Starting phenix.real_space_refine on Fri Jul 3 19:53:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uc8_64038/07_2026/9uc8_64038_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uc8_64038/07_2026/9uc8_64038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uc8_64038/07_2026/9uc8_64038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uc8_64038/07_2026/9uc8_64038.map" model { file = "/net/cci-nas-00/data/ceres_data/9uc8_64038/07_2026/9uc8_64038_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uc8_64038/07_2026/9uc8_64038_neut.cif" } resolution = 3.36 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= 0.018 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 24 5.49 5 S 64 5.16 5 C 10132 2.51 5 N 2668 2.21 5 O 2704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s 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: 15595 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2734 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 7, 'TRANS': 331} Chain breaks: 3 Chain: "B" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 831 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 239 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2734 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 7, 'TRANS': 331} Chain breaks: 3 Chain: "E" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 831 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 195 Chain: "F" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 239 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "G" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2734 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 7, 'TRANS': 331} Chain breaks: 3 Chain: "H" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 831 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 195 Chain: "I" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 239 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "J" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2734 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 7, 'TRANS': 331} Chain breaks: 3 Chain: "K" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 831 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 195 Chain: "L" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 239 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.70, per 1000 atoms: 0.24 Number of scatterers: 15595 At special positions: 0 Unit cell: (131.52, 131.52, 131.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 64 16.00 P 24 15.00 O 2704 8.00 N 2668 7.00 C 10132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 738.1 milliseconds 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3784 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 120 through 143 removed outlier: 4.490A pdb=" N VAL A 129 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER A 140 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.587A pdb=" N GLY A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 196 through 218 removed outlier: 3.545A pdb=" N ILE A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.792A pdb=" N ILE A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 260 through 284 removed outlier: 3.975A pdb=" N THR A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.967A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.932A pdb=" N CYS A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.969A pdb=" N ALA A 344 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.636A pdb=" N ALA A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 386 removed outlier: 3.768A pdb=" N GLN A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A 365 " --> pdb=" O GLN A 361 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 4.370A pdb=" N ALA A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N CYS A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 533 removed outlier: 3.973A pdb=" N ARG A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 576 removed outlier: 3.620A pdb=" N LEU A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Proline residue: A 570 - end of helix removed outlier: 3.646A pdb=" N SER A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.622A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 removed outlier: 4.171A pdb=" N PHE B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 removed outlier: 4.259A pdb=" N GLU B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.859A pdb=" N HIS B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.583A pdb=" N PHE B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 63 removed outlier: 3.797A pdb=" N VAL C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 120 through 143 removed outlier: 4.490A pdb=" N VAL D 129 " --> pdb=" O TYR D 125 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU D 131 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER D 140 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER D 143 " --> pdb=" O PHE D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 175 removed outlier: 3.586A pdb=" N GLY D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'D' and resid 196 through 218 removed outlier: 3.544A pdb=" N ILE D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 239 removed outlier: 3.791A pdb=" N ILE D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 258 Processing helix chain 'D' and resid 260 through 284 removed outlier: 3.976A pdb=" N THR D 264 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 269 " --> pdb=" O THR D 265 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU D 271 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 284 " --> pdb=" O VAL D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.967A pdb=" N ALA D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 303 " --> pdb=" O TYR D 299 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.932A