Starting phenix.real_space_refine on Sat Aug 23 00:51:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j22_35942/08_2025/8j22_35942_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j22_35942/08_2025/8j22_35942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j22_35942/08_2025/8j22_35942_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j22_35942/08_2025/8j22_35942_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j22_35942/08_2025/8j22_35942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j22_35942/08_2025/8j22_35942.map" } resolution = 3.2 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= 0.001 sd= 0.022 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 S 58 5.16 5 Cl 1 4.86 5 C 5654 2.51 5 N 1505 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8856 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1693 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2285 Classifications: {'peptide': 285} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 269} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1805 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'9UJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8856 At special positions: 0 Unit cell: (116.48, 111.28, 123.76, 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) Cl 1 17.00 S 58 16.00 O 1638 8.00 N 1505 7.00 C 5654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 213.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 38.1% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.575A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.761A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 51' Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.504A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.577A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.591A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.915A pdb=" N ALA B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.546A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 38 removed outlier: 3.820A pdb=" N MET C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Proline residue: C 23 - end of helix removed outlier: 3.585A pdb=" N LEU C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 61 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.524A pdb=" N LYS C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 113 removed outlier: 3.856A pdb=" N CYS C 82 " --> pdb=" O PRO C 78 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 122 through 152 removed outlier: 4.002A pdb=" N GLY C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 188 removed outlier: 3.655A pdb=" N LEU C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 188 through 208 removed outlier: 3.880A pdb=" N THR C 208 " --> pdb=" O TRP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 235 removed outlier: 4.050A pdb=" N LEU C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 249 removed outlier: 4.005A pdb=" N ASN C 239 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS C 242 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 273 removed outlier: 3.685A pdb=" N ASN C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 276 through 291 removed outlier: 4.058A pdb=" N VAL C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 20 Processing helix chain 'D' and resid 25 through 40 Processing helix chain 'D' and resid 41 through 44 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.650A pdb=" N ASP F 90 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'F' and resid 206 through 210 removed outlier: 3.942A pdb=" N VAL F 210 " --> pdb=" O ALA F 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 49 removed outlier: 5.312A pdb=" N THR A 45 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN A 338 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 47 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.717A pdb=" N ALA A 58 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 72 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP A 81 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS A 87 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 103 removed outlier: 7.011A pdb=" N GLY A 113 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS A 101 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA A 111 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TYR A 103 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR A 109 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS A 119 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU A 136 " --> pdb=" O CYS A 119 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 121 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 132 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 149 removed outlier: 3.500A pdb=" N ILE A 155 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 159 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP