Starting phenix.real_space_refine on Thu Aug 6 15:19:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uc8_64038/08_2026/9uc8_64038_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uc8_64038/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9uc8_64038/08_2026/9uc8_64038_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uc8_64038/08_2026/9uc8_64038_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uc8_64038/08_2026/9uc8_64038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uc8_64038/08_2026/9uc8_64038.map" } 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-2.2rc3-6140/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, 50 Unusual residues: {' K': 3, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 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: 3.55, per 1000 atoms: 0.23 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: 0.87 Conformation dependent library (CDL) restraints added in 507.4 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: 0.38 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: 1.84 Time building geometry restraints manager: 1.20 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.760 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- 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 : 0.390 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 273 average time/residue: 0.1219 time to fit residues: 48.1277 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 : 0.558 ------------------------------------------------------------------------------- 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 = 0.4859 r_free = 0.4859 target = 0.253840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.229620 restraints weight = 20232.636| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 1.55 r_work: 0.4469 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4442 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15916 Z= 0.153 Angle : 0.675 11.844 21580 Z= 0.347 Chirality : 0.040 0.178 2484 Planarity : 0.005 0.061 2644 Dihedral : 9.411 78.108 2364 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.68 % Allowed : 15.14 % Favored : 82.17 % 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: -1.34 (0.18), residues: 2004 helix: -0.19 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -2.71 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 561 TYR 0.012 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 0.00316 / 0.15 (15916) covalent geometry : angle 0.67468 / 0.35 (21580) hydrogen bonds : bond 0.06111 / 4.17 ( 936) hydrogen bonds : angle 4.50621 / 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 261 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.407 Fit side-chains 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: 244 average time/residue: 0.1223 time to fit residues: 44.1286 Evaluate side-chains 218 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 0.2980 chunk 129 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 23 optimal weight: 0.0270 chunk 103 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 187 optimal weight: 50.0000 chunk 115 optimal weight: 0.7980 chunk 134 optimal weight: 40.0000 chunk 54 optimal weight: 0.4980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN J 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.255591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.227813 restraints weight = 20439.577| |-----------------------------------------------------------------------------| r_work (start): 0.4644 rms_B_bonded: 1.76 r_work: 0.4457 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4436 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15916 Z= 0.123 Angle : 0.633 13.900 21580 Z= 0.312 Chirality : 0.039 0.157 2484 Planarity : 0.004 0.066 2644 Dihedral : 8.437 63.861 2344 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.61 % Allowed : 18.41 % Favored : 78.99 % 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: -0.27 (0.19), residues: 2004 helix: 0.61 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -2.45 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.018 0.001 TYR J 382 PHE 0.015 0.001 PHE E 13 TRP 0.013 0.001 TRP J 304 HIS 0.009 0.001 HIS J 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (15916) covalent geometry : angle 0.63306 / 0.31 (21580) hydrogen bonds : bond 0.04787 / 3.22 ( 936) hydrogen bonds : angle 4.08880 / 2.86 ( 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: 36 poor