pdb=" N CYS D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 345 removed outlier: 3.969A pdb=" N ALA D 344 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.636A pdb=" N ALA D 352 " --> pdb=" O GLY D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 386 removed outlier: 3.768A pdb=" N GLN D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS D 363 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE D 364 " --> pdb=" O ARG D 360 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN D 365 " --> pdb=" O GLN D 361 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG D 366 " --> pdb=" O LYS D 362 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN D 367 " --> pdb=" O HIS D 363 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE D 368 " --> pdb=" O PHE D 364 " (cutoff:3.500A) Proline residue: D 369 - end of helix removed outlier: 4.370A pdb=" N ALA D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP D 379 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG D 380 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS D 381 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D 386 " --> pdb=" O TYR D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 533 removed outlier: 3.972A pdb=" N ARG D 518 " --> pdb=" O ILE D 514 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 576 removed outlier: 3.619A pdb=" N LEU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS D 569 " --> pdb=" O GLN D 565 " (cutoff:3.500A) Proline residue: D 570 - end of helix removed outlier: 3.646A pdb=" N SER D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 22 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 37 through 40 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.623A pdb=" N LEU E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 75 removed outlier: 4.170A pdb=" N PHE E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 94 removed outlier: 4.259A pdb=" N GLU E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.859A pdb=" N HIS E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.583A pdb=" N PHE E 142 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 63 removed outlier: 3.797A pdb=" N VAL F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 143 removed outlier: 4.490A pdb=" N VAL G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE G 130 " --> pdb=" O HIS G 126 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU G 131 " --> pdb=" O PHE G 127 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE G 132 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL G 133 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER G 140 " --> pdb=" O CYS G 136 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER G 143 " --> pdb=" O PHE G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 175 removed outlier: 3.587A pdb=" N GLY G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 195 Processing helix chain 'G' and resid 196 through 218 removed outlier: 3.544A pdb=" N ILE G 200 " --> pdb=" O LYS G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 239 removed outlier: 3.791A pdb=" N ILE G 235 " --> pdb=" O ARG G 231 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU G 236 " --> pdb=" O PHE G 232 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 239 " --> pdb=" O ILE G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 258 Processing helix chain 'G' and resid 260 through 284 removed outlier: 3.976A pdb=" N THR G 264 " --> pdb=" O GLN G 260 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY G 269 " --> pdb=" O THR G 265 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE G 270 " --> pdb=" O LEU G 266 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU G 271 " --> pdb=" O TYR G 267 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY G 272 " --> pdb=" O ILE G 268 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU G 284 " --> pdb=" O VAL G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.966A pdb=" N ALA G 302 " --> pdb=" O SER G 298 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU G 303 " --> pdb=" O TYR G 299 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP G 304 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 336 removed outlier: 3.933A pdb=" N CYS G 331 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL G 334 " --> pdb=" O SER G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 345 removed outlier: 3.969A pdb=" N ALA G 344 " --> pdb=" O ALA G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 352 removed outlier: 3.635A pdb=" N ALA G 352 " --> pdb=" O GLY G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 386 removed outlier: 3.768A pdb=" N GLN G 359 " --> pdb=" O VAL G 355 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS G 363 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE G 364 " --> pdb=" O ARG G 360 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN G 365 " --> pdb=" O GLN G 361 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG G 366 " --> pdb=" O LYS G 362 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN G 367 " --> pdb=" O HIS G 363 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE G 368 " --> pdb=" O PHE G 364 " (cutoff:3.500A) Proline residue: G 369 - end of helix removed outlier: 4.370A pdb=" N ALA G 378 " --> pdb=" O LEU G 374 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP G 379 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG G 380 " --> pdb=" O GLN G 376 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N CYS G 381 " --> pdb=" O THR G 377 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN G 386 " --> pdb=" O TYR G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 533 removed outlier: 3.973A pdb=" N ARG G 518 " --> pdb=" O ILE G 514 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS G 528 " --> pdb=" O VAL