : bond 0.00558 ( 4) SS BOND : angle 1.72390 ( 8) hydrogen bonds : bond 0.04055 ( 373) hydrogen bonds : angle 4.82533 ( 1035) *********************** 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 182 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8288 (mpp80) REVERT: B 76 ASP cc_start: 0.6636 (t0) cc_final: 0.6404 (t0) REVERT: D 53 MET cc_start: 0.7018 (mtt) cc_final: 0.6487 (mmm) REVERT: D 229 ASP cc_start: 0.7280 (t70) cc_final: 0.6632 (t0) REVERT: D 315 ASP cc_start: 0.7336 (p0) cc_final: 0.7068 (p0) REVERT: S 21 SER cc_start: 0.7344 (p) cc_final: 0.7025 (t) REVERT: S 31 SER cc_start: 0.7362 (OUTLIER) cc_final: 0.7071 (p) REVERT: A 92 ASP cc_start: 0.5725 (p0) cc_final: 0.5518 (p0) REVERT: A 109 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6915 (tmm) REVERT: A 196 GLU cc_start: 0.8010 (pt0) cc_final: 0.7755 (pt0) outliers start: 34 outliers final: 18 residues processed: 170 average time/residue: 0.5252 time to fit residues: 95.3666 Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 295 THR 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 210 THR Chi-restraints excluded: chain A residue 109 MET 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 88 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.4408 r_free = 0.4408 target = 0.154749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.131123 restraints weight = 15251.862| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.18 r_work: 0.3979 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2464 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= 0.171 Angle : 0.687 12.131 12508 Z= 0.349 Chirality : 0.046 0.219 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.618 58.951 1263 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.74 % Allowed : 24.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.25), residues: 1130 helix: 0.49 (0.30), residues: 344 sheet: -0.11 (0.30), residues: 295 loop : -2.19 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 208 TYR 0.010 0.002 TYR D 320 PHE 0.020 0.002 PHE A 296 TRP 0.026 0.002 TRP B 82 HIS 0.007 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9239) covalent geometry : angle 0.68517 (12500) SS BOND : bond 0.00711 ( 4) SS BOND : angle 2.14680 ( 8) hydrogen bonds : bond 0.04686 ( 373) hydrogen bonds : angle 5.00009 ( 1035) *********************** 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 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8230 (mpp80) REVERT: D 53 MET cc_start: 0.6911 (mtt) cc_final: 0.6458 (mmm) REVERT: D 229 ASP cc_start: 0.7253 (t70) cc_final: 0.6589 (t0) REVERT: D 315 ASP cc_start: 0.7335 (p0) cc_final: 0.7089 (p0) REVERT: S 21 SER cc_start: 0.7335 (p) cc_final: 0.6949 (t) REVERT: S 31 SER cc_start: 0.7428 (OUTLIER) cc_final: 0.7140 (p) REVERT: S 239 PHE cc_start: 0.6902 (m-80) cc_final: 0.6502 (m-80) REVERT: A 109 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6974 (tmm) REVERT: A 198 PHE cc_start: 0.6106 (m-10) cc_final: 0.5892 (m-80) outliers start: 27 outliers final: 20 residues processed: 163 average time/residue: 0.5652 time to fit residues: 98.2093 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 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 22 CYS Chi-restraints excluded: chain S residue 31 SER 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 203 ILE Chi-restraints excluded: chain A residue 226 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 50 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN 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 = 0.4427 r_free = 0.4427 target = 0.156212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.132894 restraints weight = 15024.243| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.14 r_work: 0.4010 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9243 Z= 0.135 Angle : 0.668 11.675 12508 Z= 0.336 Chirality : 0.045 0.182 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.528 58.955 1263 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.74 % Allowed : 24.65 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.25), residues: 1130 helix: 0.69 (0.30), residues: 336 sheet: -0.12 (0.30), residues: 296 loop : -2.18 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 67 TYR 0.011 0.001 TYR S 102 PHE 0.033 0.002 PHE B 241 TRP 0.025 0.001 TRP B 82 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9239) covalent geometry : angle 0.66624 (12500) SS BOND : bond 0.00554 ( 4) SS BOND : angle 1.76597 ( 8) hydrogen bonds : bond 0.04151 ( 373) hydrogen bonds : angle 4.93728 ( 1035) ********************** 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 173 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8204 (mpp80) REVERT: C 21 MET cc_start: 0.5405 (OUTLIER) cc_final: 0.4955 (ptm) REVERT: D 53 MET cc_start: 0.6938 (mtt) cc_final: 0.6390 (mmm) REVERT: D 229 ASP cc_start: 0.7158 (t70) cc_final: 0.6574 (t0) REVERT: D 315 ASP cc_start: 0.7289 (p0) cc_final: 0.7051 (p0) REVERT: S 21 SER cc_start: 0.7370 (p) cc_final: 0.7016 (t) REVERT: S 74 ASP cc_start: 0.7810 (m-30) cc_final: 0.7597 (m-30) REVERT: A 92 ASP cc_start: 0.5735 (p0) cc_final: 0.5532 (p0) REVERT: A 109 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6885 (tmm) REVERT: A 196 GLU cc_start: 0.7976 (pt0) cc_final: 0.7674 (pt0) REVERT: A 198 PHE cc_start: 0.6099 (m-10) cc_final: 0.5883 (m-80) outliers start: 27 outliers final: 20 residues processed: 165 average time/residue: 0.6293 time to fit residues: 110.6123 Evaluate side-chains 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 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 22 CYS Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 109 MET 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 21 optimal weight: 0.0470 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN A 141 ASN A 217 GLN ** A 223 HIS ** 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 = 0.4446 r_free = 0.4446 target = 0.158879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.135492 restraints weight = 15065.699| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.19 r_work: 0.4025 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9243 Z= 0.122 Angle : 0.649 12.280 12508 Z= 0.325 Chirality : 0.044 0.167 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.476 59.989 1263 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.23 % Allowed : 25.35 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.25), residues: 1130 helix: 0.78 (0.30), residues: 336 sheet: -0.10 (0.30), residues: 296 loop : -2.15 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 67 TYR 0.010 0.001 TYR S 102 PHE 0.041 0.002 PHE S 239 TRP 0.024 0.001 TRP B 82 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9239) covalent geometry : angle 0.64832 (12500) SS BOND : bond 0.00507 ( 4) SS BOND : angle 1.60518 ( 8) hydrogen bonds : bond 0.03889 ( 373) hydrogen bonds : angle 4.85933 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4974.63 seconds wall clock time: 84 minutes 59.93 seconds (5099.93 seconds total)