Starting phenix.real_space_refine on Thu Jul 2 06:43:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jv7_36670/07_2026/8jv7_36670.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jv7_36670/07_2026/8jv7_36670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jv7_36670/07_2026/8jv7_36670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jv7_36670/07_2026/8jv7_36670.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jv7_36670/07_2026/8jv7_36670.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jv7_36670/07_2026/8jv7_36670.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jv7_36670/07_2026/8jv7_36670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jv7_36670/07_2026/8jv7_36670.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4638 2.51 5 N 1215 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7245 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2354 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ASN:plan1': 4, 'ARG:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2354 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ASN:plan1': 4, 'ARG:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2354 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ASN:plan1': 4, 'ARG:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'NAG': 2, 'UO6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'NAG': 2, 'UO6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'NAG': 2, 'UO6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.31 Number of scatterers: 7245 At special positions: 0 Unit cell: (84.66, 87.98, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1344 8.00 N 1215 7.00 C 4638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 269 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 187 " " NAG A 402 " - " ASN A 213 " " NAG B 401 " - " ASN B 187 " " NAG B 402 " - " ASN B 213 " " NAG C 401 " - " ASN C 187 " " NAG C 402 " - " ASN C 213 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 413.5 milliseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 17 sheets defined 19.7% alpha, 47.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.701A pdb=" N ALA A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 4.057A pdb=" N GLU A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.626A pdb=" N ILE A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'B' and resid 32 through 49 removed outlier: 4.190A pdb=" N PHE B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.761A pdb=" N CYS B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.808A pdb=" N GLU B 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.604A pdb=" N THR B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.729A pdb=" N VAL B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 350 removed outlier: 3.705A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 49 removed outlier: 3.515A pdb=" N PHE C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 removed outlier: 4.082A pdb=" N GLU C 186 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 241 through 248 removed outlier: 4.592A pdb=" N GLN C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 65 removed outlier: 4.160A pdb=" N TYR A 203 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 65 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 77 Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 154 removed outlier: 7.433A pdb=" N GLU A 163 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG A 151 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR A 161 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 113 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG A 307 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN A 115 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLU A 305 " --> pdb=" O GLN A 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.587A pdb=" N GLY B 250 " --> pdb=" O GLY B 314 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 322 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 324 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS B 260 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 154 removed outlier: 9.632A pdb=" N ILE B 147 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N TRP B 167 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR B 149 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N SER B 165 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 151 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU B 163 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B 313 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE B 108 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS B 311 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS B 110 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 309 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU B 112 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ARG B 