Starting phenix.real_space_refine on Tue May 13 03:24:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btw_44898/05_2025/9btw_44898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btw_44898/05_2025/9btw_44898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9btw_44898/05_2025/9btw_44898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btw_44898/05_2025/9btw_44898.map" model { file = "/net/cci-nas-00/data/ceres_data/9btw_44898/05_2025/9btw_44898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btw_44898/05_2025/9btw_44898.cif" } resolution = 3.0 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= -0.001 sd= 0.084 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 68 5.16 5 C 6156 2.51 5 N 1702 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9713 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 666 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 162 Chain: "P" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 276 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "R" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2848 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 7, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 150 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1898 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2600 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.79, per 1000 atoms: 0.60 Number of scatterers: 9713 At special positions: 0 Unit cell: (79.05, 98.6, 169.15, 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 68 16.00 O 1787 8.00 N 1702 7.00 C 6156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2398 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 13 sheets defined 45.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'E' and resid 30 through 52 Proline residue: E 38 - end of helix Processing helix chain 'E' and resid 59 through 81 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 115 through 142 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix removed outlier: 4.550A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 20 Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 131 through 137 removed outlier: 4.153A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.525A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.556A pdb=" N VAL R 205 " --> pdb=" O HIS R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 215 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.918A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 331 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 353 through 359 removed outlier: 4.167A pdb=" N VAL R 357 " --> pdb=" O GLY R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 removed outlier: 3.513A pdb=" N GLN R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.706A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.563A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.668A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.546A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.615A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.775A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.501A pdb=" N THR R 85 " --> pdb=" O CYS R 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.514A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.388A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.647A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.473A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.131A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.203A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.932A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.219A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.899A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.933A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1503 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: 2.61 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3203 1.35 - 1.46: 2406 1.46 - 1.58: 4223 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 9927 Sorted by residual: bond pdb=" C PHE R 269 " pdb=" N PRO R 270 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.08e-02 8.57e+03 4.57e+00 bond pdb=" C VAL R 272 " pdb=" N PRO R 273 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.58e+00 bond pdb=" C VAL R 206 " pdb=" N PRO R 207 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.30e-02 5.92e+03 2.66e+00 bond pdb=" C1 NAG R 501 " pdb=" O5 NAG R 501 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG R 502 " pdb=" O5 NAG R 502 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 ... (remaining 9922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 13280 1.61 - 3.22: 178 3.22 - 4.82: 25 4.82 - 6.43: 12 6.43 - 8.04: 3 Bond angle restraints: 13498 Sorted by residual: angle pdb=" C ALA P 8 " pdb=" N THR P 9 " pdb=" CA THR P 9 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" N GLN P 10 " pdb=" CA GLN P 10 " pdb=" C GLN P 10 " ideal model delta sigma weight residual 113.18 108.07 5.11 1.33e+00 5.65e-01 1.48e+01 angle pdb=" C ILE R 248 " pdb=" N VAL R 249 " pdb=" CA VAL R 249 " ideal model delta sigma weight residual 122.97 119.83 3.14 9.80e-01 1.04e+00 1.02e+01 angle pdb=" N THR P 9 " pdb=" CA THR P 9 " pdb=" CB THR P 9 " ideal model delta sigma weight residual 110.49 115.56 -5.07 1.69e+00 3.50e-01 9.01e+00 angle pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " pdb=" CG GLN B 17 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.00e+00 ... (remaining 13493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 5117 16.44 - 32.87: 587 32.87 - 49.30: 159 49.30 - 65.74: 44 65.74 - 82.17: 14 Dihedral angle restraints: 5921 sinusoidal: 2217 harmonic: 3704 Sorted by residual: dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 167.82 -74.82 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -25.51 -60.49 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 50.79 42.21 1 1.00e+01 1.00e-02 2.49e+01 ... (remaining 5918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 983 0.028 - 0.056: 355 0.056 - 0.085: 116 0.085 - 0.113: 73 0.113 - 0.141: 7 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA THR R 138 " pdb=" N THR R 138 " pdb=" C THR R 138 " pdb=" CB THR R 138 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA THR P 9 " pdb=" N THR P 9 " pdb=" C THR P 9 " pdb=" CB THR P 9 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.92e-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 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 1531 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 164 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C THR B 164 " -0.038 2.00e-02 2.50e+03 pdb=" O THR B 164 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 165 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C THR B 196 " 0.036 2.00e-02 2.50e+03 pdb=" O THR B 196 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG B 197 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 161 " -0.013 2.00e-02 2.50e+03 1.49e-02 3.88e+00 pdb=" CG PHE R 161 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE R 161 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 161 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE R 161 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE R 161 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 161 " -0.000 2.00e-02 2.50e+03 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 247 2.71 - 3.26: 9640 3.26 - 3.80: 15789 3.80 - 4.35: 19128 4.35 - 4.90: 33214 Nonbonded interactions: 78018 Sorted by model distance: nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.160 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR A 364 " pdb=" OD1 ASN A 371 " model vdw 2.256 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.284 3.120 ... (remaining 78013 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=0.00 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 23.