Starting phenix.real_space_refine on Thu Jul 2 20:30:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vb7_64918/07_2026/9vb7_64918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vb7_64918/07_2026/9vb7_64918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vb7_64918/07_2026/9vb7_64918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vb7_64918/07_2026/9vb7_64918.map" model { file = "/net/cci-nas-00/data/ceres_data/9vb7_64918/07_2026/9vb7_64918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vb7_64918/07_2026/9vb7_64918.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.087 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 6409 2.51 5 N 1724 2.21 5 O 1900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10103 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2460 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 2807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 350, 2798 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 345} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 350, 2798 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 345} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 2834 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS A 345 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 345 " occ=0.50 Time building chain proxies: 2.72, per 1000 atoms: 0.27 Number of scatterers: 10103 At special positions: 0 Unit cell: (99.6, 124.5, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 3 15.00 Mg 1 11.99 O 1900 8.00 N 1724 7.00 C 6409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.17 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 390.1 milliseconds 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 14 sheets defined 41.0% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'R' and resid 51 through 55 removed outlier: 3.762A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 89 removed outlier: 3.649A pdb=" N TYR R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 127 removed outlier: 3.846A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Proline residue: R 121 - end of helix removed outlier: 3.924A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 172 Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.881A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 206 removed outlier: 3.586A pdb=" N TRP R 193 " --> pdb=" O ILE R 189 " (cutoff:3.500A) Proline residue: R 202 - end of helix removed outlier: 3.759A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 220 No H-bonds generated for 'chain 'R' and resid 218 through 220' Processing helix chain 'R' and resid 229 through 245 removed outlier: 3.580A pdb=" N PHE R 242 " --> pdb=" O GLN R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 272 Processing helix chain 'R' and resid 296 through 329 removed outlier: 4.152A pdb=" N VAL R 302 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL R 313 " --> pdb=" O VAL R 309 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.735A pdb=" N ILE R 329 " --> pdb=" O MET R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 334 removed outlier: 3.702A pdb=" N TRP R 334 " --> pdb=" O ASP R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 365 removed outlier: 3.788A pdb=" N HIS R 343 " --> pdb=" O TYR R 339 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 375 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.552A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.888A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.811A pdb=" N ASP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 143 through 146 removed outlier: 3.808A pdb=" N TYR A 146 " --> pdb=" O SER A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.650A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 348 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.679A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.585A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.164A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 211 removed outlier: 4.182A pdb=" N GLY R 208 " --> pdb=" O THR R 225 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR R 225 " --> pdb=" O GLY R 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 8.420A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.522A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.712A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.688A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.633A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.709A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.101A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.310A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.658A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.658A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.645A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.451A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1471 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: 1.59 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.54: 9953 1.54 - 1.90: 360 1.90 - 2.26: 0 2.26 - 2.62: 0 2.62 - 2.97: 1 Bond restraints: 10314 Sorted by residual: bond pdb=" C ARG A 205 " pdb=" N GLU A 207 " ideal model delta sigma weight residual 1.332 2.974 -1.642 1.40e-02 5.10e+03 1.38e+04 bond pdb=" CB VAL R 239 " pdb=" CG2 VAL R 239 " ideal model delta sigma weight residual 1.521 1.218 0.303 3.30e-02 9.18e+02 