Starting phenix.real_space_refine on Thu Jul 31 01:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nb6_12256/07_2025/7nb6_12256.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nb6_12256/07_2025/7nb6_12256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nb6_12256/07_2025/7nb6_12256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nb6_12256/07_2025/7nb6_12256.map" model { file = "/net/cci-nas-00/data/ceres_data/7nb6_12256/07_2025/7nb6_12256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nb6_12256/07_2025/7nb6_12256.cif" } resolution = 3.3 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= 0.000 sd= 0.002 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 85 5.16 5 C 8700 2.51 5 N 2085 2.21 5 O 2150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13020 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain: "D" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain: "E" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Time building chain proxies: 8.44, per 1000 atoms: 0.65 Number of scatterers: 13020 At special positions: 0 Unit cell: (129.735, 126.387, 77.004, 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 85 16.00 O 2150 8.00 N 2085 7.00 C 8700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 2.0 seconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 88.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 30 through 57 Proline residue: A 36 - end of helix Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 60 through 94 Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.546A pdb=" N ARG A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Proline residue: A 104 - end of helix Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 129 through 147 removed outlier: 3.526A pdb=" N ALA A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE A 152 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 177 through 184 removed outlier: 3.629A pdb=" N GLU A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 218 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.836A pdb=" N VAL A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 removed outlier: 3.653A pdb=" N ILE A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 278 through 283 removed outlier: 4.405A pdb=" N ILE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.550A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) Proline residue: A 316 - end of helix removed outlier: 3.879A pdb=" N GLN A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'B' and resid 7 through 30 Processing helix chain 'B' and resid 30 through 57 Proline residue: B 36 - end of helix Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 60 through 94 Processing helix chain 'B' and resid 94 through 109 removed outlier: 3.545A pdb=" N ARG B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.526A pdb=" N ALA B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 177 through 184 removed outlier: 3.629A pdb=" N GLU B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 218 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.836A pdb=" N VAL B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.653A pdb=" N ILE B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 278 through 283 removed outlier: 4.405A pdb=" N ILE B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.551A pdb=" N MET B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL B 315 " --> pdb=" O MET B 311 " (cutoff:3.500A) Proline residue: B 316 - end of helix removed outlier: 3.879A pdb=" N GLN B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'C' and resid 7 through 30 Processing helix chain 'C' and resid 30 through 57 Proline residue: C 36 - end of helix Proline residue: C 49 - end of helix Processing helix chain 'C' and resid 60 through 94 Processing helix chain 'C' and resid 94 through 109 removed outlier: 3.546A pdb=" N ARG C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 129 through 147 removed outlier: 3.527A pdb=" N ALA C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE C 152 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 177 through 184 removed outlier: 3.628A pdb=" N GLU C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 218 Processing helix chain 'C' and resid 222 through 234 Processing helix chain 'C' and resid 238 through 245 removed outlier: 3.837A pdb=" N VAL C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 removed outlier: 3.654A pdb=" N ILE C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 275 Processing helix chain 'C' and resid 278 through 283 removed outlier: 4.406A pdb=" N ILE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 307 through 328 removed outlier: 3.550A pdb=" N MET C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) Proline residue: C 316 - end of helix