307 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLN B 114 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU B 305 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 65 removed outlier: 4.072A pdb=" N TYR B 203 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 65 removed outlier: 3.502A pdb=" N VAL B 190 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 77 Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 52 through 55 removed outlier: 6.827A pdb=" N GLY C 250 " --> pdb=" O ARG C 316 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASP C 318 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 252 " --> pdb=" O ASP C 318 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU C 320 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE C 254 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE C 322 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE C 256 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N THR C 324 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TRP C 258 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY C 326 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS C 260 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N PHE C 328 " --> pdb=" O CYS C 260 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP C 259 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG C 270 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 58 through 66 removed outlier: 3.852A pdb=" N THR C 189 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR C 203 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 58 through 66 removed outlier: 3.852A pdb=" N THR C 189 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 69 through 77 Processing sheet with id=AB8, first strand: chain 'C' and resid 147 through 154 removed outlier: 11.114A pdb=" N ILE C 147 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N TRP C 167 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N THR C 149 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N SER C 165 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ARG C 151 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY C 113 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG C 307 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN C 115 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N GLU C 305 " --> pdb=" O GLN C 115 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1149 1.31 - 1.44: 2190 1.44 - 1.57: 4040 1.57 - 1.69: 4 1.69 - 1.82: 51 Bond restraints: 7434 Sorted by residual: bond pdb=" C03 UO6 B 403 " pdb=" O32 UO6 B 403 " ideal model delta sigma weight residual 1.232 1.402 -0.170 2.00e-02 2.50e+03 7.18e+01 bond pdb=" C03 UO6 C 403 " pdb=" O32 UO6 C 403 " ideal model delta sigma weight residual 1.232 1.401 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" C03 UO6 A 403 " pdb=" O32 UO6 A 403 " ideal model delta sigma weight residual 1.232 1.401 -0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" O27 UO6 C 403 " pdb=" P26 UO6 C 403 " ideal model delta sigma weight residual 1.653 1.510 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" O27 UO6 B 403 " pdb=" P26 UO6 B 403 " ideal model delta sigma weight residual 1.653 1.510 0.143 2.00e-02 2.50e+03 5.11e+01 ... (remaining 7429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.02: 10139 11.02 - 22.04: 10 22.04 - 33.06: 0 33.06 - 44.07: 0 44.07 - 55.09: 9 Bond angle restraints: 10158 Sorted by residual: angle pdb=" C06 UO6 A 403 " pdb=" N08 UO6 A 403 " pdb=" N09 UO6 A 403 " ideal model delta sigma weight residual 174.86 119.77 55.09 3.00e+00 1.11e-01 3.37e+02 angle pdb=" C06 UO6 B 403 " pdb=" N08 UO6 B 403 " pdb=" N09 UO6 B 403 " ideal model delta sigma weight residual 174.86 119.78 55.08 3.00e+00 1.11e-01 3.37e+02 angle pdb=" C06 UO6 C 403 " pdb=" N08 UO6 C 403 " pdb=" N09 UO6 C 403 " ideal model delta sigma weight residual 174.86 119.94 54.92 3.00e+00 1.11e-01 3.35e+02 angle pdb=" O27 UO6 C 403 " pdb=" P26 UO6 C 403 " pdb=" O28 UO6 C 403 " ideal model delta sigma weight residual 55.51 109.40 -53.89 3.00e+00 1.11e-01 3.23e+02 angle pdb=" O27 UO6 B 403 " pdb=" P26 UO6 B 403 " pdb=" O28 UO6 B 403 " ideal model delta sigma weight residual 55.51 109.38 -53.87 3.00e+00 1.11e-01 3.22e+02 ... (remaining 10153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 3764 17.58 - 35.16: 446 35.16 - 52.74: 130 52.74 - 70.33: 57 70.33 - 87.91: 7 Dihedral angle restraints: 4404 sinusoidal: 1635 harmonic: 2769 Sorted by residual: dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 162 " pdb=" CB CYS B 162 " ideal model delta sinusoidal sigma weight residual -86.00 -167.65 81.65 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual -86.00 -154.33 68.33 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS B 216 " pdb=" SG CYS B 216 " pdb=" SG CYS B 226 " pdb=" CB CYS B 226 " ideal model delta sinusoidal sigma weight