8.41e+01 bond pdb=" CB VAL R 239 " pdb=" CG1 VAL R 239 " ideal model delta sigma weight residual 1.521 1.786 -0.265 3.30e-02 9.18e+02 6.44e+01 bond pdb=" CA SER D 181 " pdb=" CB SER D 181 " ideal model delta sigma weight residual 1.534 1.444 0.090 1.45e-02 4.76e+03 3.87e+01 bond pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 1.384 1.254 0.130 2.10e-02 2.27e+03 3.85e+01 ... (remaining 10309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.78: 13949 8.78 - 17.57: 40 17.57 - 26.35: 3 26.35 - 35.14: 0 35.14 - 43.92: 1 Bond angle restraints: 13993 Sorted by residual: angle pdb=" CA ARG A 205 " pdb=" C ARG A 205 " pdb=" N GLU A 207 " ideal model delta sigma weight residual 116.84 72.92 43.92 1.71e+00 3.42e-01 6.60e+02 angle pdb=" CB PHE R 174 " pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 120.70 98.53 22.17 1.70e+00 3.46e-01 1.70e+02 angle pdb=" O ARG A 205 " pdb=" C ARG A 205 " pdb=" N GLU A 207 " ideal model delta sigma weight residual 122.59 138.07 -15.48 1.33e+00 5.65e-01 1.35e+02 angle pdb=" C ASP B 291 " pdb=" CA ASP B 291 " pdb=" CB ASP B 291 " ideal model delta sigma weight residual 110.11 92.25 17.86 1.90e+00 2.77e-01 8.84e+01 angle pdb=" C ASP B 186 " pdb=" CA ASP B 186 " pdb=" CB ASP B 186 " ideal model delta sigma weight residual 109.90 96.28 13.62 1.56e+00 4.11e-01 7.63e+01 ... (remaining 13988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 5901 35.11 - 70.22: 197 70.22 - 105.32: 12 105.32 - 140.43: 4 140.43 - 175.54: 2 Dihedral angle restraints: 6116 sinusoidal: 2347 harmonic: 3769 Sorted by residual: dihedral pdb=" CA ARG A 205 " pdb=" C ARG A 205 " pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta harmonic sigma weight residual 180.00 71.36 108.64 0 5.00e+00 4.00e-02 4.72e+02 dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -175.10 89.10 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CD ARG R 182 " pdb=" NE ARG R 182 " pdb=" CZ ARG R 182 " pdb=" NH1 ARG R 182 " ideal model delta sinusoidal sigma weight residual 0.00 -79.74 79.74 1 1.00e+01 1.00e-02 7.89e+01 ... (remaining 6113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.378: 1586 0.378 - 0.756: 3 0.756 - 1.134: 0 1.134 - 1.512: 0 1.512 - 1.890: 1 Chirality restraints: 1590 Sorted by residual: chirality pdb=" CG LEU R 118 " pdb=" CB LEU R 118 " pdb=" CD1 LEU R 118 " pdb=" CD2 LEU R 118 " both_signs ideal model delta sigma weight residual False -2.59 -0.70 -1.89 2.00e-01 2.50e+01 8.93e+01 chirality pdb=" CG LEU R 366 " pdb=" CB LEU R 366 " pdb=" CD1 LEU R 366 " pdb=" CD2 LEU R 366 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" CA HIS B 142 " pdb=" N HIS B 142 " pdb=" C HIS B 142 " pdb=" CB HIS B 142 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.66e+00 ... (remaining 1587 not shown) Planarity restraints: 1771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 205 " 0.068 2.00e-02 2.50e+03 1.95e-01 3.80e+02 pdb=" C ARG A 205 " -0.324 2.00e-02 2.50e+03 pdb=" O ARG A 205 " 0.199 2.00e-02 2.50e+03 pdb=" N GLU A 207 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " -0.860 9.50e-02 1.11e+02 3.97e-01 2.02e+02 pdb=" NE ARG A 129 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " 0.193 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " -0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 182 " 1.086 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG R 182 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG R 182 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG R 182 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG R 182 " 0.019 2.00e-02 2.50e+03 ... (remaining 1768 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 380 2.72 - 3.27: 9706 3.27 - 3.81: 15622 3.81 - 4.36: 21722 4.36 - 4.90: 35543 Nonbonded interactions: 82973 Sorted by model distance: nonbonded pdb=" O ILE R 192 " pdb=" OG SER R 196 " model vdw 2.181 3.040 nonbonded pdb=" O1G GTP A 401 " pdb="MG MG A 402 " model vdw 2.281 2.170 nonbonded pdb=" OG SER A 47 " pdb="MG MG A 402 " model vdw 2.284 2.170 nonbonded pdb=" N GLU A 122 " pdb=" OE1 GLU A 122 " model vdw 2.331 3.120 nonbonded pdb=" O SER D 52 " pdb=" NH1 ARG D 72 " model vdw 2.342 3.120 ... (remaining 82968 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=0.50 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: 0.130 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 10.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 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 : 0.020 1.642 10317 Z= 1.374 Angle : 2.180 43.923 13999 Z= 1.445 Chirality : 0.125 1.890 1590 Planarity : 0.023 0.487 1771 Dihedral : 17.129 175.538 3679 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.30 % Allowed : 11.77 % Favored : 81.93 % Cbeta Deviations : 1.73 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.21), residues: 1279 helix: -2.00 (0.18), residues: 486 sheet: -1.21 (0.29), residues: 267 loop : -1.55 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.183 0.010 ARG A 129 TYR 0.038 0.008 TYR D 103 PHE 0.154 0.008 PHE R 174 TRP 0.041 0.010 TRP B 63 HIS 0.021 0.006 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.02042 / 1.37 (10314) covalent geometry : angle 2.17778 / 1.44 (13993) SS BOND : bond 0.08521 / 5.90 ( 3) SS BOND : angle 5.63435 / 3.38 ( 6) hydrogen bonds : bond 0.23655 / 15.91 ( 511) hydrogen bonds : angle 8.98210 / 6.50 ( 1471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: R 123 GLU cc_start: 0.9043 (tt0) cc_final: 0.8809 (tt0) REVERT: R 148 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8150 (ttm170) REVERT: R 149 ASP cc_start: 0.9018 (m-30) cc_final: 0.8715 (m-30) REVERT: R 165 GLU cc_start: 0.9355 (tp30) cc_final: 0.9131 (tp30) REVERT: R 187 LYS cc_start: 0.8871 (mtpm) cc_final: 0.8662 (tmtt) REVERT: R 207 MET cc_start: 0.9343 (mmt) cc_final: 0.9014 (mmm) REVERT: R 237 ILE cc_start: 0.8286 (mt) cc_final: 0.8058 (mt) REVERT: R 243 MET cc_start: 0.9333 (mmm) cc_final: 0.9103 (mmp) REVERT: R 249 MET cc_start: 0.8291 (ttp) cc_final: 0.8031 (tmm) REVERT: R 306 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7517 (mmm-85) REVERT: R 331 ASP cc_start: 0.8259 (t0) cc_final: 0.7908 (t70) REVERT: L 11 TYR cc_start: 0.8131 (p90) cc_final: 0.7905 (p90) REVERT: L 12 ILE cc_start: 0.8604 (mm) cc_final: 0.8404 (mt) REVERT: A 17 LYS cc_start: 0.9139 (mttt) cc_final: 0.8938 (mtmm) REVERT: A 84 ILE cc_start: 0.9244 (mt) cc_final: 0.9034 (tt) REVERT: A 102 ASP cc_start: 0.9816 (m-30) cc_final: 0.9470 (t0) REVERT: A 192 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8542 (mttm) REVERT: A 198 MET cc_start: 0.9030 (ttm) cc_final: 0.8784 (ttp) REVERT: A 236 GLU cc_start: 0.2276 (OUTLIER) cc_final: 0.1906 (mt-10) REVERT: A 289 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9114 (pm20) REVERT: A 313 ARG cc_start: 0.8653 (ptp90) cc_final: 0.8328 (ptt-90) REVERT: B 3 GLU cc_start: 0.8535 (mp0) cc_final: 0.8273 (tp30) REVERT: B 9 GLN cc_start: 0.9687 (mm110) cc_final: 0.9411 (pt0) REVERT: B 15 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8931 (mttt) REVERT: C 22 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8492 (mt-10) REVERT: C 32 LYS cc_start: 0.8762 (tptp) cc_final: 0.8410 (tptp) REVERT: C 36 ASP cc_start: 0.8679 (m-30) cc_final: 0.8457 (m-30) REVERT: D 137 VAL cc_start: 0.9187 (t) cc_final: 0.8985 (p) REVERT: D 178 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.9097 (p90) REVERT: D 232 LYS cc_start: 0.9081 (tttt) cc_final: 0.8625 (tttp) REVERT: D 234 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8565 (pm20) outliers start: 66 outliers final: 18 residues processed: 272 average time/residue: 0.1384 time to fit residues: 48.9177 Evaluate side-chains 171 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 GLN Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 306 ARG Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 323 ARG Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 178 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 95 GLN R 210 GLN R 217 GLN R 238 GLN R 261 ASN R 360 ASN A 213 HIS A 346 ASN B 36 ASN B 75 GLN B 88 ASN B 91 HIS B 268 ASN B 293 ASN B 311 HIS B 340 ASN D 130 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.061285 restraints weight = 38410.269| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.92 r_work: 0.2659 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10317 Z= 0.186 Angle : 0.709 10.492 13999 Z= 0.366 Chirality : 0.045 0.339 1590 Planarity : 0.005 0.084 1771 Dihedral : 11.529 164.860 1481 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.27 % Favored : 97.65 % Rotamer: Outliers : 4.26 % Allowed : 14.74 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1281 helix: 0.88 (0.23), residues: 492 sheet: -1.10 (0.28), residues: 305 loop : -0.91 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.018 0.002 TYR R 144 PHE 0.016 0.002 PHE A 336 TRP 0.026 0.002 TRP A 211 HIS 0.007 0.001 HIS R 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (10314) covalent geometry : angle 0.70826 / 0.37 (13993) SS BOND : bond 0.00545 / 0.35 ( 3) SS BOND : angle 1.56233 / 1.04 ( 6) hydrogen bonds : bond 0.05174 / 3.48 ( 511) hydrogen bonds : angle 5.04083 / 3.60 ( 1471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 88 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9007 (mt) REVERT: R 98 GLN cc_start: 0.8627 (tp40) cc_final: 0.8413 (mp10) REVERT: R 187 LYS cc_start: 0.8419 (mtpm) cc_final: 0.8174 (tmtt) REVERT: R 263 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7805 (tt) REVERT: R 323 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7214 (mtm-85) REVERT: R 333 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8419 (mm-40) REVERT: L 11 TYR cc_start: 0.8421 (p90) cc_final: 0.7978 (p90) REVERT: A 17 LYS cc_start: 0.8632 (mttt) cc_final: 0.8297 (mtmm) REVERT: A 25 GLU cc_start: 0.8593 (tt0) cc_final: 0.8130 (tm-30) REVERT: A 67 LYS cc_start: 0.9561 (mtpt) cc_final: 0.9221 (mmmm) REVERT: A 198 MET cc_start: 0.9137 (ttm) cc_final: 0.8914 (ttp) REVERT: A 253 ILE cc_start: 0.9310 (mt) cc_final: 0.8945 (mp) REVERT: A 257 LYS cc_start: 0.9178 (ptpt) cc_final: 0.8856 (ptmm) REVERT: A 350 ASP cc_start: 0.8897 (m-30) cc_final: 0.8696 (p0) REVERT: B 15 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8242 (mttp) REVERT: B 197 ARG cc_start: 0.8862 (mmm160) cc_final: 0.8655 (mmp-170) REVERT: B 323 ASP cc_start: 0.8945 (t0) cc_final: 0.8704 (t0) REVERT: C 21 MET cc_start: 0.9326 (tpp) cc_final: 0.8917 (mmm) REVERT: C 32 LYS cc_start: 0.8283 (tptp) cc_final: 0.8012 (tptp) REVERT: C 58 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8996 (mp0) REVERT: D 117 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8044 (tt) REVERT: D 174 GLN cc_start: 0.8615 (pt0) cc_final: 0.8399 (pt0) REVERT: D 234 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8149 (pm20) outliers start: 44 outliers final: 15 residues processed: 192 average time/residue: 0.1213 time to fit residues: 31.2135 Evaluate side-chains 152 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 323 ARG Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 120 optimal weight: 7.9990 chunk 42 optimal weight: 30.0000 chunk 113 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS B 36 ASN B 340 ASN D 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.057520 restraints weight = 50670.264| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 4.38 r_work: 0.2575 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10317 Z= 0.233 Angle : 0.696 9.388 13999 Z= 0.355 Chirality : 0.045 0.367 1590 Planarity : 0.004 0.033 1771 Dihedral : 9.994 161.022 1439 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 4.17 % Allowed : 16.31 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.23), residues: 1281 helix: 1.44 (0.23), residues: 499 sheet: -0.78 (0.29), residues: 283 loop : -0.77 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 8 TYR 0.016 0.002 TYR R 145 PHE 0.017 0.002 PHE B 234 TRP 0.018 0.002 TRP A 211 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (10314) covalent geometry : angle 0.69349 / 0.35 (13993) SS BOND : bond 0.01434 / 1.00 ( 3) SS BOND : angle 3.10239 / 2.59 ( 6) hydrogen bonds : bond 0.04906 / 3.27 ( 511) hydrogen bonds : angle 4.71128 / 3.37 ( 1471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 187 LYS cc_start: 0.8347 (mtpm) cc_final: 0.8088 (tmtt) REVERT: R 263 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7861 (tt) REVERT: L 11 TYR cc_start: 0.8615 (p90) cc_final: 0.8079 (p90) REVERT: A 25 GLU cc_start: 0.8568 (tt0) cc_final: 0.8133 (tm-30) REVERT: A 119 MET cc_start: 0.8468 (tmm) cc_final: 0.8225 (tmm) REVERT: A 120 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9102 (p) REVERT: A 198 MET cc_start: 0.9118 (ttm) cc_final: 0.8845 (ttp) REVERT: A 257 LYS cc_start: 0.9239 (ptpt) cc_final: 0.8907 (ptmm) REVERT: A 350 ASP cc_start: 0.8901 (m-30) cc_final: 0.8662 (p0) REVERT: B 10 GLU cc_start: 0.9251 (tp30) cc_final: 0.8944 (tp30) REVERT: B 234 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8945 (m-80) REVERT: B 286 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9146 (mt) REVERT: B 323 ASP cc_start: 0.8865 (t0) cc_final: 0.8620 (t0) REVERT: C 21 MET cc_start: 0.9282 (tpp) cc_final: 0.8837 (mmm) REVERT: C 32 LYS cc_start: 0.8283 (tptp) cc_final: 0.8049 (tptp) REVERT: D 89 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8630 (mp0) REVERT: D 98 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8688 (ptt90) REVERT: D 117 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7871 (tt) REVERT: D 234 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7988 (pm20) outliers start: 43 outliers final: 19 residues processed: 171 average time/residue: 0.1049 time to fit residues: 24.8396 Evaluate side-chains 145 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 45 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 340 ASN D 13 GLN D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.058727 restraints weight = 46856.736| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.22 r_work: 0.2605 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10317 Z= 0.168 Angle : 0.627 8.478 13999 Z= 0.317 Chirality : 0.042 0.203 1590 Planarity : 0.004 0.032 1771 Dihedral : 9.376 169.242 1428 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.34 % Allowed : 16.50 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1281 helix: 1.75 (0.24), residues: 493 sheet: -0.55 (0.29), residues: 285 loop : -0.65 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 205 TYR 0.016 0.001 TYR D 178 PHE 0.010 0.001 PHE B 234 TRP 0.014 0.001 TRP A 211 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (10314) covalent geometry : angle 0.62544 / 0.32 (13993) SS BOND : bond 0.01003 / 0.70 ( 3) SS BOND : angle 2.27554 / 1.94 ( 6) hydrogen bonds : bond 0.04273 / 2.86 ( 511) hydrogen bonds : angle 4.52312 / 3.22 ( 1471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 187 LYS cc_start: 0.8312 (mtpm) cc_final: 0.8034 (tmtt) REVERT: R 264 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8874 (p) REVERT: L 11 TYR cc_start: 0.8684 (p90) cc_final: 0.8173 (p90) REVERT: A 25 GLU cc_start: 0.8594 (tt0) cc_final: 0.8139 (tm-30) REVERT: A 119 MET cc_start: 0.8647 (tmm) cc_final: 0.8430 (tmm) REVERT: A 120 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9130 (p) REVERT: A 198 MET cc_start: 0.9081 (ttm) cc_final: 0.8843 (ttp) REVERT: A 257 LYS cc_start: 0.9362 (ptpt) cc_final: 0.9038 (ptmm) REVERT: A 310 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 350 ASP cc_start: 0.8888 (m-30) cc_final: 0.8629 (p0) REVERT: B 10 GLU cc_start: 0.9288 (tp30) cc_final: 0.8933 (tp30) REVERT: B 15 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8299 (mttp) REVERT: B 234 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.9005 (m-80) REVERT: B 286 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9085 (mt) REVERT: B 318 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8848 (pp) REVERT: B 323 ASP cc_start: 0.8823 (t0) cc_final: 0.8562 (t0) REVERT: C 21 MET cc_start: 0.9291 (tpp) cc_final: 0.9047 (mmm) REVERT: C 48 ASP cc_start: 0.9064 (t0) cc_final: 0.8703 (t0) REVERT: D 73 ASP cc_start: 0.8435 (t0) cc_final: 0.8087 (t0) REVERT: D 89 