density : 218 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6314 (mmp) cc_final: 0.5864 (mmm) REVERT: A 227 ILE cc_start: 0.6860 (tp) cc_final: 0.6558 (pt) REVERT: D 159 MET cc_start: 0.6245 (mmp) cc_final: 0.5807 (mmm) REVERT: D 227 ILE cc_start: 0.6866 (tp) cc_final: 0.6559 (pt) REVERT: G 159 MET cc_start: 0.6237 (mmp) cc_final: 0.5798 (mmm) REVERT: G 227 ILE cc_start: 0.6852 (tp) cc_final: 0.6548 (pt) REVERT: J 227 ILE cc_start: 0.6907 (tp) cc_final: 0.6595 (pt) outliers start: 36 outliers final: 12 residues processed: 244 average time/residue: 0.1300 time to fit residues: 46.5978 Evaluate side-chains 213 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 142 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 139 TYR 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 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: 1.9990 chunk 181 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 161 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 113 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- 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 112 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.250386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.216600 restraints weight = 20001.752| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 2.01 r_work: 0.4328 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.4284 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2682 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= 0.131 Angle : 0.634 12.035 21580 Z= 0.314 Chirality : 0.039 0.186 2484 Planarity : 0.004 0.067 2644 Dihedral : 8.303 64.754 2344 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.06 % Allowed : 19.35 % Favored : 76.59 % 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: 0.12 (0.19), residues: 2004 helix: 0.92 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -2.37 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 366 TYR 0.010 0.001 TYR J 171 PHE 0.011 0.001 PHE J 130 TRP 0.013 0.001 TRP J 304 HIS 0.006 0.001 HIS G 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15916) covalent geometry : angle 0.63352 / 0.31 (21580) hydrogen bonds : bond 0.04981 / 3.34 ( 936) hydrogen bonds : angle 3.97510 / 2.77 ( 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 253 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6402 (mmp) cc_final: 0.6149 (mmt) REVERT: A 227 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6658 (pt) REVERT: D 159 MET cc_start: 0.6363 (mmp) cc_final: 0.5898 (mmm) REVERT: D 227 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6649 (pt) REVERT: G 159 MET cc_start: 0.6326 (mmp) cc_final: 0.5875 (mmm) REVERT: G 227 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6647 (pt) REVERT: J 227 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6614 (pt) outliers start: 56 outliers final: 23 residues processed: 235 average time/residue: 0.1268 time to fit residues: 44.2934 Evaluate side-chains 222 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 139 TYR 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 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 139 TYR 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 139 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4805 r_free = 0.4805 target = 0.249744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.205402 restraints weight = 19883.208| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 3.14 r_work: 0.4142 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work: 0.4109 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15916 Z= 0.138 Angle : 0.664 10.439 21580 Z= 0.321 Chirality : 0.039 0.179 2484 Planarity : 0.004 0.066 2644 Dihedral : 8.201 64.154 2344 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.77 % Allowed : 20.72 % Favored : 75.51 % 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: 0.28 (0.19), residues: 2004 helix: 1.05 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.36 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 533 TYR 0.018 0.002 TYR A 382 PHE 0.010 0.001 PHE J 130 TRP 0.013 0.001 TRP G 304 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (15916) covalent geometry : angle 0.66431 / 0.32 (21580) hydrogen bonds : bond 0.05150 / 3.44 ( 936) hydrogen bonds : angle 3.93791 / 2.74 ( 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 234 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6386 (mmp) cc_final: 0.6160 (mmt) REVERT: A 533 ARG