residual -86.00 -152.28 66.28 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 4401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 825 0.044 - 0.088: 208 0.088 - 0.131: 86 0.131 - 0.175: 5 0.175 - 0.219: 1 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CA PRO A 142 " pdb=" N PRO A 142 " pdb=" C PRO A 142 " pdb=" CB PRO A 142 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1122 not shown) Planarity restraints: 1308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 141 " 0.061 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 142 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 237 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" CD GLU A 237 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 237 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 237 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 55 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 56 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " 0.025 5.00e-02 4.00e+02 ... (remaining 1305 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 198 2.70 - 3.25: 6683 3.25 - 3.80: 10838 3.80 - 4.35: 13095 4.35 - 4.90: 22724 Nonbonded interactions: 53538 Sorted by model distance: nonbonded pdb=" O GLY A 67 " pdb=" OH TYR A 93 " model vdw 2.147 3.040 nonbonded pdb=" O GLY C 67 " pdb=" OH TYR C 93 " model vdw 2.172 3.040 nonbonded pdb=" O GLY B 67 " pdb=" OH TYR B 93 " model vdw 2.223 3.040 nonbonded pdb=" OD2 ASP A 197 " pdb=" NH2 ARG C 276 " model vdw 2.251 3.120 nonbonded pdb=" O LYS B 136 " pdb=" NE2 GLN B 148 " model vdw 2.255 3.120 ... (remaining 53533 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.009 0.170 7455 Z= 0.421 Angle : 1.772 55.093 10206 Z= 0.644 Chirality : 0.045 0.219 1125 Planarity : 0.005 0.085 1302 Dihedral : 17.730 87.906 2589 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.38 % Allowed : 31.50 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.06 (0.28), residues: 954 helix: 1.50 (0.45), residues: 153 sheet: 0.56 (0.30), residues: 315 loop : -0.96 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 276 TYR 0.011 0.001 TYR C 93 PHE 0.014 0.001 PHE B 266 TRP 0.005 0.001 TRP B 167 HIS 0.012 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.42 ( 7434) covalent geometry : angle 1.77394 / 0.64 (10158) SS BOND : bond 0.00206 / 0.13 ( 15) SS BOND : angle 1.38165 / 1.10 ( 30) hydrogen bonds : bond 0.13799 / 8.44 ( 308) hydrogen bonds : angle 6.26621 / 4.42 ( 930) link_NAG-ASN : bond 0.00098 / 0.04 ( 6) link_NAG-ASN : angle 0.75700 / 0.54 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.278 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 114 average time/residue: 0.0850 time to fit residues: 13.4272 Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN A 148 GLN A 225 GLN B 116 GLN B 194 ASN C 268 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.147564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103454 restraints weight = 10691.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106789 restraints weight = 6653.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108996 restraints weight = 5002.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110454 restraints weight = 4217.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111119 restraints weight = 3794.194| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7455 Z= 0.131 Angle : 0.533 5.644 10206 Z= 0.279 Chirality : 0.045 0.142 1125 Planarity : 0.004 0.037 1302 Dihedral : 8.956 53.618 1231 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.20 % Allowed : 28.13 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.27 (0.29), residues: 954 helix: 1.92 (0.43), residues: 156 sheet: 0.44 (0.28), residues: 357 loop : -0.64 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 206 TYR 0.011 0.001 TYR C 273 PHE 0.009 0.001 PHE B 235 TRP 0.011 0.001 TRP A 258 HIS 0.013 0.001 HIS C 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 7434) covalent geometry : angle 0.52717 / 0.28 (10158) SS BOND : bond 0.00327 / 0.19 ( 15) SS BOND : angle 1.28215 / 1.02 ( 30) hydrogen bonds : bond 0.03226 / 2.13 ( 308) hydrogen bonds : angle 5.01759 / 3.56 ( 930) link_NAG-ASN : bond 0.00060 / 0.03 ( 6) link_NAG-ASN : angle 1.12475 / 0.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.316 Fit side-chains REVERT: A 148 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: B 255 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7566 (mt-10) REVERT: B 307 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7440 (ptt-90) REVERT: C 237 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7571 (tm-30) outliers start: 34 outliers final: 20 residues processed: 119 average time/residue: 0.0861 time to fit residues: 14.0160 Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 19 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN A 148 GLN C 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100553 restraints weight = 10636.