Starting phenix.real_space_refine on Thu Mar 13 18:31:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jz7_36736/03_2025/8jz7_36736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jz7_36736/03_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_36736/03_2025/8jz7_36736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jz7_36736/03_2025/8jz7_36736.map" model { file = "/net/cci-nas-00/data/ceres_data/8jz7_36736/03_2025/8jz7_36736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jz7_36736/03_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-5624/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: 5.80, per 1000 atoms: 0.64 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: 2.42 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: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 1 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.506A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.695A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 30 removed outlier: 4.018A pdb=" N ALA D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 207 through 211 Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.501A pdb=" N ALA D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 280 removed outlier: 3.953A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.578A pdb=" N ILE D 285 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 330 through 352 removed outlier: 4.080A pdb=" N VAL D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.513A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.814A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 55 removed outlier: 3.868A pdb=" N LEU A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.514A pdb=" N LEU A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.579A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 removed outlier: 4.444A pdb=" N LEU A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.588A pdb=" N PHE A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.943A pdb=" N VAL A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.547A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.776A pdb=" N THR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 4.165A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.781A pdb=" N ARG A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 Processing helix chain 'A' and resid 227 through 239 removed outlier: 3.681A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.559A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.800A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.610A pdb=" N LEU A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.512A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.709A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.967A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.909A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.585A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.542A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.654A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190 removed outlier: 3.630A pdb=" N LEU D 38 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.919A pdb=" N GLY S 16 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER S 85 " --> pdb=" O GLY S 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.985A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.554A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.929A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 12 through 13 373 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 2.79 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.090 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: 0.010 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.560 ------------------------------------------------------------------------------- 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 9239 Z= 0.400 Angle : 0.852 7.917 12500 Z= 0.489 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 *********************** 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 : 0.911 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: 1.3115 time to fit residues: 256.1652 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 : 0.898 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.156977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.135873 restraints weight = 15204.128| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.08 r_work: 0.3987 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9239 Z= 0.206 Angle : 0.677 10.903 12500 Z= 0.350 Chirality : 0.045 0.211 1398 Planarity : 0.004 0.062 1580 Dihedral : 7.022 58.002 1265 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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: -1.63 (0.24), residues: 1130 helix: -0.24 (0.29), residues: 336 sheet: -0.07 (0.30), residues: 295 loop : -2.33 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.007 0.001 HIS A 189 PHE 0.023 0.002 PHE A 117 TYR 0.013 0.001 TYR A 295 ARG 0.004 0.000 ARG B 22 *********************** 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: 22 poor density : 163 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7672 (tpt-90) cc_final: 0.7465 (tpt90) REVERT: D 53 MET cc_start: 0.6908 (mtt) cc_final: 0.6465 (mmm) REVERT: D 229 ASP cc_start: 0.7176 (t70) cc_final: 0.6595 (t0) REVERT: D 315 ASP cc_start: 0.7462 (p0) cc_final: 0.7160 (p0) REVERT: S 160 ARG cc_start: 0.6856 (ptp-170) cc_final: 0.6650 (ptm160) REVERT: S 220 GLU cc_start: 0.8291 (tt0) cc_final: 0.7948 (tt0) REVERT: S 230 MET cc_start: 0.7066 (ttp) cc_final: 0.6684 (mtp) REVERT: S 235 TYR cc_start: 0.8068 (m-80) cc_final: 0.7679 (m-80) REVERT: A 26 ILE cc_start: 0.5071 (OUTLIER) cc_final: 0.4668 (mm) REVERT: A 52 PHE cc_start: 0.6289 (m-10) cc_final: 0.6035 (m-10) REVERT: A 95 PHE cc_start: 0.7547 (m-10) cc_final: 0.7245 (m-80) REVERT: A 141 ASN cc_start: 0.7783 (p0) cc_final: 0.7537 (p0) REVERT: A 234 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.7029 (mmt) REVERT: A 295 TYR cc_start: 0.7009 (m-80) cc_final: 0.6521 (m-80) outliers start: 22 outliers final: 6 residues processed: 173 average time/residue: 1.5220 time to fit residues: 279.6779 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.0010 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.157809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.136333 restraints weight = 15354.176| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.13 r_work: 0.3999 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9239 Z= 0.195 Angle : 0.635 10.521 12500 Z= 0.327 Chirality : 0.044 0.224 1398 Planarity : 0.004 0.063 1580 Dihedral : 6.558 56.249 1263 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.84 % Allowed : 16.73 % 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: -1.38 (0.25), residues: 1130 helix: 0.19 (0.30), residues: 336 sheet: -0.01 (0.30), residues: 295 loop : -2.31 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.014 0.002 PHE A 193 TYR 0.008 0.001 TYR D 320 ARG 0.004 0.000 ARG C 62 *********************** 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 187 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: B 76 ASP cc_start: 0.6881 (t0) cc_final: 0.6650 (t0) REVERT: D 53 MET cc_start: 0.7003 (mtt) cc_final: 0.6493 (mmm) REVERT: D 229 ASP cc_start: 0.7180 (t70) cc_final: 0.6580 (t0) REVERT: D 315 ASP cc_start: 0.7427 (p0) cc_final: 0.7115 (p0) REVERT: S 21 SER cc_start: 0.7419 (p) cc_final: 0.7026 (t) REVERT: S 235 TYR cc_start: 0.7977 (m-80) cc_final: 0.7495 (m-80) REVERT: A 234 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.7031 (mmt) REVERT: A 295 TYR cc_start: 0.7041 (m-80) cc_final: 0.6547 (m-80) outliers start: 28 outliers final: 10 residues processed: 171 average time/residue: 1.2476 time to fit residues: 227.3139 Evaluate side-chains 161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain 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 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: 2.9990 chunk 109 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.155733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.134031 restraints weight = 15343.223| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.18 r_work: 0.3962 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9239 Z= 0.259 Angle : 0.673 11.199 12500 Z= 0.346 Chirality : 0.046 0.240 1398 Planarity : 0.004 0.062 1580 Dihedral : 6.620 56.761 1263 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.35 % Allowed : 19.17 % Favored : 77.48 % 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: -1.42 (0.25), residues: 1130 helix: 0.19 (0.30), residues: 339 sheet: -0.04 (0.30), residues: 288 loop : -2.34 (0.25), residues: 503 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 0.023 0.002 PHE A 117 TYR 0.010 0.002 TYR D 320 ARG 0.008 0.000 ARG S 67 *********************** 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 190 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8317 (mpp80) REVERT: B 76 ASP cc_start: 0.6907 (t0) cc_final: 0.6664 (t0) REVERT: D 53 MET cc_start: 0.6994 (mtt) cc_final: 0.6501 (mmm) REVERT: D 315 ASP cc_start: 0.7426 (p0) cc_final: 0.7093 (p0) REVERT: S 46 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6515 (pt0) REVERT: S 220 GLU cc_start: 0.8300 (tt0) cc_final: 0.7921 (tt0) REVERT: S 235 TYR cc_start: 0.8035 (m-80) cc_final: 0.7520 (m-80) REVERT: A 92 ASP cc_start: 0.5792 (p0) cc_final: 0.5588 (p0) REVERT: A 109 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7034 (tmm) REVERT: A 234 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7097 (mmt) REVERT: A 295 TYR cc_start: 0.7098 (m-80) cc_final: 0.6580 (m-80) outliers start: 33 outliers final: 17 residues processed: 176 average time/residue: 1.5175 time to fit residues: 284.9775 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 271 CYS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 241 VAL 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: 0.6980 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 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 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 195 HIS 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 = 0.4420 r_free = 0.4420 target = 0.157312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.136432 restraints weight = 15157.861| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.07 r_work: 0.3996 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9239 Z= 0.194 Angle : 0.624 10.696 12500 Z= 0.322 Chirality : 0.044 0.207 1398 Planarity : 0.004 0.061 1580 Dihedral : 6.451 56.015 1263 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.14 % Allowed : 21.10 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1130 helix: 0.34 (0.30), residues: 342 sheet: -0.06 (0.30), residues: 290 loop : -2.17 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.022 0.002 PHE A 296 TYR 0.008 0.001 TYR D 320 ARG 0.007 0.000 ARG S 67 *********************** 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 182 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8296 (mpp80) REVERT: B 76 ASP cc_start: 0.6760 (t0) cc_final: 0.6529 (t0) REVERT: D 53 MET cc_start: 0.6972 (mtt) cc_final: 0.6437 (mmm) REVERT: D 229 ASP cc_start: 0.7214 (t70) cc_final: 0.6633 (t0) REVERT: D 315 ASP cc_start: 0.7375 (p0) cc_final: 0.7051 (p0) REVERT: S 21 SER cc_start: 0.7332 (p) cc_final: 0.6958 (t) REVERT: A 109 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6982 (tmm) REVERT: A 141 ASN cc_start: 0.7858 (p0) cc_final: 0.7458 (t0) REVERT: A 295 TYR cc_start: 0.7085 (m-80) cc_final: 0.6632 (m-80) REVERT: A 296 PHE cc_start: 0.6698 (m-80) cc_final: 0.6402 (m-80) outliers start: 31 outliers final: 15 residues processed: 169 average time/residue: 1.2973 time to fit residues: 233.6111 Evaluate side-chains 160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 271 CYS 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 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 109 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 97 optimal weight: 0.0060 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 107 optimal weight: 0.4980 overall best weight: 0.2312 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.160709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.138250 restraints weight = 15257.929| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.23 r_work: 0.4043 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9239 Z= 0.152 Angle : 0.589 11.586 12500 Z= 0.302 Chirality : 0.043 0.145 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.148 55.075 1263 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.43 % Allowed : 23.02 % 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 (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: -1.04 (0.25), residues: 1130 helix: 0.58 (0.30), residues: 341 sheet: -0.01 (0.31), residues: 290 loop : -2.06 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS A 189 PHE 0.021 0.001 PHE A 74 TYR 0.013 0.001 TYR S 102 ARG 0.006 0.000 ARG S 67 *********************** 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 185 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8331 (mpp80) REVERT: B 76 ASP cc_start: 0.6287 (t0) cc_final: 0.6051 (t0) REVERT: C 21 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.4998 (ptm) REVERT: D 29 LYS cc_start: 0.8028 (tttp) cc_final: 0.7708 (tptp) REVERT: D 53 MET cc_start: 0.7057 (mtt) cc_final: 0.6547 (mmm) REVERT: D 229 ASP cc_start: 0.7177 (t70) cc_final: 0.6607 (t0) REVERT: D 315 ASP cc_start: 0.7357 (p0) cc_final: 0.7078 (p0) REVERT: S 21 SER cc_start: 0.7352 (p) cc_final: 0.7093 (t) REVERT: S 31 SER cc_start: 0.7294 (OUTLIER) cc_final: 0.6951 (p) REVERT: A 56 LEU cc_start: 0.7147 (tp) cc_final: 0.6828 (tt) REVERT: A 141 ASN cc_start: 0.7888 (p0) cc_final: 0.7591 (t0) REVERT: A 196 GLU cc_start: 0.7837 (pt0) cc_final: 0.7573 (pt0) REVERT: A 295 TYR cc_start: 0.7095 (m-80) cc_final: 0.6623 (m-80) REVERT: A 296 PHE cc_start: 0.6664 (m-80) cc_final: 0.6375 (m-80) outliers start: 24 outliers final: 13 residues processed: 177 average time/residue: 1.1370 time to fit residues: 215.4539 Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 271 CYS 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 25 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 0.0170 