removed outlier: 3.878A pdb=" N GLN C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 339 Processing helix chain 'D' and resid 7 through 30 Processing helix chain 'D' and resid 30 through 57 Proline residue: D 36 - end of helix Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 60 through 94 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.546A pdb=" N ARG D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 129 through 147 removed outlier: 3.527A pdb=" N ALA D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE D 152 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.629A pdb=" N GLU D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 218 Processing helix chain 'D' and resid 222 through 234 Processing helix chain 'D' and resid 238 through 245 removed outlier: 3.836A pdb=" N VAL D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 removed outlier: 3.654A pdb=" N ILE D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 275 Processing helix chain 'D' and resid 278 through 283 removed outlier: 4.405A pdb=" N ILE D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 307 through 328 removed outlier: 3.550A pdb=" N MET D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL D 315 " --> pdb=" O MET D 311 " (cutoff:3.500A) Proline residue: D 316 - end of helix removed outlier: 3.878A pdb=" N GLN D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 339 Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 30 through 57 Proline residue: E 36 - end of helix Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 60 through 94 Processing helix chain 'E' and resid 94 through 109 removed outlier: 3.545A pdb=" N ARG E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Proline residue: E 104 - end of helix Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 129 through 147 removed outlier: 3.525A pdb=" N ALA E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE E 152 " --> pdb=" O MET E 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 177 through 184 removed outlier: 3.628A pdb=" N GLU E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 218 Processing helix chain 'E' and resid 222 through 234 Processing helix chain 'E' and resid 238 through 245 removed outlier: 3.836A pdb=" N VAL E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 256 removed outlier: 3.653A pdb=" N ILE E 249 " --> pdb=" O ALA E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 275 Processing helix chain 'E' and resid 278 through 283 removed outlier: 4.405A pdb=" N ILE E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 306 Processing helix chain 'E' and resid 307 through 328 removed outlier: 3.551A pdb=" N MET E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 312 " --> pdb=" O PRO E 308 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL E 315 " --> pdb=" O MET E 311 " (cutoff:3.500A) Proline residue: E 316 - end of helix removed outlier: 3.878A pdb=" N GLN E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 339 1025 hydrogen bonds defined for protein. 3075 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: 4.07 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3985 1.34 - 1.46: 2394 1.46 - 1.57: 6726 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 13270 Sorted by residual: bond pdb=" C ALA A 31 " pdb=" N GLU A 32 " ideal model delta sigma weight residual 1.334 1.301 0.033 1.38e-02 5.25e+03 5.73e+00 bond pdb=" CB VAL E 14 " pdb=" CG1 VAL E 14 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.88e+00 bond pdb=" CB VAL A 14 " pdb=" CG1 VAL A 14 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.87e+00 bond pdb=" CB VAL D 14 " pdb=" CG1 VAL D 14 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.79e+00 bond pdb=" CB VAL C 14 " pdb=" CG1 VAL C 14 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.73e+00 ... (remaining 13265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 17434 2.12 - 4.24: 531 4.24 - 6.36: 118 6.36 - 8.48: 42 8.48 - 10.60: 5 Bond angle restraints: 18130 Sorted by residual: angle pdb=" N ILE A 283 " pdb=" CA ILE A 283 " pdb=" C ILE A 283 " ideal model delta sigma weight residual 108.53 103.77 4.76 1.22e+00 6.72e-01 1.53e+01 angle pdb=" N ILE D 283 " pdb=" CA ILE D 283 " pdb=" C ILE D 283 " ideal model delta sigma weight residual 108.53 103.80 4.73 1.22e+00 6.72e-01 1.50e+01 angle pdb=" N ILE C 283 " pdb=" CA ILE C 283 " pdb=" C ILE C 283 " ideal model delta sigma weight residual 108.53 103.81 4.72 1.22e+00 6.72e-01 1.49e+01 angle pdb=" N ILE E 283 " pdb=" CA ILE E 283 " pdb=" C ILE E 283 " ideal model delta sigma weight residual 108.53 103.82 4.71 1.22e+00 6.72e-01 1.49e+01 angle pdb=" N ILE B 283 " pdb=" CA ILE B 283 " pdb=" C ILE B 283 " ideal model delta sigma weight residual 108.53 103.84 4.69 1.22e+00 6.72e-01 1.48e+01 ... (remaining 18125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 7039 15.46 - 30.92: 708 30.92 - 46.38: 173 46.38 - 61.83: 18 61.83 - 77.29: 12 Dihedral angle restraints: 7950 sinusoidal: 3030 harmonic: 4920 Sorted by residual: dihedral pdb=" CA PHE C 275 " pdb=" C PHE C 275 " pdb=" N GLY C 276 " pdb=" CA GLY C 276 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PHE B 275 " pdb=" C PHE B 275 " pdb=" N GLY B 276 " pdb=" CA GLY B 276 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA PHE E 275 " pdb=" C PHE E 275 " pdb=" N GLY E 276 " pdb=" CA GLY E 276 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1268 0.035 - 0.070: 716 0.070 - 0.105: 264 0.105 - 0.141: 79 0.141 - 0.176: 18 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CB ILE C 283 " pdb=" CA ILE C 283 " pdb=" CG1 ILE C 283 " pdb=" CG2 ILE C 283 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB ILE D 283 " pdb=" CA ILE D 283 " pdb=" CG1 ILE D 283 " pdb=" CG2 ILE D 283 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB ILE B 283 " pdb=" CA ILE B 283 " pdb=" CG1 ILE B 283 " pdb=" CG2 ILE B 283 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 2342 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 178 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO B 179 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 178 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO C 179 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 178 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO E 179 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 179 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 179 " 0.028 5.00e-02 4.00e+02 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3205 2.79 - 3.32: 14859 3.32 - 3.84: 22037 3.84 - 4.37: 23352 4.37 - 4.90: 40652 Nonbonded interactions: 104105 Sorted by model distance: nonbonded pdb=" OG1 THR A 201 " pdb=" OH TYR A 235 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR C 201 " pdb=" OH TYR C 235 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR B 201 " pdb=" OH TYR B 235 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR E 201 " pdb=" OH TYR E 235 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR D 201 " pdb=" OH TYR D 235 " model vdw 2.263 3.040 ... (remaining 104100 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 3.160 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.480 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.010 0.074 13270 Z= 0.409 Angle : 0.958 10.604 18130 Z= 0.471 Chirality : 0.050 0.176 2345 Planarity : 0.005 0.050 2180 Dihedral : 13.567 77.292 4760 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.49 % Allowed : 0.77 % Favored : 98.74 % 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: 0.79 (0.21), residues: 1690 helix: 1.37 (0.14), residues: 1405 sheet: None (None), residues: 0 loop : -3.86 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 57 HIS 0.009 0.003 HIS E 126 PHE 0.015 0.002 PHE D 29 TYR 0.018 0.003 TYR C 268 ARG 0.003 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.10215 ( 1025) hydrogen bonds : angle 5.67948 ( 3075) covalent geometry : bond 0.00973 (13270) covalent geometry : angle 0.95757 (18130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 1.504 Fit side-chains REVERT: A 164 GLU cc_start: 0.7563 (pp20) cc_final: 0.7033 (pp20) REVERT: A 176 MET cc_start: 0.5510 (mpp) cc_final: 0.5146 (pmm) REVERT: B 32 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: B 89 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7127 (tm-30) REVERT: C 212 TRP cc_start: 0.8435 (t60) cc_final: 0.7846 (t60) REVERT: D 199 LEU cc_start: 0.8571 (tp) cc_final: 0.8371 (tp) outliers start: 7 outliers final: 0 residues processed: 211 average time/residue: 0.1926 time to fit residues: 63.8784 Evaluate side-chains 153 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 GLN E 106 GLN E 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.119891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082159 restraints weight = 27884.473| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.52 r_work: 0.3133 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13270 Z= 0.175 Angle : 0.767 9.924 18130 Z= 0.368 Chirality : 0.044 0.174 2345 Planarity : 0.006 0.051 2180 Dihedral : 5.437 73.446 1793 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.35 % Allowed : 10.04 % Favored : 89.61 % 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: 1.47 (0.21), residues: 1690 helix: 1.76 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.42 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 57 HIS 0.004 0.001 HIS D 126 PHE 0.009 0.001 PHE C 29 TYR 0.023 0.003 TYR D 97 ARG 0.003 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 1025) hydrogen bonds : angle 4.60223 ( 3075) covalent