Starting phenix.real_space_refine on Mon May 12 08:25:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j22_35942/05_2025/8j22_35942_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j22_35942/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j22_35942/05_2025/8j22_35942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j22_35942/05_2025/8j22_35942.map" model { file = "/net/cci-nas-00/data/ceres_data/8j22_35942/05_2025/8j22_35942_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j22_35942/05_2025/8j22_35942_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} 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: 5.42, per 1000 atoms: 0.61 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: 2.10 Conformation dependent library (CDL) restraints added in 904.7 milliseconds 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: 0.87 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: 2.30 Time building geometry restraints manager: 2.38 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: 1.010 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- 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 : 7.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (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 TRP 0.015 0.001 TRP C 75 HIS 0.002 0.000 HIS F 35 PHE 0.020 0.001 PHE C 197 TYR 0.007 0.001 TYR F 221 ARG 0.007 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.23954 ( 423) hydrogen bonds : angle 7.16797 ( 1215) SS BOND : bond 0.00294 ( 2) SS BOND : angle 1.16860 ( 4) covalent geometry : bond 0.00308 ( 9049) covalent geometry : angle 0.64402 (12274) *********************** 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 : 0.983 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: 0.2344 time to fit residues: 51.2811 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 : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.137037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119678 restraints weight = 12765.855| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.78 r_work: 0.3394 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 9051 Z= 0.174 Angle : 0.621 16.569 12278 Z= 0.326 Chirality : 0.044 0.305 1391 Planarity : 0.004 0.065 1552 Dihedral : 4.534 45.617 1255 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 3.14 % Allowed : 28.45 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.86 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1116 helix: 2.10 (0.26), residues: 398 sheet: 1.16 (0.31), residues: 303 loop : -0.58 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 47 HIS 0.004 0.001 HIS A 89 PHE 0.014 0.002 PHE A 239 TYR 0.013 0.001 TYR F 50 ARG 0.006 0.001 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 423) hydrogen bonds : angle 4.83554 ( 1215) SS BOND : bond 0.00627 ( 2) SS BOND : angle 1.46687 ( 4) covalent geometry : bond 0.00397 ( 9049) covalent geometry : angle 0.62042 (12274) *********************** 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: 30 poor density : 178 time to evaluate : 0.965 Fit side-chains REVERT: A 98 VAL cc_start: 0.8116 (m) cc_final: 0.7827 (p) REVERT: B 29 LYS cc_start: 0.8167 (tttm) cc_final: 0.7860 (ttmm) REVERT: B 35 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8270 (mttm) REVERT: C 120 SER cc_start: 0.8141 (m) cc_final: 0.7712 (p) REVERT: F 183 SER cc_start: 0.8390 (m) cc_final: 0.8109 (p) REVERT: F 205 LEU cc_start: 0.8180 (mt) cc_final: 0.7855 (mt) outliers start: 30 outliers final: 18 residues processed: 197 average time/residue: 0.2173 time to fit residues: 58.4784 Evaluate side-chains 188 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 253 ILE Chi-restraints excluded: chain B residue 274 PHE 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 91 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain F residue 125 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 0.0070 chunk 101 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 C 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116765 restraints weight = 12972.439| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.83 r_work: 0.3360 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9051 Z= 0.143 Angle : 0.571 16.185 12278 Z= 0.297 Chirality : 0.043 0.274 1391 Planarity : 0.004 0.062 1552 Dihedral : 4.502 31.824 1255 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.14 % Favored : 96.51 % Rotamer: Outliers : 3.56 % Allowed : 28.