A 168 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 174 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.977A pdb=" N SER A 187 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 200 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 218 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP A 210 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS A 216 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 232 removed outlier: 4.010A pdb=" N SER A 243 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS A 248 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 261 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 250 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 252 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 257 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.739A pdb=" N GLY A 304 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP A 296 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG A 302 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 191 removed outlier: 9.097A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.503A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 126 through 128 removed outlier: 3.647A pdb=" N VAL F 141 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 197 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 133 through 135 removed outlier: 3.758A pdb=" N GLY F 211 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP F 162 " --> pdb=" O LEU F 174 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2852 1.35 - 1.47: 2285 1.47 - 1.60: 3826 1.60 - 1.72: 3 1.72 - 1.84: 83 Bond restraints: 9049 Sorted by residual: bond pdb=" C13 9UJ C 401 " pdb=" C15 9UJ C 401 " ideal model delta sigma weight residual 1.502 1.588 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C09 9UJ C 401 " pdb=" N07 9UJ C 401 " ideal model delta sigma weight residual 1.483 1.564 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" N08 9UJ C 401 " pdb=" O06 9UJ C 401 " ideal model delta sigma weight residual 1.406 1.334 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C13 9UJ C 401 " pdb=" N07 9UJ C 401 " ideal model delta sigma weight residual 1.366 1.427 -0.061 2.00e-02 2.50e+03 9.38e+00 bond pdb=" C16 9UJ C 401 " pdb="CL01 9UJ C 401 " ideal model delta sigma weight residual 1.756 1.702 0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 9044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.45: 12252 5.45 - 10.89: 17 10.89 - 16.34: 3 16.34 - 21.79: 1 21.79 - 27.24: 1 Bond angle restraints: 12274 Sorted by residual: angle pdb=" C PHE C 73 " pdb=" N ARG C 74 " pdb=" CA ARG C 74 " ideal model delta sigma weight residual 121.70 148.94 -27.24 1.80e+00 3.09e-01 2.29e+02 angle pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta sigma weight residual 119.84 131.77 -11.93 1.25e+00 6.40e-01 9.11e+01 angle pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" C TYR F 221 " ideal model delta sigma weight residual 109.81 129.39 -19.58 2.21e+00 2.05e-01 7.85e+01 angle pdb=" C PRO F 222 " pdb=" CA PRO F 222 " pdb=" CB PRO F 222 " ideal model delta sigma weight residual 111.56 125.73 -14.17 1.65e+00 3.67e-01 7.38e+01 angle pdb=" CA PRO A 234 " pdb=" N PRO A 234 " pdb=" CD PRO A 234 " ideal model delta sigma weight residual 112.00 103.43 8.57 1.40e+00 5.10e-01 3.75e+01 ... (remaining 12269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 4809 23.85 - 47.69: 479 47.69 - 71.54: 62 71.54 - 95.39: 6 95.39 - 119.23: 1 Dihedral angle restraints: 5357 sinusoidal: 2081 harmonic: 3276 Sorted by residual: dihedral pdb=" CA TYR F 221 " pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta harmonic sigma weight residual 180.00 60.77 119.23 0 5.00e+00 4.00e-02 5.69e+02 dihedral pdb=" C TYR F 221 " pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual -122.60 -149.63 27.03 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual 122.80 149.59 -26.79 0 2.50e+00 1.60e-01 1.15e+02 ... (remaining 5354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 1387 0.250 - 0.500: 1 0.500 - 0.750: 0 0.750 - 1.000: 2 1.000 - 1.250: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA TYR F 221 " pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CB TYR F 221 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" CA PHE C 73 " pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CB PHE C 73 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA PRO F 222 " pdb=" N PRO F 222 " pdb=" C PRO F 222 " pdb=" CB PRO F 222 " both_signs ideal model delta sigma weight residual False 2.72 1.91 0.81 2.00e-01 2.50e+01 1.65e+01 ... (remaining 1388 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 233 " -0.084 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO A 234 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 221 " -0.064 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO F 222 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO F 222 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 222 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 275 " -0.014 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C PHE C 275 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE C 275 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 276 " -0.015 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 85 2.60 - 3.18: 6964 3.18 - 3.75: 13761 3.75 - 4.33: 18753 4.33 - 4.90: 31780 Nonbonded interactions: 71343 Sorted by model distance: nonbonded pdb=" OE2 GLU A 258 " pdb=" OG1 THR A 261 " model vdw 2.029 3.040 nonbonded pdb=" O ILE C 16 " pdb=" OG1 THR C 20 " model vdw 2.166 3.040 nonbonded pdb=" O SER A 96 " pdb=" OG SER A 96 " model vdw 2.226 3.040 nonbonded pdb=" O GLN C 148 " pdb=" OG1 THR C 152 " model vdw 2.257 3.040 nonbonded pdb=" O GLN A 73 " pdb=" OG SER A 96 " model vdw 2.271 3.040 ... (remaining 71338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.04 max=1.00 mean=0.99 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: 0.930 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.003 0.113 9051 Z= 0.134 Angle : 0.644 27.235 12278 Z= 0.329 Chirality : 0.061 1.250 1391 Planarity : 0.005 0.122 1552 Dihedral : 17.811 119.232 3241 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.42 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 31.07 % Favored : 68.93 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.86 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 1.17 (0.26), residues: 1116 helix: 1.69 (0.26), residues: 397 sheet: 1.36 (0.32), residues: 298 loop : -0.52 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 47 TYR 0.007 0.001 TYR F 221 PHE 0.020 0.001 PHE C 197 TRP 0.015 0.001 TRP C 75 HIS 0.002 0.000 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9049) covalent geometry : angle 0.64402 (12274) SS BOND : bond 0.00294 ( 2) SS BOND : angle 1.16860 ( 4) hydrogen bonds : bond 0.23954 ( 423) hydrogen bonds : angle 7.16797 ( 1215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6877 (m-30) cc_final: 0.6655 (m-30) REVERT: C 120 SER cc_start: 0.7960 (m) cc_final: 0.7505 (p) REVERT: F 183 SER cc_start: 0.8246 (m) cc_final: 0.7935 (p) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0901 time to fit residues: 20.0497 Evaluate side-chains 153 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 213 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118932 restraints weight = 12897.520| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.77 r_work: 0.3381 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 9051 Z= 0.191 Angle : 0.634 16.673 12278 Z= 0.333 Chirality : 0.045 0.322 1391 Planarity : 0.005 0.065 1552 Dihedral : 4.625 44.702 1255 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 3.35 % Allowed : 28.35 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.86 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 1.27 (0.25), residues: 1116 helix: 2.08 (0.26), residues: 398 sheet: 1.16 (0.31), residues: 301 loop : -0.63 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 217 TYR 0.014 0.001 TYR F 50 PHE 0.015 0.002 PHE A 239 TRP 0.017 0.002 TRP F 47 HIS 0.004 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9049) covalent geometry : angle 0.63312 (12274) SS BOND : bond 0.00635 ( 2) SS BOND : angle 1.53686 ( 4) hydrogen bonds : bond 0.05005 ( 423) hydrogen bonds : angle 4.83191 ( 1215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.374 Fit side-chains REVERT: A 98 VAL cc_start: 0.8153 (m) cc_final: 0.7869 (p) REVERT: A 117 ASN cc_start: 0.7532 (m-40) cc_final: 0.7216 (m-40) REVERT: B 29 LYS cc_start: 0.8162 (tttp) cc_final: 0.7852 (ttmm) REVERT: C 120 SER cc_start: 0.8131 (m) cc_final: 0.7713 (p) REVERT: F 183 SER cc_start: 0.8367 (m) cc_final: 0.8084 (p) outliers start: 32 outliers final: 20 residues processed: 197 average time/residue: 0.1043 time to fit residues: 28.1618 Evaluate side-chains 192 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114745 restraints weight = 12818.154| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.82 r_work: 0.3332 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9051 Z= 0.186 Angle : 0.605 16.103 12278 Z= 0.315 Chirality : 0.045 0.265 1391 Planarity : 0.004 0.061 1552 Dihedral : 4.738 31.139 1255 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 3.87 % Allowed : 27.51 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.86 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 1.04 (0.25), residues: 1116 helix: 1.99 (0.26), residues: 398 sheet: 0.85 (0.30), residues: 302 loop : -0.71 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 217 TYR 0.011 0.001 TYR A 83 PHE 0.019 0.002 PHE C 273 TRP 0.014 0.002 TRP F 47 HIS 0.004 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9049) covalent geometry : angle 0.60481 (12274) SS BOND : bond 0.00545 ( 2) SS BOND : angle 1.48959 ( 4) hydrogen bonds : bond 0.04612 ( 423) hydrogen bonds : angle 4.55634 ( 1215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.341 Fit side-chains REVERT: A 47 ARG cc_start: 0.8307 (mmt-90) cc_final: 0.8083 (mpt180) REVERT: A 98 VAL cc_start: 0.8369 (m) cc_final: 0.8156 (p) REVERT: A 153 ASN cc_start: 0.8318 (t0) cc_final: 0.8002 (t0) REVERT: B 182 THR cc_start: 0.6202 (OUTLIER) cc_final: 0.5978 (m) REVERT: C 120 SER cc_start: 0.8192 (m) cc_final: 0.7737 (p) REVERT: C 175 VAL cc_start: 0.6357 (p) cc_final: 0.6114 (t) REVERT: F 125 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8473 (p) REVERT: F 183 SER cc_start: 0.8329 (m) cc_final: 0.8048 (p) outliers start: 37 outliers final: 24 residues processed: 196 average time/residue: 0.1050 time to fit residues: 27.8035 Evaluate side-chains 193 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114234 restraints weight = 12952.781| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.83 r_work: 0.3328 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9051 Z= 0.178 Angle : 0.593 15.943 12278 Z= 0.308 Chirality : 0.044 0.305 1391 Planarity : 0.005 0.090 1552 Dihedral : 4.688 29.687 1255 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.67 % Favored : 95.97 % Rotamer: Outliers : 4.81 % Allowed : 28.35 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 aren not related in a simple way. whole: 0.91 (0.25), residues: 1116 helix: 1.95 (0.26), residues: 397 sheet: 0.66 (0.29), residues: 302 loop : -0.75 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 217 TYR 0.010 0.001 TYR A 83 PHE 0.017 0.002 PHE C 273 TRP 0.013 0.001 TRP C 134 HIS 0.005 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9049) covalent geometry : angle 0.59227 (12274) SS BOND : bond 0.00535 ( 2) SS BOND : angle 1.39296 ( 4) hydrogen bonds : bond 0.04239 ( 423) hydrogen bonds : angle 4.50367 ( 1215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.331 Fit side-chains REVERT: A 98 VAL cc_start: 0.8209 (m) cc_final: 0.7963 (p) REVERT: A 153 ASN cc_start: 0.8394 (t0) cc_final: 0.8074 (t0) REVERT: B 182 THR cc_start: 0.6472 (OUTLIER) cc_final: 0.6261 (m) REVERT: B 351 CYS cc_start: 0.7165 (p) cc_final: 0.6949 (m) REVERT: C 120 SER cc_start: 0.8254 (m) cc_final: 0.7819 (p) REVERT: F 125 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8481 (p) REVERT: F 183 SER cc_start: 0.8314 (m) cc_final: 0.8030 (p) outliers start: 46 outliers final: 31 residues processed: 203 average time/residue: 0.1060 time to fit residues: 29.1982 Evaluate side-chains 201 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113708 restraints weight = 12815.007| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.79 r_work: 0.3319 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9051 Z= 0.179 Angle : 0.600 16.187 12278 Z= 0.309 Chirality : 0.044 0.280 1391 Planarity : 0.005 0.090 1552 Dihedral : 4.701 29.850 1255 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.58 % Favored : 96.06 % Rotamer: Outliers : 5.02 % Allowed : 28.87 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 aren not related in a simple way. whole: 0.84 (0.25), residues: 1116 helix: 1.91 (0.26), residues: 397 sheet: 0.58 (0.29), residues: 301 loop : -0.77 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 217 TYR 0.010 0.001 TYR F 176 PHE 0.016 0.002 PHE C 273 TRP 0.013 0.001 TRP F 47 HIS 0.004 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9049) covalent geometry : angle 0.59917 (12274) SS BOND : bond 0.00518 ( 2) SS BOND : angle 1.35521 ( 4) hydrogen bonds : bond 0.04143 ( 423) hydrogen bonds : angle 4.51240 ( 1215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.350 Fit side-chains REVERT: A 98 VAL cc_start: 0.8272 (m) cc_final: 0.8027 (p) REVERT: A 144 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7450 (mm) REVERT: A 153 ASN cc_start: 0.8395 (t0) cc_final: 0.8110 (t0) REVERT: A 157 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8140 (m) REVERT: B 351 CYS cc_start: 0.7281 (p) cc_final: 0.7013 (m) REVERT: C 120 SER cc_start: 0.8195 (m) cc_final: 0.7771 (p) REVERT: F 125 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8560 (p) REVERT: F 183 SER cc_start: 0.8357 (m) cc_final: 0.8072 (p) outliers start: 48 outliers final: 36 residues processed: 200 average time/residue: 0.1024 time to fit residues: 28.0074 Evaluate side-chains 203 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.0270 chunk 14 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114651 restraints weight = 12740.487| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.84 r_work: 0.3330 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9051 Z= 0.125 Angle : 0.567 16.021 12278 Z= 0.293 Chirality : 0.042 0.241 1391 Planarity : 0.004 0.088 1552 Dihedral : 4.507 28.589 1255 