G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 576 removed outlier: 3.620A pdb=" N LEU G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY G 568 " --> pdb=" O ASP G 564 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS G 569 " --> pdb=" O GLN G 565 " (cutoff:3.500A) Proline residue: G 570 - end of helix removed outlier: 3.646A pdb=" N SER G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 Processing helix chain 'H' and resid 25 through 36 Processing helix chain 'H' and resid 37 through 40 Processing helix chain 'H' and resid 45 through 58 removed outlier: 3.621A pdb=" N LEU H 49 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 4.171A pdb=" N PHE H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 94 removed outlier: 4.259A pdb=" N GLU H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE H 90 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 113 removed outlier: 3.859A pdb=" N HIS H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 132 Processing helix chain 'H' and resid 138 through 149 removed outlier: 3.583A pdb=" N PHE H 142 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 63 removed outlier: 3.797A pdb=" N VAL I 47 " --> pdb=" O GLU I 43 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 115 Processing helix chain 'J' and resid 120 through 143 removed outlier: 4.490A pdb=" N VAL J 129 " --> pdb=" O TYR J 125 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE J 130 " --> pdb=" O HIS J 126 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU J 131 " --> pdb=" O PHE J 127 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE J 132 " --> pdb=" O ALA J 128 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL J 133 " --> pdb=" O VAL J 129 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER J 140 " --> pdb=" O CYS J 136 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL J 141 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER J 143 " --> pdb=" O PHE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 175 removed outlier: 3.587A pdb=" N GLY J 168 " --> pdb=" O VAL J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 195 Processing helix chain 'J' and resid 196 through 218 removed outlier: 3.544A pdb=" N ILE J 200 " --> pdb=" O LYS J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 239 removed outlier: 3.792A pdb=" N ILE J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU J 236 " --> pdb=" O PHE J 232 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU J 239 " --> pdb=" O ILE J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 258 Processing helix chain 'J' and resid 260 through 284 removed outlier: 3.976A pdb=" N THR J 264 " --> pdb=" O GLN J 260 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY J 269 " --> pdb=" O THR J 265 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE J 270 " --> pdb=" O LEU J 266 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU J 271 " --> pdb=" O TYR J 267 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY J 272 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU J 284 " --> pdb=" O VAL J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 311 removed outlier: 3.966A pdb=" N ALA J 302 " --> pdb=" O SER J 298 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU J 303 " --> pdb=" O TYR J 299 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP J 304 " --> pdb=" O ALA J 300 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR J 311 " --> pdb=" O VAL J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 336 removed outlier: 3.932A pdb=" N CYS J 331 " --> pdb=" O THR J 327 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL J 334 " --> pdb=" O SER J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 341 through 345 removed outlier: 3.969A pdb=" N ALA J 344 " --> pdb=" O ALA J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 352 removed outlier: 3.636A pdb=" N ALA J 352 " --> pdb=" O GLY J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 386 removed outlier: 3.768A pdb=" N GLN J 359 " --> pdb=" O VAL J 355 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS J 363 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE J 364 " --> pdb=" O ARG J 360 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN J 365 " --> pdb=" O GLN J 361 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG J 366 " --> pdb=" O LYS J 362 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN J 367 " --> pdb=" O HIS J 363 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE J 368 " --> pdb=" O PHE J 364 " (cutoff:3.500A) Proline residue: J 369 - end of helix removed outlier: 4.369A pdb=" N ALA J 378 " --> pdb=" O LEU J 374 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP J 379 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG J 380 " --> pdb=" O GLN J 376 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS J 381 " --> pdb=" O THR J 377 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN J 386 " --> pdb=" O TYR J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 507 through 533 removed outlier: 3.973A pdb=" N ARG J 518 " --> pdb=" O ILE J 514 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS J 528 " --> pdb=" O VAL J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 576 removed outlier: 3.619A pdb=" N LEU J 552 " --> pdb=" O GLY J 548 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY J 568 " --> pdb=" O ASP J 564 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS J 569 " --> pdb=" O GLN J 565 " (cutoff:3.500A) Proline residue: J 570 - end of helix removed outlier: 3.647A pdb=" N SER J 575 " --> pdb=" O SER J 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 22 Processing helix chain 'K' and resid 25 through 36 Processing helix chain 'K' and resid 37 through 40 Processing helix chain 'K' and resid 45 through 58 removed outlier: 3.622A