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1116 helix: 2.17 (0.26), residues: 397 sheet: 0.98 (0.30), residues: 301 loop : -0.65 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.003 0.001 HIS A 89 PHE 0.015 0.002 PHE C 273 TYR 0.010 0.001 TYR F 176 ARG 0.007 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 423) hydrogen bonds : angle 4.46544 ( 1215) SS BOND : bond 0.00462 ( 2) SS BOND : angle 1.30034 ( 4) covalent geometry : bond 0.00326 ( 9049) covalent geometry : angle 0.57043 (12274) *********************** 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 216 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.905 Fit side-chains REVERT: A 98 VAL cc_start: 0.8297 (m) cc_final: 0.8077 (p) REVERT: B 9 ASP cc_start: 0.7725 (m-30) cc_final: 0.7462 (m-30) REVERT: B 29 LYS cc_start: 0.8196 (tttm) cc_final: 0.7882 (ttmm) REVERT: B 35 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8198 (mttm) REVERT: B 182 THR cc_start: 0.6114 (OUTLIER) cc_final: 0.5893 (m) REVERT: B 330 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7578 (mttt) REVERT: C 120 SER cc_start: 0.8213 (m) cc_final: 0.7746 (p) REVERT: F 125 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8455 (p) REVERT: F 183 SER cc_start: 0.8334 (m) cc_final: 0.8054 (p) REVERT: F 205 LEU cc_start: 0.8298 (mt) cc_final: 0.7942 (mt) outliers start: 34 outliers final: 21 residues processed: 203 average time/residue: 0.2139 time to fit residues: 58.7880 Evaluate side-chains 195 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 91 ILE 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 305 VAL 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 C residue 8 SER Chi-restraints excluded: chain C residue 82 CYS 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 131 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 0.5980 chunk 103 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.133813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115755 restraints weight = 12917.580| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.83 r_work: 0.3347 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2283 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= 0.146 Angle : 0.564 15.771 12278 Z= 0.293 Chirality : 0.042 0.294 1391 Planarity : 0.004 0.090 1552 Dihedral : 4.441 30.534 1255 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.67 % Favored : 95.97 % Rotamer: Outliers : 3.87 % Allowed : 28.66 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1116 helix: 2.13 (0.26), residues: 397 sheet: 0.80 (0.30), residues: 301 loop : -0.63 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 134 HIS 0.004 0.001 HIS F 35 PHE 0.014 0.002 PHE A 239 TYR 0.009 0.001 TYR F 101 ARG 0.007 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 423) hydrogen bonds : angle 4.35297 ( 1215) SS BOND : bond 0.00488 ( 2) SS BOND : angle 1.29012 ( 4) covalent geometry : bond 0.00335 ( 9049) covalent geometry : angle 0.56385 (12274) *********************** 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 211 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.085 Fit side-chains REVERT: A 98 VAL cc_start: 0.8278 (m) cc_final: 0.8043 (p) REVERT: A 153 ASN cc_start: 0.8258 (t0) cc_final: 0.7922 (t0) REVERT: B 35 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8177 (mttm) REVERT: C 120 SER cc_start: 0.8266 (m) cc_final: 0.7823 (p) REVERT: F 125 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8458 (p) REVERT: F 183 SER cc_start: 0.8314 (m) cc_final: 0.8060 (p) outliers start: 37 outliers final: 27 residues processed: 198 average time/residue: 0.2220 time to fit residues: 59.8396 Evaluate side-chains 194 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 49 LEU Chi-restraints excluded: chain A residue 91 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 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 323 MET 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 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 F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 94 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114515 restraints weight = 12877.843| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.82 r_work: 0.3329 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9051 Z= 0.169 Angle : 0.583 15.573 12278 Z= 0.301 Chirality : 0.043 0.273 1391 Planarity : 0.005 0.088 1552 Dihedral : 4.537 28.961 1255 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 4.81 % Allowed : 28.56 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1116 helix: 2.04 (0.26), residues: 397 sheet: 0.63 (0.29), residues: 302 loop : -0.65 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 47 HIS 0.004 0.001 HIS B 244 PHE 0.014 0.002 PHE C 273 TYR 0.010 0.001 TYR F 176 ARG 0.007 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 423) hydrogen bonds : angle 4.37507 ( 1215) SS BOND : bond 0.00499 ( 2) SS BOND : angle 1.34033 ( 4) covalent geometry : bond 0.00395 ( 9049) covalent geometry : angle 0.58216 (12274) *********************** 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 217 