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 : 0.002 0.045 9937 Z= 0.114 Angle : 0.510 8.042 13520 Z= 0.279 Chirality : 0.037 0.141 1534 Planarity : 0.003 0.039 1736 Dihedral : 15.757 82.174 3499 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.10 % Allowed : 22.64 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.74 (0.24), residues: 1256 helix: 2.67 (0.23), residues: 519 sheet: 0.26 (0.33), residues: 250 loop : 0.03 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 128 HIS 0.003 0.000 HIS E 110 PHE 0.035 0.001 PHE R 161 TYR 0.018 0.001 TYR R 191 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 2) link_NAG-ASN : angle 1.50405 ( 6) hydrogen bonds : bond 0.19969 ( 524) hydrogen bonds : angle 6.48890 ( 1503) SS BOND : bond 0.00184 ( 8) SS BOND : angle 1.16124 ( 16) covalent geometry : bond 0.00218 ( 9927) covalent geometry : angle 0.50787 (13498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: E 130 THR cc_start: 0.7710 (m) cc_final: 0.7458 (m) REVERT: R 133 MET cc_start: 0.6097 (ttm) cc_final: 0.5388 (tmt) REVERT: R 141 LYS cc_start: 0.7391 (ttmt) cc_final: 0.6797 (mttm) REVERT: R 150 TYR cc_start: 0.7015 (m-10) cc_final: 0.6298 (m-10) REVERT: R 257 GLN cc_start: 0.7037 (mt0) cc_final: 0.6374 (mt0) REVERT: R 340 LYS cc_start: 0.6544 (mmmt) cc_final: 0.6230 (mmmt) REVERT: B 138 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 175 GLN cc_start: 0.8006 (tt0) cc_final: 0.7297 (pp30) REVERT: B 212 ASP cc_start: 0.7020 (t70) cc_final: 0.6810 (t70) REVERT: B 217 MET cc_start: 0.6444 (pp-130) cc_final: 0.5942 (ppp) REVERT: N 34 MET cc_start: 0.7824 (mmt) cc_final: 0.7570 (mmt) REVERT: N 87 LYS cc_start: 0.6424 (mtpt) cc_final: 0.6176 (mtpm) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 1.0515 time to fit residues: 168.1700 Evaluate side-chains 110 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 135 ASN R 226 HIS A 239 ASN A 371 ASN A 387 HIS A 390 GLN B 176 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.210124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154458 restraints weight = 10773.578| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.56 r_work: 0.3785 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9937 Z= 0.116 Angle : 0.514 6.577 13520 Z= 0.270 Chirality : 0.039 0.151 1534 Planarity : 0.004 0.033 1736 Dihedral : 3.915 36.118 1412 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.25 % Allowed : 21.62 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.94 (0.24), residues: 1256 helix: 2.86 (0.22), residues: 528 sheet: 0.38 (0.34), residues: 245 loop : 0.02 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 362 PHE 0.027 0.002 PHE R 161 TYR 0.021 0.001 TYR R 149 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 2) link_NAG-ASN : angle 1.74514 ( 6) hydrogen bonds : bond 0.04243 ( 524) hydrogen bonds : angle 4.62564 ( 1503) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.84215 ( 16) covalent geometry : bond 0.00243 ( 9927) covalent geometry : angle 0.51242 (13498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.055 Fit side-chains REVERT: E 130 THR cc_start: 0.7769 (m) cc_final: 0.7507 (m) REVERT: R 101 ASP cc_start: 0.6530 (t0) cc_final: 0.6137 (t0) REVERT: R 133 MET cc_start: 0.6560 (ttm) cc_final: 0.5641 (tmt) REVERT: R 150 TYR cc_start: 0.7242 (m-10) cc_final: 0.6544 (m-10) REVERT: R 210 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.5138 (mp0) REVERT: R 258 ARG cc_start: 0.7588 (mtm180) cc_final: 0.6409 (mmm160) REVERT: R 340 LYS cc_start: 0.6403 (mmmt) cc_final: 0.6075 (mmmt) REVERT: A 392 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8089 (mt-10) REVERT: B 118 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7365 (p0) REVERT: B 138 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 212 ASP cc_start: 0.7222 (t70) cc_final: 0.6734 (p0) REVERT: B 217 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.6113 (ppp) REVERT: G 21 MET cc_start: 0.6802 (ptt) cc_final: 0.6486 (ptt) REVERT: N 87 LYS cc_start: 0.6588 (mtpt) cc_final: 0.6242 (mtpm) outliers start: 32 outliers final: 9 residues processed: 140 average time/residue: 1.0561 time to fit residues: 160.2156 Evaluate side-chains 121 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 210 GLU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 135 ASN A 239 