Starting phenix.real_space_refine on Wed Sep 17 08:12:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfv_61441/09_2025/9jfv_61441.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfv_61441/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jfv_61441/09_2025/9jfv_61441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfv_61441/09_2025/9jfv_61441.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jfv_61441/09_2025/9jfv_61441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfv_61441/09_2025/9jfv_61441.map" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASP:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 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: {'ARG:plan': 2, 'GLU:plan': 1} 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: {'ARG:plan': 7, 'PHE:plan': 2, 'TRP:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 79 Time building chain proxies: 1.86, per 1000 atoms: 0.26 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: 0.57 Conformation dependent library (CDL) restraints added in 417.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.25 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: 1.03 Time building geometry restraints manager: 0.78 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- 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 : 16.59 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (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 ARG 0.006 0.001 ARG R 160 TYR 0.016 0.002 TYR R 251 PHE 0.018 0.002 PHE R 107 TRP 0.030 0.002 TRP R 83 HIS 0.005 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 7189) covalent geometry : angle 0.73636 ( 9784) SS BOND : bond 0.15274 ( 2) SS BOND : angle 19.49846 ( 4) hydrogen bonds : bond 0.17584 ( 357) hydrogen bonds : angle 6.30732 ( 1026) *********************** 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 : 0.255 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: 0.4860 time to fit residues: 63.7417 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 : 0.251 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.196668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.181228 restraints weight = 10029.110| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 1.57 r_work: 0.4275 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7191 Z= 0.171 Angle : 0.609 7.102 9788 Z= 0.329 Chirality : 0.044 0.218 1118 Planarity : 0.004 0.050 1258 Dihedral : 5.078 54.103 991 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.16 % Rotamer: Outliers : 4.40 % Allowed : 22.56 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.28), residues: 910 helix: 1.19 (0.27), residues: 381 sheet: -0.37 (0.43), residues: 150 loop : -1.78 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 247 TYR 0.012 0.002 TYR R 102 PHE 0.019 0.002 PHE R 107 TRP 0.014 0.002 TRP B 63 HIS 0.004 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 7189) covalent geometry : angle 0.60777 ( 9784) SS BOND : bond 0.00140 ( 2) SS BOND : angle 2.08248 ( 4) hydrogen bonds : bond 0.05422 ( 357) hydrogen bonds : angle 4.99722 ( 1026) *********************** 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 155 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7518 (p90) cc_final: 0.7070 (p90) REVERT: B 232 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7793 (tt) REVERT: R 48 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: R 115 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6827 (mtt180) REVERT: R 146 LEU cc_start: 0.7660 (mm) cc_final: 0.7435 (mt) REVERT: R 164 ASN cc_start: 0.6186 (OUTLIER) cc_final: 0.5975 (t0) outliers start: 32 outliers final: 17 residues processed: 138 average time/residue: 0.4680 time to fit residues: 68.9395 Evaluate side-chains 139 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 222 PHE Chi-restraints excluded: chain B residue 232 ILE 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 164 ASN 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 44 optimal weight: 0.0770 chunk 77 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 ** 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 = 0.4518 r_free = 0.4518 target = 0.197624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.182437 restraints weight = 9938.542| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 1.56 r_work: 0.4292 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4176 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7191 Z= 0.143 Angle : 0.563 6.277 9788 Z= 0.303 Chirality : 0.043 0.212 1118 Planarity : 0.004 0.049 1258 Dihedral : 4.856 52.295 991 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 5.64 % Allowed : 22.