Starting phenix.real_space_refine on Wed Mar 4 10:39:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nb6_12256/03_2026/7nb6_12256.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nb6_12256/03_2026/7nb6_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 { model { file = "/net/cci-nas-00/data/ceres_data/7nb6_12256/03_2026/7nb6_12256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nb6_12256/03_2026/7nb6_12256.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nb6_12256/03_2026/7nb6_12256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nb6_12256/03_2026/7nb6_12256.map" } resolution = 3.3 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.07, per 1000 atoms: 0.24 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: 1.06 Conformation dependent library (CDL) restraints added in 630.3 milliseconds 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: 0.40 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: 2.25 Time building geometry restraints manager: 1.43 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG C 92 TYR 0.018 0.003 TYR C 268 PHE 0.015 0.002 PHE D 29 TRP 0.009 0.001 TRP E 57 HIS 0.009 0.003 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00973 (13270) covalent geometry : angle 0.95757 (18130) hydrogen bonds : bond 0.10215 ( 1025) hydrogen bonds : angle 5.67948 ( 3075) *********************** 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 : 0.556 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: 0.0808 time to fit residues: 27.5725 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 : 0.370 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.119577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.080700 restraints weight = 28108.845| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.34 r_work: 0.3136 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13270 Z= 0.180 Angle : 0.774 9.930 18130 Z= 0.372 Chirality : 0.044 0.162 2345 Planarity : 0.006 0.052 2180 Dihedral : 5.481 73.970 1793 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.35 % Allowed : 9.68 % Favored : 89.96 % 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 are not related in a simple way. whole: 1.48 (0.21), residues: 1690 helix: 1.77 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.43 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.021 0.003 TYR E 97 PHE 0.010 0.001 PHE D 275 TRP 0.008 0.001 TRP C 57 HIS 0.003 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00405 (13270) covalent geometry : angle 0.77408 (18130) hydrogen bonds : bond 0.04337 ( 1025) hydrogen bonds : angle 4.63684 ( 3075) *********************** 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 168 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.5480 (mpp) cc_final: 0.4936 (pmm) REVERT: B 89 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7170 (tm-30) REVERT: B 164 GLU cc_start: 0.8077 (pp20) cc_final: 0.7856 (pp20) REVERT: C 144 LEU cc_start: 0.8216 (mt) cc_final: 0.7770 (mt) REVERT: C 214 MET cc_start: 0.8238 (tmm) cc_final: 0.7922 (tmm) REVERT: C 311 MET cc_start: 0.8711 (mtp) cc_final: 0.8468 (mtt) REVERT: E 164 GLU cc_start: 0.8081 (pp20) cc_final: 0.7764 (pp20) outliers start: 5 outliers final: 2 residues processed: 165 average time/residue: 0.0827 time to fit residues: 22.2531 Evaluate side-chains 153 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 26 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3953 r_free = 0.3953 target = 0.120097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082917 restraints weight = 28181.143| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.48 r_work: 0.3107 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13270 Z= 0.163 Angle : 0.725 9.121 18130 Z= 0.347 Chirality : 0.043 0.170 2345 Planarity : 0.006 0.053 2180 Dihedral : 4.725 23.416 1790 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.96 % Allowed : 12.70 % Favored : 85.33 % 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 are not related in a simple way. whole: 1.65 (0.21), residues: 1690 helix: 1.88 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.37 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.023 0.002 TYR C 97 PHE 0.019 0.001 PHE A 258 TRP 0.007 0.001 TRP A 57 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00368 (13270) covalent geometry : angle 0.72494 (18130) hydrogen bonds : bond 0.03776 ( 1025) hydrogen bonds : angle 4.38587 ( 3075) *********************** 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 195 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.404 