ASN A 279 ASN A 390 GLN B 176 GLN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.206739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.149397 restraints weight = 10954.534| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.59 r_work: 0.3728 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9937 Z= 0.128 Angle : 0.516 6.782 13520 Z= 0.270 Chirality : 0.040 0.152 1534 Planarity : 0.004 0.036 1736 Dihedral : 3.951 33.625 1412 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.86 % Allowed : 21.32 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.86 (0.25), residues: 1256 helix: 2.88 (0.22), residues: 527 sheet: 0.20 (0.34), residues: 247 loop : -0.02 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS R 302 PHE 0.028 0.002 PHE R 161 TYR 0.016 0.001 TYR R 149 ARG 0.010 0.000 ARG E 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 2) link_NAG-ASN : angle 1.71132 ( 6) hydrogen bonds : bond 0.04028 ( 524) hydrogen bonds : angle 4.31086 ( 1503) SS BOND : bond 0.00263 ( 8) SS BOND : angle 0.73906 ( 16) covalent geometry : bond 0.00289 ( 9927) covalent geometry : angle 0.51493 (13498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.071 Fit side-chains REVERT: E 130 THR cc_start: 0.7805 (m) cc_final: 0.7572 (m) REVERT: R 101 ASP cc_start: 0.6361 (t0) cc_final: 0.5958 (t0) REVERT: R 133 MET cc_start: 0.6586 (ttm) cc_final: 0.5563 (tmt) REVERT: R 141 LYS cc_start: 0.7153 (ttmt) cc_final: 0.6914 (ttmm) REVERT: R 150 TYR cc_start: 0.7327 (m-10) cc_final: 0.6729 (m-10) REVERT: R 202 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6262 (mp) REVERT: R 258 ARG cc_start: 0.7644 (mtm180) cc_final: 0.6427 (mmm160) REVERT: R 340 LYS cc_start: 0.6603 (mmmt) cc_final: 0.6251 (mmmt) REVERT: B 118 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7466 (p0) REVERT: B 212 ASP cc_start: 0.7465 (t70) cc_final: 0.6885 (p0) REVERT: B 215 GLU cc_start: 0.7823 (pm20) cc_final: 0.7328 (mp0) REVERT: G 21 MET cc_start: 0.6827 (ptt) cc_final: 0.6497 (ptt) REVERT: N 87 LYS cc_start: 0.6449 (mtpt) cc_final: 0.6087 (mtpm) REVERT: N 98 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7491 (ptt180) outliers start: 38 outliers final: 13 residues processed: 149 average time/residue: 1.0437 time to fit residues: 168.2413 Evaluate side-chains 124 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 135 ASN ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN B 176 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.200862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.150122 restraints weight = 10877.745| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.80 r_work: 0.3658 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9937 Z= 0.179 Angle : 0.585 7.377 13520 Z= 0.302 Chirality : 0.042 0.153 1534 Planarity : 0.004 0.045 1736 Dihedral : 4.277 32.408 1412 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.48 % Allowed : 20.71 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.55 (0.24), residues: 1256 helix: 2.62 (0.22), residues: 522 sheet: -0.01 (0.34), residues: 248 loop : -0.12 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.004 0.001 HIS R 223 PHE 0.020 0.002 PHE N 108 TYR 0.015 0.002 TYR R 149 ARG 0.008 0.001 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 2) link_NAG-ASN : angle 1.76814 ( 6) hydrogen bonds : bond 0.04486 ( 524) hydrogen bonds : angle 4.37270 ( 1503) SS BOND : bond 0.00404 ( 8) SS BOND : angle 1.11581 ( 16) covalent geometry : bond 0.00419 ( 9927) covalent geometry : angle 0.58307 (13498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 114 time to evaluate : 1.164 Fit side-chains REVERT: E 40 CYS cc_start: 0.1675 (OUTLIER) cc_final: 0.1321 (p) REVERT: R 121 HIS cc_start: 0.5159 (OUTLIER) cc_final: 0.4213 (p-80) REVERT: R 133 MET cc_start: 0.6621 (ttm) cc_final: 0.5559 (tmt) REVERT: R 150 TYR cc_start: 0.7393 (m-10) cc_final: 0.6836 (m-10) REVERT: R 202 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6239 (mp) REVERT: R 258 ARG cc_start: 0.7695 (mtm180) cc_final: 0.6426 (mmm160) REVERT: R 340 LYS cc_start: 0.6584 (mmmt) cc_final: 0.6200 (mmmt) REVERT: B 234 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8745 (t80) REVERT: B 268 ASN cc_start: 0.7512 (t0) cc_final: 0.7242 (t0) REVERT: G 21 MET cc_start: 0.6721 (ptt) cc_final: 0.6387 (ptt) REVERT: N 87 LYS cc_start: 0.6380 (mtpt) cc_final: 0.6011 (mtpm) REVERT: N 98 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7438 (ptt90) REVERT: N 117 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.4973 (m-80) outliers start: 54 outliers final: 23 residues processed: 155 average time/residue: 0.9949 time to fit residues: 167.5736 Evaluate side-chains 137 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 117 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.203352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145942 restraints weight = 10826.379| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.56 r_work: 0.3689 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9937 Z= 0.123 Angle : 0.527 8.339 13520 Z= 0.272 Chirality : 0.040 0.151 1534 Planarity : 0.004 0.045 1736 Dihedral : 4.122 33.121 1412 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.26 % Allowed : 22.34 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.77 (0.25), residues: 1256 helix: 2.83 (0.22), residues: 519 sheet: 0.07 (0.34), residues: 242 loop : 0.01 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS R 223 PHE 0.030 0.002 PHE R 161 TYR 0.016 0.001 TYR R 149 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 2) link_NAG-ASN : angle 1.73081 ( 6) hydrogen bonds : bond 0.03896 ( 524) hydrogen bonds : angle 4.19445 ( 1503) SS BOND : bond 0.00318 ( 8) SS BOND : angle 0.98349 ( 16) covalent geometry : bond 0.00277 ( 9927) covalent geometry : angle 0.52471 (13498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 1.181 Fit side-chains REVERT: E 40 CYS cc_start: 0.1664 (OUTLIER) cc_final: 0.1304 (p) REVERT: R 121 HIS cc_start: 0.5274 (OUTLIER) cc_final: 0.4406 (p-80) REVERT: R 133 MET cc_start: 0.6692 (ttm) cc_final: 0.5646 (tmt) REVERT: R 141 LYS cc_start: 0.7095 (ttmt) cc_final: 0.6865 (ttmm) REVERT: R 150 TYR cc_start: 0.7313 (m-10) cc_final: 0.6722 (m-10) REVERT: R 258 ARG cc_start: 0.7742 (mtm180) cc_final: 0.6493 (mmm160) REVERT: R 340 LYS cc_start: 0.6628 (mmmt) cc_final: 0.6264 (mmmt) REVERT: A 266 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7893 (tt) REVERT: B 217 MET cc_start: 0.6802 (pp-130) cc_final: 0.6582 (ppp) REVERT: B 234 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8867 (t80) REVERT: B 268 ASN cc_start: 0.7514 (t0) cc_final: 0.7227 (t0) REVERT: B 280 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7513 (tptt) REVERT: G 21 MET cc_start: 0.6770 (ptt) cc_final: 0.6476 (ptt) REVERT: N 87 LYS cc_start: 0.6371 (mtpt) cc_final: 0.6028 (mtpm) REVERT: N 98 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7509 (ptt180) REVERT: N 120 GLN cc_start: 0.6659 (mm110) cc_final: 0.5405 (mp10) outliers start: 42 outliers final: 15 residues processed: 149 average time/residue: 1.0256 time to fit residues: 165.6800 Evaluate side-chains 128 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 98 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 390 GLN B 176 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.204061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.157406 restraints weight = 10952.672| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.72 r_work: 0.3692 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9937 Z= 0.117 Angle : 0.511 6.946 13520 Z= 0.264 Chirality : 0.040 0.146 1534 Planarity : 0.004 0.037 1736 Dihedral : 4.067 33.280 1412 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.26 % Allowed : 22.64 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.78 (0.25), residues: 1256 helix: 2.84 (0.22), residues: 518 sheet: 0.09 (0.34), residues: 242 loop : -0.00 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS R 223 PHE 0.022 0.001 PHE R 172 TYR 0.016 0.001 TYR R 149 ARG 0.008 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 2) link_NAG-ASN : angle 1.68883 ( 6) hydrogen bonds : bond 