Starting phenix.real_space_refine on Thu Jul 2 10:03:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vba_64919/07_2026/9vba_64919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vba_64919/07_2026/9vba_64919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vba_64919/07_2026/9vba_64919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vba_64919/07_2026/9vba_64919.map" model { file = "/net/cci-nas-00/data/ceres_data/9vba_64919/07_2026/9vba_64919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vba_64919/07_2026/9vba_64919.cif" } resolution = 3.38 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= 0.007 sd= 0.031 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 55 5.16 5 C 5117 2.51 5 N 1388 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 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: 8089 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2725 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 346} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2575 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 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: "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: "R" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2300 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.42, per 1000 atoms: 0.18 Number of scatterers: 8089 At special positions: 0 Unit cell: (94.62, 88.395, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 3 15.00 O 1526 8.00 N 1388 7.00 C 5117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.58 Conformation dependent library (CDL) restraints added in 410.8 milliseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 48.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 47 through 58 removed outlier: 4.549A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 92 removed outlier: 3.609A pdb=" N LYS A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.024A pdb=" N ASP A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.767A pdb=" N GLY A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.782A pdb=" N TYR A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 removed outlier: 4.035A pdb=" N ILE A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.511A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.217A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 328 through 346 removed outlier: 3.522A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.634A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.628A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'R' and resid 51 through 55 Processing helix chain 'R' and resid 59 through 88 Processing helix chain 'R' and resid 99 through 130 Proline residue: R 121 - end of helix removed outlier: 3.572A pdb=" N TRP R 129 " --> pdb=" O TYR R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.663A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET R 180 " --> pdb=" O ALA R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 207 Proline residue: R 202 - end of helix removed outlier: 3.523A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 273 removed outlier: 3.842A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE R 247 " --> pdb=" O MET R 243 " (cutoff:3.500A) Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 295 through 328 removed outlier: 3.754A pdb=" N LEU R 317 " --> pdb=" O VAL R 313 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.743A pdb=" N CYS R 327 " --> pdb=" O ARG R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 365 Proline residue: R 361 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 5.877A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 196 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.282A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 49 removed outlier: 4.046A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.043A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.679A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.665A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.665A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.960A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.627A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.017A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 209 through 211 431 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.29: 1341 1.29 - 1.45: 2277 1.45 - 1.62: 4540 1.62 - 1.79: 8 1.79 - 1.95: 79 Bond restraints: 8245 Sorted by residual: bond pdb=" CA SER R 330 " pdb=" CB SER R 330 " ideal model delta sigma weight residual 1.529 1.836 -0.307 1.62e-02 3.81e+03 3.59e+02 bond pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 1.384 1.685 -0.301 2.10e-02 2.27e+03 2.06e+02 bond pdb=" CE1 HIS B 183 " pdb=" NE2 HIS B 183 " ideal model delta sigma weight residual 1.321 1.180 0.141 1.00e-02 1.00e+04 1.98e+02 bond pdb=" CB ILE R 60 " pdb=" CG2 ILE R 60 " ideal model delta sigma weight residual 1.521 1.953 -0.432 3.30e-02 9.18e+02 1.72e+02 bond pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta sigma weight residual 1.534 1.738 -0.205 1.57e-02 4.06e+03 1.70e+02 ... (remaining 8240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.19: 11123 9.19 - 18.38: 74 18.38 - 