Starting phenix.real_space_refine on Sat May 10 22:49:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfv_61441/05_2025/9jfv_61441.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfv_61441/05_2025/9jfv_61441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jfv_61441/05_2025/9jfv_61441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfv_61441/05_2025/9jfv_61441.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfv_61441/05_2025/9jfv_61441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfv_61441/05_2025/9jfv_61441.cif" } resolution = 2.67 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4473 2.51 5 N 1207 2.21 5 O 1311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7035 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1851 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2526 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 402 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2256 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 12, 'TRANS': 280} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 79 Time building chain proxies: 5.45, per 1000 atoms: 0.77 Number of scatterers: 7035 At special positions: 0 Unit cell: (69.6, 103.2, 138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1311 8.00 N 1207 7.00 C 4473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.25 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: 1.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 46.4% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.529A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.840A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.669A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.717A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.688A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.776A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.666A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.864A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 17 Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.792A pdb=" N LEU R 23 " --> pdb=" O PHE R 19 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 80 removed outlier: 3.960A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix removed outlier: 4.278A pdb=" N PHE R 77 " --> pdb=" O TRP R 73 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS R 80 " --> pdb=" O TYR R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 121 removed outlier: 3.701A pdb=" N CYS R 90 " --> pdb=" O GLY R 86 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA R 118 " --> pdb=" O ASP R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 150 removed outlier: 3.574A pdb=" N SER R 139 " --> pdb=" O VAL R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 176 through 188 removed outlier: 3.598A pdb=" N TRP R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 removed outlier: 3.574A pdb=" N TRP R 194 " --> pdb=" O PHE R 190 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR R 201 " --> pdb=" O MET R 197 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 254 removed outlier: 4.300A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 257 through 275 removed outlier: 4.391A pdb=" N GLU R 261 " --> pdb=" O ASP R 257 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 214 removed outlier: 9.690A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.786A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.677A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.583A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.934A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.370A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.693A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 4.033A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1026 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: 2.16 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2266 1.34 - 1.46: 1204 1.46 - 1.58: 3661 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 7189 Sorted by residual: bond pdb=" N SER R 13 " pdb=" CA SER R 13 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" N PHE R 19 " pdb=" CA PHE R 19 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.41e-02 5.03e+03 1.02e+01 bond pdb=" N ASP R 161 " pdb=" CA ASP R 161 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.18e-02 7.18e+03 8.84e+00 bond pdb=" N ASP R 75 " pdb=" CA ASP R 75 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.76e+00 bond pdb=" N TYR R 163 " pdb=" CA TYR R 163 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.57e+00 ... (remaining 7184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 9488 1.89 - 3.79: 235 3.79 - 5.68: 47 5.68 - 7.58: 12 7.58 - 9.47: 2 Bond angle restraints: 9784 Sorted by residual: angle pdb=" N LEU R 78 " pdb=" CA LEU R 78 " pdb=" C LEU R 78 " ideal model delta sigma weight residual 112.34 105.73 6.61 1.30e+00 5.92e-01 2.59e+01 angle pdb=" CA ASP R 12 " pdb=" C ASP R 12 " pdb=" O ASP R 12 " ideal model delta sigma weight residual 121.05 115.84 5.21 1.05e+00 9.07e-01 2.46e+01 angle pdb=" CA ASN R 82 " pdb=" C ASN R 82 " pdb=" O ASN R 82 " ideal model delta sigma weight residual 121.20 116.09 5.11 1.04e+00 9.25e-01 2.41e+01 angle pdb=" C HIS R 165 " pdb=" CA HIS R 165 " pdb=" CB HIS R 165 " ideal model delta sigma weight residual 110.42 100.95 9.47 1.99e+00 2.53e-01 2.26e+01 angle pdb=" CA TYR R 268 " pdb=" C TYR R 268 " pdb=" O TYR R 268 " ideal model delta sigma weight residual 121.07 115.85 5.22 1.10e+00 8.26e-01 2.25e+01 ... (remaining 9779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 3668 17.00 - 34.00: 398 34.00 - 51.00: 127 51.00 - 68.00: 34 68.00 - 85.00: 7 Dihedral angle restraints: 4234 sinusoidal: 1550 harmonic: 2684 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual -86.00 -149.23 63.23 1 1.00e+01 1.00e-02 5.28e+01 dihedral pdb=" C PHE R 19 " pdb=" N PHE R 19 " pdb=" CA PHE R 19 " pdb=" CB PHE R 19 " ideal model delta harmonic sigma weight residual -122.60 -133.46 10.86 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" C HIS R 165 " pdb=" N HIS R 165 " pdb=" CA HIS R 165 " pdb=" CB HIS R 165 " ideal model delta harmonic sigma weight residual -122.60 -111.78 -10.82 0 2.50e+00 1.60e-01 1.87e+01 ... (remaining 4231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 878 0.055 - 0.109: 198 0.109 - 0.164: 36 0.164 - 0.219: 3 0.219 - 0.273: 3 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CA VAL R 15 " pdb=" N VAL R 15 " pdb=" C VAL R 15 " pdb=" CB VAL R 15 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA HIS R 165 " pdb=" N HIS R 165 " pdb=" C HIS R 165 " pdb=" CB HIS R 165 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PHE R 19 " pdb=" N PHE R 19 " pdb=" C PHE R 19 " pdb=" CB PHE R 19 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1115 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 162 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C ARG R 162 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG R 162 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR R 163 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 20 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO R 21 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 21 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 21 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 166 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C THR R 166 " -0.033 2.00e-02 2.50e+03 pdb=" O THR R 166 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE R 167 " 0.011 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 627 2.74 - 3.28: 7191 3.28 - 3.82: 12079 3.82 - 4.36: 13980 4.36 - 4.90: 23950 Nonbonded interactions: 57827 Sorted by model distance: nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.199 3.040 nonbonded pdb=" NE2 GLN C 18 " pdb=" OE2 GLU C 22 " model vdw 2.223 3.120 nonbonded pdb=" O ARG A 273 " pdb=" ND1 HIS A 347 " model vdw 2.229 3.120 nonbonded pdb=" O GLY R 31 " pdb=" ND2 ASN R 35 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR B 289 " pdb=" NE1 TRP B 297 " model vdw 2.247 3.120 ... (remaining 57822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.750 Find NCS groups from input model: 0.100 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:14.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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 : 0.005 0.216 7191 Z= 0.280 Angle : 0.835 30.242 9788 Z= 0.478 Chirality : 0.048 0.273 1118 Planarity : 0.004 0.049 1258 Dihedral : 16.645 85.005 2490 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.38 % Favored : 94.18 % Rotamer: Outliers : 0.83 % Allowed : 26.41 % Favored : 72.76 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.27), residues: 910 helix: 1.12 (0.27), residues: 381 sheet: -0.48 (0.42), residues: 148 loop : -1.88 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 83 HIS 0.005 0.001 HIS R 165 PHE 0.018 0.002 PHE R 107 TYR 0.016 0.002 TYR R 251 ARG 0.006 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.17584 ( 357) hydrogen bonds : angle 6.30732 ( 1026) SS BOND : bond 0.15274 ( 2) SS BOND : angle 19.49846 ( 4) covalent geometry : bond 0.00417 ( 7189) covalent geometry : angle 0.73636 ( 9784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7347 (p90) cc_final: 0.6985 (p90) REVERT: R 164 ASN cc_start: 0.6253 (OUTLIER) cc_final: 0.6021 (t0) outliers start: 6 outliers final: 1 residues processed: 123 average time/residue: 0.9185 time to fit residues: 120.8419 