0.03706 ( 524) hydrogen bonds : angle 4.11066 ( 1503) SS BOND : bond 0.00313 ( 8) SS BOND : angle 0.83430 ( 16) covalent geometry : bond 0.00259 ( 9927) covalent geometry : angle 0.50957 (13498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 1.189 Fit side-chains REVERT: E 40 CYS cc_start: 0.1636 (OUTLIER) cc_final: 0.1286 (p) REVERT: E 139 TRP cc_start: 0.7458 (t60) cc_final: 0.7203 (t60) REVERT: R 121 HIS cc_start: 0.5209 (OUTLIER) cc_final: 0.4358 (p-80) REVERT: R 133 MET cc_start: 0.6578 (ttm) cc_final: 0.5626 (tmt) REVERT: R 150 TYR cc_start: 0.7359 (m-10) cc_final: 0.6743 (m-10) REVERT: R 202 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6306 (mp) REVERT: R 258 ARG cc_start: 0.7744 (mtm180) cc_final: 0.6422 (mmm160) REVERT: R 340 LYS cc_start: 0.6433 (mmmt) cc_final: 0.6060 (mmmt) REVERT: A 266 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7816 (tt) REVERT: A 299 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5481 (mm-30) REVERT: B 217 MET cc_start: 0.6782 (pp-130) cc_final: 0.6580 (ppp) REVERT: B 234 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8882 (t80) REVERT: B 268 ASN cc_start: 0.7525 (t0) cc_final: 0.7215 (t0) REVERT: B 340 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7891 (m-40) REVERT: G 21 MET cc_start: 0.6802 (ptt) cc_final: 0.6488 (ptt) REVERT: N 87 LYS cc_start: 0.6319 (mtpt) cc_final: 0.5970 (mtpm) REVERT: N 98 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7512 (ptt180) REVERT: N 120 GLN cc_start: 0.6650 (mm110) cc_final: 0.5484 (mp10) outliers start: 42 outliers final: 20 residues processed: 144 average time/residue: 0.9978 time to fit residues: 156.9611 Evaluate side-chains 134 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 19 optimal weight: 30.0000 chunk 27 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.200013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.153858 restraints weight = 11043.255| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.71 r_work: 0.3633 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9937 Z= 0.187 Angle : 0.591 7.800 13520 Z= 0.303 Chirality : 0.042 0.154 1534 Planarity : 0.004 0.042 1736 Dihedral : 4.312 32.263 1412 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.77 % Allowed : 22.13 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.49 (0.24), residues: 1256 helix: 2.61 (0.22), residues: 519 sheet: -0.08 (0.34), residues: 245 loop : -0.16 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 236 HIS 0.004 0.001 HIS R 223 PHE 0.033 0.002 PHE R 161 TYR 0.013 0.002 TYR R 149 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 2) link_NAG-ASN : angle 1.70636 ( 6) hydrogen bonds : bond 0.04449 ( 524) hydrogen bonds : angle 4.27183 ( 1503) SS BOND : bond 0.00458 ( 8) SS BOND : angle 0.73769 ( 16) covalent geometry : bond 0.00442 ( 9927) covalent geometry : angle 0.58940 (13498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 1.061 Fit side-chains REVERT: E 40 CYS cc_start: 0.1688 (OUTLIER) cc_final: 0.1307 (p) REVERT: E 139 TRP cc_start: 0.7479 (t60) cc_final: 0.7186 (t60) REVERT: R 121 HIS cc_start: 0.5385 (OUTLIER) cc_final: 0.4462 (p-80) REVERT: R 133 MET cc_start: 0.6533 (ttm) cc_final: 0.5558 (tmt) REVERT: R 150 TYR cc_start: 0.7411 (m-10) cc_final: 0.6845 (m-10) REVERT: R 202 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6239 (mp) REVERT: R 258 ARG cc_start: 0.7783 (mtm180) cc_final: 0.6403 (mmm160) REVERT: R 340 LYS cc_start: 0.6520 (mmmt) cc_final: 0.6121 (mmmt) REVERT: A 266 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7899 (tt) REVERT: B 217 MET cc_start: 0.6788 (pp-130) cc_final: 0.6559 (ppp) REVERT: B 234 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8846 (t80) REVERT: B 268 ASN cc_start: 0.7520 (t0) cc_final: 0.7248 (t0) REVERT: G 21 MET cc_start: 0.6879 (ptt) cc_final: 0.6566 (ptt) REVERT: N 87 LYS cc_start: 0.6284 (mtpt) cc_final: 0.5919 (mtpm) REVERT: N 98 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7460 (ptt90) REVERT: N 117 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.5199 (m-80) outliers start: 47 