Starting phenix.real_space_refine on Wed Apr 30 15:25:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btw_44898/04_2025/9btw_44898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btw_44898/04_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_44898/04_2025/9btw_44898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btw_44898/04_2025/9btw_44898.map" model { file = "/net/cci-nas-00/data/ceres_data/9btw_44898/04_2025/9btw_44898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btw_44898/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.74, per 1000 atoms: 0.59 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 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: 0.97 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: 2.71 Time building geometry restraints manager: 2.67 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: 1.580 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.660 ------------------------------------------------------------------------------- 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 : 1.037 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: 1.0873 time to fit residues: 173.7062 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 : 1.141 ------------------------------------------------------------------------------- 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: 0.8980 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4450 r_free = 0.4450 target = 0.210253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.154794 restraints weight = 10770.311| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.54 r_work: 0.3790 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9937 Z= 0.118 Angle : 0.513 6.510 13520 Z= 0.270 Chirality : 0.039 0.151 1534 Planarity : 0.004 0.034 1736 Dihedral : 3.906 36.609 1412 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.05 % Allowed : 21.83 % 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: 1.97 (0.24), residues: 1256 helix: 2.86 (0.22), residues: 528 sheet: 0.47 (0.34), residues: 240 loop : 0.03 (0.29), residues: 488 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 0.001 PHE R 161 TYR 0.020 0.001 TYR R 149 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 2) link_NAG-ASN : angle 1.72852 ( 6) hydrogen bonds : bond 0.04347 ( 524) hydrogen bonds : angle 4.64902 ( 1503) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.84378 ( 16) covalent geometry : bond 0.00245 ( 9927) covalent geometry : angle 0.51180 (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 150 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.980 Fit side-chains REVERT: E 130 THR cc_start: 0.7771 (m) cc_final: 0.7508 (m) REVERT: R 101 ASP cc_start: 0.6586 (t0) cc_final: 0.6203 (t0) REVERT: R 133 MET cc_start: 0.6562 (ttm) cc_final: 0.5628 (tmt) REVERT: R 150 TYR cc_start: 0.7228 (m-10) cc_final: 0.6537 (m-10) REVERT: R 258 ARG cc_start: 0.7587 (mtm180) cc_final: 0.6425 (mmm160) REVERT: R 340 LYS cc_start: 0.6408 (mmmt) cc_final: 0.6085 (mmmt) REVERT: A 392 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8074 (mt-10) REVERT: B 118 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7404 (p0) REVERT: B 138 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7184 (mt-10) REVERT: B 212 ASP cc_start: 0.7227 (t70) cc_final: 0.6743 (p0) REVERT: B 217 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6121 (ppp) REVERT: G 21 MET cc_start: 0.6829 (ptt) cc_final: 0.6522 (ptt) REVERT: N 87 LYS cc_start: 0.6605 (mtpt) cc_final: 0.6259 (mtpm) outliers start: 30 outliers final: 9 residues processed: 138 average time/residue: 1.0755 time to fit residues: 160.6695 Evaluate side-chains 121 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 254 THR Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 176 GLN 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 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: 8.