Evaluate side-chains 118 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain R residue 164 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 347 HIS A 367 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.195275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.180004 restraints weight = 9776.276| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 1.53 r_work: 0.4265 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4147 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7191 Z= 0.200 Angle : 0.638 7.245 9788 Z= 0.346 Chirality : 0.045 0.222 1118 Planarity : 0.004 0.052 1258 Dihedral : 5.199 54.466 991 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.05 % Favored : 94.84 % Rotamer: Outliers : 4.68 % Allowed : 22.42 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.27), residues: 910 helix: 1.07 (0.27), residues: 381 sheet: -0.43 (0.43), residues: 150 loop : -1.82 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.004 0.001 HIS A 352 PHE 0.023 0.002 PHE R 107 TYR 0.013 0.002 TYR R 102 ARG 0.004 0.001 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.05880 ( 357) hydrogen bonds : angle 5.10847 ( 1026) SS BOND : bond 0.00190 ( 2) SS BOND : angle 2.23730 ( 4) covalent geometry : bond 0.00439 ( 7189) covalent geometry : angle 0.63658 ( 9784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7536 (p90) cc_final: 0.7035 (p90) REVERT: B 232 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7807 (tt) REVERT: R 48 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: R 115 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6826 (mtt180) REVERT: R 146 LEU cc_start: 0.7715 (mm) cc_final: 0.7480 (mt) outliers start: 34 outliers final: 18 residues processed: 135 average time/residue: 0.8954 time to fit residues: 129.5984 Evaluate side-chains 136 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 48 GLN Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 278 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 55 optimal weight: 0.6980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS B 17 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.196350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.181292 restraints weight = 9936.906| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 1.53 r_work: 0.4276 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4158 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7191 Z= 0.161 Angle : 0.585 6.481 9788 Z= 0.316 Chirality : 0.043 0.221 1118 Planarity : 0.004 0.050 1258 Dihedral : 4.922 53.336 989 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 6.05 % Allowed : 22.56 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.27), residues: 910 helix: 1.22 (0.27), residues: 383 sheet: -0.28 (0.43), residues: 138 loop : -1.90 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 63 HIS 0.004 0.001 HIS A 352 PHE 0.018 0.002 PHE R 107 TYR 0.013 0.002 TYR R 102 ARG 0.003 0.000 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.05291 ( 357) hydrogen bonds : angle 4.86835 ( 1026) SS BOND : bond 0.00058 ( 2) SS BOND : angle 0.78099 ( 4) covalent geometry : bond 0.00343 ( 7189) covalent geometry : angle 0.58533 ( 9784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7460 (p90) cc_final: 0.6980 (p90) REVERT: B 232 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7805 (tt) REVERT: B 234 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: R 115 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6842 (mtt180) REVERT: R 146 LEU cc_start: 0.7641 (mm) cc_final: 0.7409 (mt) outliers start: 44 outliers final: 21 residues processed: 140 average time/residue: 0.9767 time to fit residues: 146.5508 Evaluate side-chains 136 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 278 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 87 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 347 HIS B 88 ASN ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.196386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.181073 restraints weight = 10010.668| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 1.57 r_work: 0.4272 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7191 Z= 0.160 Angle : 0.577 5.825 9788 Z= 0.312 Chirality : 0.043 0.223 1118 Planarity : 0.004 0.050 1258 Dihedral : 4.879 52.291 989 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % Rotamer: Outliers : 5.09 % Allowed : 23.80 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 910 helix: 1.33 (0.27), residues: 383 sheet: -0.43 (0.43), residues: 143 loop : -1.89 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 63 HIS 0.003 0.001 HIS A 352 PHE 0.018 0.002 PHE R 107 TYR 0.012 0.002 TYR R 102 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.05146 ( 357) hydrogen bonds : angle 4.77120 ( 1026) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.50070 ( 4) covalent geometry : bond 0.00342 ( 7189) covalent geometry : angle 0.57743 ( 9784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7433 (p90) cc_final: 0.6956 (p90) REVERT: B 222 PHE cc_start: 0.5769 (OUTLIER) cc_final: 0.5554 (m-80) REVERT: B 234 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: R 115 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6830 (mtt180) REVERT: R 146 LEU cc_start: 0.7671 (mm) cc_final: 0.7443 (mt) outliers start: 37 outliers final: 24 residues processed: 137 average time/residue: 0.8410 time to fit residues: 123.8865 Evaluate side-chains 146 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 278 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 79 optimal weight: 0.0770 chunk 57 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 347 HIS ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.197347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.182410 restraints weight = 9891.928| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 1.52 r_work: 0.4291 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4174 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7191 Z= 0.138 Angle : 0.556 5.633 9788 Z= 0.299 Chirality : 0.043 0.220 1118 Planarity : 0.004 0.049 1258 Dihedral : 4.793 50.577 989 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.60 % Rotamer: Outliers : 6.05 % Allowed : 23.93 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.24 (0.28), residues: 910 helix: 1.55 (0.27), residues: 378 sheet: -0.34 (0.43), residues: 143 loop : -1.87 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 63 HIS 0.003 0.001 HIS R 269 PHE 0.015 0.002 PHE R 107 TYR 0.012 0.002 TYR R 251 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 357) hydrogen bonds : angle 4.61032 ( 1026) SS BOND : bond 0.00049 ( 2) SS BOND : angle 0.40141 ( 4) covalent geometry : bond 0.00292 ( 7189) covalent geometry : angle 0.55643 ( 9784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7404 (p90) cc_final: 0.6908 (p90) REVERT: B 222 PHE cc_start: 0.5753 (OUTLIER) cc_final: 0.5548 (m-80) REVERT: B 234 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: R 48 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6799 (mp10) REVERT: R 115 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6723 (mtt180) REVERT: R 146 LEU cc_start: 0.7607 (mm) cc_final: 0.7379 (mt) outliers start: 44 outliers final: 25 residues processed: 138 average time/residue: 0.8453 time to fit residues: 125.4391 Evaluate side-chains 145 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 48 GLN Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 278 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 347 HIS ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.194772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.179546 restraints weight = 9812.769| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 1.54 r_work: 0.4254 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7191 Z= 0.204 Angle : 0.623 5.844 9788 Z= 0.338 Chirality : 0.046 0.240 1118 Planarity : 0.004 0.048 1258 Dihedral : 5.040 52.303 989 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.82 % Favored : 94.07 % Rotamer: Outliers : 6.05 % Allowed : 24.76 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.28), residues: 910 helix: 1.28 (0.27), residues: 382 sheet: -0.39 (0.43), residues: 143 loop : -1.99 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 63 HIS 0.004 0.001 HIS R 241 PHE 0.025 0.002 PHE R 107 TYR 0.024 0.002 TYR R 66 ARG 0.004 0.001 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.05744 ( 357) hydrogen bonds : angle 4.85612 ( 1026) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.32163 ( 4) covalent geometry : bond 0.00447 ( 7189) covalent geometry : angle 0.62296 ( 9784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7553 (p90) cc_final: 0.7122 (p90) REVERT: A 305 PHE cc_start: 0.5267 (t80) cc_final: 0.4933 (t80) REVERT: A 373 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.6168 (mm) REVERT: B 59 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.7248 (t80) REVERT: B 61 MET cc_start: 0.7874 (pp-130) cc_final: 0.7393 (ppp) REVERT: B 234 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: B 338 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8113 (mm) REVERT: R 115 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6977 (mtt180) REVERT: R 146 LEU cc_start: 0.7743 (mm) cc_final: 0.7520 (mt) outliers start: 44 outliers final: 25 residues processed: 138 average time/residue: 0.8871 time to fit residues: 132.0468 Evaluate side-chains 144 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 