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8743 (mp0) REVERT: D 117 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7742 (tt) REVERT: D 234 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8069 (pm20) outliers start: 34 outliers final: 16 residues processed: 159 average time/residue: 0.1026 time to fit residues: 22.3279 Evaluate side-chains 143 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 0.0670 chunk 47 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 340 ASN D 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.058627 restraints weight = 38868.387| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.95 r_work: 0.2597 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10317 Z= 0.201 Angle : 0.639 8.247 13999 Z= 0.324 Chirality : 0.042 0.183 1590 Planarity : 0.004 0.032 1771 Dihedral : 9.240 177.650 1428 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.17 % Allowed : 16.87 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1281 helix: 1.82 (0.24), residues: 494 sheet: -0.46 (0.30), residues: 283 loop : -0.64 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 90 TYR 0.014 0.001 TYR D 178 PHE 0.014 0.001 PHE B 234 TRP 0.013 0.002 TRP A 211 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (10314) covalent geometry : angle 0.63696 / 0.32 (13993) SS BOND : bond 0.01132 / 0.79 ( 3) SS BOND : angle 2.27782 / 1.93 ( 6) hydrogen bonds : bond 0.04377 / 2.92 ( 511) hydrogen bonds : angle 4.51030 / 3.21 ( 1471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 187 LYS cc_start: 0.8297 (mtpm) cc_final: 0.7997 (tmtt) REVERT: R 238 GLN cc_start: 0.8344 (pt0) cc_final: 0.7989 (pt0) REVERT: L 11 TYR cc_start: 0.8779 (p90) cc_final: 0.8423 (p90) REVERT: A 25 GLU cc_start: 0.8579 (tt0) cc_final: 0.8093 (tm-30) REVERT: A 106 GLN cc_start: 0.9665 (tp-100) cc_final: 0.9355 (tp-100) REVERT: A 120 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.9163 (p) REVERT: A 198 MET cc_start: 0.9078 (ttm) cc_final: 0.8810 (ttp) REVERT: A 257 LYS cc_start: 0.9383 (ptpt) cc_final: 0.9044 (ptmm) REVERT: A 310 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 350 ASP cc_start: 0.8895 (m-30) cc_final: 0.8633 (p0) REVERT: B 10 GLU cc_start: 0.9318 (tp30) cc_final: 0.8948 (tp30) REVERT: B 15 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8313 (mttp) REVERT: B 142 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.6806 (t-90) REVERT: B 234 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: B 286 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9057 (mt) REVERT: B 318 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8826 (pp) REVERT: B 323 ASP cc_start: 0.8788 (t0) cc_final: 0.8552 (t0) REVERT: C 21 MET cc_start: 0.9290 (tpp) cc_final: 0.9046 (mmm) REVERT: C 48 ASP cc_start: 0.9076 (t0) cc_final: 0.8579 (t0) REVERT: D 46 GLU cc_start: 0.8752 (tt0) cc_final: 0.8484 (tt0) REVERT: D 73 ASP cc_start: 0.8419 (t0) cc_final: 0.8094 (t70) REVERT: D 89 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8668 (mp0) REVERT: D 117 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7752 (tt) REVERT: D 234 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8071 (pm20) outliers start: 43 outliers final: 26 residues processed: 160 average time/residue: 0.1105 time to fit residues: 24.4366 Evaluate side-chains 153 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 48 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.056781 restraints weight = 45564.327| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 4.26 r_work: 0.2555 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10317 Z= 0.274 Angle : 0.674 8.283 13999 Z= 0.343 Chirality : 0.044 0.176 1590 Planarity : 0.004 0.033 1771 Dihedral : 9.178 174.252 1427 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.36 % Allowed : 17.24 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1281 helix: 1.74 (0.24), residues: 501 sheet: -0.46 (0.30), residues: 294 loop : -0.54 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 105 TYR 0.014 0.001 TYR D 178 PHE 0.017 0.002 PHE B 234 TRP 0.015 0.002 TRP B 63 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.27 (10314) covalent geometry : angle 0.67208 / 0.34 (13993) SS BOND : bond 0.01564 / 1.10 ( 3) SS BOND : angle 2.70792 / 2.28 ( 6) hydrogen bonds : bond 0.04580 / 3.06 ( 511) hydrogen bonds : angle 4.58786 / 3.28 ( 1471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: R 187 LYS cc_start: 0.8431 (mtpm) cc_final: 0.8080 (tmtt) REVERT: R 238 GLN cc_start: 0.8221 (pt0) cc_final: 0.7890 (pt0) REVERT: R 264 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8746 (p) REVERT: L 11 TYR cc_start: 0.8827 (p90) cc_final: 0.8495 (p90) REVERT: A 25 GLU cc_start: 0.8603 (tt0) cc_final: 0.8112 (tm-30) REVERT: A 105 ARG cc_start: 0.9492 (mtm110) cc_final: 0.9287 (mtm110) REVERT: A 106 GLN cc_start: 0.9661 (tp-100) cc_final: 0.9358 (tp-100) REVERT: A 120 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9143 (p) REVERT: A 198 MET cc_start: 0.9103 (ttm) cc_final: 0.8833 (ttp) REVERT: A 257 LYS cc_start: 0.9402 (ptpt) cc_final: 0.9065 (ptmm) REVERT: A 310 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 350 ASP cc_start: 0.8909 (m-30) cc_final: 0.8556 (p0) REVERT: B 10 GLU cc_start: 0.9332 (tp30) cc_final: 0.8958 (tp30) REVERT: B 146 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 234 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8935 (m-80) REVERT: B 286 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9119 (mt) REVERT: B 291 ASP cc_start: 0.8656 (t0) cc_final: 0.8393 (t0) REVERT: B 318 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8848 (pp) REVERT: B 323 ASP cc_start: 0.8830 (t0) cc_final: 0.8597 (t0) REVERT: C 21 MET cc_start: 0.9305 (tpp) cc_final: 0.9067 (mmm) REVERT: C 36 ASP cc_start: 0.8133 (m-30) cc_final: 0.7929 (m-30) REVERT: C 48 ASP cc_start: 0.9102 (t0) cc_final: 0.8606 (t0) REVERT: D 73 ASP cc_start: 0.8426 (t0) cc_final: 0.8118 (t70) REVERT: D 89 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8727 (mp0) REVERT: D 117 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7842 (tt) REVERT: D 234 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8073 (pm20) outliers start: 45 outliers final: 30 residues processed: 161 average time/residue: 0.1016 time to fit residues: 23.0375 Evaluate side-chains 159 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 9 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.060233 restraints weight = 39331.280| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.91 r_work: 0.2643 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10317 Z= 0.141 Angle : 0.610 8.151 13999 Z= 0.309 Chirality : 0.041 0.183 1590 Planarity : 0.003 0.032 1771 Dihedral : 8.987 177.292 1427 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.15 % Allowed : 18.44 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.24), residues: 1281 helix: 1.92 (0.24), residues: 494 sheet: -0.29 (0.29), residues: 297 loop : -0.61 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 105 TYR 0.014 0.001 TYR D 178 PHE 0.011 0.001 PHE A 267 TRP 0.014 0.002 TRP B 63 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10314) covalent geometry : angle 0.60933 / 0.31 (13993) SS BOND : bond 0.00845 / 0.58 ( 3) SS BOND : angle 1.66884 / 1.44 ( 6) hydrogen bonds : bond 0.03981 / 2.67 ( 511) hydrogen bonds : angle 4.43400 / 3.16 ( 1471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 120 MET cc_start: 0.9254 (tpp) cc_final: 0.9006 (tpt) REVERT: R 126 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8845 (t0) REVERT: R 187 LYS cc_start: 0.8387 (mtpm) cc_final: 0.8095 (tmtt) REVERT: R 238 GLN cc_start: 0.8326 (pt0) cc_final: 0.8044 (pt0) REVERT: L 11 TYR cc_start: 0.8899 (p90) cc_final: 0.8681 (p90) REVERT: A 25 GLU cc_start: 0.8720 (tt0) cc_final: 0.8241 (tm-30) REVERT: A 106 GLN cc_start: 0.9641 (tp-100) cc_final: 0.9388 (mt0) REVERT: A 119 MET cc_start: 0.8579 (tmm) cc_final: 0.8324 (tmm) REVERT: A 120 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.9169 (p) REVERT: A 198 MET cc_start: 0.9201 (ttm) cc_final: 0.8982 (ttp) REVERT: A 257 LYS cc_start: 0.9415 (ptpt) cc_final: 0.9103 (ptmm) REVERT: A 310 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8741 (mm) REVERT: A 350 ASP cc_start: 0.8868 (m-30) cc_final: 0.8594 (p0) REVERT: B 10 GLU cc_start: 0.9314 (tp30) cc_final: 0.8915 (tp30) REVERT: B 15 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8365 (mttp) REVERT: B 142 HIS cc_start: 0.9094 (OUTLIER) cc_final: 0.7449 (t-90) REVERT: B 146 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8708 (mp) REVERT: B 234 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9104 (m-80) REVERT: B 261 LEU cc_start: 0.9046 (tp) cc_final: 0.8749 (mp) REVERT: B 291 ASP cc_start: 0.8613 (t0) cc_final: 0.8274 (p0) REVERT: B 318 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8956 (pp) REVERT: B 323 ASP cc_start: 0.8918 (t0) cc_final: 0.8666 (t0) REVERT: C 21 MET cc_start: 0.9369 (tpp) cc_final: 0.9102 (mmm) REVERT: C 32 LYS cc_start: 0.8234 (tptp) cc_final: 0.7751 (tptp) REVERT: C 48 ASP cc_start: 0.9101 (t0) cc_final: 0.8593 (t0) REVERT: D 73 ASP cc_start: 0.8484 (t0) cc_final: 0.8194 (t0) REVERT: D 89 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8741 (mp0) REVERT: D 117 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7986 (tt) REVERT: D 234 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8144 (pm20) outliers start: 32 outliers final: 15 residues processed: 159 average time/residue: 0.1006 time to fit residues: 22.4648 Evaluate side-chains 146 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 5 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 17 optimal weight: 20.0000 chunk 117 optimal weight: 0.0000 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 113 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 13 GLN D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.058620 restraints weight = 33073.821| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.63 r_work: 0.2619 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10317 Z= 0.186 Angle : 0.632 8.224 13999 Z= 0.320 Chirality : 0.042 0.158 1590 Planarity : 0.004 0.032 1771 Dihedral : 8.875 173.329 1425 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.34 % Allowed : 18.44 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.24), residues: 1281 helix: 1.92 (0.24), residues: 495 sheet: -0.25 (0.30), residues: 292 loop : -0.64 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 105 TYR 0.014 0.001 TYR R 125 PHE 0.013 0.001 PHE B 234 TRP 0.012 0.001 TRP D 47 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (10314) covalent geometry : angle 0.63007 / 0.32 (13993) SS BOND : bond 0.01121 / 0.79 ( 3) SS BOND : angle 2.15123 / 1.83 ( 6) hydrogen bonds : bond 0.04131 / 2.76 ( 511) hydrogen bonds : angle 4.41126 / 3.15 ( 1471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: R 126 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8686 (t0) REVERT: R 187 LYS cc_start: 0.8412 (mtpm) cc_final: 0.8069 (tmtt) REVERT: R 229 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6902 (p-80) REVERT: R 238 GLN cc_start: 0.8247 (pt0) cc_final: 0.7869 (pt0) REVERT: L 12 ILE cc_start: 0.8726 (mm) cc_final: 0.8511 (mp) REVERT: A 25 GLU cc_start: 0.8590 (tt0) cc_final: 0.8100 (tm-30) REVERT: A 106 GLN cc_start: 0.9664 (tp-100) cc_final: 0.9427 (mt0) REVERT: A 119 MET cc_start: 0.8573 (tmm) cc_final: 0.8303 (tmm) REVERT: A 120 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9160 (p) REVERT: A 198 MET cc_start: 0.9083 (ttm) cc_final: 0.8851 (ttp) REVERT: A 257 LYS cc_start: 0.9400 (ptpt) cc_final: 0.9057 (ptmm) REVERT: A 310 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8564 (mm) REVERT: A 350 ASP cc_start: 0.8852 (m-30) cc_final: 0.8535 (p0) REVERT: A 354 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7852 (p90) REVERT: B 10 GLU cc_start: 0.9327 (tp30) cc_final: 0.8928 (tp30) REVERT: B 12 GLU cc_start: 0.8643 (tp30) cc_final: 0.7987 (tp30) REVERT: B 15 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8399 (mttp) REVERT: B 142 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.7403 (t-90) REVERT: B 146 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 234 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.8976 (m-80) REVERT: B 261 LEU cc_start: 0.9116 (tp) cc_final: 0.8760 (mp) REVERT: B 291 ASP cc_start: 0.8572 (t0) cc_final: 0.8152 (p0) REVERT: B 318 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8878 (pp) REVERT: B 323 ASP cc_start: 0.8860 (t0) cc_final: 0.8575 (t0) REVERT: C 21 MET cc_start: 0.9299 (tpp) cc_final: 0.9046 (mmm) REVERT: C 32 LYS cc_start: 0.8071 (tptp) cc_final: 0.7638 (tptp) REVERT: C 36 ASP cc_start: 0.8119 (m-30) cc_final: 0.7759 (m-30) REVERT: C 48 ASP cc_start: 0.9057 (t0) cc_final: 0.8522 (t0) REVERT: C 58 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8728 (pm20) REVERT: D 73 ASP cc_start: 0.8413 (t0) cc_final: 0.8070 (t0) REVERT: D 89 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8713 (mp0) REVERT: D 117 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7722 (tt) REVERT: D 234 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8107 (pm20) outliers start: 34 outliers final: 22 residues processed: 152 average time/residue: 0.0905 time to fit residues: 19.3034 Evaluate side-chains 153 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 17 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.0770 chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.060748 restraints weight = 27757.208| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.38 r_work: 0.2671 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10317 Z= 0.131 Angle : 0.607 8.102 13999 Z= 0.308 Chirality : 0.041 0.151 1590 Planarity : 0.003 0.032 1771 Dihedral : 8.825 175.734 1425 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.78 % Allowed : 19.28 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.24), residues: 1281 helix: 1.96 (0.24), residues: 495 sheet: -0.17 (0.30), residues: 290 loop : -0.61 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 105 TYR 0.016 0.001 TYR R 125 PHE 0.009 0.001 PHE A 267 TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10314) covalent geometry : angle 0.60655 / 0.31 (13993) SS BOND : bond 0.00810 / 0.56 ( 3) SS BOND : angle 1.62280 / 1.41 ( 6) hydrogen bonds : bond 0.03857 / 2.58 ( 511) hydrogen bonds : angle 4.32868 / 3.09 ( 1471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: R 126 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8554 (t0) REVERT: R 187 LYS cc_start: 0.8284 (mtpm) cc_final: 0.7984 (tmtt) REVERT: R 229 HIS cc_start: 0.7284 (OUTLIER) cc_final: 0.6882 (p-80) REVERT: R 238 GLN cc_start: 0.8191 (pt0) cc_final: 0.7843 (pt0) REVERT: A 25 GLU cc_start: 0.8555 (tt0) cc_final: 0.8052 (tm-30) REVERT: A 106 GLN cc_start: 0.9669 (tp-100) cc_final: 0.9426 (mt0) REVERT: A 119 MET cc_start: 0.8593 (tmm) cc_final: 0.8339 (tmm) REVERT: A 120 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9157 (p) REVERT: A 198 MET cc_start: 0.9038 (ttm) cc_final: 0.8835 (ttp) REVERT: A 257 LYS cc_start: 0.9405 (ptpt) cc_final: 0.9057 (ptmm) REVERT: A 310 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8601 (mm) REVERT: A 350 ASP cc_start: 0.8849 (m-30) cc_final: 0.8509 (p0) REVERT: A 354 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7904 (p90) REVERT: B 8 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8397 (mtt90) REVERT: B 10 GLU cc_start: 0.9389 (tp30) cc_final: 0.9033 (tp30) REVERT: B 15 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8436 (mttp) REVERT: B 124 TYR cc_start: 0.9262 (m-80) cc_final: 0.9024 (m-80) REVERT: B 142 HIS cc_start: 0.8952 (OUTLIER) cc_final: 0.7407 (t-90) REVERT: B 146 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8436 (mp) REVERT: B 217 MET cc_start: 0.9097 (pmm) cc_final: 0.8511 (pmm) REVERT: B 234 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8916 (m-80) REVERT: B 261 LEU cc_start: 0.9031 (tp) cc_final: 0.8719 (mp) REVERT: B 291 ASP cc_start: 0.8519 (t0) cc_final: 0.8162 (p0) REVERT: B 318 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8872 (pp) REVERT: B 323 ASP cc_start: 0.8870 (t0) cc_final: 