pdb=" N LEU K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 75 removed outlier: 4.171A pdb=" N PHE K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 94 removed outlier: 4.260A pdb=" N GLU K 83 " --> pdb=" O ASP K 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE K 90 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 113 removed outlier: 3.858A pdb=" N HIS K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 138 through 149 removed outlier: 3.582A pdb=" N PHE K 142 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 63 removed outlier: 3.797A pdb=" N VAL L 47 " --> pdb=" O GLU L 43 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE L 54 " --> pdb=" O VAL L 50 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2784 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2336 1.31 - 1.43: 4519 1.43 - 1.56: 8921 1.56 - 1.68: 36 1.68 - 1.81: 104 Bond restraints: 15916 Sorted by residual: bond pdb=" C TRP G 158 " pdb=" N MET G 159 " ideal model delta sigma weight residual 1.334 1.232 0.103 1.27e-02 6.20e+03 6.54e+01 bond pdb=" C TRP J 158 " pdb=" N MET J 159 " ideal model delta sigma weight residual 1.334 1.232 0.103 1.27e-02 6.20e+03 6.54e+01 bond pdb=" C TRP A 158 " pdb=" N MET A 159 " ideal model delta sigma weight residual 1.334 1.232 0.103 1.27e-02 6.20e+03 6.54e+01 bond pdb=" C GLN A 560 " pdb=" N ARG A 561 " ideal model delta sigma weight residual 1.335 1.230 0.105 1.30e-02 5.92e+03 6.49e+01 bond pdb=" C GLN D 560 " pdb=" N ARG D 561 " ideal model delta sigma weight residual 1.335 1.230 0.105 1.30e-02 5.92e+03 6.49e+01 ... (remaining 15911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 20436 2.39 - 4.78: 767 4.78 - 7.17: 302 7.17 - 9.56: 47 9.56 - 11.95: 28 Bond angle restraints: 21580 Sorted by residual: angle pdb=" N ILE G 257 " pdb=" CA ILE G 257 " pdb=" C ILE G 257 " ideal model delta sigma weight residual 110.42 116.53 -6.11 9.60e-01 1.09e+00 4.05e+01 angle pdb=" N ILE J 257 " pdb=" CA ILE J 257 " pdb=" C ILE J 257 " ideal model delta sigma weight residual 110.42 116.52 -6.10 9.60e-01 1.09e+00 4.03e+01 angle pdb=" N ILE A 257 " pdb=" CA ILE A 257 " pdb=" C ILE A 257 " ideal model delta sigma weight residual 110.42 116.50 -6.08 9.60e-01 1.09e+00 4.01e+01 angle pdb=" N ILE D 257 " pdb=" CA ILE D 257 " pdb=" C ILE D 257 " ideal model delta sigma weight residual 110.42 116.49 -6.07 9.60e-01 1.09e+00 3.99e+01 angle pdb=" N VAL J 141 " pdb=" CA VAL J 141 " pdb=" C VAL J 141 " ideal model delta sigma weight residual 113.07 104.62 8.45 1.36e+00 5.41e-01 3.86e+01 ... (remaining 21575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 8208 16.89 - 33.78: 664 33.78 - 50.67: 168 50.67 - 67.56: 48 67.56 - 84.45: 12 Dihedral angle restraints: 9100 sinusoidal: 3220 harmonic: 5880 Sorted by residual: dihedral pdb=" CA SER H 102 " pdb=" C SER H 102 " pdb=" N ALA H 103 " pdb=" CA ALA H 103 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA SER E 102 " pdb=" C SER E 102 " pdb=" N ALA E 103 " pdb=" CA ALA E 103 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA SER K 102 " pdb=" C SER K 102 " pdb=" N ALA K 103 " pdb=" CA ALA K 103 " ideal model delta harmonic sigma weight residual -180.00 -154.99 -25.01 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 9097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2005 0.059 - 0.118: 392 0.118 - 0.177: 63 0.177 - 0.236: 16 0.236 - 0.295: 8 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CA ARG D 231 " pdb=" N ARG D 231 " pdb=" C ARG D 231 " pdb=" CB ARG D 231 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ARG G 231 " pdb=" N ARG G 231 " pdb=" C ARG G 231 " pdb=" CB ARG G 231 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ARG A 231 " pdb=" N ARG A 231 " pdb=" C ARG A 231 " pdb=" CB ARG A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2481 not shown) Planarity restraints: 2644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 232 " -0.016 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C PHE G 232 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE G 232 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU G 233 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 232 " 0.016 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C PHE A 232 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE A 232 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 233 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 232 " -0.016 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C PHE D 232 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE D 232 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU D 233 " -0.018 2.00e-02 2.50e+03 ... (remaining 2641 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 4783 2.81 - 3.39: 17485 3.39 - 3.98: 25072 3.98 - 4.56: 33644 4.56 - 5.14: 49492 Nonbonded interactions: 130476 Sorted by model distance: nonbonded pdb=" CG LYS J 557 " pdb=" NH1 ARG J 561 " model vdw 2.229 3.520 nonbonded pdb=" CG LYS A 557 " pdb=" NH1 ARG A 561 " model vdw 2.229 3.520 nonbonded pdb=" CG LYS G 557 " pdb=" NH1 ARG G 561 " model vdw 2.229 3.520 nonbonded pdb=" CG LYS D 557 " pdb=" NH1 ARG D 561 " model vdw 2.230 3.520 nonbonded pdb=" O LEU A 572 " pdb=" OG SER A 575 " model vdw 2.296 3.040 ... (remaining 130471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 104 through 701) selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.200 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 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 0.105 15916 Z= 0.551 Angle : 1.257 11.948 21580 Z= 0.737 Chirality : 0.051 0.295 2484 Planarity : 0.006 0.072 2644 Dihedral : 14.138 84.452 5316 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.59 % Favored : 94.21 % Rotamer: Outliers : 1.45 % Allowed : 9.64 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.16), residues: 