278 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 347 HIS ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.193338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.178121 restraints weight = 10072.502| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 1.65 r_work: 0.4234 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4113 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7191 Z= 0.189 Angle : 0.610 6.524 9788 Z= 0.332 Chirality : 0.045 0.234 1118 Planarity : 0.004 0.048 1258 Dihedral : 5.046 54.065 989 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.50 % Allowed : 25.86 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.27), residues: 910 helix: 1.31 (0.26), residues: 382 sheet: -0.51 (0.43), residues: 145 loop : -2.00 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 63 HIS 0.009 0.001 HIS R 269 PHE 0.022 0.002 PHE R 107 TYR 0.014 0.002 TYR R 251 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.05471 ( 357) hydrogen bonds : angle 4.78303 ( 1026) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.33984 ( 4) covalent geometry : bond 0.00415 ( 7189) covalent geometry : angle 0.61044 ( 9784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7545 (p90) cc_final: 0.7042 (p90) REVERT: A 263 PHE cc_start: 0.4739 (OUTLIER) cc_final: 0.4173 (m-80) REVERT: A 305 PHE cc_start: 0.5238 (t80) cc_final: 0.4878 (t80) REVERT: A 373 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.6150 (mm) REVERT: B 59 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7358 (t80) REVERT: B 61 MET cc_start: 0.7983 (pp-130) cc_final: 0.7399 (ppp) REVERT: B 234 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: B 325 MET cc_start: 0.7122 (mtp) cc_final: 0.6705 (mmt) REVERT: B 338 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8155 (mm) REVERT: R 115 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6937 (mtt180) REVERT: R 146 LEU cc_start: 0.7748 (mm) cc_final: 0.7520 (mt) outliers start: 40 outliers final: 27 residues processed: 132 average time/residue: 0.8455 time to fit residues: 120.0457 Evaluate side-chains 144 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 278 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.0370 chunk 21 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 347 HIS R 80 HIS ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.194128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.178657 restraints weight = 10127.880| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 1.71 r_work: 0.4241 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4120 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7191 Z= 0.165 Angle : 0.588 6.996 9788 Z= 0.318 Chirality : 0.044 0.227 1118 Planarity : 0.004 0.048 1258 Dihedral : 4.950 53.418 989 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.36 % Allowed : 26.13 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.28), residues: 910 helix: 1.41 (0.27), residues: 378 sheet: -0.53 (0.43), residues: 145 loop : -1.98 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 63 HIS 0.005 0.001 HIS R 269 PHE 0.019 0.002 PHE R 107 TYR 0.022 0.002 TYR R 66 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 357) hydrogen bonds : angle 4.68352 ( 1026) SS BOND : bond 0.00059 ( 2) SS BOND : angle 0.42477 ( 4) covalent geometry : bond 0.00357 ( 7189) covalent geometry : angle 0.58769 ( 9784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7458 (p90) cc_final: 0.6951 (p90) REVERT: A 263 PHE cc_start: 0.4708 (OUTLIER) cc_final: 0.4197 (m-80) REVERT: B 59 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7322 (t80) REVERT: B 62 HIS cc_start: 0.8178 (t-170) cc_final: 0.7960 (t-90) REVERT: B 234 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: B 325 MET cc_start: 0.7082 (mtp) cc_final: 0.6684 (mmt) REVERT: R 115 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6912 (mtt180) REVERT: R 146 LEU cc_start: 0.7689 (mm) cc_final: 0.7451 (mt) outliers start: 39 outliers final: 22 residues processed: 132 average time/residue: 0.8266 time to fit residues: 117.3399 Evaluate side-chains 141 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 278 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 77 optimal weight: 0.0570 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 347 HIS ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.194898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.179541 restraints weight = 10221.603| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 1.70 r_work: 0.4250 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4131 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7191 Z= 0.148 Angle : 0.578 8.998 9788 Z= 0.311 Chirality : 0.043 0.223 1118 Planarity : 0.004 