27.58: 4 27.58 - 36.77: 4 36.77 - 45.96: 2 Bond angle restraints: 11207 Sorted by residual: angle pdb=" CG GLU A 238 " pdb=" CD GLU A 238 " pdb=" OE2 GLU A 238 " ideal model delta sigma weight residual 118.40 72.44 45.96 2.30e+00 1.89e-01 3.99e+02 angle pdb=" N GLU R 332 " pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta sigma weight residual 111.31 78.13 33.18 1.67e+00 3.59e-01 3.95e+02 angle pdb=" CG GLU A 238 " pdb=" CD GLU A 238 " pdb=" OE1 GLU A 238 " ideal model delta sigma weight residual 118.40 162.10 -43.70 2.30e+00 1.89e-01 3.61e+02 angle pdb=" CB PHE R 174 " pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 120.70 143.74 -23.04 1.70e+00 3.46e-01 1.84e+02 angle pdb=" CB ILE R 237 " pdb=" CG1 ILE R 237 " pdb=" CD1 ILE R 237 " ideal model delta sigma weight residual 113.80 142.12 -28.32 2.10e+00 2.27e-01 1.82e+02 ... (remaining 11202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 4722 35.90 - 71.80: 159 71.80 - 107.71: 12 107.71 - 143.61: 2 143.61 - 179.51: 1 Dihedral angle restraints: 4896 sinusoidal: 1823 harmonic: 3073 Sorted by residual: dihedral pdb=" N GLU R 332 " pdb=" C GLU R 332 " pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta harmonic sigma weight residual 122.80 80.59 42.21 0 2.50e+00 1.60e-01 2.85e+02 dihedral pdb=" C GLU R 332 " pdb=" N GLU R 332 " pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta harmonic sigma weight residual -122.60 -94.76 -27.84 0 2.50e+00 1.60e-01 1.24e+02 dihedral pdb=" C PHE A 196 " pdb=" N PHE A 196 " pdb=" CA PHE A 196 " pdb=" CB PHE A 196 " ideal model delta harmonic sigma weight residual -122.60 -98.05 -24.55 0 2.50e+00 1.60e-01 9.64e+01 ... (remaining 4893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.358: 1262 0.358 - 0.715: 32 0.715 - 1.073: 6 1.073 - 1.430: 2 1.430 - 1.788: 2 Chirality restraints: 1304 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 -0.80 -1.79 2.00e-01 2.50e+01 7.99e+01 chirality pdb=" CB VAL R 239 " pdb=" CA VAL R 239 " pdb=" CG1 VAL R 239 " pdb=" CG2 VAL R 239 " both_signs ideal model delta sigma weight residual False -2.63 -0.93 -1.70 2.00e-01 2.50e+01 7.23e+01 chirality pdb=" CB ILE R 60 " pdb=" CA ILE R 60 " pdb=" CG1 ILE R 60 " pdb=" CG2 ILE R 60 " both_signs ideal model delta sigma weight residual False 2.64 3.98 -1.33 2.00e-01 2.50e+01 4.45e+01 ... (remaining 1301 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 86 " 1.068 9.50e-02 1.11e+02 4.79e-01 1.38e+02 pdb=" NE ARG A 86 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 86 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 86 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 86 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 100 " -0.654 9.50e-02 1.11e+02 3.01e-01 1.08e+02 pdb=" NE ARG A 100 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 100 " 0.136 2.00e-02 2.50e+03 pdb=" NH1 ARG A 100 " -0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG A 100 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 144 " 0.656 9.50e-02 1.11e+02 3.00e-01 9.57e+01 pdb=" NE ARG A 144 " -0.080 2.00e-02 2.50e+03 pdb=" CZ ARG A 144 " 0.105 2.00e-02 2.50e+03 pdb=" NH1 ARG A 144 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG A 144 " -0.014 2.00e-02 2.50e+03 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 736 2.80 - 3.32: 8951 3.32 - 3.85: 13296 3.85 - 4.37: 16095 4.37 - 4.90: 25838 Nonbonded interactions: 64916 Sorted by model distance: nonbonded pdb=" C VAL R 64 " pdb=" CG1 VAL R 64 " model vdw 2.273 2.952 nonbonded pdb=" O GLN R 98 " pdb=" N VAL R 101 " model vdw 2.307 3.120 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.373 3.040 nonbonded pdb=" OD2 ASP R 149 " pdb=" ND2 ASN R 240 " model vdw 2.373 3.120 nonbonded pdb=" C SER R 99 " pdb=" OG SER R 99 " model vdw 2.425 2.616 ... (remaining 64911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.860 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.017 0.432 8245 Z= 0.974 Angle : 2.762 45.962 11207 Z= 1.817 Chirality : 0.179 1.788 1304 Planarity : 0.025 0.479 1420 Dihedral : 18.377 179.507 2906 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 9.83 % Allowed : 12.80 % Favored : 77.37 % Cbeta Deviations : 5.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -3.64 (0.21), residues: 1038 helix: -2.16 (0.19), residues: 478 sheet: -3.53 (0.48), residues: 81 loop : -2.37 (0.24), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.128 0.009 ARG A 100 TYR 0.114 0.010 TYR A 61 PHE 0.085 0.010 PHE A 95 TRP 0.088 0.010 TRP B 99 HIS 0.040 0.008 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.01737 / 0.97 ( 8245) covalent geometry : angle 2.76240 / 1.82 (11207) hydrogen bonds : bond 0.22090 / 14.19 ( 427) hydrogen bonds : angle 8.72068 / 6.53 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 261 time to evaluate : 0.299 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8636 (m-30) cc_final: 0.8404 (t70) REVERT: A 26 ASP cc_start: 0.9374 (m-30) cc_final: 0.8664 (m-30) REVERT: A 105 ARG cc_start: 0.9699 (mtm180) cc_final: 0.9477 (mtm-85) REVERT: A 130 LEU cc_start: 0.9503 (mt) cc_final: 0.9254 (mt) REVERT: A 160 ASP cc_start: 0.8817 (p0) cc_final: 0.8319 (t0) REVERT: A 181 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7520 (p) REVERT: A 188 HIS cc_start: 0.7557 (m90) cc_final: 0.6382 (m-70) REVERT: A 229 ASP cc_start: 0.7979 (p0) cc_final: 0.7642 (p0) REVERT: A 243 MET cc_start: 0.8177 (mmt) cc_final: 0.7874 (mmt) REVERT: A 256 ASN cc_start: 0.7909 (t0) cc_final: 0.7541 (t0) REVERT: B 3 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8942 (tm-30) REVERT: B 137 ARG cc_start: 0.8318 (mmm160) cc_final: 0.8040 (mmm160) REVERT: B 170 ASP cc_start: 0.8525 (t70) cc_final: 0.8269 (t0) REVERT: B 178 THR cc_start: 0.9244 (m) cc_final: 0.9018 (p) REVERT: B 227 SER cc_start: 0.8549 (t) cc_final: 0.8196 (p) REVERT: B 266 HIS cc_start: 0.8300 (t-90) cc_final: 0.7944 (t-90) REVERT: B 275 SER cc_start: 0.9099 (t) cc_final: 0.8522 (p) REVERT: B 304 ARG cc_start: 0.9125 (ttp-170) cc_final: 0.8723 (tpp80) REVERT: C 13 ARG cc_start: 0.9530 (mtm180) cc_final: 0.9255 (mtt180) REVERT: C 47 GLU cc_start: 0.8479 (pt0) cc_final: 0.7895 (pp20) REVERT: R 61 TYR cc_start: 0.7887 (m-80) cc_final: 0.7439 (p90) REVERT: R 97 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4633 (mp) REVERT: R 131 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7066 (m170) REVERT: R 136 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8922 (t80) REVERT: R 144 TYR cc_start: 0.8485 (t80) cc_final: 0.8248 (t80) REVERT: R 201 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8396 (m) REVERT: R 207 MET cc_start: 0.9095 (mmt) cc_final: 0.8219 (mmm) REVERT: R 237 ILE cc_start: 0.8139 (mp) cc_final: 0.7855 (mm) REVERT: R 244 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8168 (m) REVERT: R 252 ILE cc_start: 0.9058 (tt) cc_final: 0.8647 (tt) REVERT: R 312 PHE cc_start: 0.9130 (t80) cc_final: 0.8898 (t80) REVERT: R 339 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.7094 (p90) REVERT: R 345 PHE cc_start: 0.9448 (t80) cc_final: 0.9144 (t80) outliers start: 83 outliers final: 25 residues processed: 320 average time/residue: 0.0960 time to fit residues: 40.2565 Evaluate side-chains 214 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 50 PRO Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.0050 chunk 61 optimal weight: 7.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 294 ASN B 13 GLN B 91 HIS B 295 ASN B 340 ASN C 18 GLN R 102 HIS R 104 HIS R 131 HIS R 172 HIS R 217 GLN R 218 HIS R 261 ASN ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.092503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075917 restraints weight = 30456.203| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 4.64 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8245 Z= 0.197 Angle : 0.823 12.009 11207 Z= 0.431 Chirality : 0.048 0.188 1304 Planarity : 0.005 0.073 1420 Dihedral : 12.519 171.074 1215 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.21 % Allowed : 20.38 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.29 (0.25), residues: 1038 helix: 0.48 (0.22), residues: 484 sheet: -2.14 (0.39), residues: 159 loop : -1.92 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.041 0.002 TYR A 74 PHE 0.029 0.002 PHE A 336 TRP 0.017 0.002 TRP B 99 HIS 0.007 0.002 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 ( 8245) covalent geometry : angle 0.82267 / 0.43 (11207) hydrogen bonds : bond 0.05885 / 3.95 ( 427) hydrogen bonds : angle 5.73835 / 4.24 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.335 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9129 (m-30) cc_final: 0.8892 (m-30) REVERT: A 23 LEU cc_start: 0.8972 (mp) cc_final: 0.8729 (mt) REVERT: A 36 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8299 (mt) REVERT: A 88 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7379 (tmm) REVERT: A 186 GLU cc_start: 0.8555 (tt0) cc_final: 0.8210 (tt0) REVERT: A 197 LYS cc_start: 0.8860 (tttp) cc_final: 0.8173 (tttm) REVERT: A 205 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8381 (mtp180) REVERT: A 256 ASN cc_start: 0.7404 (t0) cc_final: 0.7078 (t0) REVERT: A 336 PHE cc_start: 0.7843 (t80) cc_final: 0.7592 (t80) REVERT: B 8 ARG cc_start: 0.9761 (mtm110) cc_final: 0.9387 (ptp-110) REVERT: B 170 ASP cc_start: 0.8450 (t70) cc_final: 0.8000 (t0) REVERT: B 188 MET cc_start: 0.7983 (mmm) cc_final: 0.7644 (mtp) REVERT: B 227 SER cc_start: 0.8001 (t) cc_final: 0.7607 (p) REVERT: B 266 HIS cc_start: 0.7922 (t-90) cc_final: 0.7277 (t70) REVERT: B 275 SER cc_start: 0.8272 (t) cc_final: 0.7448 (p) REVERT: B 304 ARG cc_start: 0.8637 (ttp-170) cc_final: 0.8370 (tpp80) REVERT: L 12 ILE cc_start: 0.9202 (mm) cc_final: 0.8707 (mm) REVERT: R 131 HIS cc_start: 0.7633 (OUTLIER) cc_final: 0.6536 (m-70) REVERT: R 207 MET cc_start: 0.8040 (mmt) cc_final: 0.7525 (mmp) REVERT: R 252 ILE cc_start: 0.8853 (tt) cc_final: 0.8196 (tt) REVERT: R 312 PHE cc_start: 0.8613 (t80) cc_final: 0.7915 (t80) REVERT: R 313 VAL cc_start: 0.8651 (t) cc_final: 0.8097 (p) REVERT: R 325 MET cc_start: 0.8650 (tmm) cc_final: 0.8130 (tmm) REVERT: R 339 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6191 (p90) outliers start: 44 outliers final: 18 residues processed: 205 average time/residue: 0.0917 time to fit residues: 24.8909 Evaluate side-chains 171 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 11 