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.28), residues: 910 helix: 1.38 (0.27), residues: 383 sheet: -0.17 (0.44), residues: 138 loop : -1.83 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 270 TYR 0.019 0.002 TYR R 66 PHE 0.016 0.002 PHE R 107 TRP 0.029 0.002 TRP B 63 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7189) covalent geometry : angle 0.56271 ( 9784) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.81655 ( 4) hydrogen bonds : bond 0.04908 ( 357) hydrogen bonds : angle 4.73461 ( 1026) *********************** 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: 41 poor density : 119 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7417 (p90) cc_final: 0.6929 (p90) REVERT: B 234 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: R 115 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6723 (mtt180) outliers start: 41 outliers final: 22 residues processed: 139 average time/residue: 0.4468 time to fit residues: 66.3558 Evaluate side-chains 138 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 338 ILE 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 114 CYS 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 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 336 LEU Chi-restraints excluded: chain R residue 105 ILE 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 64 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 79 optimal weight: 0.0070 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 27 optimal weight: 0.0010 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4604 ------------------------------------------------------------------------------- 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 17 GLN ** 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 = 0.4513 r_free = 0.4513 target = 0.197214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.181973 restraints weight = 9999.258| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 1.55 r_work: 0.4284 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4166 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7191 Z= 0.149 Angle : 0.561 5.695 9788 Z= 0.302 Chirality : 0.043 0.220 1118 Planarity : 0.004 0.048 1258 Dihedral : 4.777 51.713 989 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 5.09 % Allowed : 22.83 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.28), residues: 910 helix: 1.54 (0.27), residues: 377 sheet: -0.17 (0.44), residues: 138 loop : -1.80 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 270 TYR 0.013 0.002 TYR R 268 PHE 0.017 0.002 PHE R 107 TRP 0.015 0.002 TRP A 267 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7189) covalent geometry : angle 0.56146 ( 9784) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.47685 ( 4) hydrogen bonds : bond 0.04925 ( 357) hydrogen bonds : angle 4.65361 ( 1026) *********************** 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 155 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7394 (p90) cc_final: 0.6883 (p90) REVERT: B 234 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: R 115 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6740 (mtt180) outliers start: 37 outliers final: 22 residues processed: 135 average time/residue: 0.4434 time to fit residues: 64.1482 Evaluate side-chains 138 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 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 159 PHE Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 83 optimal weight: 0.5980 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 17 GLN R 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.198816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.183671 restraints weight = 9981.672| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 1.54 r_work: 0.4301 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4185 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.1913 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= 0.128 Angle : 0.540 5.603 9788 Z= 0.290 Chirality : 0.042 0.217 1118 Planarity : 0.004 0.047 1258 Dihedral : 4.669 50.157 989 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.60 % Rotamer: Outliers : 6.05 % Allowed : 23.66 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.28), residues: 910 helix: 1.71 (0.27), residues: 377 sheet: -0.43 (0.42), residues: 146 loop : -1.73 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 270 TYR 0.020 0.002 TYR R 66 PHE 0.013 0.002 PHE R 107 TRP 0.037 0.002 TRP B 63 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7189) covalent geometry : angle 0.54017 ( 9784) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.39711 ( 4) hydrogen bonds : bond 0.04458 ( 357) hydrogen bonds : angle 4.51238 ( 1026) *********************** 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 167 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7392 (p90) cc_final: 0.6843 (p90) REVERT: B 234 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: R 48 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6771 (mp10) outliers start: 44 outliers final: 23 residues processed: 145 average time/residue: 0.4457 time to fit residues: 69.2075 Evaluate side-chains 142 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 114 CYS 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 17 GLN ** 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 = 0.4505 r_free = 0.4505 target = 0.196442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.181159 restraints weight = 9943.407| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.55 r_work: 0.4275 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.2019 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= 0.169 Angle : 0.580 5.695 9788 Z= 0.314 Chirality : 0.044 0.228 1118 Planarity : 0.004 0.046 1258 Dihedral : 4.825 51.374 989 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 4.95 % Allowed : 25.72 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.28), residues: 910 helix: 1.55 (0.27), residues: 378 sheet: -0.32 (0.43), residues: 143 loop : -1.80 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 115 TYR 0.014 0.002 TYR R 251 PHE 0.021 0.002 PHE R 107 TRP 0.026 0.002 TRP B 63 HIS 0.004 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7189) covalent geometry : angle 0.58013 ( 