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.0270 chunk 89 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 279 ASN 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 = 0.4430 r_free = 0.4430 target = 0.208427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.160265 restraints weight = 10940.488| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.79 r_work: 0.3756 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1615 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= 0.112 Angle : 0.498 6.609 13520 Z= 0.260 Chirality : 0.039 0.150 1534 Planarity : 0.004 0.042 1736 Dihedral : 3.857 34.509 1412 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.94 % Allowed : 22.34 % Favored : 74.72 % 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 (0.25), residues: 1256 helix: 2.92 (0.22), residues: 527 sheet: 0.30 (0.34), residues: 245 loop : 0.01 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS R 302 PHE 0.028 0.001 PHE R 161 TYR 0.017 0.001 TYR R 149 ARG 0.008 0.000 ARG E 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 2) link_NAG-ASN : angle 1.70454 ( 6) hydrogen bonds : bond 0.03840 ( 524) hydrogen bonds : angle 4.31955 ( 1503) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.72850 ( 16) covalent geometry : bond 0.00243 ( 9927) covalent geometry : angle 0.49655 (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 152 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.079 Fit side-chains REVERT: E 130 THR cc_start: 0.7708 (m) cc_final: 0.7463 (m) REVERT: R 101 ASP cc_start: 0.6390 (t0) cc_final: 0.5978 (t0) REVERT: R 133 MET cc_start: 0.6563 (ttm) cc_final: 0.5517 (tmt) REVERT: R 141 LYS cc_start: 0.7117 (ttmt) cc_final: 0.6895 (ttmm) REVERT: R 150 TYR cc_start: 0.7320 (m-10) cc_final: 0.6653 (m-10) REVERT: R 202 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6158 (mp) REVERT: R 258 ARG cc_start: 0.7577 (mtm180) cc_final: 0.6330 (mmm160) REVERT: R 340 LYS cc_start: 0.6567 (mmmt) cc_final: 0.6208 (mmmt) REVERT: A 392 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8060 (mt-10) REVERT: B 212 ASP cc_start: 0.7287 (t70) cc_final: 0.6686 (p0) REVERT: B 215 GLU cc_start: 0.7817 (pm20) cc_final: 0.7261 (mp0) REVERT: G 21 MET cc_start: 0.6787 (ptt) cc_final: 0.6434 (ptt) REVERT: N 34 MET cc_start: 0.8092 (mmm) cc_final: 0.7867 (mmm) REVERT: N 87 LYS cc_start: 0.6512 (mtpt) cc_final: 0.6150 (mtpm) outliers start: 29 outliers final: 11 residues processed: 143 average time/residue: 1.0633 time to fit residues: 164.5493 Evaluate side-chains 124 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 202 LEU 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 B residue 275 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 83 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 390 GLN 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 = 0.4402 r_free = 0.4402 target = 0.205448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.154280 restraints weight = 10783.074| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.62 r_work: 0.3722 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9937 Z= 0.127 Angle : 0.517 6.997 13520 Z= 0.268 Chirality : 0.040 0.148 1534 Planarity : 0.004 0.040 1736 Dihedral : 3.984 33.178 1412 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.37 % Allowed : 21.83 % 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: 1.89 (0.25), residues: 1256 helix: 2.92 (0.22), residues: 522 sheet: 0.16 (0.34), residues: 242 loop : 0.03 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS R 302 PHE 0.016 0.002 PHE R 172 TYR 0.015 0.001 TYR R 149 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 2) link_NAG-ASN : angle 1.69110 ( 6) hydrogen bonds : bond 0.03896 ( 524) hydrogen bonds : angle 4.18474 ( 1503) SS BOND : bond 0.00283 ( 8) SS BOND : angle 0.69663 ( 16) covalent geometry : bond 0.00289 ( 9927) covalent geometry : angle 0.51517 (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 161 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.958 Fit side-chains REVERT: E 40 CYS cc_start: 0.1546 (OUTLIER) cc_final: 0.1240 (p) REVERT: E 130 THR cc_start: 0.7757 (m) cc_final: 0.7544 (m) REVERT: R 101 ASP cc_start: 0.6181 (t0) cc_final: 0.5772 (t0) REVERT: R 133 MET cc_start: 0.6609 (ttm) cc_final: 0.5557 (tmt) REVERT: R 141 LYS cc_start: 0.6988 (ttmt) cc_final: 0.6443 (mtmm) REVERT: R 150 TYR cc_start: 0.7377 (m-10) cc_final: 0.6784 (m-10) REVERT: R 157 SER cc_start: 0.8122 (m) cc_final: 0.7888 (p) REVERT: R 202 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6205 (mp) REVERT: R 258 ARG cc_start: 0.7637 (mtm180) cc_final: 0.6416 (mmm160) REVERT: R 340 LYS cc_start: 0.6599 (mmmt) cc_final: 0.6219 (mmmt) REVERT: R 403 LYS cc_start: 0.5577 (mmtm) cc_final: 0.5301 (mptm) REVERT: B 212 ASP cc_start: 0.7512 (t70) cc_final: 0.6804 (p0) REVERT: B 215 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: B 234 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8744 (t80) REVERT: B 268 ASN cc_start: 0.7480 (t0) cc_final: 0.7172 (t0) REVERT: G 21 MET cc_start: 0.6725 (ptt) cc_final: 0.6383 (ptt) REVERT: N 34 MET cc_start: 0.8090 (mmm) cc_final: 0.7875 (mmm) REVERT: N 87 LYS cc_start: 0.6384 (mtpt) cc_final: 0.6033 (mtpm) REVERT: N 120 GLN cc_start: 0.6667 (mm110) cc_final: 0.5601 (mp10) outliers start: 43 outliers final: 17 residues processed: 148 average time/residue: 0.9974 time to fit residues: 160.2820 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 : 0.836 ------------------------------------------------------------------------------- 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 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 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 198 LEU Chi-restraints excluded: chain B residue 215 GLU 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 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 3 optimal weight: 50.0000 chunk 20 optimal weight: 0.0170 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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** A 390 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 = 0.4416 r_free = 0.4416 target = 0.206279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149074 restraints weight = 10808.730| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.55 r_work: 0.3712 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2158 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= 0.114 Angle : 0.501 6.758 13520 Z= 0.259 Chirality : 0.039 0.148 1534 Planarity : 0.004 0.046 1736 Dihedral : 3.952 33.247 1412 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.37 % Allowed : 21.93 % Favored : 73.71 % 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: 1.91 (0.25), residues: 1256 helix: 2.90 (0.22), residues: 522 sheet: 0.17 (0.34), residues: 242 loop : 0.09 (0.29), residues: 492 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 0.032 0.001 PHE R 161 TYR 0.015 0.001 TYR R 149 ARG 0.010 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 2) link_NAG-ASN : angle 1.68205 ( 6) hydrogen bonds : bond 0.03637 ( 524) hydrogen bonds : angle 4.10328 ( 1503) SS BOND : bond 0.00268 ( 8) SS BOND : angle 0.94874 ( 16) covalent geometry : bond 0.00251 ( 9927) covalent geometry : angle 0.49953 (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 160 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 1.078 Fit side-chains REVERT: E 40 CYS cc_start: 0.1648 (OUTLIER) cc_final: 0.1305 (p) REVERT: E 130 THR cc_start: 0.7697 (m) cc_final: 0.7485 (m) REVERT: R 101 ASP cc_start: 0.6181 (t0) cc_final: 0.5788 (t0) REVERT: R 121 HIS cc_start: 0.5304 (OUTLIER) cc_final: 0.4356 (p-80) REVERT: R 133 MET cc_start: 0.6605 (ttm) cc_final: 0.5542 (tmt) REVERT: R 150 TYR cc_start: 0.7356 (m-10) cc_final: 0.6734 (m-10) REVERT: R 157 SER cc_start: 0.8131 (m) cc_final: 0.7930 (p) REVERT: R 202 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6353 (mp) REVERT: R 258 ARG cc_start: 0.7692 (mtm180) cc_final: 0.6510 (mmm160) REVERT: R 340 LYS cc_start: 0.6552 (mmmt) cc_final: 0.6208 (mmmt) REVERT: A 266 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7844 (tt) REVERT: B 212 ASP cc_start: 0.7628 (t70) cc_final: 0.6998 (p0) REVERT: B 215 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: B 234 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8764 (t80) REVERT: B 268 ASN cc_start: 0.7466 (t0) cc_final: 0.7154 (t0) REVERT: B 340 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7845 (m-40) REVERT: G 21 MET cc_start: 0.6783 (ptt) cc_final: 0.6479 (ptt) REVERT: N 34 MET cc_start: 0.8097 (mmm) cc_final: 0.7892 (mmm) REVERT: N 87 LYS cc_start: 0.6406 (mtpt) cc_final: 0.6050 (mtpm) REVERT: N 98 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7399 (ptt90) REVERT: N 120 GLN cc_start: 0.6697 (mm110) cc_final: 0.5686 (mp10) outliers start: 43 outliers final: 13 residues processed: 150 average time/residue: 1.0616 time to fit residues: 172.7685 Evaluate side-chains 132 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 217 VAL 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 A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 340 ASN 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 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.200222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142074 restraints weight = 10948.731| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.56 r_work: 0.3640 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9937 Z= 0.208 Angle : 0.605 7.776 13520 Z= 0.312 Chirality : 0.043 0.153 1534 Planarity : 0.004 0.048 1736 Dihedral : 4.260 31.856 1412 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.77 % Allowed : 22.23 % Favored : 72.99 % 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: 1.58 (0.24), residues: 1256 helix: 2.63 (0.22), residues: 519 sheet: -0.02 (0.33), residues: 246 loop : -0.05 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 236 HIS 0.003 0.001 HIS B 266 PHE 0.020 0.002 PHE B 151 TYR 0.013 0.002 TYR R 149 ARG 0.014 0.001 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 2) link_NAG-ASN : angle 1.73462 ( 6) hydrogen bonds : bond 0.04555 ( 524) hydrogen bonds : angle 4.30821 ( 1503) SS BOND : bond 0.00589 ( 8) SS BOND : angle 1.10132 ( 16) covalent geometry : bond 0.00489 ( 9927) covalent geometry : angle 0.60348 (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 159 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 1.012 Fit side-chains REVERT: E 40 CYS cc_start: 0.1680 (OUTLIER) cc_final: 0.1316 (p) REVERT: R 121 HIS cc_start: 0.5313 (OUTLIER) cc_final: 0.4445 (p-80) REVERT: R 133 MET cc_start: 0.6612 (ttm) cc_final: 0.5591 (tmt) REVERT: R 141 LYS cc_start: 0.7092 (ttmt) cc_final: 0.6883 (ttmm) REVERT: R 150 TYR cc_start: 0.7375 (m-10) cc_final: 0.6819 (m-10) REVERT: R 202 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6300 (mp) REVERT: R 258 ARG cc_start: 0.7763 (mtm180) cc_final: 0.6516 (mmm160) REVERT: R 340 LYS cc_start: 0.6584 (mmmt) cc_final: 0.6199 (mmmt) REVERT: A 266 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7903 (tt) REVERT: B 234 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8746 (t80) REVERT: B 268 ASN cc_start: 0.7560 (t0) cc_final: 0.7273 (t0) REVERT: G 21 MET cc_start: 0.6766 (ptt) cc_final: 0.6475 (ptt) REVERT: N 34 MET cc_start: 0.8121 (mmm) cc_final: 0.7894 (mmm) REVERT: N 87 LYS cc_start: 0.6351 (mtpt) cc_final: 0.5978 (mtpm) REVERT: N 98 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7492 (ptt90) outliers start: 47 outliers final: 22 residues processed: 148 average time/residue: 1.0499 time to fit residues: 169.1634 Evaluate side-chains 131 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 198 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 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 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 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 120 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 20.0000 chunk 117 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 111 optimal weight: 0.0040 chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.205076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.154342 restraints weight = 11045.995| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.94 r_work: 0.3694 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2472 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= 0.116 Angle : 0.527 7.549 13520 Z= 0.272 Chirality : 0.040 0.147 1534 Planarity : 0.004 0.049 1736 Dihedral : 4.104 32.886 1412 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.96 % Allowed : 22.94 % 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: 1.79 (0.25), residues: 1256 helix: 2.82 (0.22), residues: 