geometry : bond 0.00394 (13270) covalent geometry : angle 0.76700 (18130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 1.386 Fit side-chains REVERT: A 176 MET cc_start: 0.5467 (mpp) cc_final: 0.4946 (pmm) REVERT: B 89 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7169 (tm-30) REVERT: C 144 LEU cc_start: 0.8169 (mt) cc_final: 0.7720 (mt) REVERT: C 214 MET cc_start: 0.8259 (tmm) cc_final: 0.7940 (tmm) REVERT: C 311 MET cc_start: 0.8772 (mtp) cc_final: 0.8523 (mtt) REVERT: D 199 LEU cc_start: 0.8905 (tp) cc_final: 0.8701 (tp) outliers start: 5 outliers final: 2 residues processed: 166 average time/residue: 0.1893 time to fit residues: 50.0831 Evaluate side-chains 151 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain E residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 117 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN E 126 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.117064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079132 restraints weight = 28158.206| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.49 r_work: 0.3054 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13270 Z= 0.247 Angle : 0.800 10.608 18130 Z= 0.382 Chirality : 0.045 0.178 2345 Planarity : 0.006 0.054 2180 Dihedral : 4.916 25.061 1790 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.61 % Allowed : 13.82 % Favored : 84.56 % 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: 1.25 (0.21), residues: 1690 helix: 1.59 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.43 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 57 HIS 0.004 0.002 HIS B 53 PHE 0.016 0.002 PHE E 258 TYR 0.017 0.003 TYR E 259 ARG 0.002 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 1025) hydrogen bonds : angle 4.62288 ( 3075) covalent geometry : bond 0.00601 (13270) covalent geometry : angle 0.79974 (18130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.540 Fit side-chains REVERT: A 141 LEU cc_start: 0.8752 (tp) cc_final: 0.7967 (pp) REVERT: B 89 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7300 (tm-30) REVERT: C 164 GLU cc_start: 0.8476 (pp20) cc_final: 0.8272 (pp20) REVERT: C 265 LEU cc_start: 0.8191 (tp) cc_final: 0.7978 (tt) REVERT: C 311 MET cc_start: 0.9119 (mtp) cc_final: 0.8917 (mtt) REVERT: D 258 PHE cc_start: 0.6164 (p90) cc_final: 0.5750 (p90) outliers start: 23 outliers final: 14 residues processed: 183 average time/residue: 0.1975 time to fit residues: 57.3692 Evaluate side-chains 163 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 327 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 5 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 65 optimal weight: 0.2980 chunk 18 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 HIS D 126 HIS E 126 HIS E 251 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.120041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082392 restraints weight = 27827.047| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.72 r_work: 0.3112 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13270 Z= 0.140 Angle : 0.712 9.477 18130 Z= 0.338 Chirality : 0.041 0.173 2345 Planarity : 0.006 0.049 2180 Dihedral : 4.675 22.936 1790 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.67 % Allowed : 16.56 % Favored : 80.77 % 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: 1.70 (0.21), residues: 1690 helix: 1.91 (0.14), residues: 1415 sheet: None (None), residues: 0 loop : -3.27 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.002 0.000 HIS E 126 PHE 0.021 0.001 PHE E 258 TYR 0.027 0.002 TYR D 97 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 1025) hydrogen bonds : angle 4.35832 ( 3075) covalent geometry : bond 0.00293 (13270) covalent geometry : angle 0.71169 (18130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 1.442 Fit side-chains REVERT: B 89 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7194 (tm-30) REVERT: C 311 MET cc_start: 0.9099 (mtp) cc_final: 0.8870 (mtt) REVERT: D 47 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8831 (mp) outliers start: 38 outliers final: 16 residues processed: 189 average time/residue: 0.2169 time to fit residues: 65.0031 Evaluate side-chains 164 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 327 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 79 optimal weight: 3.9990 chunk 163 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 18 optimal weight: 0.0060 chunk 104 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.120897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084216 restraints weight = 27950.666| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.61 r_work: 0.3137 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13270 Z= 0.136 Angle : 0.690 9.308 18130 Z= 0.327 Chirality : 0.041 0.166 