Starting phenix.real_space_refine on Thu Jan 15 11:54:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc7_36150/01_2026/8jc7_36150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc7_36150/01_2026/8jc7_36150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jc7_36150/01_2026/8jc7_36150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc7_36150/01_2026/8jc7_36150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jc7_36150/01_2026/8jc7_36150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc7_36150/01_2026/8jc7_36150.map" } resolution = 2.06 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= 0.084 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 Ca 7 9.91 5 K 7 8.98 5 S 49 5.16 5 C 15631 2.51 5 N 4375 2.21 5 O 5554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 223 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25623 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3574 Classifications: {'peptide': 448} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 434} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3574 Classifications: {'peptide': 448} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 434} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3574 Classifications: {'peptide': 448} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 434} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3574 Classifications: {'peptide': 448} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 434} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3574 Classifications: {'peptide': 448} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 434} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3574 Classifications: {'peptide': 448} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 434} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3574 Classifications: {'peptide': 448} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 434} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "G" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Time building chain proxies: 5.33, per 1000 atoms: 0.21 Number of scatterers: 25623 At special positions: 0 Unit cell: (117.771, 117.771, 151.723, 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) Ca 7 19.99 K 7 19.00 S 49 16.00 O 5554 8.00 N 4375 7.00 C 15631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 482 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 468 " - pdb=" SG CYS D 482 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 468 " - pdb=" SG CYS E 482 " distance=2.03 Simple disulfide: pdb=" SG CYS F 153 " - pdb=" SG CYS F 171 " distance=2.03 Simple disulfide: pdb=" SG CYS F 468 " - pdb=" SG CYS F 482 " distance=2.03 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 171 " distance=2.03 Simple disulfide: pdb=" SG CYS G 468 " - pdb=" SG CYS G 482 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 78 sheets defined 6.0% alpha, 57.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 486 through 489 Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 486 through 489 Processing helix chain 'B' and resid 523 through 526 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 448 through 453 Processing helix chain 'C' and resid 486 through 489 Processing helix chain 'C' and resid 523 through 526 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 486 through 489 Processing helix chain 'D' and resid 523 through 526 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 346 through 350 Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 448 through 453 Processing helix chain 'E' and resid 486 through 489 Processing helix chain 'E' and resid 523 through 526 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 346 through 350 Processing helix chain 'F' and resid 365 through 369 Processing helix chain 'F' and resid 448 through 453 Processing helix chain 'F' and resid 486 through 489 Processing helix chain 'F' and resid 523 through 526 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 346 through 350 Processing helix chain 'G' and resid 365 through 369 Processing helix chain 'G' and resid 448 through 453 Processing helix chain 'G' and resid 486 through 489 Processing helix chain 'G' and resid 523 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 147 Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 147 removed outlier: 6.133A pdb=" N ASP A 382 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 266 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 384 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 156 Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 228 removed outlier: 9.600A pdb=" N ARG A 239 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS A 414 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N TRP A 241 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA A 412 " --> pdb=" O TRP A 241 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR A 243 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN A 410 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 245 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 408 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA A 247 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG A 406 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 249 " --> pdb=" O ASN A 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 330 removed outlier: 6.920A pdb=" N THR A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLN A 248 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ARG A 239 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS A 414 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N TRP A 241 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA A 412 " --> pdb=" O TRP A 241 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR A 243 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN A 410 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 245 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 408 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA A 247 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG A 406 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 249 " --> pdb=" O ASN A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 294 removed outlier: 6.862A pdb=" N LYS A 275 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN A 318 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS G 275 " --> pdb=" O ASN G 318 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN G 318 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS F 275 " --> pdb=" O ASN F 318 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASN F 318 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS E 275 " --> pdb=" O ASN E 318 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASN E 318 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS D 275 " --> pdb=" O ASN D 318 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN D 318 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS C 275 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN C 318 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS B 275 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN B 318 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 457 through 461 removed outlier: 3.664A pdb=" N ALA A 572 " --> pdb=" O ASN A 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 471 Processing sheet with id=AA9, first strand: chain 'A' and resid 491 through 493 Processing sheet with id=AB1, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AB2, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AB3, first strand: chain 'A' and resid 555 through 558 Processing sheet with id=AB4, first strand: chain 'B' and resid 138 through 147 Processing sheet with id=AB5, first strand: chain 'B' and resid 138 through 147 removed outlier: 6.127A pdb=" N ASP B 382 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 266 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 384 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 154 through 156 Processing sheet with id=AB7, first strand: chain 'B' and resid 224 through 228 removed outlier: 6.277A pdb=" N TYR B 237 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS B 414 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 239 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA B 245 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG B 406 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA B 247 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN B 404 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP B 249 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER B 402 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 251 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP B 400 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 253 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 398 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS B 255 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP B 396 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 322 through 330 removed outlier: 6.916A pdb=" N THR B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLN B 248 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR B 237 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS B 414 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 239 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA B 245 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG B 406 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA B 247 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN B 404 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP B 249 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER B 402 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 251 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP B 400 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 253 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 398 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS B 255 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP B 396 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 457 through 461 removed outlier: 3.653A pdb=" N ALA B 572 " --> pdb=" O ASN B 458 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 468 through 471 Processing sheet with id=AC2, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AC3, first strand: chain 'B' and resid 507 through 508 Processing sheet with id=AC4, first strand: chain 'B' and resid 528 through 530 Processing sheet with id=AC5, first strand: chain 'B' and resid 555 through 558 Processing sheet with id=AC6, first strand: chain 'C' and resid 138 through 147 Processing sheet with id=AC7, first strand: chain 'C' and resid 138 through 147 removed outlier: 6.143A pdb=" N ASP C 382 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR C 266 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C 384 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AC9, first strand: chain 'C' and resid 224 through 228 removed outlier: 9.610A pdb=" N ARG C 239 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LYS C 414 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N TRP C 241 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA C 412 " --> pdb=" O TRP C 241 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR C 243 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASN C 410 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA C 245 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 408 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA C 247 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG C 406 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP C 249 " --> pdb=" O ASN C 404 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 322 through 330 removed outlier: 6.924A pdb=" N THR C 333 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLN C 248 " --> pdb=" O ARG C 340 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N ARG C 239 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LYS C 414 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N TRP C 241 