Fit side-chains REVERT: A 141 LEU cc_start: 0.8734 (tp) cc_final: 0.7952 (pp) REVERT: B 89 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7215 (tm-30) REVERT: B 269 LEU cc_start: 0.8648 (tp) cc_final: 0.8123 (mt) REVERT: C 214 MET cc_start: 0.8134 (tmm) cc_final: 0.7847 (tmm) REVERT: C 311 MET cc_start: 0.9027 (mtp) cc_final: 0.8749 (mtt) REVERT: D 265 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7825 (tp) REVERT: E 148 MET cc_start: 0.8522 (tpt) cc_final: 0.8278 (tpt) outliers start: 28 outliers final: 11 residues processed: 188 average time/residue: 0.0768 time to fit residues: 23.4315 Evaluate side-chains 159 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 327 GLN Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 327 GLN 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 157 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 44 optimal weight: 0.0570 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 HIS D 174 GLN 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 = 0.3970 r_free = 0.3970 target = 0.121230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083536 restraints weight = 27925.780| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.67 r_work: 0.3147 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13270 Z= 0.137 Angle : 0.691 9.265 18130 Z= 0.330 Chirality : 0.041 0.184 2345 Planarity : 0.006 0.050 2180 Dihedral : 4.537 22.419 1790 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.33 % Allowed : 16.84 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.21), residues: 1690 helix: 2.05 (0.14), residues: 1415 sheet: None (None), residues: 0 loop : -3.18 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.019 0.002 TYR A 259 PHE 0.021 0.001 PHE A 258 TRP 0.004 0.001 TRP A 226 HIS 0.002 0.000 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00285 (13270) covalent geometry : angle 0.69126 (18130) hydrogen bonds : bond 0.03489 ( 1025) hydrogen bonds : angle 4.27519 ( 3075) *********************** 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 174 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.524 Fit side-chains REVERT: B 89 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7192 (tm-30) REVERT: B 235 TYR cc_start: 0.8733 (m-80) cc_final: 0.8524 (m-80) REVERT: B 269 LEU cc_start: 0.8647 (tp) cc_final: 0.8128 (mt) REVERT: C 214 MET cc_start: 0.8170 (tmm) cc_final: 0.7937 (tmm) REVERT: C 258 PHE cc_start: 0.5858 (p90) cc_final: 0.5464 (p90) REVERT: C 311 MET cc_start: 0.8995 (mtp) cc_final: 0.8710 (mtt) REVERT: D 265 LEU cc_start: 0.8479 (mt) cc_final: 0.8159 (tp) REVERT: D 311 MET cc_start: 0.8925 (mtp) cc_final: 0.8546 (mtt) REVERT: E 148 MET cc_start: 0.8517 (tpt) cc_final: 0.8301 (tpt) outliers start: 19 outliers final: 6 residues processed: 168 average time/residue: 0.0803 time to fit residues: 21.8864 Evaluate side-chains 152 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 190 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.118663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078942 restraints weight = 28081.810| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.30 r_work: 0.3105 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13270 Z= 0.191 Angle : 0.733 9.117 18130 Z= 0.350 Chirality : 0.043 0.172 2345 Planarity : 0.006 0.048 2180 Dihedral : 4.550 22.689 1790 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.32 % Allowed : 17.75 % Favored : 79.93 % 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 are not related in a simple way. whole: 1.66 (0.22), residues: 1690 helix: 1.87 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.28 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.019 0.002 TYR A 259 PHE 0.023 0.002 PHE E 258 TRP 0.005 0.001 TRP B 57 HIS 0.003 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00455 (13270) covalent geometry : angle 0.73309 (18130) hydrogen bonds : bond 0.03726 ( 1025) hydrogen bonds : angle 4.37464 ( 3075) *********************** 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 188 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.479 Fit side-chains REVERT: A 16 MET cc_start: 0.8841 (tpp) cc_final: 0.8630 (tpp) REVERT: A 141 LEU cc_start: 0.8707 (tp) cc_final: 0.7958 (pp) REVERT: B 89 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7302 (tm-30) REVERT: C 127 TYR cc_start: 0.3673 (OUTLIER) cc_final: 0.1479 (t80) REVERT: C 311 MET cc_start: 0.9026 (mtp) cc_final: 0.8798 (mtt) REVERT: D 47 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8987 (mp) REVERT: D 265 LEU cc_start: 