2345 Planarity : 0.006 0.048 2180 Dihedral : 4.445 21.360 1790 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.60 % Allowed : 18.18 % Favored : 79.23 % 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: 1.94 (0.22), residues: 1690 helix: 2.08 (0.14), residues: 1415 sheet: None (None), residues: 0 loop : -3.16 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.002 0.000 HIS C 126 PHE 0.020 0.001 PHE E 258 TYR 0.021 0.002 TYR E 259 ARG 0.001 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 1025) hydrogen bonds : angle 4.21520 ( 3075) covalent geometry : bond 0.00280 (13270) covalent geometry : angle 0.68957 (18130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.387 Fit side-chains REVERT: B 89 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7152 (tm-30) REVERT: C 127 TYR cc_start: 0.3630 (OUTLIER) cc_final: 0.1423 (t80) REVERT: C 258 PHE cc_start: 0.5911 (p90) cc_final: 0.5493 (p90) REVERT: D 47 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8869 (mp) outliers start: 37 outliers final: 20 residues processed: 189 average time/residue: 0.2035 time to fit residues: 61.0828 Evaluate side-chains 169 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 327 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 54 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.120385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083654 restraints weight = 28218.569| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.65 r_work: 0.3125 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13270 Z= 0.139 Angle : 0.689 9.256 18130 Z= 0.324 Chirality : 0.041 0.164 2345 Planarity : 0.006 0.047 2180 Dihedral : 4.319 21.929 1790 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.74 % Allowed : 19.44 % Favored : 77.82 % 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: 1.98 (0.21), residues: 1690 helix: 2.11 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.29 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.001 0.000 HIS B 53 PHE 0.022 0.001 PHE B 258 TYR 0.020 0.002 TYR A 259 ARG 0.001 0.000 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 1025) hydrogen bonds : angle 4.20172 ( 3075) covalent geometry : bond 0.00300 (13270) covalent geometry : angle 0.68903 (18130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.637 Fit side-chains REVERT: B 89 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7138 (tm-30) REVERT: B 181 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6986 (pt0) REVERT: C 127 TYR cc_start: 0.3530 (OUTLIER) cc_final: 0.1458 (t80) REVERT: C 181 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6972 (pt0) REVERT: C 311 MET cc_start: 0.9092 (mtm) cc_final: 0.8773 (mtt) REVERT: D 47 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8904 (mp) REVERT: D 127 TYR cc_start: 0.3829 (OUTLIER) cc_final: 0.1861 (t80) REVERT: D 311 MET cc_start: 0.9045 (mtp) cc_final: 0.8723 (mtt) outliers start: 39 outliers final: 22 residues processed: 176 average time/residue: 0.1984 time to fit residues: 55.2231 Evaluate side-chains 172 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 TRP Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 327 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 44 optimal weight: 0.2980 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.120119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082285 restraints weight = 28011.302| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.51 r_work: 0.3120 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13270 Z= 0.143 Angle : 0.697 9.118 18130 Z= 0.326 Chirality : 0.041 0.164 2345 Planarity : 0.005 0.046 2180 Dihedral : 4.265 20.918 1790 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.81 % Allowed : 19.86 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1690 helix: 2.11 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.21 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.001 0.000 HIS A 53 PHE 0.022 0.001 PHE E 258 TYR 0.021 0.002 TYR E 259 ARG 0.001 0.000 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 1025) hydrogen bonds : angle 4.18811 ( 3075) covalent geometry : bond 0.00316 (13270) covalent geometry : angle 0.69698 (18130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.558 Fit side-chains REVERT: A 89 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 181 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6454 (pt0) REVERT: A 222 PHE cc_start: 0.7487 (m-80) cc_final: 0.7227 (m-80) REVERT: B 89 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7159 (tm-30) REVERT: B 127 TYR cc_start: 0.3393 (OUTLIER) cc_final: 0.1456 (t80) REVERT: B 141 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7722 (pp) REVERT: B 181 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: C 127 TYR cc_start: 0.3640 (OUTLIER) cc_final: 0.1485 (t80) REVERT: C 181 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6914 (pt0) REVERT: C 311 MET cc_start: 0.9083 (mtm) cc_final: 0.8761 (mtt) REVERT: D 47 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8891 (mp) REVERT: D 127 TYR cc_start: 0.3544 (OUTLIER) cc_final: 0.1467 (t80) outliers start: 40 outliers final: 21 residues processed: 186 average time/residue: 0.2007 time to fit residues: 58.8855 Evaluate side-chains 180 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 TRP Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 327 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 162 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 40 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.121006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084369 restraints weight = 27809.719| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.64 r_work: 0.3139 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13270 Z= 0.132 Angle : 0.704 10.109 18130 Z= 0.327 Chirality : 0.041 0.192 2345 Planarity : 0.005 0.045 2180 Dihedral : 4.201 20.576 1790 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.60 % Allowed : 19.86 % Favored : 77.54 % 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: 2.05 (0.21), residues: 1690 helix: 2.09 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -3.30 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 226 HIS 0.001 0.000 HIS E 195 PHE 0.022 0.001 PHE B 258 TYR 0.018 0.001 TYR A 259 ARG 0.001 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 1025) hydrogen bonds : angle 4.15369 ( 3075) covalent geometry : bond 0.00276 (13270) covalent geometry : angle 0.70396 (18130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.497 Fit side-chains REVERT: A 89 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 181 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6494 (pt0) REVERT: A 222 PHE cc_start: 0.7460 (m-80) cc_final: 0.7194 (m-80) REVERT: A 259 TYR cc_start: 0.7940 (t80) cc_final: 0.7734 (t80) REVERT: B 89 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7136 (tm-30) REVERT: B 127 TYR cc_start: 0.3269 (OUTLIER) cc_final: 0.1362 (t80) REVERT: B 141 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7775 (pp) REVERT: B 181 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6623 (pt0) REVERT: B 305 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8265 (tp) REVERT: B 311 MET cc_start: 0.8940 (mtp) cc_final: 0.8586 (mtt) REVERT: C 127 TYR cc_start: 0.3619 (OUTLIER) cc_final: 0.1501 (t80) REVERT: C 181 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6882 (pt0) REVERT: C 311 MET cc_start: 0.9049 (mtm) cc_final: 0.8730 (mtt) REVERT: D 47 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8893 (mp) REVERT: D 127 TYR cc_start: 0.3593 (OUTLIER) cc_final: 0.1494 (t80) REVERT: E 311 MET cc_start: 0.9020 (mtm) cc_final: 0.8660 (mtt) outliers start: 37 outliers final: 16 residues processed: 185 average time/residue: 0.2170 time to fit residues: 63.8459 Evaluate side-chains 180 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 TRP Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 214 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 68 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 45 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.120780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082892 restraints weight = 27805.704| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.65 r_work: 0.3126 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13270 Z= 0.136 Angle : 0.724 10.355 18130 Z= 0.335 Chirality : 0.041 0.237 2345 Planarity : 0.005 0.046 2180 Dihedral : 4.133 19.871 1790 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.60 % Allowed : 20.63 % Favored : 76.77 % 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: 2.11 (0.21), residues: 1690 helix: 2.14 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -3.27 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 304 HIS 0.003 0.001 HIS D 195 PHE 0.023 0.001 PHE E 258 TYR 0.020 0.001 TYR C 97 ARG 0.003 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 1025) hydrogen bonds : angle 4.15344 ( 3075) covalent geometry : bond 0.00290 (13270) covalent geometry : angle 0.72388 (18130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.520 Fit side-chains REVERT: A 89 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 141 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.7931 (pp) REVERT: A 181 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6388 (pt0) REVERT: A 222 PHE cc_start: 0.7498 (m-80) cc_final: 0.7228 (m-80) REVERT: B 89 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7150 (tm-30) REVERT: B 127 TYR cc_start: 0.3083 (OUTLIER) cc_final: 0.1355 (t80) REVERT: B 141 