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103762 restraints weight = 6680.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105850 restraints weight = 5053.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107254 restraints weight = 4284.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107919 restraints weight = 3861.621| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7455 Z= 0.159 Angle : 0.527 5.132 10206 Z= 0.282 Chirality : 0.046 0.151 1125 Planarity : 0.004 0.038 1302 Dihedral : 7.855 53.599 1219 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 7.49 % Allowed : 27.37 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.29 (0.29), residues: 954 helix: 1.96 (0.43), residues: 156 sheet: 0.45 (0.28), residues: 357 loop : -0.64 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 206 TYR 0.013 0.001 TYR A 93 PHE 0.013 0.001 PHE C 242 TRP 0.011 0.001 TRP A 258 HIS 0.012 0.001 HIS C 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 7434) covalent geometry : angle 0.52085 / 0.28 (10158) SS BOND : bond 0.00476 / 0.26 ( 15) SS BOND : angle 1.32837 / 1.02 ( 30) hydrogen bonds : bond 0.03365 / 2.19 ( 308) hydrogen bonds : angle 4.90858 / 3.49 ( 930) link_NAG-ASN : bond 0.00116 / 0.07 ( 6) link_NAG-ASN : angle 1.17177 / 0.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 93 time to evaluate : 0.275 Fit side-chains REVERT: A 122 PHE cc_start: 0.7818 (t80) cc_final: 0.7510 (t80) REVERT: A 148 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: B 34 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7943 (m-70) REVERT: B 307 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7722 (ptt-90) REVERT: C 237 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7691 (tm-30) REVERT: C 339 SER cc_start: 0.7162 (OUTLIER) cc_final: 0.6933 (m) outliers start: 49 outliers final: 31 residues processed: 127 average time/residue: 0.0780 time to fit residues: 13.9066 Evaluate side-chains 124 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.0070 chunk 44 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 overall best weight: 2.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.140184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096964 restraints weight = 10882.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100082 restraints weight = 6834.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102176 restraints weight = 5158.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103278 restraints weight = 4363.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104094 restraints weight = 3975.135| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7455 Z= 0.201 Angle : 0.572 4.744 10206 Z= 0.306 Chirality : 0.047 0.160 1125 Planarity : 0.004 0.038 1302 Dihedral : 7.607 57.981 1219 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 7.95 % Allowed : 26.30 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.13 (0.28), residues: 954 helix: 1.09 (0.40), residues: 174 sheet: 0.41 (0.28), residues: 342 loop : -0.96 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 206 TYR 0.013 0.001 TYR B 93 PHE 0.017 0.002 PHE C 242 TRP 0.011 0.001 TRP C 258 HIS 0.002 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 7434) covalent geometry : angle 0.56478 / 0.30 (10158) SS BOND : bond 0.00452 / 0.27 ( 15) SS BOND : angle 1.48881 / 1.17 ( 30) hydrogen bonds : bond 0.03792 / 2.45 ( 308) hydrogen bonds : angle 4.97090 / 3.54 ( 930) link_NAG-ASN : bond 0.00147 / 0.08 ( 6) link_NAG-ASN : angle 1.28218 / 0.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 83 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7836 (t80) cc_final: 0.7502 (t80) REVERT: B 34 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.8109 (m-70) REVERT: B 186 GLU cc_start: 0.8371 (pt0) cc_final: 0.8123 (pt0) REVERT: B 237 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 252 MET cc_start: 0.8054 (tpp) cc_final: 0.7842 (tpp) REVERT: B 307 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7867 (ptt-90) REVERT: C 122 PHE cc_start: 0.8186 (t80) cc_final: 0.7916 (t80) REVERT: C 237 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7845 (tm-30) REVERT: C 344 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7397 (t80) outliers start: 52 outliers final: 31 residues processed: 125 average time/residue: 0.0732 time to fit residues: 13.1056 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN A 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.098477 restraints weight = 10713.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101593 restraints weight = 6755.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.103696 restraints weight = 5119.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104829 restraints weight = 4328.