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS A 106 GLN B 295 ASN ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.092319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075895 restraints weight = 30423.455| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.62 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8245 Z= 0.164 Angle : 0.743 11.671 11207 Z= 0.383 Chirality : 0.045 0.189 1304 Planarity : 0.004 0.038 1420 Dihedral : 10.598 161.842 1171 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.38 % Allowed : 21.09 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.60 (0.26), residues: 1038 helix: 1.15 (0.23), residues: 488 sheet: -1.82 (0.38), residues: 172 loop : -1.74 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 148 TYR 0.030 0.002 TYR A 74 PHE 0.020 0.002 PHE R 312 TRP 0.035 0.002 TRP B 332 HIS 0.019 0.002 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 8245) covalent geometry : angle 0.74278 / 0.38 (11207) hydrogen bonds : bond 0.04683 / 3.17 ( 427) hydrogen bonds : angle 5.34073 / 3.93 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7088 (mt-10) REVERT: A 35 LYS cc_start: 0.9097 (mttp) cc_final: 0.8868 (mttm) REVERT: A 197 LYS cc_start: 0.8755 (tttp) cc_final: 0.8318 (tttt) REVERT: A 207 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: A 320 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7405 (m-10) REVERT: B 3 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: B 12 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8889 (mp0) REVERT: B 47 THR cc_start: 0.8971 (m) cc_final: 0.8656 (t) REVERT: B 59 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: B 170 ASP cc_start: 0.8515 (t70) cc_final: 0.8010 (t0) REVERT: B 266 HIS cc_start: 0.7947 (t-90) cc_final: 0.7502 (t-90) REVERT: B 275 SER cc_start: 0.8266 (t) cc_final: 0.7277 (p) REVERT: B 304 ARG cc_start: 0.8591 (ttp-170) cc_final: 0.8330 (tpp80) REVERT: B 311 HIS cc_start: 0.6708 (m-70) cc_final: 0.6446 (m-70) REVERT: B 325 MET cc_start: 0.8035 (tpp) cc_final: 0.7733 (tpp) REVERT: C 13 ARG cc_start: 0.9244 (mtm180) cc_final: 0.8922 (mtt180) REVERT: C 21 MET cc_start: 0.8509 (tmm) cc_final: 0.8269 (tmm) REVERT: L 12 ILE cc_start: 0.9105 (mm) cc_final: 0.8723 (mm) REVERT: R 108 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9045 (tt) REVERT: R 120 MET cc_start: 0.7781 (mmt) cc_final: 0.7389 (mmm) REVERT: R 131 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.6505 (m-70) REVERT: R 151 CYS cc_start: 0.9278 (m) cc_final: 0.9034 (p) REVERT: R 177 LYS cc_start: 0.9290 (mtmm) cc_final: 0.8907 (mtmm) REVERT: R 207 MET cc_start: 0.7788 (mmt) cc_final: 0.7283 (mmp) REVERT: R 312 PHE cc_start: 0.8741 (t80) cc_final: 0.8466 (t80) REVERT: R 339 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6290 (p90) outliers start: 37 outliers final: 15 residues processed: 199 average time/residue: 0.0940 time to fit residues: 24.5225 Evaluate side-chains 171 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 72 optimal weight: 0.1980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.0030 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN R 104 HIS ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.093046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.076449 restraints weight = 30721.019| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 4.68 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8245 Z= 0.136 Angle : 0.716 11.898 11207 Z= 0.362 Chirality : 0.043 0.160 1304 Planarity : 0.004 0.032 1420 Dihedral : 10.138 156.683 1168 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.50 % Allowed : 20.73 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.27), residues: 1038 helix: 1.44 (0.24), residues: 483 sheet: -1.43 (0.39), residues: 176 loop : -1.67 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 322 TYR 0.028 0.002 TYR R 354 PHE 0.021 0.001 PHE A 336 TRP 0.050 0.002 TRP B 332 HIS 0.014 0.002 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 8245) covalent geometry : angle 0.71612 / 0.36 (11207) hydrogen bonds : bond 0.04186 / 2.88 ( 427) hydrogen bonds : angle 5.09471 / 3.72 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.249 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7495 (m-30) cc_final: 0.5022 (m-30) REVERT: A 186 GLU cc_start: 0.8330 (tt0) cc_final: 0.8055 (tt0) REVERT: A 197 LYS cc_start: 0.8609 (tttp) cc_final: 0.7871 (tttm) REVERT: A 240 MET cc_start: 0.8082 (tpp) cc_final: 0.7324 (tpp) REVERT: A 320 TYR cc_start: 0.7746 (m-10) cc_final: 0.7417 (m-10) REVERT: B 3 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: B 47 THR cc_start: 0.8922 (m) cc_final: 0.8686 (t) REVERT: B 59 TYR cc_start: 0.8382 (m-80) cc_final: 0.8123 (m-80) REVERT: B 170 ASP cc_start: 0.8598 (t70) cc_final: 0.8009 (t0) REVERT: B 198 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8519 (mp) REVERT: B 266 HIS cc_start: 0.7987 (t-90) cc_final: 0.7534 (t-90) REVERT: B 304 ARG cc_start: 0.8599 (ttp-170) cc_final: 0.8310 (tpp80) REVERT: B 325 MET cc_start: 0.7842 (tpp) cc_final: 0.7088 (tpp) REVERT: B 340 ASN cc_start: 0.6195 (OUTLIER) cc_final: 0.4553 (t0) REVERT: C 13 ARG cc_start: 0.9255 (mtm180) cc_final: 0.8839 (mtm-85) REVERT: L 12 ILE cc_start: 0.8946 (mm) cc_final: 0.8619 (mm) REVERT: R 120 MET cc_start: 0.7883 (mmt) cc_final: 0.7449 (mmm) REVERT: R 131 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.6564 (m-70) REVERT: R 177 LYS cc_start: 0.9259 (mtmm) cc_final: 0.8875 (mtmm) REVERT: R 207 MET cc_start: 0.7722 (mmt) cc_final: 0.7358 (tpp) REVERT: R 312 PHE cc_start: 0.8717 (t80) cc_final: 0.8415 (t80) REVERT: R 325 MET cc_start: 0.8042 (tmm) cc_final: 0.7725 (tmm) REVERT: R 339 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.5778 (p90) REVERT: R 356 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8515 (p) outliers start: 38 outliers final: 19 residues processed: 197 average time/residue: 0.0970 time to fit residues: 24.8933 Evaluate side-chains 165 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN R 240 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.092517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.076171 restraints weight = 30810.209| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.74 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8245 Z= 0.147 Angle : 0.713 11.753 11207 Z= 0.364 Chirality : 0.043 0.150 1304 Planarity : 0.004 0.031 1420 Dihedral : 9.753 155.072 1165 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.79 % Allowed : 22.16 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.27), residues: 1038 helix: 1.40 (0.24), residues: 491 sheet: -1.23 (0.40), residues: 176 loop : -1.77 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 100 TYR 0.021 0.002 TYR A 74 PHE 0.015 0.001 PHE A 336 TRP 0.056 0.002 TRP B 332 HIS 0.013 0.002 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 8245) covalent geometry : angle 0.71303 / 0.36 (11207) hydrogen bonds : bond 0.04003 / 2.78 ( 427) hydrogen bonds : angle 4.99674 / 3.64 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.9006 (mttm) cc_final: 0.8785 (mmtm) REVERT: A 240 MET cc_start: 0.8270 (tpp) cc_final: 0.7564 (tpp) REVERT: A 320 TYR cc_start: 0.7764 (m-10) cc_final: 0.7379 (m-10) REVERT: B 12 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: B 59 TYR cc_start: 0.8436 (m-80) cc_final: 0.8117 (m-80) REVERT: B 89 LYS cc_start: 0.9263 (mtmm) cc_final: 0.8767 (mtpp) REVERT: B 170 ASP cc_start: 0.8588 (t70) cc_final: 0.8102 (t0) REVERT: B 183 HIS cc_start: 0.5599 (OUTLIER) cc_final: 0.5338 (t-90) REVERT: B 198 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8483 (mp) REVERT: B 230 ASN cc_start: 0.8435 (m-40) cc_final: 0.7914 (t0) REVERT: B 266 HIS cc_start: 0.8003 (t-90) cc_final: 0.7547 (t-90) REVERT: B 304 ARG cc_start: 0.8621 (ttp-170) cc_final: 0.8293 (tpp80) REVERT: B 325 MET cc_start: 0.8007 (tpp) cc_final: 0.7173 (tpp) REVERT: B 340 ASN cc_start: 0.6246 (OUTLIER) cc_final: 0.4700 (t0) REVERT: L 12 ILE cc_start: 0.8959 (mm) cc_final: 0.8650 (mm) REVERT: R 108 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8991 (tt) REVERT: R 120 MET cc_start: 0.7946 (mmt) cc_final: 0.7521 (mmm) REVERT: R 131 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.6773 (m-70) REVERT: R 165 GLU cc_start: 0.8805 (tp30) cc_final: 0.8597 (tp30) REVERT: R 177 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8868 (mtmm) REVERT: R 203 MET cc_start: 0.8718 (tpp) cc_final: 0.8474 (tpp) REVERT: R 207 MET cc_start: 0.7658 (mmt) cc_final: 0.7150 (mmp) REVERT: R 312 PHE cc_start: 0.8765 (t80) cc_final: 0.8379 (t80) REVERT: R 325 MET cc_start: 0.8204 (tmm) cc_final: 0.7950 (tmm) REVERT: R 339 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.5820 (p90) REVERT: R 356 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8397 (p) outliers start: 32 outliers final: 21 residues processed: 185 average time/residue: 0.0990 time to fit residues: 23.8629 Evaluate side-chains 174 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.089798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.073141 restraints weight = 30560.024| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.68 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8245 Z= 0.211 Angle : 0.756 13.089 11207 Z= 0.383 Chirality : 0.044 0.184 1304 Planarity : 0.004 0.033 1420 Dihedral : 9.689 153.055 1165 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.15 % Allowed : 22.75 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.27), residues: 1038 helix: 1.30 (0.23), residues: 485 sheet: -1.35 (0.39), residues: 179 loop : -1.68 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 24 TYR 0.022 0.002 TYR A 74 PHE 0.015 0.002 PHE B 335 TRP 0.038 0.002 TRP B 332 HIS 0.011 0.002 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 ( 8245) covalent geometry : angle 0.75617 / 0.38 (11207) hydrogen bonds : bond 0.04220 / 2.92 ( 427) hydrogen bonds : angle 5.01848 / 3.65 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.9096 (mttm) cc_final: 0.8862 (mmtm) REVERT: A 103 ASP cc_start: 0.6857 (m-30) cc_final: 0.4843 (m-30) REVERT: A 160 ASP cc_start: 0.8873 (p0) cc_final: 0.8362 (t0) REVERT: A 181 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7846 (p) REVERT: A 194 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7700 (mm) REVERT: A 240 MET cc_start: 0.8296 (tpp) cc_final: 0.7654 (tpp) REVERT: A 320 TYR cc_start: 0.7858 (m-10) cc_final: 0.7496 (m-10) REVERT: B 8 ARG cc_start: 0.9812 (mtm110) cc_final: 0.9587 (ptt-90) REVERT: B 59 TYR cc_start: 0.8430 (m-80) cc_final: 0.8002 (m-80) REVERT: B 78 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7382 (mmmt) REVERT: B 89 LYS cc_start: 0.9338 (mtmm) cc_final: 0.8879 (mtpp) REVERT: B 170 ASP cc_start: 0.8535 (t70) cc_final: 0.8064 (t0) REVERT: B 198 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8649 (mp) REVERT: B 230 ASN cc_start: 0.8547 (m-40) cc_final: 0.7915 (t0) REVERT: B 266 HIS cc_start: 0.7965 (t-90) cc_final: 0.7742 (t-90) REVERT: B 304 ARG cc_start: 0.8560 (ttp-170) cc_final: 0.8221 (tpp80) REVERT: B 325 MET cc_start: 0.8055 (tpp) cc_final: 0.7114 (tpp) REVERT: B 340 ASN cc_start: 0.6254 (OUTLIER) cc_final: 0.4882 (t0) REVERT: C 20 LYS cc_start: 0.9632 (mtpp) cc_final: 0.9312 (mmmm) REVERT: L 12 ILE cc_start: 0.8942 (mm) cc_final: 0.8575 (mm) REVERT: R 120 MET cc_start: 0.7957 (mmt) cc_final: 0.7550 (mmm) REVERT: R 131 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.6848 (m-70) REVERT: R 165 GLU cc_start: 0.8882 (tp30) cc_final: 0.8674 (tp30) REVERT: R 177 LYS cc_start: 0.9349 (mtmm) cc_final: 0.8892 (mtmm) REVERT: R 207 MET cc_start: 0.7964 (mmt) cc_final: 0.7367 (tpp) REVERT: R 312 PHE cc_start: 0.8798 (t80) cc_final: 0.8409 (t80) REVERT: R 339 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.5880 (p90) REVERT: R 356 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8606 (p) outliers start: 35 outliers final: 22 residues processed: 174 average time/residue: 0.0989 time to fit residues: 22.5047 Evaluate side-chains 168 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 87 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 141 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.090126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.073383 restraints weight = 30991.969| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.79 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8245 Z= 0.178 Angle : 0.747 12.721 11207 Z= 0.376 Chirality : 0.043 0.168 1304 Planarity : 0.004 0.059 1420 Dihedral : 9.519 151.175 1164 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.44 % Allowed : 23.93 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.27), residues: 1038 helix: 1.29 (0.24), residues: 476 sheet: -1.33 (0.39), residues: 180 loop : -1.59 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.022 0.002 TYR A 74 PHE 0.028 0.002 PHE A 334 TRP 0.027 0.002 TRP B 332 HIS 0.011 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 8245) covalent geometry : angle 0.74689 / 0.38 (11207) hydrogen bonds : bond 0.04054 / 2.80 ( 427) hydrogen bonds : angle 5.03174 / 3.67 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.9148 (mttm) cc_final: 0.8867 (mmtm) REVERT: A 103 ASP cc_start: 0.7008 (m-30) cc_final: 0.5690 (m-30) REVERT: A 160 ASP cc_start: 0.8991 (p0) cc_final: 0.8511 (t0) REVERT: A 181 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 194 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7675 (mm) REVERT: A 240 MET cc_start: 0.8383 (tpp) cc_final: 0.7763 (tpp) REVERT: A 320 TYR cc_start: 0.7803 (m-10) cc_final: 0.7468 (m-10) REVERT: B 59 TYR cc_start: 0.8414 (m-80) cc_final: 0.7831 (m-80) REVERT: B 89 LYS cc_start: 0.9259 (mtmm) cc_final: 0.8846 (mtpp) REVERT: B 137 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8238 (mmm160) REVERT: B 170 ASP cc_start: 0.8555 (t70) cc_final: 0.8092 (t0) REVERT: B 198 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8543 (mt) REVERT: B 230 ASN cc_start: 0.8610 (m-40) cc_final: 0.7899 (t0) REVERT: B 304 ARG cc_start: 0.8619 (ttp-170) cc_final: 0.8230 (tpp80) REVERT: B 325 MET cc_start: 0.8137 (tpp) cc_final: 0.7175 (tpp) REVERT: B 335 PHE cc_start: 0.8125 (m-80) cc_final: 0.7913 (m-80) REVERT: B 340 ASN cc_start: 0.6342 (OUTLIER) cc_final: 0.4890 (t0) REVERT: C 20 LYS cc_start: 0.9634 (mtpp) cc_final: 0.9310 (mmmm) REVERT: L 12 ILE cc_start: 0.8944 (mm) cc_final: 0.8660 (mm) REVERT: R 120 MET cc_start: 0.7957 (mmt) cc_final: 0.7570 (mmm) REVERT: R 131 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.6909 (m-70) REVERT: R 165 GLU cc_start: 0.8848 (tp30) cc_final: 0.8595 (tp30) REVERT: R 177 LYS cc_start: 0.9307 (mtmm) cc_final: 0.8963 (mtmm) REVERT: R 187 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8934 (pttp) REVERT: R 207 MET cc_start: 0.8000 (mmt) cc_final: 0.7227 (mmp) REVERT: R 312 PHE cc_start: 0.8826 (t80) cc_final: 0.8463 (t80) REVERT: R 339 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5724 (p90) REVERT: R 356 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8430 (p) outliers start: 29 outliers final: 20 residues processed: 170 average time/residue: 0.0916 time to fit residues: 20.3257 Evaluate side-chains 166 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 95 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.089855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.073240 restraints weight = 30836.415| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 4.70 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8245 Z= 0.179 Angle : 0.778 12.805 11207 Z= 0.387 Chirality : 0.043 0.167 1304 Planarity : 0.004 0.033 