9784) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.31746 ( 4) hydrogen bonds : bond 0.05120 ( 357) hydrogen bonds : angle 4.64394 ( 1026) *********************** 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 151 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7518 (p90) cc_final: 0.7036 (p90) REVERT: B 59 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.6359 (t80) REVERT: B 61 MET cc_start: 0.7833 (pp-130) cc_final: 0.7252 (ppp) REVERT: B 234 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7627 (m-80) outliers start: 36 outliers final: 24 residues processed: 129 average time/residue: 0.4127 time to fit residues: 57.4828 Evaluate side-chains 137 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS 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 318 LEU Chi-restraints excluded: chain R residue 15 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 27 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 17 GLN ** 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 = 0.4478 r_free = 0.4478 target = 0.194220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.178705 restraints weight = 10143.032| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 1.69 r_work: 0.4241 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7191 Z= 0.177 Angle : 0.592 5.968 9788 Z= 0.321 Chirality : 0.044 0.231 1118 Planarity : 0.004 0.047 1258 Dihedral : 4.909 54.476 989 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.23 % Allowed : 25.45 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.28), residues: 910 helix: 1.55 (0.27), residues: 371 sheet: -0.46 (0.43), residues: 145 loop : -1.85 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 270 TYR 0.015 0.002 TYR R 251 PHE 0.021 0.002 PHE R 107 TRP 0.021 0.002 TRP B 63 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7189) covalent geometry : angle 0.59192 ( 9784) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.32144 ( 4) hydrogen bonds : bond 0.05254 ( 357) hydrogen bonds : angle 4.67294 ( 1026) *********************** 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 154 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7485 (p90) cc_final: 0.6977 (p90) REVERT: A 253 TYR cc_start: 0.6332 (m-80) cc_final: 0.6125 (m-80) REVERT: A 263 PHE cc_start: 0.4546 (OUTLIER) cc_final: 0.4085 (m-80) REVERT: B 59 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.6375 (t80) REVERT: B 61 MET cc_start: 0.7842 (pp-130) cc_final: 0.7264 (ppp) REVERT: B 234 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7639 (m-80) outliers start: 38 outliers final: 26 residues processed: 132 average time/residue: 0.4173 time to fit residues: 59.3056 Evaluate side-chains 142 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 74 SER 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 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 15 VAL 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 163 TYR 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 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 67 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 26 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 46 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.197980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.182945 restraints weight = 10251.943| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 1.66 r_work: 0.4290 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.2348 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= 0.115 Angle : 0.530 7.898 9788 Z= 0.285 Chirality : 0.042 0.212 1118 Planarity : 0.004 0.046 1258 Dihedral : 4.587 51.360 989 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.68 % Allowed : 27.24 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.28), residues: 910 helix: 1.94 (0.27), residues: 372 sheet: -0.46 (0.43), residues: 148 loop : -1.67 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 270 TYR 0.017 0.001 TYR R 251 PHE 0.014 0.001 PHE B 241 TRP 0.014 0.002 TRP A 271 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7189) covalent geometry : angle 0.53019 ( 9784) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.40897 ( 4) hydrogen bonds : bond 0.04047 ( 357) hydrogen bonds : angle 4.34392 ( 1026) *********************** 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 149 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7288 (p90) cc_final: 0.6746 (p90) REVERT: A 253 TYR cc_start: 0.5989 (m-80) cc_final: 0.5788 (m-80) REVERT: A 383 LEU cc_start: 0.6922 (tp) cc_final: 0.6476 (OUTLIER) REVERT: B 325 MET cc_start: 0.6911 (mtp) cc_final: 0.6630 (mmt) outliers start: 34 outliers final: 25 residues processed: 131 average time/residue: 0.3946 time to fit residues: 55.6706 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 : 0.249 ------------------------------------------------------------------------------- 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 74 SER 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 269 ILE Chi-restraints excluded: chain R residue 15 VAL 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 163 TYR Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 217 GLN 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 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS C 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.193867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178360 restraints weight = 10132.484| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 1.67 