0.8534 (mt) cc_final: 0.8237 (tp) REVERT: D 311 MET cc_start: 0.9000 (mtp) cc_final: 0.8661 (mtt) REVERT: E 311 MET cc_start: 0.9055 (mtp) cc_final: 0.8782 (mtt) outliers start: 33 outliers final: 18 residues processed: 181 average time/residue: 0.0743 time to fit residues: 21.8821 Evaluate side-chains 168 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 277 ASN Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 259 TYR 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 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 24 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.118520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080049 restraints weight = 28035.331| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.67 r_work: 0.3094 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13270 Z= 0.180 Angle : 0.725 9.126 18130 Z= 0.342 Chirality : 0.042 0.169 2345 Planarity : 0.006 0.054 2180 Dihedral : 4.516 23.310 1790 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.67 % Allowed : 19.58 % Favored : 77.75 % 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 are not related in a simple way. whole: 1.65 (0.21), residues: 1690 helix: 1.87 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.35 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 98 TYR 0.016 0.002 TYR A 259 PHE 0.016 0.001 PHE C 258 TRP 0.004 0.001 TRP C 57 HIS 0.002 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00426 (13270) covalent geometry : angle 0.72470 (18130) hydrogen bonds : bond 0.03536 ( 1025) hydrogen bonds : angle 4.33163 ( 3075) *********************** 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 199 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.502 Fit side-chains REVERT: B 89 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7215 (tm-30) REVERT: C 127 TYR cc_start: 0.3644 (OUTLIER) cc_final: 0.1444 (t80) REVERT: C 181 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7049 (pt0) REVERT: C 258 PHE cc_start: 0.5698 (p90) cc_final: 0.5462 (p90) REVERT: C 311 MET cc_start: 0.9071 (mtp) cc_final: 0.8839 (mtt) REVERT: D 47 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8984 (mp) REVERT: D 265 LEU cc_start: 0.8549 (mt) cc_final: 0.8065 (tp) REVERT: D 311 MET cc_start: 0.9056 (mtp) cc_final: 0.8707 (mtt) REVERT: E 311 MET cc_start: 0.9092 (mtp) cc_final: 0.8804 (mtt) outliers start: 38 outliers final: 21 residues processed: 188 average time/residue: 0.0809 time to fit residues: 24.4881 Evaluate side-chains 175 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET 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 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 190 ILE 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 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 36 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.119949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.080392 restraints weight = 28065.580| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.39 r_work: 0.3128 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4073 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 : 0.703 11.469 18130 Z= 0.329 Chirality : 0.041 0.166 2345 Planarity : 0.005 0.047 2180 Dihedral : 4.384 21.746 1790 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.67 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.21), residues: 1690 helix: 1.96 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -3.46 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 28 TYR 0.020 0.002 TYR E 259 PHE 0.022 0.001 PHE A 222 TRP 0.005 0.001 TRP A 226 HIS 0.001 0.000 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00301 (13270) covalent geometry : angle 0.70296 (18130) hydrogen bonds : bond 0.03365 ( 1025) hydrogen bonds : angle 4.23024 ( 3075) *********************** 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 199 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.488 Fit side-chains REVERT: A 181 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6589 (pt0) REVERT: B 89 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7140 (tm-30) REVERT: B 127 TYR cc_start: 0.3381 (OUTLIER) cc_final: 0.1393 (t80) REVERT: B 181 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6640 (pt0) REVERT: C 127 TYR cc_start: 0.3649 (OUTLIER) cc_final: 0.1361 (t80) REVERT: C 181 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7014 (pt0) REVERT: C 311 MET cc_start: 0.9050 (mtp) cc_final: 0.8798 (mtt) REVERT: D 127 TYR cc_start: 0.3651 (OUTLIER) cc_final: 0.1528 (t80) REVERT: D 311 MET cc_start: 