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA C 412 " --> pdb=" O TRP C 241 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR C 243 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASN C 410 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA C 245 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 408 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA C 247 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG C 406 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP C 249 " --> pdb=" O ASN C 404 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 457 through 461 removed outlier: 3.648A pdb=" N ALA C 572 " --> pdb=" O ASN C 458 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 468 through 471 Processing sheet with id=AD4, first strand: chain 'C' and resid 491 through 493 Processing sheet with id=AD5, first strand: chain 'C' and resid 507 through 508 Processing sheet with id=AD6, first strand: chain 'C' and resid 528 through 530 Processing sheet with id=AD7, first strand: chain 'C' and resid 555 through 558 Processing sheet with id=AD8, first strand: chain 'D' and resid 138 through 147 Processing sheet with id=AD9, first strand: chain 'D' and resid 138 through 147 removed outlier: 6.146A pdb=" N ASP D 382 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR D 266 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE D 384 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 154 through 156 Processing sheet with id=AE2, first strand: chain 'D' and resid 224 through 228 removed outlier: 9.596A pdb=" N ARG D 239 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS D 414 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N TRP D 241 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA D 412 " --> pdb=" O TRP D 241 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR D 243 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN D 410 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA D 245 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 408 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ALA D 247 " --> pdb=" O ARG D 406 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG D 406 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D 249 " --> pdb=" O ASN D 404 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 322 through 330 removed outlier: 6.922A pdb=" N THR D 333 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLN D 248 " --> pdb=" O ARG D 340 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N ARG D 239 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS D 414 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N TRP D 241 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA D 412 " --> pdb=" O TRP D 241 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR D 243 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN D 410 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA D 245 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 408 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ALA D 247 " --> pdb=" O ARG D 406 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG D 406 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D 249 " --> pdb=" O ASN D 404 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 457 through 461 removed outlier: 3.664A pdb=" N ALA D 572 " --> pdb=" O ASN D 458 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 468 through 471 Processing sheet with id=AE6, first strand: chain 'D' and resid 491 through 493 Processing sheet with id=AE7, first strand: chain 'D' and resid 507 through 508 Processing sheet with id=AE8, first strand: chain 'D' and resid 528 through 530 Processing sheet with id=AE9, first strand: chain 'D' and resid 555 through 558 Processing sheet with id=AF1, first strand: chain 'E' and resid 138 through 147 Processing sheet with id=AF2, first strand: chain 'E' and resid 138 through 147 removed outlier: 6.131A pdb=" N ASP E 382 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR E 266 " --> pdb=" O ASP E 382 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE E 384 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 154 through 156 Processing sheet with id=AF4, first strand: chain 'E' and resid 224 through 228 removed outlier: 7.415A pdb=" N PHE E 238 " --> pdb=" O LYS E 414 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LYS E 414 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU E 240 " --> pdb=" O ALA E 412 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA E 412 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER E 242 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN E 410 " --> pdb=" O SER E 242 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP E 244 " --> pdb=" O ILE E 408 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE E 408 " --> pdb=" O ASP E 244 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN E 404 " --> pdb=" O GLN E 248 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR E 250 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER E 402 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE E 252 " --> pdb=" O ASP E 400 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP E 400 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE E 254 " --> pdb=" O ILE E 398 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 398 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR E 256 " --> pdb=" O ASP E 396 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP E 396 " --> pdb=" O THR E 256 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 322 through 330 removed outlier: 6.917A pdb=" N THR E 333 " --> pdb=" O LYS E 329 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N GLN E 248 " --> pdb=" O ARG E 340 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE E 238 " --> pdb=" O LYS E 414 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LYS E 414 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU E 240 " --> pdb=" O ALA E 412 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA E 412 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER E 242 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN E 410 " --> pdb=" O SER E 242 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP E 244 " --> pdb=" O ILE E 408 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE E 408 " --> pdb=" O ASP E 244 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN E 404 " --> pdb=" O GLN E 248 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR E 250 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER E 402 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE E 252 " --> pdb=" O ASP E 400 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP E 400 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE E 254 " --> pdb=" O ILE E 398 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 398 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR E 256 " --> pdb=" O ASP E 396 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP E 396 " --> pdb=" O THR E 256 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 457 through 461 removed outlier: 3.650A pdb=" N ALA E 572 " --> pdb=" O ASN E 458 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 468 through 471 Processing sheet with id=AF8, first strand: chain 'E' and resid 491 through 493 Processing sheet with id=AF9, first strand: chain 'E' and resid 507 through 508 Processing sheet with id=AG1, first strand: chain 'E' and resid 528 through 530 Processing sheet with id=AG2, first strand: chain 'E' and resid 555 through 558 Processing sheet with id=AG3, first strand: chain 'F' and resid 138 through 147 Processing sheet with id=AG4, first strand: chain 'F' and resid 138 through 147 removed outlier: 6.136A pdb=" N ASP F 382 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR F 266 " --> pdb=" O ASP F 382 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE F 384 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 154 through 156 Processing sheet with id=AG6, first strand: chain 'F' and resid 224 through 228 removed outlier: 7.409A pdb=" N PHE F 238 " --> pdb=" O LYS F 414 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS F 414 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU F 240 " --> pdb=" O ALA F 412 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA F 412 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER F 242 " --> pdb=" O ASN F 410 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN F 410 " --> pdb=" O SER F 242 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASP F 244 " --> pdb=" O ILE F 408 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE F 408 " --> pdb=" O ASP F 244 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN F 404 " --> pdb=" O GLN F 248 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR F 250 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER F 402 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE F 252 " --> pdb=" O ASP F 400 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP F 400 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE F 254 " --> pdb=" O ILE F 398 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE F 398 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR F 256 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP F 396 " --> pdb=" O THR F 256 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 322 through 330 removed outlier: 6.922A pdb=" N THR F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLN F 248 " --> pdb=" O ARG F 340 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE F 238 " --> pdb=" O LYS F 414 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS F 414 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU F 240 " --> pdb=" O ALA F 412 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA F 412 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER F 242 " --> pdb=" O ASN F 410 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN F 410 " --> pdb=" O SER F 242 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASP F 244 " --> pdb=" O ILE F 408 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE F 408 " --> pdb=" O ASP F 244 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN F 404 " --> pdb=" O GLN F 248 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR F 250 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER F 402 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE F 252 " --> pdb=" O ASP F 400 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP F 400 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE F 254 " --> pdb=" O ILE F 398 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE F 398 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR F 256 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP F 396 " --> pdb=" O THR F 256 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 457 through 461 removed outlier: 3.659A pdb=" N ALA F 572 " --> pdb=" O ASN F 458 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 468 through 471 Processing sheet with id=AH1, first strand: chain 'F' and resid 491 through 493 Processing sheet with id=AH2, first strand: chain 'F' and resid 507 through 508 Processing sheet with id=AH3, first strand: chain 'F' and resid 528 through 530 Processing sheet with id=AH4, first strand: chain 'F' and resid 555 through 558 Processing sheet with id=AH5, first strand: chain 'G' and resid 138 through 147 Processing sheet with id=AH6, first strand: chain 'G' and resid 138 through 147 removed outlier: 6.135A pdb=" N ASP G 382 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR G 266 " --> pdb=" O ASP G 382 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE G 384 " --> pdb=" O LEU G 264 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 154 through 156 Processing sheet with id=AH8, first strand: chain 'G' and resid 224 through 228 removed outlier: 7.404A pdb=" N PHE G 238 " --> pdb=" O LYS G 414 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LYS G 414 " --> pdb=" O PHE G 238 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU G 240 " --> pdb=" O ALA G 412 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA G 412 " --> pdb=" O GLU G 240 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER G 242 " --> pdb=" O ASN G 410 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASN G 410 " --> pdb=" O SER G 242 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASP G 244 " --> pdb=" O ILE G 408 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE G 408 " --> pdb=" O ASP G 244 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN G 404 " --> pdb=" O GLN G 248 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR G 250 " --> pdb=" O SER G 402 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER G 402 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE G 252 " --> pdb=" O ASP G 400 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP G 400 " --> pdb=" O PHE G 252 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE G 254 " --> pdb=" O ILE G 398 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE G 398 " --> pdb=" O PHE G 254 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR G 256 " --> pdb=" O ASP G 396 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP G 396 " --> pdb=" O THR G 256 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 322 through 330 removed outlier: 6.919A pdb=" N THR G 333 " --> pdb=" O LYS G 329 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLN G 248 " --> pdb=" O ARG G 340 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE G 238 " --> pdb=" O LYS G 414 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LYS G 414 " --> pdb=" O PHE G 238 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU G 240 " --> pdb=" O ALA G 412 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA G 412 " --> pdb=" O GLU G 240 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER G 242 " --> pdb=" O ASN G 410 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASN G 410 " --> pdb=" O SER G 242 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASP G 244 " --> pdb=" O ILE G 408 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE G 408 " --> pdb=" O ASP G 244 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN G 404 " --> pdb=" O GLN G 248 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR G 250 " --> pdb=" O SER G 402 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER G 402 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE G 252 " --> pdb=" O ASP G 400 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP G 400 " --> pdb=" O PHE G 252 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE G 254 " --> pdb=" O ILE G 398 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE G 398 " --> pdb=" O PHE G 254 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR G 256 " --> pdb=" O ASP G 396 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP G 396 " --> pdb=" O THR G 256 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 457 through 461 removed outlier: 3.672A pdb=" N ALA G 572 " --> pdb=" O ASN G 458 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 468 through 471 Processing sheet with id=AI3, first strand: chain 'G' and resid 491 through 493 Processing sheet with id=AI4, first strand: chain 'G' and resid 507 through 508 Processing sheet with id=AI5, first strand: chain 'G' and resid 528 through 530 Processing sheet with id=AI6, first strand: chain 'G' and resid 555 through 558 1099 hydrogen bonds defined for protein. 2871 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: 5.66 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 6068 1.32 - 1.44: 5624 1.44 - 1.55: 13819 1.55 - 1.67: 4 1.67 - 1.79: 56 Bond restraints: 25571 Sorted by residual: bond pdb=" C TYR B 499 " pdb=" N VAL B 500 " ideal model delta sigma weight residual 1.329 1.277 0.052 1.69e-02 3.50e+03 9.48e+00 bond pdb=" C TYR F 499 " pdb=" N VAL F 500 " ideal model delta sigma weight residual 1.329 1.278 0.051 1.69e-02 3.50e+03 9.03e+00 bond pdb=" C TYR G 499 " pdb=" N VAL G 500 " ideal model delta sigma weight residual 1.329 1.278 0.051 1.69e-02 3.50e+03 8.94e+00 bond pdb=" CB ASP D 321 " pdb=" CG ASP D 321 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.57e+00 bond pdb=" CB ASP E 321 " pdb=" CG ASP E 321 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.55e+00 ... (remaining 25566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 34126 1.72 - 3.44: 575 3.44 - 5.17: 58 5.17 - 6.89: 6 6.89 - 8.61: 4 Bond angle restraints: 34769 Sorted by residual: angle pdb=" N ASP A 515 " pdb=" CA ASP A 515 " pdb=" C ASP A 515 " ideal model delta sigma weight residual 114.56 109.55 5.01 1.27e+00 6.20e-01 1.56e+01 angle pdb=" N ASP G 515 " pdb=" CA ASP G 515 " pdb=" C ASP G 515 " ideal model delta sigma weight residual 114.56 109.61 4.95 1.27e+00 6.20e-01 1.52e+01 angle pdb=" N ASP B 515 " pdb=" CA ASP B 515 " pdb=" C ASP B 515 " ideal model delta sigma weight residual 114.56 109.61 4.95 1.27e+00 6.20e-01 1.52e+01 angle pdb=" N ASP D 515 " pdb=" CA ASP D 515 " pdb=" C ASP D 515 " ideal model delta sigma weight residual 114.56 109.62 4.94 1.27e+00 6.20e-01 1.51e+01 angle pdb=" N ASP E 515 " pdb=" CA ASP E 515 " pdb=" C ASP E 515 " ideal model delta sigma weight residual 114.56 109.66 4.90 1.27e+00 6.20e-01 1.49e+01 ... (remaining 34764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13395 17.95 - 35.91: 1268 35.91 - 53.86: 374 53.86 - 71.81: 104 71.81 - 89.77: 42 Dihedral angle restraints: 15183 sinusoidal: 5950 harmonic: 9233 Sorted by residual: dihedral pdb=" CB CYS C 153 " pdb=" SG CYS C 153 " pdb=" SG CYS C 171 " pdb=" CB CYS C 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.77 89.77 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS F 153 " pdb=" SG CYS F 153 " pdb=" SG CYS F 171 " pdb=" CB CYS F 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.62 89.62 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS A 153 " pdb=" SG CYS A 153 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.49 89.49 1 1.00e+01 1.00e-02 9.51e+01 ... (remaining 15180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2087 0.034 - 0.068: 1050 0.068 - 0.101: 555 0.101 - 0.135: 88 0.135 - 0.169: 7 Chirality restraints: 3787 Sorted by residual: chirality pdb=" CA THR F 505 " pdb=" N THR F 505 " pdb=" C THR F 505 " pdb=" CB THR F 505 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA THR B 505 " pdb=" N THR B 505 " pdb=" C THR B 505 " pdb=" CB THR B 505 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA THR G 505 " pdb=" N THR G 505 " pdb=" C THR G 505 " pdb=" CB THR G 505 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 3784 not shown) Planarity restraints: 4564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 298 " -0.052 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO E 299 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO E 299 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 299 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 284 " -0.009 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE B 284 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 284 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 284 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 284 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 284 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 284 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 448 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 449 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " -0.021 5.00e-02 4.00e+02 ... (remaining 4561 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 7485 2.79 - 3.38: 24925 3.38 - 3.97: 54811 3.97 - 4.55: 74484 4.55 - 5.14: 112551 Nonbonded interactions: 274256 Sorted by model distance: nonbonded pdb=" O HOH E 982 " pdb=" O HOH E 985 " model vdw 2.209 3.040 nonbonded pdb=" O HOH C 981 " pdb=" O HOH C 984 " model vdw 2.209 3.040 nonbonded pdb=" O HOH A 977 " pdb=" O HOH A 980 " model vdw 2.209 3.040 nonbonded pdb=" O HOH F 980 " pdb=" O HOH F 983 " model vdw 2.209 3.040 nonbonded pdb=" O HOH G 983 " pdb=" O HOH G 986 " model vdw 2.210 3.040 ... (remaining 274251 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 21.340 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 24.190 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 : 0.011 0.065 25585 Z= 0.483 Angle : 0.606 8.612 34797 Z= 0.349 Chirality : 0.047 0.169 3787 Planarity : 0.004 0.079 4564 Dihedral : 16.570 87.343 9205 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.88 % Allowed : 18.57 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.25 (0.15), residues: 3122 helix: -4.32 (0.28), residues: 126 sheet: 0.83 (0.13), residues: 1498 loop : -0.02 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 476 TYR 0.012 0.002 TYR G 499 PHE 0.028 0.002 PHE B 284 TRP 0.016 0.002 TRP C 358 HIS 0.005 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.01094 (25571) covalent geometry : angle 0.59987 (34769) SS BOND : bond 0.00193 ( 14) SS BOND : angle 2.96818 ( 28) hydrogen bonds : bond 0.14886 ( 994) hydrogen bonds : angle 7.74850 ( 2871) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 398 time to evaluate : 1.078 Fit side-chains REVERT: A 151 GLU cc_start: 0.5869 (pm20) cc_final: 0.5601 (tp30) REVERT: A 210 ASP cc_start: 0.6696 (m-30) cc_final: 0.6492 (m-30) REVERT: A 221 GLN cc_start: 0.7323 (pm20) cc_final: 0.7094 (pm20) REVERT: A 225 ARG cc_start: 0.6791 (mmm-85) cc_final: 0.6510 (mmt90) REVERT: A 226 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7005 (ttp80) REVERT: A 265 GLU cc_start: 0.7361 (pt0) cc_final: 0.6275 (pp20) REVERT: A 272 LEU cc_start: 0.7326 (tp) cc_final: 0.7047 (mt) REVERT: A 275 LYS cc_start: 0.7246 (tppt) cc_final: 0.6718 (tppt) REVERT: A 279 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7492 (ttm-80) REVERT: A 310 THR cc_start: 0.7230 (m) cc_final: 0.6862 (t) REVERT: A 313 ARG cc_start: 0.7312 (mmt-90) cc_final: 0.7104 (mmt-90) REVERT: A 329 LYS cc_start: 0.7656 (mtpp) cc_final: 0.6623 (tptt) REVERT: A 445 ASP cc_start: 0.6639 (t0) cc_final: 0.6371 (t0) REVERT: A 470 GLN cc_start: 0.7813 (tt0) cc_final: 0.7391 (tt0) REVERT: A 472 ASP cc_start: 0.6644 (p0) cc_final: 0.6293 (p0) REVERT: A 516 VAL cc_start: 0.7488 (m) cc_final: 0.7272 (p) REVERT: A 550 LYS cc_start: 0.6966 (mttt) cc_final: 0.6748 (mttm) REVERT: A 554 GLU cc_start: 0.6620 (tt0) cc_final: 0.6318 (tt0) REVERT: A 579 VAL cc_start: 0.6497 (OUTLIER) cc_final: 0.6180 (t) REVERT: B 151 GLU cc_start: 0.5880 (pm20) cc_final: 0.5595 (tp30) REVERT: B 220 ASP cc_start: 0.7318 (m-30) cc_final: 0.7030 (m-30) REVERT: B 225 ARG cc_start: 0.6858 (mmm-85) cc_final: 0.6506 (mmt90) REVERT: B 226 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7195 (ttp80) REVERT: B 265 GLU cc_start: 0.7351 (pt0) cc_final: 0.6277 (pp20) REVERT: B 272 LEU cc_start: 0.7255 (tp) cc_final: 0.6915 (mt) REVERT: B 275 LYS cc_start: 0.7279 (tppt) cc_final: 0.6754 (tppt) REVERT: B 309 ILE cc_start: 0.7340 (mm) cc_final: 0.7137 (tp) REVERT: B 310 THR cc_start: 0.7283 (m) cc_final: 0.6906 (t) REVERT: B 311 GLN cc_start: 0.7618 (tt0) cc_final: 0.7343 (mt0) REVERT: B 313 ARG cc_start: 0.7380 (mmt-90) cc_final: 0.7167 (mmt-90) REVERT: B 329 LYS cc_start: 0.7676 (mtpp) cc_final: 0.6649 (tptt) REVERT: B 380 LYS cc_start: 0.7921 (mmtp) cc_final: 0.7711 (mmtp) REVERT: B 429 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6570 (mm-30) REVERT: B 445 ASP cc_start: 0.6707 (t0) cc_final: 0.6441 (t0) REVERT: B 470 GLN cc_start: 0.7850 (tt0) cc_final: 0.7417 (tt0) REVERT: B 472 ASP cc_start: 0.6620 (p0) cc_final: 0.6305 (p0) REVERT: B 476 ARG cc_start: 0.6822 (mtp85) cc_final: 0.6610 (mmm160) REVERT: B 550 LYS cc_start: 0.6906 (mttt) cc_final: 0.6644 (mttm) REVERT: B 554 GLU cc_start: 0.6656 (tt0) cc_final: 0.6318 (tt0) REVERT: C 151 GLU cc_start: 0.5919 (pm20) cc_final: 0.5662 (tp30) REVERT: C 220 ASP cc_start: 0.7269 (m-30) cc_final: 0.6944 (m-30) REVERT: C 221 GLN cc_start: 0.7272 (pm20) cc_final: 0.7058 (pm20) REVERT: C 225 ARG cc_start: 0.6919 (mmm-85) cc_final: 0.6552 (mmt90) REVERT: C 226 ARG cc_start: 0.7473 (ttp80) cc_final: 0.7102 (ttp80) REVERT: C 265 GLU cc_start: 0.7323 (pt0) cc_final: 0.6944 (pt0) REVERT: C 272 LEU cc_start: 0.7223 (tp) cc_final: 0.6979 (mt) REVERT: C 275 LYS cc_start: 0.7298 (tppt) cc_final: 0.6728 (tppt) REVERT: C 279 ARG cc_start: 0.7762 (ttm-80) cc_final: 0.7545 (ttm-80) REVERT: C 306 ARG cc_start: 0.6022 (mtm-85) cc_final: 0.5500 (mtm-85) REVERT: C 310 THR cc_start: 0.7195 (m) cc_final: 0.6814 (t) REVERT: C 311 GLN cc_start: 0.7584 (tt0) cc_final: 0.7325 (tt0) REVERT: C 313 ARG cc_start: 0.7344 (mmt-90) cc_final: 0.7062 (mmt-90) REVERT: C 329 LYS cc_start: 0.7709 (mtpp) cc_final: 0.6626 (tptt) REVERT: C 445 ASP cc_start: 0.6670 (t0) cc_final: 0.6373 (t0) REVERT: C 470 GLN cc_start: 0.7835 (tt0) cc_final: 0.7287 (tt0) REVERT: C 472 ASP cc_start: 0.6668 (p0) cc_final: 0.6437 (p0) REVERT: C 476 ARG cc_start: 0.6785 (mtp85) cc_final: 0.6541 (mmm160) REVERT: C 550 LYS cc_start: 0.7003 (mttt) cc_final: 0.6749 (mttm) REVERT: C 551 GLN cc_start: 0.7130 (mp10) cc_final: 0.6922 (mp10) REVERT: C 554 GLU cc_start: 0.6674 (tt0) cc_final: 0.6338 (tt0) REVERT: D 151 GLU cc_start: 0.5858 (pm20) cc_final: 0.5599 (tp30) REVERT: D 204 ARG cc_start: 0.6994 (ttm110) cc_final: 0.6155 (ttm-80) REVERT: D 210 ASP cc_start: 0.6669 (m-30) cc_final: 0.6464 (m-30) REVERT: D 220 ASP cc_start: 0.7326 (m-30) cc_final: 0.7015 (m-30) REVERT: D 221 GLN cc_start: 0.7337 (pm20) cc_final: 0.6968 (pm20) REVERT: D 225 ARG cc_start: 0.6881 (mmm-85) cc_final: 0.6548 (mmt90) REVERT: D 226 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7069 (ttp80) REVERT: D 265 GLU cc_start: 0.7418 (pt0) cc_final: 0.7041 (pt0) REVERT: D 272 LEU cc_start: 0.7277 (tp) cc_final: 0.7077 (mt) REVERT: D 275 LYS cc_start: 0.7276 (tppt) cc_final: 0.6742 (tppt) REVERT: D 279 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7448 (ttm-80) REVERT: D 310 THR cc_start: 0.7187 (m) cc_final: 0.6785 (t) REVERT: D 311 GLN cc_start: 0.7596 (tt0) cc_final: 0.7355 (tt0) REVERT: D 329 LYS cc_start: 0.7678 (mtpp) cc_final: 0.6641 (tptt) REVERT: D 380 LYS cc_start: 0.7938 (mmtp) cc_final: 0.7729 (mmtp) REVERT: D 445 ASP cc_start: 0.6674 (t0) cc_final: 0.6387 (t0) REVERT: D 470 GLN cc_start: 0.7800 (tt0) cc_final: 0.7413 (tt0) REVERT: D 472 ASP cc_start: 0.6652 (p0) cc_final: 0.6346 (p0) REVERT: D 550 LYS cc_start: 0.7043 (mttt) cc_final: 0.6748 (mttm) REVERT: D 551 GLN cc_start: 0.7120 (mp10) cc_final: 0.6904 (mp10) REVERT: D 554 GLU cc_start: 0.6641 (tt0) cc_final: 0.6257 (tt0) REVERT: E 151 GLU cc_start: 0.5896 (pm20) cc_final: 0.5613 (tp30) REVERT: E 172 LYS cc_start: 0.6912 (tptt) cc_final: 0.6682 (tptt) REVERT: E 221 GLN cc_start: 0.7343 (pm20) cc_final: 0.7018 (pm20) REVERT: E 225 ARG cc_start: 0.6852 (mmm-85) cc_final: 0.6524 (mmt90) REVERT: E 226 ARG cc_start: 0.7449 (ttp80) cc_final: 0.7191 (ttp80) REVERT: E 265 GLU cc_start: 0.7332 (pt0) cc_final: 0.6180 (pp20) REVERT: E 272 LEU cc_start: 0.7241 (tp) cc_final: 0.7024 (mt) REVERT: E 275 LYS cc_start: 0.7303 (tppt) cc_final: 0.6771 (tppt) REVERT: E 279 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7505 (ttm-80) REVERT: E 310 THR cc_start: 0.7136 (m) cc_final: 0.6723 (t) REVERT: E 311 GLN cc_start: 0.7545 (tt0) cc_final: 0.7312 (tt0) REVERT: E 321 ASP cc_start: 0.7356 (p0) cc_final: 0.7075 (p0) REVERT: E 329 LYS cc_start: 0.7696 (mtpp) cc_final: 0.6712 (tptt) REVERT: E 380 LYS cc_start: 0.7928 (mmtp) cc_final: 0.7718 (mmtp) REVERT: E 429 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6632 (mm-30) REVERT: E 445 ASP cc_start: 0.6641 (t0) cc_final: 0.6367 (t0) REVERT: E 470 GLN cc_start: 0.7881 (tt0) cc_final: 0.7243 (tt0) REVERT: E 472 ASP cc_start: 0.6588 (p0) cc_final: 0.6231 (p0) REVERT: E 550 LYS cc_start: 0.6945 (mttt) cc_final: 0.6579 (mttm) REVERT: E 551 GLN cc_start: 0.7104 (mp10) cc_final: 0.6896 (mp10) REVERT: E 554 GLU cc_start: 0.6587 (tt0) cc_final: 0.6220 (tt0) REVERT: F 151 GLU cc_start: 0.5933 (pm20) cc_final: 0.5641 (tp30) REVERT: F 221 GLN cc_start: 0.7348 (pm20) cc_final: 0.7026 (pm20) REVERT: F 225 ARG cc_start: 0.6856 (mmm-85) cc_final: 0.6503 (mmt90) REVERT: F 226 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7148 (ttp80) REVERT: F 272 LEU cc_start: 0.7281 (tp) cc_final: 0.7002 (mt) REVERT: F 275 LYS cc_start: 0.7230 (tppt) cc_final: 0.6679 (tppt) REVERT: F 279 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7442 (ttm-80) REVERT: F 310 THR cc_start: 0.7172 (m) cc_final: 0.6781 (t) REVERT: F 311 GLN cc_start: 0.7580 (tt0) cc_final: 0.7260 (mt0) REVERT: F 329 LYS cc_start: 0.7664 (mtpp) cc_final: 0.6553 (tptt) REVERT: F 445 ASP cc_start: 0.6729 (t0) cc_final: 0.6474 (t0) REVERT: F 470 GLN cc_start: 0.7775 (tt0) cc_final: 0.7338 (tt0) REVERT: F 472 ASP cc_start: 0.6662 (p0) cc_final: 0.6415 (p0) REVERT: F 516 VAL cc_start: 0.7577 (m) cc_final: 0.7344 (t) REVERT: F 551 GLN cc_start: 0.7119 (mp10) cc_final: 0.6908 (mp10) REVERT: F 554 GLU cc_start: 0.6661 (tt0) cc_final: 0.6348 (tt0) REVERT: G 151 GLU cc_start: 0.5934 (pm20) cc_final: 0.5630 (tp30) REVERT: G 220 ASP cc_start: 0.7291 (m-30) cc_final: 0.7052 (m-30) REVERT: G 225 ARG cc_start: 0.6828 (mmm-85) cc_final: 0.6495 (mmt90) REVERT: G 226 ARG cc_start: 0.7414 (ttp80) cc_final: 0.7127 (ttp80) REVERT: G 265 GLU cc_start: 0.7285 (pt0) cc_final: 0.6912 (pt0) REVERT: G 272 LEU cc_start: 0.7336 (tp) cc_final: 0.7093 (mt) REVERT: G 275 LYS cc_start: 0.7275 (tppt) cc_final: 0.6751 (tppt) REVERT: G 279 ARG cc_start: 0.7750 (ttm-80) cc_final: 0.7469 (ttm-80) REVERT: G 309 ILE cc_start: 0.7277 (mm) cc_final: 0.7076 (tp) REVERT: G 310 THR cc_start: 0.7118 (m) cc_final: 0.6725 (t) REVERT: G 313 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.7106 (mmt-90) REVERT: G 329 LYS cc_start: 0.7681 (mtpp) cc_final: 0.6657 (tptt) REVERT: G 445 ASP cc_start: 0.6730 (t0) cc_final: 0.6437 (t0) REVERT: G 470 GLN cc_start: 0.7817 (tt0) cc_final: 0.7440 (tt0) REVERT: G 472 ASP cc_start: 0.6657 (p0) cc_final: 0.6373 (p0) REVERT: G 476 ARG cc_start: 0.6816 (mtp85) cc_final: 0.6609 (mmm160) REVERT: G 516 VAL cc_start: 0.7527 (m) cc_final: 0.7282 (p) REVERT: G 550 LYS cc_start: 0.6979 (mttt) cc_final: 0.6721 (mttm) REVERT: G 551 GLN cc_start: 0.7065 (mp10) cc_final: 