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7745 (pp) REVERT: B 181 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6573 (pt0) REVERT: B 305 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8257 (tp) REVERT: B 311 MET cc_start: 0.8936 (mtp) cc_final: 0.8589 (mtt) REVERT: C 127 TYR cc_start: 0.3531 (OUTLIER) cc_final: 0.1517 (t80) REVERT: C 181 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6912 (pt0) REVERT: C 305 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8339 (tp) REVERT: C 311 MET cc_start: 0.9030 (mtm) cc_final: 0.8736 (mtt) REVERT: D 47 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8927 (mp) REVERT: D 127 TYR cc_start: 0.3457 (OUTLIER) cc_final: 0.1430 (t80) REVERT: D 305 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8389 (tp) REVERT: E 311 MET cc_start: 0.9030 (mtm) cc_final: 0.8662 (mtt) outliers start: 37 outliers final: 15 residues processed: 187 average time/residue: 0.1983 time to fit residues: 58.4415 Evaluate side-chains 182 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 TRP Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 63 optimal weight: 0.9980 chunk 161 optimal weight: 0.0570 chunk 115 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.121623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082510 restraints weight = 27721.989| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.36 r_work: 0.3167 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13270 Z= 0.130 Angle : 0.723 11.871 18130 Z= 0.333 Chirality : 0.041 0.218 2345 Planarity : 0.005 0.046 2180 Dihedral : 4.045 19.613 1790 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.96 % Allowed : 21.19 % Favored : 76.84 % 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: 2.19 (0.21), residues: 1690 helix: 2.19 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -3.26 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 226 HIS 0.001 0.000 HIS D 195 PHE 0.023 0.001 PHE B 258 TYR 0.015 0.001 TYR A 97 ARG 0.002 0.000 ARG B 178 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 1025) hydrogen bonds : angle 4.11033 ( 3075) covalent geometry : bond 0.00270 (13270) covalent geometry : angle 0.72319 (18130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.477 Fit side-chains REVERT: A 89 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 141 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7918 (pp) REVERT: A 181 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6550 (pt0) REVERT: A 222 PHE cc_start: 0.7501 (m-80) cc_final: 0.7228 (m-80) REVERT: A 284 MET cc_start: 0.7807 (ptm) cc_final: 0.7558 (ptt) REVERT: B 89 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7117 (tm-30) REVERT: B 127 TYR cc_start: 0.3087 (OUTLIER) cc_final: 0.1361 (t80) REVERT: B 141 LEU cc_start: 0.8424 (tp) cc_final: 0.7768 (pp) REVERT: B 181 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6725 (pt0) REVERT: B 305 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8088 (tp) REVERT: B 311 MET cc_start: 0.8867 (mtp) cc_final: 0.8525 (mtt) REVERT: C 127 TYR cc_start: 0.3369 (OUTLIER) cc_final: 0.1421 (t80) REVERT: C 311 MET cc_start: 0.8945 (mtm) cc_final: 0.8658 (mtt) REVERT: D 47 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8931 (mp) REVERT: D 127 TYR cc_start: 0.3432 (OUTLIER) cc_final: 0.1364 (t80) REVERT: E 89 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7291 (tm-30) REVERT: E 311 MET cc_start: 0.8962 (mtm) cc_final: 0.8656 (mtt) outliers start: 28 outliers final: 17 residues processed: 179 average time/residue: 0.2002 time to fit residues: 56.6287 Evaluate side-chains 178 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 277 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.120906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082658 restraints weight = 28040.576| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.70 r_work: 0.3133 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13270 Z= 0.136 Angle : 0.729 9.975 18130 Z= 0.335 Chirality : 0.041 0.187 2345 Planarity : 0.005 0.046 2180 Dihedral : 4.042 19.796 1790 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.18 % Allowed : 21.82 % Favored : 76.00 % 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: 2.18 (0.21), residues: 1690 helix: 2.19 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -3.32 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 304 HIS 0.002 0.000 HIS D 195 PHE 0.016 0.001 PHE C 258 TYR 0.017 0.001 TYR A 97 ARG 0.001 0.000 ARG E 178 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 1025) hydrogen bonds : angle 4.10766 ( 3075) covalent geometry : bond 0.00293 (13270) covalent geometry : angle 0.72856 (18130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6856.17 seconds wall clock time: 118 minutes 32.15 seconds (7112.15 seconds total)