518 sheet: 0.07 (0.34), residues: 242 loop : 0.05 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.003 0.001 HIS R 223 PHE 0.032 0.001 PHE R 161 TYR 0.016 0.001 TYR R 149 ARG 0.012 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 2) link_NAG-ASN : angle 1.70487 ( 6) hydrogen bonds : bond 0.03761 ( 524) hydrogen bonds : angle 4.11396 ( 1503) SS BOND : bond 0.00321 ( 8) SS BOND : angle 0.95653 ( 16) covalent geometry : bond 0.00254 ( 9927) covalent geometry : angle 0.52564 (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 150 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 1.106 Fit side-chains REVERT: E 40 CYS cc_start: 0.1668 (OUTLIER) cc_final: 0.1303 (p) REVERT: E 113 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7519 (t0) REVERT: E 139 TRP cc_start: 0.7465 (t60) cc_final: 0.6854 (t-100) REVERT: R 101 ASP cc_start: 0.6090 (t0) cc_final: 0.5226 (t0) REVERT: R 121 HIS cc_start: 0.5255 (OUTLIER) cc_final: 0.4407 (p-80) REVERT: R 133 MET cc_start: 0.6513 (ttm) cc_final: 0.5557 (tmt) REVERT: R 135 ASN cc_start: 0.6401 (t0) cc_final: 0.6194 (m-40) REVERT: R 141 LYS cc_start: 0.6926 (ttmt) cc_final: 0.6700 (ttmm) REVERT: R 150 TYR cc_start: 0.7379 (m-10) cc_final: 0.6738 (m-10) REVERT: R 202 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6240 (mp) REVERT: R 258 ARG cc_start: 0.7752 (mtm180) cc_final: 0.6434 (mmm160) REVERT: R 340 LYS cc_start: 0.6435 (mmmt) cc_final: 0.6057 (mmmt) REVERT: A 266 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7804 (tt) REVERT: B 212 ASP cc_start: 0.7398 (t70) cc_final: 0.7039 (p0) REVERT: B 234 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8786 (t80) REVERT: B 268 ASN cc_start: 0.7531 (t0) cc_final: 0.7254 (t0) REVERT: G 21 MET cc_start: 0.6801 (ptt) cc_final: 0.6492 (ptt) REVERT: N 87 LYS cc_start: 0.6283 (mtpt) cc_final: 0.5923 (mtpm) REVERT: N 98 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7353 (ptt90) REVERT: N 117 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.5125 (m-80) outliers start: 39 outliers final: 15 residues processed: 142 average time/residue: 0.9754 time to fit residues: 151.2411 Evaluate side-chains 131 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 113 ASP 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 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 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 176 GLN Chi-restraints excluded: chain B residue 234 PHE 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 52 SER Chi-restraints excluded: chain N residue 98 ARG 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: 1.9990 chunk 98 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.203663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.145841 restraints weight = 10958.628| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.60 r_work: 0.3692 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2537 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= 0.125 Angle : 0.535 9.256 13520 Z= 0.274 Chirality : 0.040 0.159 1534 Planarity : 0.004 0.056 1736 Dihedral : 4.037 32.780 1412 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.37 % Allowed : 23.05 % 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: 2.86 (0.22), residues: 518 sheet: 0.06 (0.34), residues: 242 loop : -0.02 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.002 0.001 HIS R 223 PHE 0.015 0.001 PHE B 151 TYR 0.015 0.001 TYR R 149 ARG 0.013 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 2) link_NAG-ASN : angle 1.64819 ( 6) hydrogen bonds : bond 0.03794 ( 524) hydrogen bonds : angle 4.07506 ( 1503) SS BOND : bond 0.00331 ( 8) SS BOND : angle 1.07042 ( 16) covalent geometry : bond 0.00281 ( 9927) covalent geometry : angle 0.53276 (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 152 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 1.091 Fit side-chains REVERT: E 40 CYS cc_start: 0.1637 (OUTLIER) cc_final: 0.1258 (p) REVERT: R 101 ASP cc_start: 0.6150 (t0) cc_final: 0.5652 (t0) REVERT: R 121 HIS cc_start: 0.5437 (OUTLIER) cc_final: 0.4523 (p-80) REVERT: R 133 MET cc_start: 0.6614 (ttm) cc_final: 0.5686 (tmt) REVERT: R 141 LYS