0.048 1258 Dihedral : 4.875 53.535 989 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.68 % Allowed : 27.37 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.28), residues: 910 helix: 1.55 (0.27), residues: 379 sheet: -0.51 (0.42), residues: 145 loop : -1.92 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 63 HIS 0.003 0.001 HIS R 269 PHE 0.017 0.002 PHE R 97 TYR 0.016 0.002 TYR R 251 ARG 0.005 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 357) hydrogen bonds : angle 4.58740 ( 1026) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.35736 ( 4) covalent geometry : bond 0.00318 ( 7189) covalent geometry : angle 0.57759 ( 9784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7475 (p90) cc_final: 0.6961 (p90) REVERT: A 263 PHE cc_start: 0.4574 (OUTLIER) cc_final: 0.4132 (m-80) REVERT: A 383 LEU cc_start: 0.7298 (tp) cc_final: 0.7041 (mt) REVERT: B 59 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.7283 (t80) REVERT: B 61 MET cc_start: 0.7829 (pp-130) cc_final: 0.7310 (ppp) REVERT: B 234 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: B 325 MET cc_start: 0.7053 (mtp) cc_final: 0.6680 (mmt) REVERT: R 115 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6858 (mtt180) REVERT: R 146 LEU cc_start: 0.7662 (mm) cc_final: 0.7432 (mt) outliers start: 34 outliers final: 23 residues processed: 133 average time/residue: 0.8382 time to fit residues: 120.1210 Evaluate side-chains 143 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 278 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 0.0050 chunk 86 optimal weight: 0.8980 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 347 HIS B 62 HIS ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.197976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.182918 restraints weight = 10390.563| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 1.68 r_work: 0.4288 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7191 Z= 0.118 Angle : 0.546 8.380 9788 Z= 0.291 Chirality : 0.042 0.215 1118 Planarity : 0.004 0.047 1258 Dihedral : 4.625 51.015 989 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.60 % Rotamer: Outliers : 4.13 % Allowed : 28.47 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.03 (0.28), residues: 910 helix: 1.93 (0.27), residues: 372 sheet: -0.59 (0.41), residues: 154 loop : -1.70 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 63 HIS 0.004 0.001 HIS R 241 PHE 0.017 0.001 PHE B 241 TYR 0.020 0.002 TYR R 66 ARG 0.007 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 357) hydrogen bonds : angle 4.32600 ( 1026) SS BOND : bond 0.00017 ( 2) SS BOND : angle 0.54853 ( 4) covalent geometry : bond 0.00244 ( 7189) covalent geometry : angle 0.54574 ( 9784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7288 (p90) cc_final: 0.6802 (p90) REVERT: A 254 ASN cc_start: 0.7513 (p0) cc_final: 0.7250 (p0) REVERT: A 383 LEU cc_start: 0.7125 (tp) cc_final: 0.6790 (mt) REVERT: B 325 MET cc_start: 0.6978 (mtp) cc_final: 0.6743 (mmt) REVERT: R 146 LEU cc_start: 0.7536 (mm) cc_final: 0.7312 (mt) outliers start: 30 outliers final: 21 residues processed: 131 average time/residue: 0.8673 time to fit residues: 122.2010 Evaluate side-chains 136 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 278 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 8 optimal weight: 0.0050 chunk 73 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.0000 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 347 HIS B 62 HIS ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.198044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.183118 restraints weight = 10156.279| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 1.65 r_work: 0.4287 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4167 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7191 Z= 0.127 Angle : 0.577 10.895 9788 Z= 0.306 Chirality : 0.042 0.215 1118 Planarity : 0.004 0.046 1258 Dihedral : 4.610 50.681 989 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 3.99 % Allowed : 28.75 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.04 (0.28), residues: 910 helix: 1.88 (0.27), residues: 378 sheet: -0.52 (0.42), residues: 154 loop : -1.72 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 63 HIS 0.005 0.001 HIS B 62 PHE 0.022 0.002 PHE A 305 TYR 0.016 0.002 TYR R 251 ARG 0.012 0.001 ARG R 202 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 357) hydrogen bonds : angle 4.32162 ( 1026) SS BOND : bond 0.00020 ( 2) SS BOND : angle 0.43563 ( 4) covalent geometry : bond 0.00271 ( 7189) covalent geometry : angle 0.57695 ( 9784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5832.98 seconds wall clock time: 101 minutes 8.32 seconds (6068.32 seconds total)