1420 Dihedral : 9.373 149.930 1164 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.15 % Allowed : 23.46 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.27), residues: 1038 helix: 1.27 (0.24), residues: 476 sheet: -1.34 (0.38), residues: 180 loop : -1.55 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 314 TYR 0.021 0.002 TYR A 74 PHE 0.030 0.002 PHE A 334 TRP 0.024 0.002 TRP B 332 HIS 0.011 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 8245) covalent geometry : angle 0.77805 / 0.39 (11207) hydrogen bonds : bond 0.04145 / 2.86 ( 427) hydrogen bonds : angle 5.06424 / 3.70 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.363 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: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.9033 (mttm) cc_final: 0.8800 (mmtm) REVERT: A 160 ASP cc_start: 0.8989 (p0) cc_final: 0.8523 (t0) REVERT: A 181 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7868 (p) REVERT: A 194 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 247 MET cc_start: 0.9109 (mtt) cc_final: 0.8818 (mtm) REVERT: A 320 TYR cc_start: 0.7766 (m-10) cc_final: 0.7463 (m-10) REVERT: B 59 TYR cc_start: 0.8330 (m-80) cc_final: 0.7899 (m-80) REVERT: B 89 LYS cc_start: 0.9265 (mtmm) cc_final: 0.8877 (mtpp) REVERT: B 137 ARG cc_start: 0.8678 (mmm160) cc_final: 0.8266 (mmm160) REVERT: B 160 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 170 ASP cc_start: 0.8560 (t70) cc_final: 0.8133 (t0) REVERT: B 198 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8576 (mt) REVERT: B 266 HIS cc_start: 0.7968 (t-90) cc_final: 0.7043 (t-90) REVERT: B 304 ARG cc_start: 0.8577 (ttp-170) cc_final: 0.8190 (tpp80) REVERT: B 325 MET cc_start: 0.8089 (tpp) cc_final: 0.7335 (tpp) REVERT: B 340 ASN cc_start: 0.6244 (OUTLIER) cc_final: 0.4571 (t0) REVERT: C 20 LYS cc_start: 0.9643 (mtpp) cc_final: 0.9268 (mmmm) REVERT: R 120 MET cc_start: 0.8007 (mmt) cc_final: 0.7591 (mmm) REVERT: R 131 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7203 (m-70) REVERT: R 165 GLU cc_start: 0.8909 (tp30) cc_final: 0.8679 (tp30) REVERT: R 177 LYS cc_start: 0.9294 (mtmm) cc_final: 0.8952 (mtmm) REVERT: R 207 MET cc_start: 0.8044 (mmt) cc_final: 0.7806 (mmm) REVERT: R 296 GLN cc_start: 0.9187 (mm110) cc_final: 0.8887 (pp30) REVERT: R 312 PHE cc_start: 0.8874 (t80) cc_final: 0.8504 (t80) REVERT: R 339 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.5635 (p90) REVERT: R 356 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8471 (p) outliers start: 35 outliers final: 22 residues processed: 183 average time/residue: 0.0943 time to fit residues: 22.8791 Evaluate side-chains 176 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 340 ASP Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 54 optimal weight: 0.0970 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.091731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.074973 restraints weight = 30509.058| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.76 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8245 Z= 0.147 Angle : 0.804 12.865 11207 Z= 0.401 Chirality : 0.044 0.234 1304 Planarity : 0.004 0.034 1420 Dihedral : 9.286 150.552 1164 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.20 % Allowed : 25.59 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.27), residues: 1038 helix: 1.29 (0.24), residues: 472 sheet: -1.28 (0.38), residues: 180 loop : -1.56 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 184 TYR 0.021 0.001 TYR A 74 PHE 0.033 0.001 PHE A 334 TRP 0.070 0.002 TRP B 332 HIS 0.011 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8245) covalent geometry : angle 0.80383 / 0.40 (11207) hydrogen bonds : bond 0.04021 / 2.80 ( 427) hydrogen bonds : angle 5.03257 / 3.69 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.9003 (mttm) cc_final: 0.8784 (mmtm) REVERT: A 129 ARG cc_start: 0.8095 (ptm160) cc_final: 0.7734 (ptm160) REVERT: A 181 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7778 (p) REVERT: A 194 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7791 (mm) REVERT: A 240 MET cc_start: 0.7197 (tpp) cc_final: 0.6883 (tpp) REVERT: A 320 TYR cc_start: 0.7621 (m-10) cc_final: 0.7250 (m-10) REVERT: B 45 MET cc_start: 0.8192 (mtm) cc_final: 0.7928 (mmp) REVERT: B 89 LYS cc_start: 0.9221 (mtmm) cc_final: 0.8810 (mtpp) REVERT: B 137 ARG cc_start: 0.8596 (mmm160) cc_final: 0.8276 (mmm160) REVERT: B 170 ASP cc_start: 0.8525 (t70) cc_final: 0.8092 (t0) REVERT: B 198 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8546 (mt) REVERT: B 266 HIS cc_start: 0.7778 (t-90) cc_final: 0.7475 (t-90) REVERT: B 289 TYR cc_start: 0.7522 (m-80) cc_final: 0.6794 (m-80) REVERT: B 304 ARG cc_start: 0.8554 (ttp-170) cc_final: 0.8205 (tpp80) REVERT: B 325 MET cc_start: 0.8015 (tpp) cc_final: 0.7144 (tpp) REVERT: B 340 ASN cc_start: 0.6186 (OUTLIER) cc_final: 0.4474 (t0) REVERT: C 20 LYS cc_start: 0.9643 (mtpp) cc_final: 0.9269 (mmmm) REVERT: L 12 ILE cc_start: 0.8786 (mm) cc_final: 0.8449 (mm) REVERT: R 120 MET cc_start: 0.7991 (mmt) cc_final: 0.7596 (mmm) REVERT: R 131 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.6951 (m-70) REVERT: R 165 GLU cc_start: 0.8861 (tp30) cc_final: 