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.32 % Favored : 96.33 % Rotamer: Outliers : 4.39 % Allowed : 30.02 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 aren not related in a simple way. whole: 0.95 (0.25), residues: 1116 helix: 2.10 (0.26), residues: 397 sheet: 0.55 (0.29), residues: 297 loop : -0.72 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 132 TYR 0.009 0.001 TYR F 176 PHE 0.013 0.001 PHE C 275 TRP 0.012 0.001 TRP C 134 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9049) covalent geometry : angle 0.56680 (12274) SS BOND : bond 0.00425 ( 2) SS BOND : angle 1.22074 ( 4) hydrogen bonds : bond 0.03729 ( 423) hydrogen bonds : angle 4.33673 ( 1215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.335 Fit side-chains REVERT: A 98 VAL cc_start: 0.8188 (m) cc_final: 0.7917 (p) REVERT: A 144 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7305 (mm) REVERT: A 153 ASN cc_start: 0.8389 (t0) cc_final: 0.8090 (t0) REVERT: A 157 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8158 (m) REVERT: A 186 MET cc_start: 0.7749 (mmm) cc_final: 0.7037 (mmm) REVERT: B 351 CYS cc_start: 0.7193 (p) cc_final: 0.6992 (m) REVERT: C 120 SER cc_start: 0.8225 (m) cc_final: 0.7829 (p) REVERT: C 136 MET cc_start: 0.6446 (mmt) cc_final: 0.6215 (mmm) REVERT: F 125 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (p) REVERT: F 183 SER cc_start: 0.8360 (m) cc_final: 0.8078 (p) outliers start: 42 outliers final: 33 residues processed: 195 average time/residue: 0.1142 time to fit residues: 29.7225 Evaluate side-chains 204 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 216 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113671 restraints weight = 12749.735| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.79 r_work: 0.3316 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9051 Z= 0.174 Angle : 0.603 15.772 12278 Z= 0.308 Chirality : 0.044 0.258 1391 Planarity : 0.005 0.085 1552 Dihedral : 4.626 30.077 1255 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.76 % Favored : 95.88 % Rotamer: Outliers : 4.92 % Allowed : 29.39 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 aren not related in a simple way. whole: 0.87 (0.25), residues: 1116 helix: 2.00 (0.26), residues: 400 sheet: 0.47 (0.29), residues: 301 loop : -0.73 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 217 TYR 0.011 0.001 TYR F 101 PHE 0.015 0.002 PHE C 273 TRP 0.012 0.001 TRP F 47 HIS 0.004 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9049) covalent geometry : angle 0.60251 (12274) SS BOND : bond 0.00510 ( 2) SS BOND : angle 1.36551 ( 4) hydrogen bonds : bond 0.03984 ( 423) hydrogen bonds : angle 4.40918 ( 1215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.332 Fit side-chains REVERT: A 98 VAL cc_start: 0.8251 (m) cc_final: 0.8010 (p) REVERT: A 153 ASN cc_start: 0.8475 (t0) cc_final: 0.8227 (t0) REVERT: A 157 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8111 (m) REVERT: C 120 SER cc_start: 0.8203 (m) cc_final: 0.7775 (p) REVERT: C 206 MET cc_start: 0.8324 (tpp) cc_final: 0.7981 (mmm) REVERT: F 183 SER cc_start: 0.8338 (m) cc_final: 0.8057 (p) outliers start: 47 outliers final: 39 residues processed: 202 average time/residue: 0.0970 time to fit residues: 26.9666 Evaluate side-chains 211 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 216 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113782 restraints weight = 12743.268| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.79 r_work: 0.3312 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9051 Z= 0.170 Angle : 0.612 15.627 12278 Z= 0.310 Chirality : 0.043 0.256 1391 Planarity : 0.005 0.083 1552 Dihedral : 4.619 29.687 1255 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.67 % Favored : 95.97 % Rotamer: Outliers : 4.29 % Allowed : 29.81 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 aren not related in a simple way. whole: 0.84 (0.25), residues: 1116 helix: 1.97 (0.26), residues: 400 sheet: 0.44 (0.29), residues: 296 loop : -0.71 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 177 TYR 0.009 0.001 TYR F 60 PHE 0.014 0.002 PHE A 149 TRP 0.013 0.001 TRP C 98 HIS 0.004 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9049) covalent geometry : angle 0.61123 (12274) SS BOND : bond 0.00492 ( 2) SS BOND : angle 1.33691 ( 4) hydrogen bonds : bond 0.03953 ( 423) hydrogen bonds : angle 4.41265 ( 1215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.342 Fit side-chains REVERT: A 98 VAL cc_start: 0.8235 (m) cc_final: 0.7994 (p) REVERT: A 153 ASN cc_start: 0.8442 (t0) cc_final: 0.8223 (t0) REVERT: A 157 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8126 (m) REVERT: C 120 SER cc_start: 0.8225 (m) cc_final: 0.7831 (p) REVERT: C 136 MET cc_start: 0.6211 (mmm) cc_final: 0.5922 (tpp) REVERT: C 206 MET cc_start: 0.8326 (tpp) cc_final: 0.8016 (mmm) REVERT: F 183 SER cc_start: 