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105787 restraints weight = 3936.406| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7455 Z= 0.142 Angle : 0.524 4.707 10206 Z= 0.279 Chirality : 0.046 0.161 1125 Planarity : 0.004 0.036 1302 Dihedral : 7.197 59.838 1217 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 7.34 % Allowed : 26.61 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.04 (0.28), residues: 954 helix: 1.29 (0.40), residues: 174 sheet: 0.37 (0.28), residues: 351 loop : -0.74 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 206 TYR 0.014 0.001 TYR A 93 PHE 0.014 0.001 PHE B 344 TRP 0.010 0.001 TRP C 258 HIS 0.002 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 7434) covalent geometry : angle 0.51700 / 0.28 (10158) SS BOND : bond 0.00346 / 0.20 ( 15) SS BOND : angle 1.40973 / 1.10 ( 30) hydrogen bonds : bond 0.03319 / 2.18 ( 308) hydrogen bonds : angle 4.80028 / 3.42 ( 930) link_NAG-ASN : bond 0.00090 / 0.05 ( 6) link_NAG-ASN : angle 1.15479 / 0.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 87 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7846 (t80) cc_final: 0.7518 (t80) REVERT: A 148 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7734 (pm20) REVERT: B 186 GLU cc_start: 0.8355 (pt0) cc_final: 0.8064 (pt0) REVERT: B 237 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B 307 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7894 (ptt-90) REVERT: C 122 PHE cc_start: 0.8192 (t80) cc_final: 0.7912 (t80) REVERT: C 237 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7866 (tm-30) REVERT: C 344 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7431 (t80) outliers start: 48 outliers final: 35 residues processed: 122 average time/residue: 0.0845 time to fit residues: 13.9751 Evaluate side-chains 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099178 restraints weight = 10621.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.102373 restraints weight = 6676.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104462 restraints weight = 5039.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105565 restraints weight = 4266.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106602 restraints weight = 3878.054| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7455 Z= 0.127 Angle : 0.517 4.757 10206 Z= 0.274 Chirality : 0.046 0.145 1125 Planarity : 0.004 0.036 1302 Dihedral : 7.050 58.247 1217 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 7.34 % Allowed : 26.30 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.13 (0.28), residues: 954 helix: 1.38 (0.40), residues: 174 sheet: 0.38 (0.28), residues: 354 loop : -0.66 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 206 TYR 0.014 0.001 TYR B 93 PHE 0.012 0.001 PHE C 242 TRP 0.009 0.001 TRP C 258 HIS 0.002 0.000 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7434) covalent geometry : angle 0.50980 / 0.27 (10158) SS BOND : bond 0.00307 / 0.18 ( 15) SS BOND : angle 1.51808 / 1.24 ( 30) hydrogen bonds : bond 0.03155 / 2.07 ( 308) hydrogen bonds : angle 4.77409 / 3.39 ( 930) link_NAG-ASN : bond 0.00076 / 0.05 ( 6) link_NAG-ASN : angle 1.09286 / 0.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7786 (t80) cc_final: 0.7441 (t80) REVERT: A 277 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7584 (ttt90) REVERT: B 122 PHE cc_start: 0.7596 (t80) cc_final: 0.6951 (t80) REVERT: B 186 GLU cc_start: 0.8339 (pt0) cc_final: 0.8126 (pt0) REVERT: B 237 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 252 MET cc_start: 0.7687 (tpp) cc_final: 0.7370 (tpp) REVERT: B 307 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7979 (ptt-90) REVERT: C 122 PHE cc_start: 0.8165 (t80) cc_final: 0.7875 (t80) REVERT: C 237 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 344 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7647 (t80) outliers start: 48 outliers final: 38 residues processed: 121 average time/residue: 0.0846 time to fit residues: 14.0859 Evaluate side-chains 121 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN A 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098496 restraints weight = 10780.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101647 restraints weight = 6789.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.103487 restraints weight = 5124.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.104986 restraints weight = 4374.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105659 restraints weight = 3941.017| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7455 Z= 0.141 Angle : 0.528 4.962 10206 Z= 0.280 Chirality : 0.046 0.146 1125 Planarity : 0.004 0.037 1302 Dihedral : 6.963 55.648 1217 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 8.10 % Allowed : 25.84 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.18 (0.28), residues: 954 helix: 1.43 (0.40), residues: 174 sheet: 0.39 (0.28), residues: 354 loop : -0.60 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 206 TYR 0.014 0.001 TYR B 93 PHE 0.014 0.001 PHE C 242 TRP 0.010 0.001 TRP C 258 HIS 0.002 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 7434) covalent geometry : angle 0.52113 / 0.28 (10158) SS BOND : bond 0.00371 / 0.22 ( 15) SS BOND : angle 1.48309 / 1.20 ( 30) hydrogen bonds : bond 0.03269 / 2.15 ( 308) hydrogen bonds : angle 4.75886 / 3.37 ( 930) link_NAG-ASN : bond 0.00085 / 0.05 ( 6) link_NAG-ASN : angle 1.13744 / 0.