2004 helix: -1.54 (0.11), residues: 1416 sheet: None (None), residues: 0 loop : -2.95 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.022 0.002 TYR G 315 PHE 0.015 0.002 PHE D 232 TRP 0.024 0.003 TRP G 304 HIS 0.012 0.002 HIS J 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00874 / 0.55 (15916) covalent geometry : angle 1.25734 / 0.74 (21580) hydrogen bonds : bond 0.16336 / 10.55 ( 936) hydrogen bonds : angle 6.52282 / 4.62 ( 2784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 253 time to evaluate : 0.596 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 273 average time/residue: 0.1399 time to fit residues: 55.1322 Evaluate side-chains 219 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 211 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 234 GLN Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 234 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS A 531 GLN A 560 GLN B 108 HIS D 126 HIS D 531 GLN D 560 GLN E 108 HIS G 126 HIS G 531 GLN G 560 GLN H 108 HIS J 126 HIS J 531 GLN J 560 GLN K 108 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.254069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.226797 restraints weight = 20055.840| |-----------------------------------------------------------------------------| r_work (start): 0.4635 rms_B_bonded: 1.67 r_work: 0.4451 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4430 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15916 Z= 0.151 Angle : 0.676 12.115 21580 Z= 0.348 Chirality : 0.041 0.175 2484 Planarity : 0.005 0.062 2644 Dihedral : 9.392 77.150 2364 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.68 % Allowed : 15.07 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.18), residues: 2004 helix: -0.16 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -2.66 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.013 0.001 TYR J 111 PHE 0.014 0.002 PHE H 66 TRP 0.015 0.001 TRP J 304 HIS 0.008 0.001 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (15916) covalent geometry : angle 0.67570 / 0.35 (21580) hydrogen bonds : bond 0.06082 / 4.15 ( 936) hydrogen bonds : angle 4.49685 / 3.15 ( 2784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 12 residues processed: 245 average time/residue: 0.1315 time to fit residues: 47.4485 Evaluate side-chains 217 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain K residue 139 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 133 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 178 optimal weight: 10.0000 chunk 187 optimal weight: 50.0000 chunk 115 optimal weight: 0.9990 chunk 134 optimal weight: 30.0000 chunk 54 optimal weight: 0.0060 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN ** J 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.254815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.227672 restraints weight = 20613.448| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 1.75 r_work: 0.4448 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4426 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15916 Z= 0.127 Angle : 0.634 13.490 21580 Z= 0.314 Chirality : 0.039 0.154 2484 Planarity : 0.004 0.066 2644 Dihedral : 8.468 63.376 2344 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.90 % Allowed : 18.33 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 2004 helix: 0.59 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -2.44 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.015 0.001 TYR A 382 PHE 0.014 0.001 PHE E 13 TRP 0.013 0.001 TRP G 304 HIS 0.010 0.001 HIS J 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (15916) covalent geometry : angle 0.63413 / 0.31 (21580) hydrogen bonds : bond 0.05042 / 3.39 ( 936) hydrogen bonds : angle 4.12297 / 2.88 ( 2784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.554 Fit side-chains REVERT: A 159 MET cc_start: 0.6361 (mmp) cc_final: 0.5903 (mmm) REVERT: A 227 ILE cc_start: 0.6943 (tp) cc_final: 0.6590 (pt) REVERT: D 159 MET cc_start: 0.6291 (mmp) cc_final: 0.5846 (mmm) REVERT: D 227 ILE cc_start: 0.6938 (tp) cc_final: 0.6586 (pt) REVERT: G 159 MET cc_start: 0.6280 (mmp) cc_final: 0.5838 (mmm) REVERT: G 227 ILE cc_start: 0.6939 (tp) cc_final: 0.6585 (pt) REVERT: J 227 ILE cc_start: 0.6950 (tp) cc_final: 0.6598 (pt) outliers start: 40 outliers final: 19 residues processed: 242 average time/residue: 0.1275 time to fit residues: 45.7458 Evaluate side-chains 211 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain D residue 105 HIS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain J residue 105 HIS Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain K residue 139 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 127 optimal weight: 0.8980 chunk 181 optimal weight: 0.0980 chunk 153 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 113 optimal weight: 0.0040 chunk 72 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.253102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.209743 restraints weight = 20031.825| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 3.15 r_work: 0.4196 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15916 Z= 0.111 Angle : 0.594 11.948 21580 Z= 0.294 Chirality : 0.037 0.157 2484 Planarity : 0.004 0.067 2644 Dihedral : 8.193 66.393 2344 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.55 % Allowed : 20.00 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 2004 helix: 1.05 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -2.30 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 366 TYR 0.011 0.001 TYR D 382 PHE 0.010 0.001 PHE D 573 TRP 0.011 0.001 TRP J 304 HIS 0.006 0.001 HIS G 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (15916) covalent geometry : angle 0.59391 / 0.29 (21580) hydrogen bonds : bond 0.04075 / 2.74 ( 936) hydrogen bonds : angle 3.86034 / 