r_work: 0.4233 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7191 Z= 0.201 Angle : 0.623 8.947 9788 Z= 0.337 Chirality : 0.046 0.239 1118 Planarity : 0.004 0.046 1258 Dihedral : 4.941 54.612 989 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.40 % Allowed : 27.24 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.28), residues: 910 helix: 1.47 (0.27), residues: 383 sheet: -0.37 (0.43), residues: 145 loop : -1.81 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 115 TYR 0.027 0.002 TYR R 66 PHE 0.024 0.002 PHE A 305 TRP 0.016 0.002 TRP B 332 HIS 0.005 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 7189) covalent geometry : angle 0.62348 ( 9784) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.29141 ( 4) hydrogen bonds : bond 0.05534 ( 357) hydrogen bonds : angle 4.71057 ( 1026) *********************** 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 147 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7538 (p90) cc_final: 0.7007 (p90) REVERT: A 253 TYR cc_start: 0.6285 (m-80) cc_final: 0.6029 (m-80) REVERT: A 263 PHE cc_start: 0.4631 (OUTLIER) cc_final: 0.4104 (m-80) REVERT: A 305 PHE cc_start: 0.5138 (t80) cc_final: 0.4859 (t80) REVERT: A 364 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.5384 (ttp80) REVERT: A 373 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6176 (mm) REVERT: B 59 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6359 (t80) REVERT: B 61 MET cc_start: 0.7846 (pp-130) cc_final: 0.7328 (ppp) REVERT: R 197 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6573 (ttt) outliers start: 32 outliers final: 21 residues processed: 130 average time/residue: 0.4250 time to fit residues: 59.3988 Evaluate side-chains 140 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 A residue 364 ARG Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER 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 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 163 TYR Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 197 MET 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 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS C 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.194526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.179019 restraints weight = 10178.886| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 1.68 r_work: 0.4243 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4123 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7191 Z= 0.170 Angle : 0.596 10.263 9788 Z= 0.323 Chirality : 0.044 0.230 1118 Planarity : 0.004 0.047 1258 Dihedral : 4.894 54.513 989 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.99 % Allowed : 28.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.28), residues: 910 helix: 1.61 (0.27), residues: 371 sheet: -0.41 (0.43), residues: 145 loop : -1.85 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 115 TYR 0.018 0.002 TYR R 251 PHE 0.020 0.002 PHE A 305 TRP 0.019 0.002 TRP A 267 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7189) covalent geometry : angle 0.59654 ( 9784) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.28043 ( 4) hydrogen bonds : bond 0.05086 ( 357) hydrogen bonds : angle 4.62683 ( 1026) ********************** 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 145 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7550 (p90) cc_final: 0.7033 (p90) REVERT: A 263 PHE cc_start: 0.4569 (OUTLIER) cc_final: 0.4090 (m-80) REVERT: A 383 LEU cc_start: 0.7306 (tp) cc_final: 0.7078 (OUTLIER) REVERT: B 59 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 325 MET cc_start: 0.7059 (mtp) cc_final: 0.6722 (mmt) REVERT: R 197 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6518 (ttt) outliers start: 29 outliers final: 22 residues processed: 128 average time/residue: 0.4117 time to fit residues: 56.6814 Evaluate side-chains 139 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 74 SER 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 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 163 TYR Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 197 MET 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 19 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 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 ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS R 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.193892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178368 restraints weight = 10027.297| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 1.67 r_work: 0.4235 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7191 Z= 0.188 Angle : 0.616 9.105 9788 Z= 0.333 Chirality : 0.045 0.237 1118 Planarity : 0.004 0.046 1258 Dihedral : 4.968 54.496 989 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.54 % Allowed : 27.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.28), residues: 910 helix: 1.40 (0.26), residues: 383 sheet: -0.40 (0.43), residues: 145 loop : -1.86 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 115 TYR 0.028 0.002 TYR R 66 PHE 0.022 0.002 PHE R 107 TRP 0.017 0.002 TRP A 267 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 7189) covalent geometry : angle 0.61600 ( 9784) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.32000 ( 4) hydrogen bonds : bond 0.05416 ( 357) hydrogen bonds : angle 4.70098 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.13 seconds wall clock time: 52 minutes 43.67 seconds (3163.67 seconds total)