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 86 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7771 (t80) cc_final: 0.7445 (t80) REVERT: A 277 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7643 (ttt90) REVERT: B 122 PHE cc_start: 0.7618 (t80) cc_final: 0.7001 (t80) REVERT: B 132 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: B 186 GLU cc_start: 0.8356 (pt0) cc_final: 0.8026 (pt0) REVERT: B 237 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 307 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8016 (ptt-90) REVERT: C 122 PHE cc_start: 0.8158 (t80) cc_final: 0.7864 (t80) REVERT: C 237 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 344 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7754 (t80) outliers start: 53 outliers final: 43 residues processed: 125 average time/residue: 0.0830 time to fit residues: 14.4518 Evaluate side-chains 126 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 79 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN B 52 GLN C 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.097057 restraints weight = 10835.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.100203 restraints weight = 6817.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.102307 restraints weight = 5146.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.103598 restraints weight = 4338.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104293 restraints weight = 3935.174| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7455 Z= 0.186 Angle : 0.572 5.693 10206 Z= 0.305 Chirality : 0.048 0.155 1125 Planarity : 0.004 0.047 1302 Dihedral : 7.078 53.530 1217 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 8.56 % Allowed : 25.84 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.06 (0.29), residues: 954 helix: 1.34 (0.40), residues: 174 sheet: 0.22 (0.28), residues: 360 loop : -0.60 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 206 TYR 0.017 0.001 TYR A 93 PHE 0.015 0.002 PHE C 242 TRP 0.012 0.001 TRP C 258 HIS 0.002 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 7434) covalent geometry : angle 0.56475 / 0.30 (10158) SS BOND : bond 0.00419 / 0.25 ( 15) SS BOND : angle 1.54987 / 1.25 ( 30) hydrogen bonds : bond 0.03719 / 2.44 ( 308) hydrogen bonds : angle 4.91360 / 3.47 ( 930) link_NAG-ASN : bond 0.00153 / 0.07 ( 6) link_NAG-ASN : angle 1.29783 / 0.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 85 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7771 (t80) cc_final: 0.7433 (t80) REVERT: A 277 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7692 (ttt90) REVERT: B 122 PHE cc_start: 0.7565 (t80) cc_final: 0.6935 (t80) REVERT: B 186 GLU cc_start: 0.8344 (pt0) cc_final: 0.8127 (pt0) REVERT: B 237 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 307 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7981 (ptt-90) REVERT: C 122 PHE cc_start: 0.8162 (t80) cc_final: 0.7868 (t80) REVERT: C 237 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 344 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7757 (t80) outliers start: 56 outliers final: 45 residues processed: 127 average time/residue: 0.0826 time to fit residues: 14.4593 Evaluate side-chains 128 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 80 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.0670 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN C 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100048 restraints weight = 10670.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103195 restraints weight = 6719.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105306 restraints weight = 5083.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106570 restraints weight = 4292.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.107474 restraints weight = 3877.220| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7455 Z= 0.105 Angle : 0.516 5.441 10206 Z= 0.275 Chirality : 0.046 0.244 1125 Planarity : 0.004 0.039 1302 Dihedral : 6.790 52.459 1217 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.66 % Allowed : 28.44 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.28 (0.29), residues: 954 helix: 1.61 (0.41), residues: 174 sheet: 0.41 (0.28), residues: 354 loop : -0.56 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 206 TYR 0.015 0.001 TYR A 93 PHE 0.012 0.001 PHE C 242 TRP 0.006 0.001 TRP B 258 HIS 0.002 0.000 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 7434) covalent geometry : angle 0.51004 / 0.27 (10158) SS BOND : bond 0.00279 / 0.16 ( 15) SS BOND : angle 1.38368 / 1.10 ( 30) hydrogen bonds : bond 0.02911 / 1.94 ( 308) hydrogen bonds : angle 4.76256 / 3.35 ( 930) link_NAG-ASN : bond 0.00081 / 0.06 ( 6) link_NAG-ASN : angle 0.99186 / 0.