2.69 ( 2784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.592 Fit side-chains REVERT: A 159 MET cc_start: 0.6263 (mmp) cc_final: 0.5803 (mmm) REVERT: A 227 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6760 (pt) REVERT: D 159 MET cc_start: 0.6237 (mmp) cc_final: 0.5766 (mmm) REVERT: D 227 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6755 (pt) REVERT: G 159 MET cc_start: 0.6235 (mmp) cc_final: 0.5769 (mmm) REVERT: G 227 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6754 (pt) REVERT: J 227 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6771 (pt) outliers start: 49 outliers final: 20 residues processed: 237 average time/residue: 0.1088 time to fit residues: 40.7460 Evaluate side-chains 220 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain D residue 105 HIS Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain K residue 139 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 181 optimal weight: 0.2980 chunk 190 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.252950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.211925 restraints weight = 20130.222| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 3.12 r_work: 0.4196 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15916 Z= 0.111 Angle : 0.600 10.093 21580 Z= 0.293 Chirality : 0.037 0.162 2484 Planarity : 0.004 0.067 2644 Dihedral : 7.990 66.542 2344 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.41 % Allowed : 21.52 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 2004 helix: 1.22 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -2.03 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 231 TYR 0.013 0.001 TYR J 171 PHE 0.018 0.001 PHE E 13 TRP 0.011 0.001 TRP D 304 HIS 0.006 0.001 HIS G 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (15916) covalent geometry : angle 0.60031 / 0.29 (21580) hydrogen bonds : bond 0.04135 / 2.78 ( 936) hydrogen bonds : angle 3.76818 / 2.62 ( 2784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.604 Fit side-chains REVERT: A 159 MET cc_start: 0.6267 (mmp) cc_final: 0.6034 (mmt) REVERT: A 227 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6842 (pt) REVERT: A 520 MET cc_start: 0.5065 (mtt) cc_final: 0.4337 (ttt) REVERT: D 159 MET cc_start: 0.6176 (mmp) cc_final: 0.5736 (mmm) REVERT: D 227 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6824 (pt) REVERT: D 520 MET cc_start: 0.5058 (mtt) cc_final: 0.4329 (ttt) REVERT: G 159 MET cc_start: 0.6170 (mmp) cc_final: 0.5730 (mmm) REVERT: G 227 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6834 (pt) REVERT: G 520 MET cc_start: 0.5083 (mtt) cc_final: 0.4344 (ttt) REVERT: J 227 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.6867 (pt) REVERT: J 520 MET cc_start: 0.5051 (mtt) cc_final: 0.4333 (ttt) outliers start: 47 outliers final: 24 residues processed: 241 average time/residue: 0.1123 time to fit residues: 41.9338 Evaluate side-chains 224 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 366 ARG Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain J residue 105 HIS Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 366 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 150 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.251107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.205929 restraints weight = 19649.596| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 3.15 r_work: 0.4155 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15916 Z= 0.129 Angle : 0.642 12.942 21580 Z= 0.311 Chirality : 0.039 0.181 2484 Planarity : 0.004 0.065 2644 Dihedral : 7.919 64.489 2344 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.48 % Allowed : 22.61 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 2004 helix: 1.23 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -1.98 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 231 TYR 0.022 0.002 TYR J 382 PHE 0.011 0.001 PHE D 130 TRP 0.012 0.001 TRP A 304 HIS 0.008 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15916) covalent geometry : angle 0.64161 / 0.31 (21580) hydrogen bonds : bond 0.04790 / 3.19 ( 936) hydrogen bonds : angle 3.79175 / 2.63 ( 2784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 0.620 Fit side-chains REVERT: A 159 MET cc_start: 0.6348 (mmp) cc_final: 0.6088 (mmt) REVERT: A 227 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6823 (pt) REVERT: A 520 MET cc_start: 0.5186 (mtt) cc_final: 0.4387 (ttt) REVERT: B 64 ILE cc_start: 0.3275 (OUTLIER) cc_final: 0.2656 (tp) REVERT: D 159 MET cc_start: 0.6243 (mmp) cc_final: 0.5781 (mmm) REVERT: D 227 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6818 (pt) REVERT: D 520 MET cc_start: 0.5126 (mtt) cc_final: 0.4333 (ttt) REVERT: E 64 ILE cc_start: 0.3207 (OUTLIER) cc_final: 0.2605 (tp) REVERT: G 159 MET cc_start: 0.6234 (mmp) cc_final: 0.5777 (mmm) REVERT: G 227 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6810 (pt) REVERT: G 520 MET cc_start: 0.5219 (mtt) cc_final: 0.4404 (ttt) REVERT: H 64 ILE cc_start: 0.3273 (OUTLIER) cc_final: 0.2662 (tp) REVERT: J 227 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6827 (pt) REVERT: J 520 MET cc_start: 0.5158 (mtt) cc_final: 0.4374 (ttt) REVERT: K 64 ILE cc_start: 0.3167 (OUTLIER) cc_final: 0.2566 (tp) outliers start: 48 outliers final: 28 residues processed: 227 average time/residue: 0.1193 time to fit residues: 41.4701 Evaluate side-chains 223 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain D residue 105 HIS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 366 ARG Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain J residue 105 HIS Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 366 ARG Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 139 TYR Chi-restraints excluded: chain K residue 143 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 