cc_start: 0.7139 (ttmt) cc_final: 0.6820 (ttmm) REVERT: R 150 TYR cc_start: 0.7326 (m-10) cc_final: 0.6740 (m-10) REVERT: R 202 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6357 (mp) REVERT: R 258 ARG cc_start: 0.7775 (mtm180) cc_final: 0.6511 (mmm160) REVERT: R 340 LYS cc_start: 0.6492 (mmmt) cc_final: 0.6115 (mmmt) REVERT: A 266 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 299 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.5653 (mm-30) REVERT: B 212 ASP cc_start: 0.7599 (t70) cc_final: 0.7185 (p0) REVERT: B 234 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8773 (t80) REVERT: B 268 ASN cc_start: 0.7560 (t0) cc_final: 0.7322 (t0) REVERT: B 340 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7814 (m-40) REVERT: G 21 MET cc_start: 0.6863 (ptt) cc_final: 0.6552 (ptt) REVERT: N 87 LYS cc_start: 0.6039 (mtpt) cc_final: 0.5726 (mtpm) REVERT: N 98 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7439 (ptt90) REVERT: N 117 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.5223 (m-80) outliers start: 43 outliers final: 20 residues processed: 145 average time/residue: 1.0354 time to fit residues: 163.1136 Evaluate side-chains 133 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 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 288 ILE Chi-restraints excluded: chain A residue 299 GLU 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 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 113 THR Chi-restraints excluded: chain N residue 117 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 6.9990 chunk 100 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 0.0870 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.206019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149131 restraints weight = 10885.250| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.58 r_work: 0.3716 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 9937 Z= 0.107 Angle : 0.520 10.409 13520 Z= 0.268 Chirality : 0.040 0.158 1534 Planarity : 0.004 0.059 1736 Dihedral : 3.966 33.187 1412 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.84 % Allowed : 24.57 % 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: 1.86 (0.25), residues: 1256 helix: 2.92 (0.23), residues: 519 sheet: 0.17 (0.34), residues: 235 loop : -0.00 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 290 HIS 0.004 0.001 HIS R 156 PHE 0.037 0.001 PHE R 161 TYR 0.016 0.001 TYR R 149 ARG 0.014 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 2) link_NAG-ASN : angle 1.61070 ( 6) hydrogen bonds : bond 0.03446 ( 524) hydrogen bonds : angle 4.00546 ( 1503) SS BOND : bond 0.00281 ( 8) SS BOND : angle 0.73183 ( 16) covalent geometry : bond 0.00232 ( 9927) covalent geometry : angle 0.51826 (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 141 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: E 40 CYS cc_start: 0.1522 (OUTLIER) cc_final: 0.1140 (p) REVERT: E 139 TRP cc_start: 0.7477 (t60) cc_final: 0.6943 (t-100) REVERT: R 101 ASP cc_start: 0.6173 (t0) cc_final: 0.5623 (t0) REVERT: R 121 HIS cc_start: 0.5561 (OUTLIER) cc_final: 0.4606 (p-80) REVERT: R 133 MET cc_start: 0.6602 (ttm) cc_final: 0.5687 (tmt) REVERT: R 141 LYS cc_start: 0.7194 (ttmt) cc_final: 0.6945 (ttmm) REVERT: R 150 TYR cc_start: 0.7323 (m-10) cc_final: 0.6727 (m-10) REVERT: R 202 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6404 (mp) REVERT: R 258 ARG cc_start: 0.7784 (mtm180) cc_final: 0.6514 (mmm160) REVERT: R 340 LYS cc_start: 0.6447 (mmmt) cc_final: 0.6085 (mmmt) REVERT: A 266 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7872 (tt) REVERT: A 299 GLU cc_start: 0.5889 (OUTLIER) cc_final: 0.5663 (mm-30) REVERT: B 212 ASP cc_start: 0.7601 (t70) cc_final: 0.7218 (p0) REVERT: B 234 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8683 (t80) REVERT: B 268 ASN cc_start: 0.7539 (t0) cc_final: 0.7331 (t0) REVERT: B 280 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7822 (ptmm) REVERT: G 21 MET cc_start: 0.6852 (ptt) cc_final: 0.6545 (ptt) REVERT: N 87 LYS cc_start: 0.6017 (mtpt) cc_final: 0.5738 (mtpm) outliers start: 28 outliers final: 16 residues processed: 135 