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.158642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.136129 restraints weight = 15569.370| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.25 r_work: 0.4025 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9239 Z= 0.174 Angle : 0.623 10.703 12500 Z= 0.315 Chirality : 0.043 0.150 1398 Planarity : 0.004 0.060 1580 Dihedral : 6.114 54.422 1263 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.14 % Allowed : 23.53 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1130 helix: 0.66 (0.30), residues: 340 sheet: 0.00 (0.31), residues: 289 loop : -2.08 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 93 HIS 0.006 0.001 HIS A 189 PHE 0.025 0.002 PHE S 239 TYR 0.009 0.001 TYR S 102 ARG 0.003 0.000 ARG S 67 *********************** 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 177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8313 (mpp80) REVERT: B 59 TYR cc_start: 0.7435 (m-80) cc_final: 0.7204 (m-80) REVERT: B 76 ASP cc_start: 0.6439 (t0) cc_final: 0.6167 (t0) REVERT: C 21 MET cc_start: 0.5350 (OUTLIER) cc_final: 0.4951 (ptm) REVERT: D 25 GLU cc_start: 0.7514 (tp30) cc_final: 0.7299 (tm-30) REVERT: D 53 MET cc_start: 0.7037 (mtt) cc_final: 0.6426 (mmm) REVERT: D 229 ASP cc_start: 0.7187 (t70) cc_final: 0.6573 (t0) REVERT: D 315 ASP cc_start: 0.7334 (p0) cc_final: 0.7055 (p0) REVERT: S 21 SER cc_start: 0.7418 (p) cc_final: 0.7141 (t) REVERT: S 31 SER cc_start: 0.7358 (OUTLIER) cc_final: 0.7001 (p) REVERT: A 56 LEU cc_start: 0.7177 (tp) cc_final: 0.6843 (tt) REVERT: A 196 GLU cc_start: 0.7835 (pt0) cc_final: 0.7550 (pt0) outliers start: 31 outliers final: 16 residues processed: 165 average time/residue: 1.1694 time to fit residues: 206.3507 Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 190 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 210 THR Chi-restraints excluded: chain S residue 230 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 6.9990 chunk 38 optimal weight: 0.0470 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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** C 18 GLN A 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.160670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.138226 restraints weight = 15610.276| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.27 r_work: 0.4040 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9239 Z= 0.158 Angle : 0.615 10.166 12500 Z= 0.308 Chirality : 0.043 0.140 1398 Planarity : 0.004 0.059 1580 Dihedral : 5.969 52.864 1263 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.54 % Allowed : 24.04 % Favored : 73.43 % 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: -0.94 (0.25), residues: 1130 helix: 0.80 (0.30), residues: 339 sheet: 0.04 (0.30), residues: 289 loop : -2.08 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP S 176 HIS 0.007 0.001 HIS A 189 PHE 0.024 0.001 PHE A 74 TYR 0.011 0.001 TYR S 102 ARG 0.002 0.000 ARG D 208 *********************** 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: 25 poor density : 144 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8270 (mpp80) REVERT: B 76 ASP cc_start: 0.6273 (t0) cc_final: 0.6040 (t0) REVERT: C 21 MET cc_start: 0.5395 (OUTLIER) cc_final: 0.4982 (ptm) REVERT: D 53 MET cc_start: 0.6992 (mtt) cc_final: 0.6503 (mmm) REVERT: D 229 ASP cc_start: 0.7211 (t70) cc_final: 0.6608 (t0) REVERT: D 315 ASP cc_start: 0.7358 (p0) cc_final: 0.7086 (p0) REVERT: S 21 SER cc_start: 0.7369 (p) cc_final: 0.7140 (t) REVERT: S 230 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6560 (mmm) REVERT: A 56 LEU cc_start: 0.7100 (tp) cc_final: 0.6827 (tt) REVERT: A 196 GLU cc_start: 0.7765 (pt0) cc_final: 0.7505 (pt0) outliers start: 25 outliers final: 18 residues processed: 161 average time/residue: 1.3602 time to fit residues: 233.8951 Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 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 190 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 210 THR Chi-restraints excluded: chain S residue 230 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 85 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.157289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.135913 restraints weight = 15103.501| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.09 r_work: 0.4005 rms_B_bonded: 2.80 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: 0.7318 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9239 Z= 0.213 Angle : 0.663 11.037 12500 Z= 0.333 Chirality : 0.045 0.179 1398 Planarity : 0.004 0.059 1580 Dihedral : 6.092 52.608 1263 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.74 % Allowed : 25.15 % 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: -1.00 (0.25), residues: 1130 helix: 0.72 (0.30), residues: 339 