0.9011 (mtp) cc_final: 0.8646 (mtt) REVERT: E 148 MET cc_start: 0.8609 (tpt) cc_final: 0.8390 (tpt) outliers start: 38 outliers final: 18 residues processed: 191 average time/residue: 0.0773 time to fit residues: 23.9093 Evaluate side-chains 173 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 57 TRP 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 327 GLN 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 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 76 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.118152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078757 restraints weight = 27874.273| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.26 r_work: 0.3100 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13270 Z= 0.184 Angle : 0.766 11.219 18130 Z= 0.356 Chirality : 0.042 0.235 2345 Planarity : 0.005 0.048 2180 Dihedral : 4.410 22.074 1790 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.60 % Allowed : 21.12 % Favored : 76.28 % 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 are not related in a simple way. whole: 1.65 (0.21), residues: 1690 helix: 1.83 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -3.57 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 286 TYR 0.016 0.002 TYR A 97 PHE 0.019 0.001 PHE A 222 TRP 0.004 0.001 TRP E 57 HIS 0.004 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00436 (13270) covalent geometry : angle 0.76627 (18130) hydrogen bonds : bond 0.03568 ( 1025) hydrogen bonds : angle 4.31860 ( 3075) *********************** 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 193 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.481 Fit side-chains REVERT: A 141 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.7932 (pp) REVERT: B 89 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 127 TYR cc_start: 0.3406 (OUTLIER) cc_final: 0.1415 (t80) REVERT: B 181 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6770 (pt0) REVERT: C 127 TYR cc_start: 0.3632 (OUTLIER) cc_final: 0.1320 (t80) REVERT: C 181 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7126 (pt0) REVERT: C 311 MET cc_start: 0.9023 (mtp) cc_final: 0.8803 (mtt) REVERT: D 127 TYR cc_start: 0.3714 (OUTLIER) cc_final: 0.1410 (t80) REVERT: D 311 MET cc_start: 0.8986 (mtp) cc_final: 0.8665 (mtt) outliers start: 37 outliers final: 21 residues processed: 182 average time/residue: 0.0768 time to fit residues: 22.6569 Evaluate side-chains 177 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET 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 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 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 327 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 37 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.120179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081614 restraints weight = 28093.773| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.77 r_work: 0.3105 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13270 Z= 0.140 Angle : 0.738 10.745 18130 Z= 0.341 Chirality : 0.041 0.225 2345 Planarity : 0.005 0.045 2180 Dihedral : 4.287 21.340 1790 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.89 % Allowed : 21.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.21), residues: 1690 helix: 1.98 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -3.42 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 286 TYR 0.017 0.001 TYR D 97 PHE 0.022 0.001 PHE B 258 TRP 0.006 0.001 TRP C 226 HIS 0.003 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00303 (13270) covalent geometry : angle 0.73758 (18130) hydrogen bonds : bond 0.03278 ( 1025) hydrogen bonds : angle 4.21655 ( 3075) *********************** 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 188 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.548 Fit side-chains REVERT: A 141 LEU cc_start: 0.8606 (tp) cc_final: 0.7935 (pp) REVERT: A 311 MET cc_start: 0.9089 (mtm) cc_final: 0.8731 (mtt) REVERT: B 89 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7242 (tm-30) REVERT: B 127 TYR cc_start: 0.3160 (OUTLIER) cc_final: 0.1367 (t80) REVERT: B 181 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6638 (pt0) REVERT: B 311 MET cc_start: 0.8967 (mtp) cc_final: 0.8599 (mtt) REVERT: C 127 TYR cc_start: 0.3371 (OUTLIER) cc_final: 0.1248 (t80) REVERT: C 181 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6949 (pt0) REVERT: C 311 MET cc_start: 0.9107 (mtp) cc_final: 0.8828 (mtt) REVERT: D 127 TYR cc_start: 0.3607 (OUTLIER) cc_final: 0.1351 (t80) REVERT: E 