average time/residue: 0.9975 time to fit residues: 146.7451 Evaluate side-chains 127 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 299 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.213349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.158948 restraints weight = 10934.062| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.44 r_work: 0.3739 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2631 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= 0.116 Angle : 0.531 11.595 13520 Z= 0.270 Chirality : 0.040 0.155 1534 Planarity : 0.004 0.061 1736 Dihedral : 3.963 32.661 1412 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.54 % Allowed : 25.08 % Favored : 72.39 % 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: 1.82 (0.25), residues: 1256 helix: 2.91 (0.23), residues: 518 sheet: 0.07 (0.34), residues: 243 loop : -0.02 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 236 HIS 0.003 0.001 HIS R 223 PHE 0.014 0.001 PHE R 99 TYR 0.015 0.001 TYR R 149 ARG 0.014 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 2) link_NAG-ASN : angle 1.56662 ( 6) hydrogen bonds : bond 0.03574 ( 524) hydrogen bonds : angle 3.98742 ( 1503) SS BOND : bond 0.00310 ( 8) SS BOND : angle 0.75346 ( 16) covalent geometry : bond 0.00258 ( 9927) covalent geometry : angle 0.52984 (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 134 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: E 40 CYS cc_start: 0.1420 (OUTLIER) cc_final: 0.1096 (p) REVERT: E 139 TRP cc_start: 0.7479 (t60) cc_final: 0.6819 (t-100) REVERT: R 101 ASP cc_start: 0.5847 (t0) cc_final: 0.5000 (t0) REVERT: R 121 HIS cc_start: 0.5500 (OUTLIER) cc_final: 0.4550 (p-80) REVERT: R 133 MET cc_start: 0.6593 (ttm) cc_final: 0.5633 (tmt) REVERT: R 150 TYR cc_start: 0.7540 (m-10) cc_final: 0.6885 (m-10) REVERT: R 202 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6043 (mp) REVERT: R 258 ARG cc_start: 0.7795 (mtm180) cc_final: 0.6293 (mmm160) REVERT: R 340 LYS cc_start: 0.6295 (mmmt) cc_final: 0.5905 (mmmt) REVERT: A 266 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7734 (tt) REVERT: B 212 ASP cc_start: 0.7473 (t70) cc_final: 0.6908 (p0) REVERT: B 234 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8756 (t80) REVERT: B 268 ASN cc_start: 0.7539 (t0) cc_final: 0.7327 (t0) REVERT: B 280 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7841 (ptmm) REVERT: G 21 MET cc_start: 0.6763 (ptt) cc_final: 0.6502 (ptt) REVERT: N 87 LYS cc_start: 0.5754 (mtpt) cc_final: 0.5464 (mtpm) outliers start: 25 outliers final: 16 residues processed: 130 average time/residue: 1.0329 time to fit residues: 146.1034 Evaluate side-chains 127 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.7980 chunk 50 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 0.0030 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 119 optimal weight: 0.0970 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.214614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160514 restraints weight = 10857.806| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.45 r_work: 0.3758 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2689 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= 0.103 Angle : 0.513 11.138 13520 Z= 0.262 Chirality : 0.039 0.147 1534 Planarity : 0.004 0.061 1736 Dihedral : 3.884 32.600 1412 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.64 % Allowed : 24.87 % 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: 1.91 (0.25), residues: 1256 helix: 2.93 (0.23), residues: 522 sheet: 0.20 (0.34), residues: 236 loop : 0.03 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS R 223 PHE 0.036 0.001 PHE R 161 TYR 0.015 0.001 TYR R 149 ARG 0.014 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 2) link_NAG-ASN : angle 1.55329 ( 6) hydrogen bonds : bond 0.03358 ( 524) hydrogen bonds : angle 3.92209 ( 1503) SS BOND : bond 0.00280 ( 8) SS BOND : angle 0.81435 ( 16) covalent geometry : bond 0.00222 ( 9927) covalent geometry : angle 0.51193 (13498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7114.71 seconds wall clock time: 122 minutes 18.89 seconds (7338.89 seconds total)