134 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.248187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.202726 restraints weight = 19439.457| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 3.20 r_work: 0.4111 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work: 0.4077 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15916 Z= 0.174 Angle : 0.688 10.957 21580 Z= 0.339 Chirality : 0.041 0.197 2484 Planarity : 0.004 0.064 2644 Dihedral : 8.029 60.895 2344 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.84 % Allowed : 22.75 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 2004 helix: 1.12 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -1.97 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 231 TYR 0.029 0.002 TYR G 382 PHE 0.014 0.002 PHE J 130 TRP 0.013 0.001 TRP J 304 HIS 0.010 0.001 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (15916) covalent geometry : angle 0.68751 / 0.34 (21580) hydrogen bonds : bond 0.05934 / 3.94 ( 936) hydrogen bonds : angle 3.91893 / 2.72 ( 2784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 0.695 Fit side-chains REVERT: A 142 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6550 (mp) REVERT: A 159 MET cc_start: 0.6320 (mmp) cc_final: 0.5848 (mmm) REVERT: A 520 MET cc_start: 0.5261 (mtt) cc_final: 0.4437 (ttt) REVERT: B 64 ILE cc_start: 0.3150 (OUTLIER) cc_final: 0.2536 (tp) REVERT: D 159 MET cc_start: 0.6340 (mmp) cc_final: 0.5880 (mmm) REVERT: D 520 MET cc_start: 0.5179 (mtt) cc_final: 0.4366 (ttt) REVERT: E 64 ILE cc_start: 0.3108 (OUTLIER) cc_final: 0.2503 (tp) REVERT: G 142 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6544 (mp) REVERT: G 159 MET cc_start: 0.6321 (mmp) cc_final: 0.5871 (mmm) REVERT: G 520 MET cc_start: 0.5258 (mtt) cc_final: 0.4435 (ttt) REVERT: H 64 ILE cc_start: 0.3163 (OUTLIER) cc_final: 0.2547 (tp) REVERT: J 520 MET cc_start: 0.5222 (mtt) cc_final: 0.4416 (ttt) REVERT: K 64 ILE cc_start: 0.3119 (OUTLIER) cc_final: 0.2515 (tp) outliers start: 53 outliers final: 38 residues processed: 223 average time/residue: 0.1183 time to fit residues: 40.2922 Evaluate side-chains 229 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain D residue 105 HIS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 366 ARG Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain J residue 105 HIS Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 366 ARG Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 139 TYR Chi-restraints excluded: chain K residue 143 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 37 optimal weight: 40.0000 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 148 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.256705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.232312 restraints weight = 20500.099| |-----------------------------------------------------------------------------| r_work (start): 0.4679 rms_B_bonded: 1.60 r_work: 0.4489 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4462 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15916 Z= 0.110 Angle : 0.603 9.951 21580 Z= 0.292 Chirality : 0.037 0.222 2484 Planarity : 0.004 0.065 2644 Dihedral : 7.686 62.118 2344 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.97 % Allowed : 23.84 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.20), residues: 2004 helix: 1.33 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -2.03 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 231 TYR 0.021 0.001 TYR G 382 PHE 0.010 0.001 PHE J 167 TRP 0.013 0.001 TRP J 304 HIS 0.010 0.001 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (15916) covalent geometry : angle 0.60328 / 0.29 (21580) hydrogen bonds : bond 0.04018 / 2.66 ( 936) hydrogen bonds : angle 3.74927 / 2.60 ( 2784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.622 Fit side-chains REVERT: A 159 MET cc_start: 0.6221 (mmp) cc_final: 0.5779 (mmm) REVERT: A 227 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6834 (pt) REVERT: A 520 MET cc_start: 0.3841 (mtt) cc_final: 0.3630 (ttt) REVERT: B 64 ILE cc_start: 0.2889 (OUTLIER) cc_final: 0.2238 (tp) REVERT: D 159 MET cc_start: 0.6103 (mmp) cc_final: 0.5662 (mmm) REVERT: D 227 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6826 (pt) REVERT: D 520 MET cc_start: 0.3776 (mtt) cc_final: 0.3570 (ttt) REVERT: E 64 ILE cc_start: 0.2844 (OUTLIER) cc_final: 0.2200 (tp) REVERT: G 159 MET cc_start: 0.6100 (mmp) cc_final: 0.5658 (mmm) REVERT: G 227 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6833 (pt) REVERT: G 520 MET cc_start: 0.3851 (mtt) cc_final: 0.3636 (ttt) REVERT: H 64 ILE cc_start: 0.2895 (OUTLIER) cc_final: 0.2243 (tp) REVERT: J 227 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6832 (pt) REVERT: J 520 MET cc_start: 0.3873 (mtt) cc_final: 0.3646 (ttt) REVERT: K 64 ILE cc_start: 0.2863 (OUTLIER) cc_final: 0.2218 (tp) outliers start: 41 outliers final: 28 residues processed: 219 average time/residue: 0.1263 time to fit residues: 41.5172 Evaluate side-chains 226 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 366 ARG Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 366 ARG Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 139 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 163 optimal weight: 0.0670 chunk 103 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 147 optimal weight: 0.2980 chunk 195 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.257300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.232554 restraints weight = 20510.304| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 1.63 r_work: 0.4495 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4472 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15916 Z= 0.112 Angle : 0.607 10.758 21580 Z= 0.295 Chirality : 0.038 0.210 2484 Planarity : 0.004 0.065 2644 