outliers final: 21 residues processed: 144 average time/residue: 0.8939 time to fit residues: 141.0847 Evaluate side-chains 134 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 117 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 117 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.208126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.150577 restraints weight = 10962.664| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.65 r_work: 0.3697 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9937 Z= 0.112 Angle : 0.517 9.466 13520 Z= 0.267 Chirality : 0.039 0.147 1534 Planarity : 0.004 0.038 1736 Dihedral : 4.078 33.067 1412 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.05 % Allowed : 24.37 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.72 (0.25), residues: 1256 helix: 2.83 (0.23), residues: 518 sheet: 0.05 (0.35), residues: 234 loop : -0.08 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.004 0.001 HIS R 223 PHE 0.027 0.001 PHE R 172 TYR 0.016 0.001 TYR R 149 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 2) link_NAG-ASN : angle 1.66263 ( 6) hydrogen bonds : bond 0.03654 ( 524) hydrogen bonds : angle 4.07200 ( 1503) SS BOND : bond 0.00307 ( 8) SS BOND : angle 0.63614 ( 16) covalent geometry : bond 0.00246 ( 9927) covalent geometry : angle 0.51549 (13498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.048 Fit side-chains REVERT: E 40 CYS cc_start: 0.1507 (OUTLIER) cc_final: 0.1179 (p) REVERT: E 139 TRP cc_start: 0.7459 (t60) cc_final: 0.7239 (t60) REVERT: R 133 MET cc_start: 0.6646 (ttm) cc_final: 0.5714 (tmt) REVERT: R 141 LYS cc_start: 0.7060 (ttmt) cc_final: 0.6826 (ttmm) REVERT: R 150 TYR cc_start: 0.7313 (m-10) cc_final: 0.6734 (m-10) REVERT: R 258 ARG cc_start: 0.7791 (mtm180) cc_final: 0.6445 (mmm160) REVERT: R 340 LYS cc_start: 0.6402 (mmmt) cc_final: 0.6036 (mmmt) REVERT: A 266 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7858 (tt) REVERT: A 299 GLU cc_start: 0.5831 (OUTLIER) cc_final: 0.5517 (mm-30) REVERT: B 217 MET cc_start: 0.6750 (pp-130) cc_final: 0.6546 (ppp) REVERT: B 268 ASN cc_start: 0.7573 (t0) cc_final: 0.7345 (t0) REVERT: G 21 MET cc_start: 0.6915 (ptt) cc_final: 0.6606 (ptt) REVERT: N 87 LYS cc_start: 0.6011 (mtpt) cc_final: 0.5731 (mtpm) outliers start: 30 outliers final: 15 residues processed: 136 average time/residue: 0.9722 time to fit residues: 144.3057 Evaluate side-chains 123 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 19 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.211402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159387 restraints weight = 10837.231| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.88 r_work: 0.3704 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9937 Z= 0.125 Angle : 0.533 10.607 13520 Z= 0.273 Chirality : 0.040 0.151 1534 Planarity : 0.004 0.039 1736 Dihedral : 4.073 32.724 1412 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.84 % Allowed : 24.47 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.69 (0.25), residues: 1256 helix: 2.83 (0.23), residues: 518 sheet: -0.06 (0.34), residues: 240 loop : -0.06 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.004 0.001 HIS R 223 PHE 0.034 0.002 PHE R 161 TYR 0.015 0.001 TYR R 149 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 2) link_NAG-ASN : angle 1.59749 ( 6) hydrogen bonds : bond 0.03773 ( 524) hydrogen bonds : angle 4.06828 ( 1503) SS BOND : bond 0.00340 ( 8) SS BOND : angle 0.61462 ( 16) covalent geometry : bond 0.00281 ( 9927) covalent geometry : angle 0.53180 (13498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 1.143 Fit side-chains REVERT: E 40 CYS cc_start: 0.1432 (OUTLIER) cc_final: 0.1105 (p) REVERT: E 139 TRP cc_start: 0.7408 (t60) cc_final: 0.7159 (t60) REVERT: R 133 MET cc_start: 0.6601 (ttm) cc_final: 0.5639 (tmt) REVERT: R 141 LYS cc_start: 0.6767 (ttmt) cc_final: 0.6497 (ttmm) REVERT: R 150 TYR cc_start: 0.7406 (m-10) cc_final: 0.6772 (m-10) REVERT: R 258 ARG cc_start: 0.7766 (mtm180) cc_final: 0.6319 (mmm160) REVERT: R 340 LYS cc_start: 0.6295 (mmmt) cc_final: 0.5894 (mmmt) REVERT: A 266 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7704 (tt) REVERT: A 299 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5434 (mm-30) REVERT: B 217 MET cc_start: 0.6585 (pp-130) cc_final: 0.6320 (ppp) REVERT: B 268 ASN cc_start: 0.7497 (t0) cc_final: 0.7264 (t0) REVERT: G 21 MET cc_start: 0.6812 (ptt) cc_final: 0.6544 (ptt) REVERT: N 87 LYS cc_start: 0.5814 (mtpt) cc_final: 0.5543 (mtpm) outliers start: 28 outliers final: 16 residues processed: 126 average time/residue: 1.0681 time to fit residues: 146.9924 Evaluate side-chains 120 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.212491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.158237 restraints weight = 10907.915| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.46 r_work: 0.3741 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9937 Z= 0.112 Angle : 0.524 10.235 13520 Z= 0.269 Chirality : 0.040 0.147 1534 Planarity : 0.004 0.038 1736 Dihedral : 3.974 32.601 1412 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.54 % Allowed : 24.87 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.77 (0.25), residues: 1256 helix: 2.89 (0.23), residues: 518 sheet: -0.01 (0.35), residues: 237 loop : -0.03 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.004 0.001 HIS R 223 PHE 0.027 0.001 PHE R 172 TYR 0.016 0.001 TYR R 149 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 2) link_NAG-ASN : angle 1.56590 ( 6) hydrogen bonds : bond 0.03546 ( 524) hydrogen bonds : angle 3.99540 ( 1503) SS BOND : bond 0.00293 ( 8) SS BOND : angle 0.63075 ( 16) covalent geometry : bond 0.00245 ( 9927) covalent geometry : angle 0.52289 (13498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: E 40 CYS cc_start: 0.1436 (OUTLIER) cc_final: 0.1062 (p) REVERT: E 139 TRP cc_start: 0.7411 (t60) cc_final: 0.7171 (t60) REVERT: R 121 HIS cc_start: 0.5433 (OUTLIER) cc_final: 0.4485 (p-80) REVERT: R 133 MET cc_start: 0.6598 (ttm) cc_final: 0.5633 (tmt) REVERT: R 141 LYS cc_start: 0.6802 (ttmt) cc_final: 0.6563 (ttmm) REVERT: R 150 TYR cc_start: 0.7511 (m-10) cc_final: 0.6898 (m-10) REVERT: R 202 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6100 (mp) REVERT: R 258 ARG cc_start: 0.7857 (mtm180) cc_final: 0.6332 (mmm160) REVERT: R 340 LYS cc_start: 0.6308 (mmmt) cc_final: 0.5913 (mmmt) REVERT: A 266 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7740 (tt) REVERT: B 217 MET cc_start: 0.6693 (pp-130) cc_final: 0.6420 (ppp) REVERT: G 21 MET cc_start: 0.6752 (ptt) cc_final: 0.6485 (ptt) REVERT: N 87 LYS cc_start: 0.5754 (mtpt) cc_final: 0.5483 (mtpm) outliers start: 25 outliers final: 18 residues processed: 127 average time/residue: 1.0029 time to fit residues: 138.5676 Evaluate side-chains 126 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** 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 = 0.4451 r_free = 0.4451 target = 0.210804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158744 restraints weight = 10822.357| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.94 r_work: 0.3691 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9937 Z= 0.135 Angle : 0.553 12.375 13520 Z= 0.282 Chirality : 0.040 0.156 1534 Planarity : 0.004 0.045 1736 Dihedral : 4.061 31.943 1412 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.54 % Allowed : 24.97 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.67 (0.25), residues: 1256 helix: 2.78 (0.23), residues: 519 sheet: -0.14 (0.34), residues: 245 loop : -0.01 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.004 0.001 HIS R 223 PHE 0.035 0.002 PHE R 161 TYR 0.015 0.001 TYR R 149 ARG 0.012 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 2) link_NAG-ASN : angle 1.54220 ( 6) hydrogen bonds : bond 0.03857 ( 524) hydrogen bonds : angle 4.07534 ( 1503) SS BOND : bond 0.00361 ( 8) SS BOND : angle 0.62797 ( 16) covalent geometry : bond 0.00308 ( 9927) covalent geometry : angle 0.55212 (13498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6572.67 seconds wall clock time: 113 minutes 53.36 seconds (6833.36 seconds total)