0.8346 (m) cc_final: 0.8066 (p) outliers start: 41 outliers final: 38 residues processed: 199 average time/residue: 0.0977 time to fit residues: 26.7672 Evaluate side-chains 211 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 0.0170 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114786 restraints weight = 12741.355| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.83 r_work: 0.3329 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9051 Z= 0.128 Angle : 0.581 12.536 12278 Z= 0.293 Chirality : 0.042 0.231 1391 Planarity : 0.004 0.080 1552 Dihedral : 4.536 27.865 1255 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.41 % Favored : 96.33 % Rotamer: Outliers : 4.29 % Allowed : 30.23 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 aren not related in a simple way. whole: 0.91 (0.25), residues: 1116 helix: 2.07 (0.26), residues: 397 sheet: 0.46 (0.29), residues: 296 loop : -0.68 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 217 TYR 0.008 0.001 TYR F 60 PHE 0.012 0.001 PHE C 275 TRP 0.026 0.001 TRP C 75 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9049) covalent geometry : angle 0.58108 (12274) SS BOND : bond 0.00408 ( 2) SS BOND : angle 1.20962 ( 4) hydrogen bonds : bond 0.03645 ( 423) hydrogen bonds : angle 4.32838 ( 1215) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.341 Fit side-chains REVERT: A 98 VAL cc_start: 0.8193 (m) cc_final: 0.7937 (p) REVERT: A 144 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7425 (mm) REVERT: A 153 ASN cc_start: 0.8401 (t0) cc_final: 0.8133 (t0) REVERT: A 157 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8157 (m) REVERT: C 120 SER cc_start: 0.8236 (m) cc_final: 0.7814 (p) REVERT: C 206 MET cc_start: 0.8233 (tpp) cc_final: 0.7905 (mmm) REVERT: F 183 SER cc_start: 0.8353 (m) cc_final: 0.8076 (p) outliers start: 41 outliers final: 35 residues processed: 204 average time/residue: 0.1034 time to fit residues: 28.4106 Evaluate side-chains 215 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 95 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114250 restraints weight = 12702.421| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.81 r_work: 0.3324 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9051 Z= 0.145 Angle : 0.579 11.066 12278 Z= 0.293 Chirality : 0.042 0.183 1391 Planarity : 0.004 0.072 1552 Dihedral : 4.587 28.818 1255 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.67 % Favored : 96.15 % Rotamer: Outliers : 4.60 % Allowed : 30.23 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 aren not related in a simple way. whole: 0.88 (0.25), residues: 1116 helix: 2.02 (0.26), residues: 400 sheet: 0.43 (0.29), residues: 296 loop : -0.68 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 217 TYR 0.017 0.001 TYR F 221 PHE 0.013 0.002 PHE C 275 TRP 0.014 0.001 TRP C 134 HIS 0.004 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9049) covalent geometry : angle 0.57838 (12274) SS BOND : bond 0.00459 ( 2) SS BOND : angle 1.38619 ( 4) hydrogen bonds : bond 0.03745 ( 423) hydrogen bonds : angle 4.34701 ( 1215) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 98 VAL cc_start: 0.8200 (m) cc_final: 0.7967 (p) REVERT: A 144 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7549 (mm) REVERT: A 153 ASN cc_start: 0.8407 (t0) cc_final: 0.8144 (t0) REVERT: A 157 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8146 (m) REVERT: C 120 SER cc_start: 0.8240 (m) cc_final: 0.7826 (p) REVERT: C 206 MET cc_start: 0.8286 (tpp) cc_final: 0.7950 (mmm) REVERT: F 183 SER cc_start: 0.8362 (m) cc_final: 0.8087 (p) outliers start: 44 outliers final: 39 residues processed: 205 average time/residue: 0.1097 time to fit residues: 30.3408 Evaluate side-chains 220 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115267 restraints weight = 12563.562| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.78 r_work: 0.3333 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9051 Z= 0.132 Angle : 0.564 10.607 12278 Z= 0.285 Chirality : 0.042 0.177 1391 Planarity : 0.004 0.079 1552 Dihedral : 4.541 30.158 1255 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.41 % Favored : 96.42 % Rotamer: Outliers : 4.08 % Allowed : 30.54 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.91 (0.25), residues: 1116 helix: 2.07 (0.26), residues: 400 sheet: 0.44 (0.29), residues: 296 loop : -0.69 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 217 TYR 0.011 0.001 TYR F 221 PHE 0.012 0.001 PHE C 275 TRP 0.015 0.001 TRP C 134 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9049) covalent geometry : angle 0.56367 (12274) SS BOND : bond 0.00414 ( 2) SS BOND : angle 1.34628 ( 4) hydrogen bonds : bond 0.03646 ( 423) hydrogen bonds : angle 4.30048 ( 1215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.94 seconds wall clock time: 43 minutes 55.75 seconds (2635.75 seconds total)