Dihedral : 7.509 61.773 2344 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.90 % Allowed : 23.70 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 2004 helix: 1.39 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -2.04 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 109 TYR 0.019 0.001 TYR G 382 PHE 0.013 0.001 PHE G 167 TRP 0.012 0.001 TRP J 304 HIS 0.010 0.001 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (15916) covalent geometry : angle 0.60683 / 0.30 (21580) hydrogen bonds : bond 0.04141 / 2.75 ( 936) hydrogen bonds : angle 3.70429 / 2.57 ( 2784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.618 Fit side-chains REVERT: A 159 MET cc_start: 0.6486 (mmp) cc_final: 0.6013 (mmm) REVERT: A 227 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6883 (pt) REVERT: B 64 ILE cc_start: 0.2844 (OUTLIER) cc_final: 0.2197 (tp) REVERT: D 159 MET cc_start: 0.6222 (mmp) cc_final: 0.5805 (mmm) REVERT: D 227 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6854 (pt) REVERT: E 64 ILE cc_start: 0.2818 (OUTLIER) cc_final: 0.2203 (tp) REVERT: G 227 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6877 (pt) REVERT: H 64 ILE cc_start: 0.2862 (OUTLIER) cc_final: 0.2213 (tp) REVERT: J 227 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6869 (pt) REVERT: K 64 ILE cc_start: 0.2840 (OUTLIER) cc_final: 0.2230 (tp) outliers start: 40 outliers final: 28 residues processed: 212 average time/residue: 0.1276 time to fit residues: 40.3399 Evaluate side-chains 219 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain D residue 105 HIS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 366 ARG Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain J residue 105 HIS Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 366 ARG Chi-restraints excluded: chain K residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 142 optimal weight: 0.0470 chunk 190 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.255812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.228268 restraints weight = 20462.508| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 1.68 r_work: 0.4481 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4460 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15916 Z= 0.120 Angle : 0.622 11.313 21580 Z= 0.300 Chirality : 0.038 0.209 2484 Planarity : 0.004 0.065 2644 Dihedral : 7.436 59.516 2344 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.12 % Allowed : 23.70 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.77 (0.20), residues: 2004 helix: 1.36 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.01 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.019 0.001 TYR G 382 PHE 0.009 0.001 PHE A 130 TRP 0.012 0.001 TRP J 304 HIS 0.009 0.001 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (15916) covalent geometry : angle 0.62232 / 0.30 (21580) hydrogen bonds : bond 0.04381 / 2.90 ( 936) hydrogen bonds : angle 3.69472 / 2.56 ( 2784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.581 Fit side-chains REVERT: A 227 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6855 (pt) REVERT: B 64 ILE cc_start: 0.2856 (OUTLIER) cc_final: 0.2206 (tp) REVERT: D 159 MET cc_start: 0.6135 (mmp) cc_final: 0.5674 (mmm) REVERT: D 227 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6875 (pt) REVERT: E 64 ILE cc_start: 0.2807 (OUTLIER) cc_final: 0.2195 (tp) REVERT: G 227 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.6856 (pt) REVERT: H 64 ILE cc_start: 0.2877 (OUTLIER) cc_final: 0.2231 (tp) REVERT: J 227 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.6885 (pt) REVERT: K 64 ILE cc_start: 0.2843 (OUTLIER) cc_final: 0.2227 (tp) outliers start: 43 outliers final: 29 residues processed: 203 average time/residue: 0.1260 time to fit residues: 37.4132 Evaluate side-chains 208 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 366 ARG Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain J residue 105 HIS Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 366 ARG Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 139 TYR Chi-restraints excluded: chain K residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 51 optimal weight: 0.0470 chunk 112 optimal weight: 0.3980 chunk 61 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 188 optimal weight: 40.0000 chunk 164 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 overall best weight: 1.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 HIS ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS ** D 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 HIS ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS ** J 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.250309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.225329 restraints weight = 20136.338| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 1.57 r_work: 0.4431 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4406 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15916 Z= 0.207 Angle : 0.742 12.482 21580 Z= 0.368 Chirality : 0.043 0.190 2484 Planarity : 0.005 0.063 2644 Dihedral : 7.834 58.775 2344 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.62 % Allowed : 24.06 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 2004 helix: 1.05 (0.14), residues: 1460 sheet: None (None), residues: 0 loop : -2.08 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 109 TYR 0.018 0.002 TYR G 382 PHE 0.017 0.002 PHE A 296 TRP 0.013 0.002 TRP J 304 HIS 0.009 0.001 HIS G 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (15916) covalent geometry : angle 0.74207 / 0.37 (21580) hydrogen bonds : bond 0.06744 / 4.47 ( 936) hydrogen bonds : angle 4.05160 / 2.81 ( 2784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4131.25 seconds wall clock time: 71 minutes 21.91 seconds (4281.91 seconds total)