cc_start: 0.7720 (tpt90) cc_final: 0.7399 (tpt90) REVERT: D 159 MET cc_start: 0.6336 (mmp) cc_final: 0.5894 (mmm) REVERT: G 159 MET cc_start: 0.6324 (mmp) cc_final: 0.5886 (mmm) REVERT: G 533 ARG cc_start: 0.7656 (tpt90) cc_final: 0.7326 (tpt90) outliers start: 52 outliers final: 26 residues processed: 227 average time/residue: 0.1268 time to fit residues: 43.0040 Evaluate side-chains 208 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 139 TYR 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 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 139 TYR 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 366 ARG Chi-restraints excluded: chain K residue 139 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4801 r_free = 0.4801 target = 0.249068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.204843 restraints weight = 19550.817| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 3.17 r_work: 0.4142 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work: 0.4115 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15916 Z= 0.147 Angle : 0.662 10.955 21580 Z= 0.323 Chirality : 0.039 0.169 2484 Planarity : 0.004 0.064 2644 Dihedral : 8.189 63.109 2344 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.70 % Allowed : 22.10 % Favored : 74.20 % 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: 0.40 (0.19), residues: 2004 helix: 1.12 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -2.20 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 231 TYR 0.023 0.002 TYR A 382 PHE 0.012 0.001 PHE G 130 TRP 0.014 0.001 TRP J 304 HIS 0.010 0.002 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (15916) covalent geometry : angle 0.66249 / 0.32 (21580) hydrogen bonds : bond 0.05367 / 3.57 ( 936) hydrogen bonds : angle 3.93119 / 2.73 ( 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 235 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6326 (mmp) cc_final: 0.6075 (mmt) REVERT: A 520 MET cc_start: 0.5120 (mtt) cc_final: 0.4321 (ttt) REVERT: B 64 ILE cc_start: 0.3385 (OUTLIER) cc_final: 0.2723 (tp) REVERT: D 159 MET cc_start: 0.6326 (mmp) cc_final: 0.5865 (mmm) REVERT: E 64 ILE cc_start: 0.3304 (OUTLIER) cc_final: 0.2649 (tp) REVERT: G 159 MET cc_start: 0.6322 (mmp) cc_final: 0.5862 (mmm) REVERT: G 520 MET cc_start: 0.5144 (mtt) cc_final: 0.4341 (ttt) REVERT: H 64 ILE cc_start: 0.3274 (OUTLIER) cc_final: 0.2663 (tp) REVERT: J 520 MET cc_start: 0.5114 (mtt) cc_final: 0.4322 (ttt) REVERT: K 64 ILE cc_start: 0.3338 (OUTLIER) cc_final: 0.2681 (tp) outliers start: 51 outliers final: 35 residues processed: 224 average time/residue: 0.1268 time to fit residues: 42.4063 Evaluate side-chains 221 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain B residue 64 ILE 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 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 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 139 TYR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 10.0000 chunk 170 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 191 optimal weight: 0.0020 chunk 43 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 530 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 = 0.4813 r_free = 0.4813 target = 0.250767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.205433 restraints weight = 19639.979| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 3.20 r_work: 0.4152 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15916 Z= 0.124 Angle : 0.623 10.213 21580 Z= 0.303 Chirality : 0.038 0.177 2484 Planarity : 0.004 0.065 2644 Dihedral : 7.965 63.296 2344 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.48 % Allowed : 22.75 % Favored : 73.77 % 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: 0.59 (0.20), residues: 2004 helix: 1.25 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -2.12 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 533 TYR 0.023 0.001 TYR A 382 PHE 0.009 0.001 PHE D 130 TRP 0.013 0.001 TRP J 304 HIS 0.007 0.001 HIS J 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15916) covalent geometry : angle 0.62303 / 0.30 (21580) hydrogen bonds : bond 0.04617 / 3.07 ( 936) hydrogen bonds : angle 3.81794 / 2.65 ( 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 233 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6250 (mmp) cc_final: 0.5996 (mmt) REVERT: A 520 MET cc_start: 0.5171 (mtt) cc_final: 0.4368 (ttt) REVERT: B 64 ILE cc_start: 0.3312 (OUTLIER) cc_final: 0.2691 (tp) REVERT: D 159 MET cc_start: 0.6215 (mmp) cc_final: 0.5733 (mmm) REVERT: E 64 ILE cc_start: 0.3084 (OUTLIER) cc_final: 0.2510 (tp) REVERT: G 159 MET cc_start: 0.6220 (mmp) cc_final: 0.5742 (mmm) REVERT: G 520 MET cc_start: 0.5226 (mtt) cc_final: 0.4404 (ttt) REVERT: H 64 ILE cc_start: 0.3302 (OUTLIER) cc_final: 0.2686 (tp) REVERT: J 520 MET cc_start: 0.5182 (mtt) cc_final: 0.4377 (ttt) REVERT: K 64 ILE cc_start: 0.3266 (OUTLIER) cc_final: 0.2655 (tp) outliers start: 48 outliers final: 33 residues processed: 222 average time/residue: 0.1216 time to fit residues: 40.1783 Evaluate side-chains 215 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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: 0.6980 chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 54 optimal weight: 0.0050 chunk 105 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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** ** 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 = 0.4823 r_free = 0.4823 target = 0.251862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.208184 restraints weight = 19761.075| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 3.27 r_work: 0.4162 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15916 Z= 0.123 Angle : 0.651 14.992 21580 Z= 0.311 Chirality : 0.039 0.177 2484 Planarity : 0.004 0.065 2644 Dihedral : 7.811 63.203 2344 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.12 % Allowed : 23.62 % Favored : 73.26 % 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: 0.65 (0.20), residues: 2004 helix: 1.28 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -2.07 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 533 TYR 0.029 0.001 TYR A 382 PHE 0.012 0.001 PHE D 167 TRP 0.013 0.001 TRP D 304 HIS 0.013 0.001 HIS G 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15916) covalent geometry : angle 0.65109 / 0.31 (21580) hydrogen bonds : bond 0.04667 / 3.11 ( 936) hydrogen bonds : angle 3.82019 / 2.65 ( 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 233 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6337 (mmp) cc_final: 0.5855 (mmm) REVERT: A 520 MET cc_start: 0.5098 (mtt) cc_final: 0.4337 (ttt) REVERT: B 64 ILE cc_start: 0.3136 (OUTLIER) cc_final: 0.2510 (tp) REVERT: D 159 MET cc_start: 0.6274 (mmp) cc_final: 0.5990 (mmt) REVERT: E 64 ILE cc_start: 0.3086 (OUTLIER) cc_final: 0.2506 (tp) REVERT: G 159 MET cc_start: 0.6286 (mmp) cc_final: 0.6008 (mmt) REVERT: G 520 MET cc_start: 0.5132 (mtt) cc_final: 0.4355 (ttt) REVERT: H 64 ILE cc_start: 0.3139 (OUTLIER) cc_final: 0.2511 (tp) REVERT: J 227 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.6945 (pt) REVERT: J 520 MET cc_start: 0.5096 (mtt) cc_final: 0.4329 (ttt) REVERT: K 64 ILE cc_start: 0.3257 (OUTLIER) cc_final: 0.2633 (tp) outliers start: 43 outliers final: 36 residues processed: 223 average time/residue: 0.1268 time to fit residues: 41.6197 Evaluate side-chains 223 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 163 optimal weight: 0.0170 chunk 103 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 92 optimal weight: 0.0020 chunk 147 optimal weight: 0.7980 chunk 195 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 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 = 0.4887 r_free = 0.4887 target = 0.257452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.233623 restraints weight = 20641.666| |-----------------------------------------------------------------------------| r_work (start): 0.4689 rms_B_bonded: 1.58 r_work: 0.4506 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4476 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15916 Z= 0.109 Angle : 0.636 14.822 21580 Z= 0.297 Chirality : 0.037 0.177 2484 Planarity : 0.004 0.065 2644 Dihedral : 7.572 62.910 2344 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.19 % Allowed : 24.71 % Favored : 72.10 % 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: 0.75 (0.20), residues: 2004 helix: 1.36 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -2.10 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.032 0.002 TYR A 382 PHE 0.009 0.001 PHE H 13 TRP 0.012 0.001 TRP D 304 HIS 0.012 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (15916) covalent geometry : angle 0.63576 / 0.30 (21580) hydrogen bonds : bond 0.03832 / 2.53 ( 936) hydrogen bonds : angle 3.69621 / 2.56 ( 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 238 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ILE