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 1.046 Fit side-chains REVERT: A 98 VAL cc_start: 0.8329 (m) cc_final: 0.8106 (p) REVERT: A 153 ASN cc_start: 0.8400 (t0) cc_final: 0.8096 (t0) REVERT: A 157 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8165 (m) REVERT: B 35 LYS cc_start: 0.8423 (mtmm) cc_final: 0.8197 (mttm) REVERT: B 351 CYS cc_start: 0.7170 (p) cc_final: 0.6941 (m) REVERT: C 120 SER cc_start: 0.8223 (m) cc_final: 0.7771 (p) REVERT: C 229 LEU cc_start: 0.7062 (tp) cc_final: 0.6833 (tp) REVERT: F 105 SER cc_start: -0.0042 (OUTLIER) cc_final: -0.0974 (p) REVERT: F 125 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8469 (p) REVERT: F 183 SER cc_start: 0.8375 (m) cc_final: 0.8089 (p) outliers start: 46 outliers final: 35 residues processed: 202 average time/residue: 0.2219 time to fit residues: 60.9210 Evaluate side-chains 203 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 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 44 VAL 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 F residue 105 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 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113177 restraints weight = 12828.358| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.82 r_work: 0.3316 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9051 Z= 0.204 Angle : 0.612 15.522 12278 Z= 0.316 Chirality : 0.044 0.288 1391 Planarity : 0.005 0.087 1552 Dihedral : 4.732 30.505 1255 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.03 % Favored : 95.61 % Rotamer: Outliers : 4.81 % Allowed : 28.97 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1116 helix: 1.91 (0.26), residues: 401 sheet: 0.54 (0.29), residues: 301 loop : -0.80 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 47 HIS 0.005 0.001 HIS B 244 PHE 0.017 0.002 PHE C 273 TYR 0.011 0.001 TYR A 83 ARG 0.006 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 423) hydrogen bonds : angle 4.43531 ( 1215) SS BOND : bond 0.00552 ( 2) SS BOND : angle 1.46215 ( 4) covalent geometry : bond 0.00481 ( 9049) covalent geometry : angle 0.61127 (12274) *********************** 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 214 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.995 Fit side-chains REVERT: A 98 VAL cc_start: 0.8264 (m) cc_final: 0.8030 (p) REVERT: A 144 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7484 (mm) REVERT: A 153 ASN cc_start: 0.8475 (t0) cc_final: 0.8239 (t0) REVERT: A 157 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8139 (m) REVERT: B 35 LYS cc_start: 0.8414 (mtmm) cc_final: 0.8202 (mttm) REVERT: C 120 SER cc_start: 0.8259 (m) cc_final: 0.7838 (p) REVERT: C 136 MET cc_start: 0.6490 (mmt) cc_final: 0.6253 (mmm) REVERT: C 229 LEU cc_start: 0.7085 (tp) cc_final: 0.6842 (tp) REVERT: F 105 SER cc_start: 0.0170 (OUTLIER) cc_final: -0.0396 (p) REVERT: F 125 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8568 (p) REVERT: F 183 SER cc_start: 0.8361 (m) cc_final: 0.8076 (p) outliers start: 46 outliers final: 34 residues processed: 199 average time/residue: 0.2270 time to fit residues: 60.7886 Evaluate side-chains 204 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 157 THR 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 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 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 44 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 ARG 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 105 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 57 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.132823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114466 restraints weight = 12835.217| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.83 r_work: 0.3324 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- 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: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9051 Z= 0.155 Angle : 0.577 15.337 12278 Z= 0.299 Chirality : 0.043 0.255 1391 Planarity : 0.004 0.084 1552 Dihedral : 4.596 28.779 1255 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.32 % Favored : 96.33 % Rotamer: Outliers : 5.13 % Allowed : 28.66 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1116 helix: 2.00 (0.26), residues: 400 sheet: 0.48 (0.29), residues: 301 loop : -0.79 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 47 HIS 0.003 0.001 HIS A 89 PHE 0.014 0.002 PHE A 149 TYR 0.010 0.001 TYR F 60 ARG 0.007 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 423) hydrogen bonds : angle 4.33943 ( 1215) SS BOND : bond 0.00461 ( 2) SS BOND : angle 1.30718 ( 4) covalent geometry : bond 0.00360 ( 9049) covalent geometry : angle 0.57623 (12274) *********************** 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 217 