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7764 (t80) cc_final: 0.7421 (t80) REVERT: A 277 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7685 (ttt90) REVERT: B 122 PHE cc_start: 0.7566 (t80) cc_final: 0.6931 (t80) REVERT: B 186 GLU cc_start: 0.8339 (pt0) cc_final: 0.7979 (pt0) REVERT: B 237 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7954 (tm-30) REVERT: B 307 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7984 (ptt-90) REVERT: C 122 PHE cc_start: 0.8119 (t80) cc_final: 0.7795 (t80) REVERT: C 148 GLN cc_start: 0.8371 (pm20) cc_final: 0.8056 (pm20) REVERT: C 237 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7980 (tm-30) outliers start: 37 outliers final: 30 residues processed: 116 average time/residue: 0.0875 time to fit residues: 13.8267 Evaluate side-chains 115 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 0.0000 chunk 79 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 overall best weight: 0.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101047 restraints weight = 10640.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104228 restraints weight = 6698.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.106337 restraints weight = 5048.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107746 restraints weight = 4259.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108163 restraints weight = 3834.277| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7455 Z= 0.098 Angle : 0.511 4.732 10206 Z= 0.272 Chirality : 0.046 0.235 1125 Planarity : 0.004 0.042 1302 Dihedral : 6.436 52.675 1215 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.89 % Allowed : 29.66 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.68 (0.29), residues: 954 helix: 2.57 (0.41), residues: 156 sheet: 0.50 (0.28), residues: 354 loop : -0.30 (0.33), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 206 TYR 0.011 0.001 TYR A 93 PHE 0.021 0.001 PHE C 344 TRP 0.006 0.001 TRP C 258 HIS 0.001 0.000 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 7434) covalent geometry : angle 0.50542 / 0.27 (10158) SS BOND : bond 0.00258 / 0.15 ( 15) SS BOND : angle 1.29982 / 1.03 ( 30) hydrogen bonds : bond 0.02760 / 1.84 ( 308) hydrogen bonds : angle 4.68956 / 3.31 ( 930) link_NAG-ASN : bond 0.00101 / 0.07 ( 6) link_NAG-ASN : angle 0.90087 / 0.65 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7707 (t80) cc_final: 0.7372 (t80) REVERT: A 277 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7564 (ttt90) REVERT: B 122 PHE cc_start: 0.7533 (t80) cc_final: 0.6904 (t80) REVERT: B 186 GLU cc_start: 0.8267 (pt0) cc_final: 0.8026 (pt0) REVERT: B 237 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 307 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7965 (ptt-90) REVERT: C 122 PHE cc_start: 0.8082 (t80) cc_final: 0.7770 (t80) REVERT: C 148 GLN cc_start: 0.8317 (pm20) cc_final: 0.8086 (pm20) REVERT: C 237 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7952 (tm-30) outliers start: 32 outliers final: 29 residues processed: 110 average time/residue: 0.0884 time to fit residues: 13.2986 Evaluate side-chains 122 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096210 restraints weight = 10824.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099283 restraints weight = 6847.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101309 restraints weight = 5189.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.102449 restraints weight = 4388.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102845 restraints weight = 3991.894| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7455 Z= 0.218 Angle : 0.609 6.769 10206 Z= 0.325 Chirality : 0.049 0.237 1125 Planarity : 0.004 0.058 1302 Dihedral : 6.863 52.847 1215 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.96 % Allowed : 28.90 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.19 (0.29), residues: 954 helix: 1.43 (0.39), residues: 174 sheet: 0.33 (0.28), residues: 360 loop : -0.53 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 206 TYR 0.018 0.002 TYR A 93 PHE 0.017 0.002 PHE C 344 TRP 0.015 0.001 TRP C 258 HIS 0.002 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 ( 7434) covalent geometry : angle 0.60167 / 0.32 (10158) SS BOND : bond 0.00463 / 0.28 ( 15) SS BOND : angle 1.50853 / 1.21 ( 30) hydrogen bonds : bond 0.03957 / 2.57 ( 308) hydrogen bonds : angle 4.93457 / 3.49 ( 930) link_NAG-ASN : bond 0.00176 / 0.08 ( 6) link_NAG-ASN : angle 1.37672 / 0.96 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1415.48 seconds wall clock time: 25 minutes 11.57 seconds (1511.57 seconds total)