cc_start: 0.7247 (tp) cc_final: 0.6865 (pt) REVERT: B 64 ILE cc_start: 0.2875 (OUTLIER) cc_final: 0.2249 (tp) REVERT: D 159 MET cc_start: 0.6061 (mmp) cc_final: 0.5624 (mmm) REVERT: D 227 ILE cc_start: 0.7243 (tp) cc_final: 0.6857 (pt) REVERT: E 64 ILE cc_start: 0.2832 (OUTLIER) cc_final: 0.2218 (tp) REVERT: G 159 MET cc_start: 0.6059 (mmp) cc_final: 0.5620 (mmm) REVERT: G 227 ILE cc_start: 0.7238 (tp) cc_final: 0.6850 (pt) REVERT: H 64 ILE cc_start: 0.2898 (OUTLIER) cc_final: 0.2267 (tp) REVERT: J 227 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6872 (pt) REVERT: K 64 ILE cc_start: 0.3126 (OUTLIER) cc_final: 0.2408 (tp) outliers start: 44 outliers final: 35 residues processed: 225 average time/residue: 0.1192 time to fit residues: 39.0921 Evaluate side-chains 228 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 3 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 197 optimal weight: 0.0980 chunk 142 optimal weight: 0.1980 chunk 190 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 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 = 0.4879 r_free = 0.4879 target = 0.256175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.229867 restraints weight = 20504.390| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 1.69 r_work: 0.4478 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4454 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3758 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= 0.115 Angle : 0.629 11.300 21580 Z= 0.300 Chirality : 0.038 0.184 2484 Planarity : 0.004 0.065 2644 Dihedral : 7.485 60.886 2344 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.48 % Allowed : 24.13 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 2004 helix: 1.39 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.033 0.002 TYR A 382 PHE 0.008 0.001 PHE K 13 TRP 0.012 0.001 TRP G 304 HIS 0.011 0.001 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (15916) covalent geometry : angle 0.62904 / 0.30 (21580) hydrogen bonds : bond 0.04181 / 2.76 ( 936) hydrogen bonds : angle 3.69608 / 2.57 ( 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 231 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ILE cc_start: 0.7278 (tp) cc_final: 0.6887 (pt) REVERT: B 64 ILE cc_start: 0.2896 (OUTLIER) cc_final: 0.2262 (tp) REVERT: D 227 ILE cc_start: 0.7274 (tp) cc_final: 0.6880 (pt) REVERT: E 64 ILE cc_start: 0.2981 (OUTLIER) cc_final: 0.2275 (tp) REVERT: G 227 ILE cc_start: 0.7279 (tp) cc_final: 0.6887 (pt) REVERT: H 64 ILE cc_start: 0.2902 (OUTLIER) cc_final: 0.2271 (tp) REVERT: J 227 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6872 (pt) REVERT: K 64 ILE cc_start: 0.3126 (OUTLIER) cc_final: 0.2404 (tp) outliers start: 48 outliers final: 29 residues processed: 218 average time/residue: 0.1269 time to fit residues: 39.8511 Evaluate side-chains 213 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 L residue 65 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 51 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 0.0980 chunk 90 optimal weight: 8.9990 chunk 188 optimal weight: 30.0000 chunk 164 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 100 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 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 = 0.4859 r_free = 0.4859 target = 0.253413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.228188 restraints weight = 20317.300| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 1.63 r_work: 0.4457 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4433 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15916 Z= 0.144 Angle : 0.667 10.638 21580 Z= 0.323 Chirality : 0.039 0.206 2484 Planarity : 0.004 0.065 2644 Dihedral : 7.554 59.422 2344 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.12 % Allowed : 24.57 % 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: 0.65 (0.20), residues: 2004 helix: 1.29 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -2.08 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.032 0.002 TYR A 382 PHE 0.011 0.001 PHE A 296 TRP 0.011 0.001 TRP G 304 HIS 0.011 0.001 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15916) covalent geometry : angle 0.66659 / 0.32 (21580) hydrogen bonds : bond 0.05091 / 3.37 ( 936) hydrogen bonds : angle 3.84041 / 2.65 ( 2784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3848.82 seconds wall clock time: 66 minutes 24.39 seconds (3984.39 seconds total)