0.8579 (tp30) REVERT: R 177 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8915 (mtmm) REVERT: R 203 MET cc_start: 0.8533 (tpp) cc_final: 0.8186 (tpp) REVERT: R 296 GLN cc_start: 0.9217 (mm110) cc_final: 0.8874 (pp30) REVERT: R 312 PHE cc_start: 0.8854 (t80) cc_final: 0.8479 (t80) REVERT: R 339 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.5606 (p90) REVERT: R 345 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8872 (t80) REVERT: R 346 TYR cc_start: 0.8924 (t80) cc_final: 0.8699 (t80) REVERT: R 356 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8435 (p) outliers start: 27 outliers final: 16 residues processed: 168 average time/residue: 0.0958 time to fit residues: 20.9421 Evaluate side-chains 166 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 85 optimal weight: 0.0670 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 overall best weight: 2.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.091826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.075333 restraints weight = 30427.155| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.75 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8245 Z= 0.162 Angle : 0.863 16.324 11207 Z= 0.425 Chirality : 0.044 0.235 1304 Planarity : 0.004 0.061 1420 Dihedral : 9.163 149.852 1164 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.08 % Allowed : 26.18 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.27), residues: 1038 helix: 1.12 (0.24), residues: 472 sheet: -1.22 (0.38), residues: 180 loop : -1.52 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 105 TYR 0.022 0.001 TYR A 74 PHE 0.032 0.002 PHE A 334 TRP 0.046 0.002 TRP B 332 HIS 0.009 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8245) covalent geometry : angle 0.86284 / 0.43 (11207) hydrogen bonds : bond 0.04065 / 2.86 ( 427) hydrogen bonds : angle 5.06171 / 3.69 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.219 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: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.9014 (mttm) cc_final: 0.8783 (mmtm) REVERT: A 106 GLN cc_start: 0.9454 (tp40) cc_final: 0.8890 (mp10) REVERT: A 119 MET cc_start: 0.4942 (mmp) cc_final: 0.3496 (mmp) REVERT: A 181 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7778 (p) REVERT: A 194 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7798 (mm) REVERT: A 320 TYR cc_start: 0.7605 (m-10) cc_final: 0.7290 (m-10) REVERT: B 45 MET cc_start: 0.8125 (mtm) cc_final: 0.7894 (mmp) REVERT: B 89 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8787 (mtpp) REVERT: B 170 ASP cc_start: 0.8494 (t70) cc_final: 0.8047 (t0) REVERT: B 183 HIS cc_start: 0.5878 (OUTLIER) cc_final: 0.5496 (t-90) REVERT: B 198 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8544 (mt) REVERT: B 266 HIS cc_start: 0.7726 (t-90) cc_final: 0.7440 (t-90) REVERT: B 289 TYR cc_start: 0.7541 (m-80) cc_final: 0.6884 (m-80) REVERT: B 304 ARG cc_start: 0.8541 (ttp-170) cc_final: 0.8198 (tpp80) REVERT: B 325 MET cc_start: 0.8042 (tpp) cc_final: 0.7157 (tpp) REVERT: B 340 ASN cc_start: 0.6214 (OUTLIER) cc_final: 0.4304 (t0) REVERT: C 20 LYS cc_start: 0.9650 (mtpp) cc_final: 0.9278 (mmmm) REVERT: L 12 ILE cc_start: 0.8793 (mm) cc_final: 0.8523 (mm) REVERT: R 120 MET cc_start: 0.7964 (mmt) cc_final: 0.7566 (mmm) REVERT: R 131 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7065 (m-70) REVERT: R 165 GLU cc_start: 0.8858 (tp30) cc_final: 0.8595 (tp30) REVERT: R 177 LYS cc_start: 0.9241 (mtmm) cc_final: 0.8913 (mtmm) REVERT: R 296 GLN cc_start: 0.9212 (mm110) cc_final: 0.8855 (pp30) REVERT: R 312 PHE cc_start: 0.8879 (t80) cc_final: 0.8504 (t80) REVERT: R 339 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.5530 (p90) REVERT: R 345 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8910 (t80) REVERT: R 356 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8596 (p) outliers start: 26 outliers final: 16 residues processed: 166 average time/residue: 0.0986 time to fit residues: 21.2751 Evaluate side-chains 166 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 8.9990 chunk 25 optimal weight: 0.0870 chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.091382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.074842 restraints weight = 30333.363| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.74 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8245 Z= 0.171 Angle : 0.855 12.981 11207 Z= 0.421 Chirality : 0.044 0.225 1304 Planarity : 0.005 0.082 1420 Dihedral : 9.035 148.243 1164 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.08 % Allowed : 25.95 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1038 helix: 1.09 (0.24), residues: 476 sheet: -1.45 (0.37), residues: 190 loop : -1.49 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 8 TYR 0.021 0.001 TYR A 74 PHE 0.033 0.002 PHE A 334 TRP 0.042 0.002 TRP B 332 HIS 0.009 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 8245) covalent geometry : angle 0.85533 / 0.42 (11207) hydrogen bonds : bond 0.04033 / 2.82 ( 427) hydrogen bonds : angle 4.99914 / 3.64 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1393.45 seconds wall clock time: 24 minutes 47.93 seconds (1487.93 seconds total)