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.995 Fit side-chains REVERT: A 98 VAL cc_start: 0.8234 (m) cc_final: 0.7997 (p) REVERT: A 144 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7521 (mm) REVERT: A 153 ASN cc_start: 0.8452 (t0) cc_final: 0.8251 (t0) REVERT: A 157 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8182 (m) REVERT: B 9 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: B 35 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8181 (mttm) REVERT: C 120 SER cc_start: 0.8214 (m) cc_final: 0.7756 (p) REVERT: C 206 MET cc_start: 0.8283 (tpp) cc_final: 0.8083 (tpt) REVERT: C 229 LEU cc_start: 0.7078 (tp) cc_final: 0.6828 (tp) REVERT: F 183 SER cc_start: 0.8367 (m) cc_final: 0.8080 (p) outliers start: 49 outliers final: 37 residues processed: 198 average time/residue: 0.2118 time to fit residues: 57.6662 Evaluate side-chains 206 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 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 9 ASP Chi-restraints excluded: chain B residue 49 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 44 VAL 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 184 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 60 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.133067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114766 restraints weight = 12872.294| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.84 r_work: 0.3330 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2940 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= 0.137 Angle : 0.588 15.173 12278 Z= 0.300 Chirality : 0.042 0.239 1391 Planarity : 0.004 0.082 1552 Dihedral : 4.515 28.327 1255 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.58 % Favored : 96.06 % Rotamer: Outliers : 4.50 % Allowed : 29.18 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1116 helix: 2.04 (0.26), residues: 400 sheet: 0.50 (0.29), residues: 301 loop : -0.72 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 134 HIS 0.003 0.001 HIS F 35 PHE 0.013 0.001 PHE C 275 TYR 0.009 0.001 TYR F 60 ARG 0.007 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 423) hydrogen bonds : angle 4.29931 ( 1215) SS BOND : bond 0.00441 ( 2) SS BOND : angle 1.27915 ( 4) covalent geometry : bond 0.00313 ( 9049) covalent geometry : angle 0.58748 (12274) *********************** 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 211 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.923 Fit side-chains REVERT: A 98 VAL cc_start: 0.8214 (m) cc_final: 0.7976 (p) REVERT: A 144 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7492 (mm) REVERT: A 153 ASN cc_start: 0.8487 (t0) cc_final: 0.8245 (t0) REVERT: A 157 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8178 (m) REVERT: B 35 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8183 (mttm) REVERT: C 120 SER cc_start: 0.8242 (m) cc_final: 0.7807 (p) REVERT: C 136 MET cc_start: 0.6059 (mmm) cc_final: 0.5791 (tpp) REVERT: F 183 SER cc_start: 0.8333 (m) cc_final: 0.8056 (p) outliers start: 43 outliers final: 36 residues processed: 193 average time/residue: 0.2133 time to fit residues: 56.2521 Evaluate side-chains 205 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 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 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 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 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 184 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 144 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 58 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.132795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114965 restraints weight = 12789.245| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.80 r_work: 0.3326 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2998 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= 0.128 Angle : 0.571 12.338 12278 Z= 0.290 Chirality : 0.042 0.229 1391 Planarity : 0.004 0.080 1552 Dihedral : 4.488 28.094 1255 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.49 % Favored : 96.24 % Rotamer: Outliers : 4.50 % Allowed : 29.50 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1116 helix: 2.14 (0.26), residues: 397 sheet: 0.52 (0.29), residues: 295 loop : -0.71 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 75 HIS 0.003 0.001 HIS F 35 PHE 0.013 0.001 PHE C 275 TYR 0.008 0.001 TYR F 60 ARG 0.007 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 423) hydrogen bonds : angle 4.22018 ( 1215) SS BOND : bond 0.00419 ( 2) SS BOND : angle 1.22922 ( 4) covalent geometry : bond 0.00291 ( 9049) covalent geometry : angle 0.57044 (12274) *********************** 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 217 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.982 