0.8608 (t0) REVERT: C 21 MET cc_start: 0.9285 (tpp) cc_final: 0.9023 (mmm) REVERT: C 32 LYS cc_start: 0.8024 (tptp) cc_final: 0.7566 (tptp) REVERT: C 36 ASP cc_start: 0.8086 (m-30) cc_final: 0.7708 (m-30) REVERT: C 48 ASP cc_start: 0.8960 (t0) cc_final: 0.8420 (t0) REVERT: C 58 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8746 (pm20) REVERT: D 73 ASP cc_start: 0.8414 (t0) cc_final: 0.8093 (t0) REVERT: D 89 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8716 (mp0) REVERT: D 117 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7734 (tt) REVERT: D 234 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8115 (pm20) outliers start: 28 outliers final: 15 residues processed: 157 average time/residue: 0.1025 time to fit residues: 22.8266 Evaluate side-chains 152 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 0.3980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.090710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.060280 restraints weight = 28732.003| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.41 r_work: 0.2660 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10317 Z= 0.150 Angle : 0.615 8.625 13999 Z= 0.311 Chirality : 0.041 0.149 1590 Planarity : 0.003 0.032 1771 Dihedral : 8.711 173.872 1425 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.78 % Allowed : 19.65 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.24), residues: 1281 helix: 1.94 (0.24), residues: 495 sheet: -0.14 (0.30), residues: 292 loop : -0.59 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 105 TYR 0.019 0.001 TYR L 11 PHE 0.029 0.001 PHE R 127 TRP 0.014 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10314) covalent geometry : angle 0.61435 / 0.31 (13993) SS BOND : bond 0.00916 / 0.64 ( 3) SS BOND : angle 1.74609 / 1.51 ( 6) hydrogen bonds : bond 0.03906 / 2.61 ( 511) hydrogen bonds : angle 4.33230 / 3.08 ( 1471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 187 LYS cc_start: 0.8400 (mtpm) cc_final: 0.8056 (tmtt) REVERT: R 229 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6892 (p-80) REVERT: R 238 GLN cc_start: 0.8124 (pt0) cc_final: 0.7780 (pt0) REVERT: A 25 GLU cc_start: 0.8570 (tt0) cc_final: 0.8067 (tm-30) REVERT: A 106 GLN cc_start: 0.9671 (tp-100) cc_final: 0.9396 (tp-100) REVERT: A 119 MET cc_start: 0.8591 (tmm) cc_final: 0.8337 (tmm) REVERT: A 120 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9156 (p) REVERT: A 198 MET cc_start: 0.9049 (ttm) cc_final: 0.8829 (ttp) REVERT: A 257 LYS cc_start: 0.9410 (ptpt) cc_final: 0.9060 (ptmm) REVERT: A 310 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 350 ASP cc_start: 0.8836 (m-30) cc_final: 0.8407 (p0) REVERT: A 354 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7784 (p90) REVERT: B 10 GLU cc_start: 0.9385 (tp30) cc_final: 0.9021 (tp30) REVERT: B 15 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8474 (mttp) REVERT: B 124 TYR cc_start: 0.9269 (m-80) cc_final: 0.9033 (m-80) REVERT: B 142 HIS cc_start: 0.8962 (OUTLIER) cc_final: 0.7488 (t-90) REVERT: B 146 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8560 (mp) REVERT: B 217 MET cc_start: 0.9097 (pmm) cc_final: 0.8499 (pmm) REVERT: B 234 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8934 (m-80) REVERT: B 261 LEU cc_start: 0.8989 (tp) cc_final: 0.8674 (mp) REVERT: B 291 ASP cc_start: 0.8516 (t0) cc_final: 0.8173 (p0) REVERT: B 318 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8862 (pp) REVERT: B 323 ASP cc_start: 0.8867 (t0) cc_final: 0.8609 (t0) REVERT: C 21 MET cc_start: 0.9285 (tpp) cc_final: 0.9025 (mmm) REVERT: C 48 ASP cc_start: 0.8972 (t0) cc_final: 0.8425 (t0) REVERT: C 58 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: D 73 ASP cc_start: 0.8432 (t0) cc_final: 0.8117 (t0) REVERT: D 89 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8763 (mp0) REVERT: D 117 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7685 (tt) REVERT: D 234 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8087 (pm20) outliers start: 28 outliers final: 16 residues processed: 149 average time/residue: 0.1013 time to fit residues: 21.3536 Evaluate side-chains 150 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 40 optimal weight: 0.0000 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN A 241 ASN B 340 ASN D 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.062067 restraints weight = 38185.112| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.92 r_work: 0.2684 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10317 Z= 0.118 Angle : 0.602 8.670 13999 Z= 0.307 Chirality : 0.040 0.145 1590 Planarity : 0.003 0.032 1771 Dihedral : 8.541 176.537 1425 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.59 % Allowed : 20.30 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1281 helix: 2.03 (0.24), residues: 497 sheet: 0.06 (0.31), residues: 282 loop : -0.57 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 105 TYR 0.012 0.001 TYR D 178 PHE 0.029 0.001 PHE R 127 TRP 0.014 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10314) covalent geometry : angle 0.60115 / 0.31 (13993) SS BOND : bond 0.00615 / 0.42 ( 3) SS BOND : angle 1.27418 / 1.10 ( 6) hydrogen bonds : bond 0.03572 / 2.40 ( 511) hydrogen bonds : angle 4.28030 / 3.02 ( 1471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2786.09 seconds wall clock time: 48 minutes 31.74 seconds (2911.74 seconds total)