69 MET cc_start: 0.8802 (tpp) cc_final: 0.8594 (mmm) REVERT: E 311 MET cc_start: 0.9076 (mtm) cc_final: 0.8702 (mtt) outliers start: 27 outliers final: 19 residues processed: 182 average time/residue: 0.0783 time to fit residues: 23.1158 Evaluate side-chains 178 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 141 LEU 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 259 TYR Chi-restraints excluded: chain C residue 327 GLN 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 214 MET Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 327 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 148 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.119878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082961 restraints weight = 28252.850| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.70 r_work: 0.3106 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4494 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= 0.143 Angle : 0.751 13.939 18130 Z= 0.346 Chirality : 0.041 0.221 2345 Planarity : 0.005 0.046 2180 Dihedral : 4.232 20.957 1790 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.04 % Allowed : 21.54 % Favored : 76.42 % 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 are not related in a simple way. whole: 1.90 (0.21), residues: 1690 helix: 2.00 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -3.41 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 178 TYR 0.020 0.001 TYR B 97 PHE 0.017 0.001 PHE A 222 TRP 0.005 0.001 TRP E 57 HIS 0.002 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00315 (13270) covalent geometry : angle 0.75136 (18130) hydrogen bonds : bond 0.03299 ( 1025) hydrogen bonds : angle 4.19924 ( 3075) ********************** 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 184 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.472 Fit side-chains REVERT: A 141 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7934 (pp) REVERT: A 311 MET cc_start: 0.9062 (mtm) cc_final: 0.8703 (mtt) REVERT: B 89 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7258 (tm-30) REVERT: B 127 TYR cc_start: 0.2935 (OUTLIER) cc_final: 0.1232 (t80) REVERT: B 181 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6602 (pt0) REVERT: B 311 MET cc_start: 0.8980 (mtp) cc_final: 0.8612 (mtt) REVERT: C 127 TYR cc_start: 0.3351 (OUTLIER) cc_final: 0.1297 (t80) REVERT: C 181 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: C 311 MET cc_start: 0.9121 (mtp) cc_final: 0.8859 (mtt) REVERT: D 127 TYR cc_start: 0.3535 (OUTLIER) cc_final: 0.1339 (t80) REVERT: E 311 MET cc_start: 0.9098 (mtm) cc_final: 0.8733 (mtt) outliers start: 29 outliers final: 21 residues processed: 175 average time/residue: 0.0779 time to fit residues: 22.0423 Evaluate side-chains 181 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 57 TRP 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 327 GLN 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 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 141 LEU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 327 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 167 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 133 optimal weight: 0.0870 chunk 23 optimal weight: 0.4980 chunk 138 optimal weight: 0.7980 chunk 98 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.2894 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.121761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083102 restraints weight = 27979.668| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.37 r_work: 0.3180 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4702 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= 0.131 Angle : 0.738 13.514 18130 Z= 0.339 Chirality : 0.041 0.188 2345 Planarity : 0.005 0.047 2180 Dihedral : 4.080 19.619 1790 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.68 % Allowed : 22.18 % Favored : 76.14 % 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 are not related in a simple way. whole: 2.09 (0.21), residues: 1690 helix: 2.13 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -3.35 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 178 TYR 0.017 0.001 TYR A 97 PHE 0.028 0.001 PHE E 222 TRP 0.011 0.001 TRP E 226 HIS 0.001 0.000 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00261 (13270) covalent geometry : angle 0.73830 (18130) hydrogen bonds : bond 0.03077 ( 1025) hydrogen bonds : angle 4.09391 ( 3075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.57 seconds wall clock time: 52 minutes 29.26 seconds (3149.26 seconds total)