Fit side-chains REVERT: A 98 VAL cc_start: 0.8195 (m) cc_final: 0.7949 (p) REVERT: A 144 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7446 (mm) REVERT: A 153 ASN cc_start: 0.8441 (t0) cc_final: 0.8226 (t0) REVERT: A 157 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8160 (m) REVERT: B 35 LYS cc_start: 0.8423 (mtmm) cc_final: 0.8208 (mttm) REVERT: C 120 SER cc_start: 0.8251 (m) cc_final: 0.7819 (p) REVERT: F 183 SER cc_start: 0.8392 (m) cc_final: 0.8107 (p) outliers start: 43 outliers final: 37 residues processed: 199 average time/residue: 0.2246 time to fit residues: 60.3646 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 : 0.940 ------------------------------------------------------------------------------- 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 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 261 THR Chi-restraints excluded: chain A residue 267 ILE 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 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 8 SER 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 169 THR Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 144 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 86 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 95 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.131477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113191 restraints weight = 12699.225| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.81 r_work: 0.3314 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 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 = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9051 Z= 0.164 Angle : 0.585 10.978 12278 Z= 0.300 Chirality : 0.043 0.187 1391 Planarity : 0.004 0.071 1552 Dihedral : 4.600 28.933 1255 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.88 % Rotamer: Outliers : 4.39 % Allowed : 29.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1116 helix: 1.98 (0.26), residues: 400 sheet: 0.42 (0.29), residues: 301 loop : -0.72 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 47 HIS 0.004 0.001 HIS B 244 PHE 0.015 0.002 PHE A 149 TYR 0.016 0.001 TYR F 221 ARG 0.007 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 423) hydrogen bonds : angle 4.37351 ( 1215) SS BOND : bond 0.00487 ( 2) SS BOND : angle 1.45633 ( 4) covalent geometry : bond 0.00387 ( 9049) covalent geometry : angle 0.58431 (12274) ********************** 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 216 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 98 VAL cc_start: 0.8234 (m) cc_final: 0.7976 (p) REVERT: A 144 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7574 (mm) REVERT: A 153 ASN cc_start: 0.8425 (t0) cc_final: 0.8202 (t0) REVERT: A 157 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8118 (m) REVERT: B 35 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8197 (mttm) REVERT: C 120 SER cc_start: 0.8259 (m) cc_final: 0.7849 (p) REVERT: F 183 SER cc_start: 0.8394 (m) cc_final: 0.8111 (p) outliers start: 42 outliers final: 36 residues processed: 197 average time/residue: 0.2163 time to fit residues: 58.0595 Evaluate side-chains 212 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 267 ILE 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 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 330 LYS Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 74 ARG 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 105 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 104 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 0.0970 chunk 67 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.132370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114062 restraints weight = 12663.451| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.82 r_work: 0.3320 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9051 Z= 0.147 Angle : 0.577 10.277 12278 Z= 0.293 Chirality : 0.042 0.184 1391 Planarity : 0.004 0.078 1552 Dihedral : 4.583 28.573 1255 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.58 % Favored : 96.24 % Rotamer: Outliers : 4.60 % Allowed : 29.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1116 helix: 2.04 (0.26), residues: 400 sheet: 0.40 (0.29), residues: 301 loop : -0.72 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 134 HIS 0.003 0.001 HIS F 35 PHE 0.013 0.002 PHE A 232 TYR 0.012 0.001 TYR F 221 ARG 0.008 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 423) hydrogen bonds : angle 4.34376 ( 1215) SS BOND : bond 0.00448 ( 2) SS BOND : angle 1.40069 ( 4) covalent geometry : bond 0.00345 ( 9049) covalent geometry : angle 0.57645 (12274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5019.43 seconds wall clock time: 87 minutes 35.82 seconds (5255.82 seconds total)