sheet: -0.01 (0.30), residues: 290 loop : -2.10 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 176 HIS 0.007 0.001 HIS A 189 PHE 0.028 0.002 PHE B 241 TYR 0.014 0.001 TYR B 59 ARG 0.004 0.000 ARG S 67 *********************** 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 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8291 (mpp80) REVERT: B 338 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7997 (mt) REVERT: D 25 GLU cc_start: 0.7569 (tp30) cc_final: 0.7356 (tm-30) REVERT: D 53 MET cc_start: 0.7008 (mtt) cc_final: 0.6507 (mmm) REVERT: D 229 ASP cc_start: 0.7183 (t70) cc_final: 0.6570 (t0) REVERT: D 315 ASP cc_start: 0.7322 (p0) cc_final: 0.7057 (p0) REVERT: S 21 SER cc_start: 0.7449 (p) cc_final: 0.7126 (t) REVERT: S 31 SER cc_start: 0.7459 (OUTLIER) cc_final: 0.7155 (p) REVERT: S 94 TYR cc_start: 0.7510 (m-80) cc_final: 0.7286 (m-80) REVERT: A 92 ASP cc_start: 0.5497 (p0) cc_final: 0.5296 (p0) REVERT: A 196 GLU cc_start: 0.7894 (pt0) cc_final: 0.7632 (pt0) outliers start: 27 outliers final: 17 residues processed: 158 average time/residue: 1.3568 time to fit residues: 228.5813 Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 B residue 338 ILE Chi-restraints excluded: chain C residue 21 MET 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 31 SER Chi-restraints excluded: chain S residue 177 PHE 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: 0.9980 chunk 6 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 51 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 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 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 = 0.4430 r_free = 0.4430 target = 0.156929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.134360 restraints weight = 15198.633| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.18 r_work: 0.4008 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9239 Z= 0.220 Angle : 0.675 11.558 12500 Z= 0.339 Chirality : 0.045 0.204 1398 Planarity : 0.004 0.058 1580 Dihedral : 6.130 51.814 1263 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.74 % Allowed : 24.95 % 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: -1.04 (0.25), residues: 1130 helix: 0.70 (0.30), residues: 339 sheet: -0.03 (0.30), residues: 290 loop : -2.13 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 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 B 59 ARG 0.006 0.000 ARG S 67 ********************** 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 164 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8222 (mpp80) REVERT: B 338 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7986 (mt) REVERT: D 4 THR cc_start: 0.6701 (OUTLIER) cc_final: 0.6475 (p) REVERT: D 25 GLU cc_start: 0.7577 (tp30) cc_final: 0.7376 (tm-30) REVERT: D 53 MET cc_start: 0.6884 (mtt) cc_final: 0.6415 (mmm) REVERT: D 229 ASP cc_start: 0.7199 (t70) cc_final: 0.6583 (t0) REVERT: D 315 ASP cc_start: 0.7331 (p0) cc_final: 0.7073 (p0) REVERT: S 21 SER cc_start: 0.7365 (p) cc_final: 0.7116 (t) REVERT: S 31 SER cc_start: 0.7427 (OUTLIER) cc_final: 0.7120 (p) REVERT: S 94 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: A 92 ASP cc_start: 0.5486 (p0) cc_final: 0.5285 (p0) REVERT: A 196 GLU cc_start: 0.7922 (pt0) cc_final: 0.7650 (pt0) outliers start: 27 outliers final: 18 residues processed: 155 average time/residue: 1.2995 time to fit residues: 215.2545 Evaluate side-chains 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 B residue 338 ILE Chi-restraints excluded: chain C residue 21 MET 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 31 SER Chi-restraints excluded: chain S residue 94 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.0370 chunk 105 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 49 optimal weight: 0.0040 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 141 ASN ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.162059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.139622 restraints weight = 15343.849| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.18 r_work: 0.4051 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9239 Z= 0.170 Angle : 0.634 11.469 12500 Z= 0.316 Chirality : 0.044 0.185 1398 Planarity : 0.004 0.059 1580 Dihedral : 5.833 48.753 1263 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.33 % Allowed : 25.46 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1130 helix: 0.90 (0.30), residues: 337 sheet: 0.01 (0.30), residues: 289 loop : -2.06 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP S 176 HIS 0.006 0.001 HIS A 189 PHE 0.028 0.001 PHE B 241 TYR 0.011 0.001 TYR S 102 ARG 0.003 0.000 ARG C 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12106.92 seconds wall clock time: 212 minutes 2.22 seconds (12722.22 seconds total)