0.6859 (mp10) REVERT: G 554 GLU cc_start: 0.6596 (tt0) cc_final: 0.6216 (tt0) outliers start: 24 outliers final: 10 residues processed: 422 average time/residue: 0.9146 time to fit residues: 429.6949 Evaluate side-chains 347 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 336 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 471 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 ASN D 219 ASN E 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112287 restraints weight = 22268.964| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.45 r_work: 0.3225 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25585 Z= 0.117 Angle : 0.459 5.124 34797 Z= 0.260 Chirality : 0.043 0.168 3787 Planarity : 0.003 0.060 4564 Dihedral : 4.751 32.287 3504 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.22 % Allowed : 15.86 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.43 (0.15), residues: 3122 helix: -4.97 (0.15), residues: 84 sheet: 0.86 (0.14), residues: 1435 loop : 0.16 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 476 TYR 0.008 0.001 TYR A 385 PHE 0.020 0.002 PHE G 284 TRP 0.008 0.001 TRP C 358 HIS 0.002 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00241 (25571) covalent geometry : angle 0.45825 (34769) SS BOND : bond 0.00107 ( 14) SS BOND : angle 1.13027 ( 28) hydrogen bonds : bond 0.03648 ( 994) hydrogen bonds : angle 5.44653 ( 2871) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 380 time to evaluate : 1.027 Fit side-chains REVERT: A 152 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: A 265 GLU cc_start: 0.8529 (pt0) cc_final: 0.8250 (pp20) REVERT: A 303 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7430 (tp) REVERT: A 554 GLU cc_start: 0.7938 (tt0) cc_final: 0.7659 (tt0) REVERT: A 579 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6978 (p) REVERT: B 152 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: B 265 GLU cc_start: 0.8499 (pt0) cc_final: 0.8248 (pp20) REVERT: B 303 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7345 (tp) REVERT: B 329 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8248 (tptt) REVERT: B 476 ARG cc_start: 0.8268 (mtp85) cc_final: 0.8026 (mmm160) REVERT: B 554 GLU cc_start: 0.7887 (tt0) cc_final: 0.7666 (tt0) REVERT: C 225 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7947 (mmt90) REVERT: C 303 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7390 (tp) REVERT: C 306 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.6998 (mtm-85) REVERT: C 470 GLN cc_start: 0.9060 (tt0) cc_final: 0.8818 (tt0) REVERT: C 476 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8053 (mmm160) REVERT: C 554 GLU cc_start: 0.7917 (tt0) cc_final: 0.7681 (tt0) REVERT: D 225 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7963 (mmt90) REVERT: D 306 ARG cc_start: 0.7387 (mtm110) cc_final: 0.6983 (mtm-85) REVERT: D 554 GLU cc_start: 0.7969 (tt0) cc_final: 0.7700 (tt0) REVERT: E 152 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: E 225 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7974 (mmt90) REVERT: E 265 GLU cc_start: 0.8525 (pt0) cc_final: 0.8095 (pp20) REVERT: E 303 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7409 (tp) REVERT: E 311 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8348 (mt0) REVERT: E 550 LYS cc_start: 0.8293 (mttt) cc_final: 0.8067 (mttm) REVERT: E 554 GLU cc_start: 0.7958 (tt0) cc_final: 0.7716 (tt0) REVERT: E 579 VAL cc_start: 0.7190 (OUTLIER) cc_final: 0.6825 (t) REVERT: F 152 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: F 225 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7951 (mmt90) REVERT: F 272 LEU cc_start: 0.8806 (tp) cc_final: 0.8596 (mt) REVERT: F 329 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8252 (tptt) REVERT: F 554 GLU cc_start: 0.7979 (tt0) cc_final: 0.7682 (tt0) REVERT: G 220 ASP cc_start: 0.8384 (m-30) cc_final: 0.8177 (m-30) REVERT: G 225 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7924 (mmt90) REVERT: G 476 ARG cc_start: 0.8245 (mtp85) cc_final: 0.8005 (mmm160) REVERT: G 554 GLU cc_start: 0.7975 (tt0) cc_final: 0.7723 (tt0) outliers start: 88 outliers final: 33 residues processed: 438 average time/residue: 0.8504 time to fit residues: 416.8712 Evaluate side-chains 354 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 579 VAL Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 481 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 4 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 273 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS B 311 GLN B 426 HIS C 426 HIS E 426 HIS F 311 GLN F 426 HIS G 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.143388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.108194 restraints weight = 22138.465| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.43 r_work: 0.3169 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25585 Z= 0.279 Angle : 0.611 6.430 34797 Z= 0.339 Chirality : 0.048 0.159 3787 Planarity : 0.005 0.053 4564 Dihedral : 5.325 21.093 3495 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.92 % Allowed : 15.90 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.46 (0.15), residues: 3122 helix: -5.00 (0.15), residues: 84 sheet: 0.84 (0.13), residues: 1435 loop : 0.22 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 204 TYR 0.013 0.002 TYR F 499 PHE 0.027 0.003 PHE E 252 TRP 0.010 0.002 TRP E 530 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00606 (25571) covalent geometry : angle 0.60870 (34769) SS BOND : bond 0.00337 ( 14) SS BOND : angle 1.78804 ( 28) hydrogen bonds : bond 0.04534 ( 994) hydrogen bonds : angle 5.76938 ( 2871) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 327 time to evaluate : 1.023 Fit side-chains REVERT: A 303 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7489 (tp) REVERT: A 309 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8456 (pt) REVERT: A 476 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7391 (mtm180) REVERT: A 554 GLU cc_start: 0.7958 (tt0) cc_final: 0.7669 (tt0) REVERT: A 578 ASN cc_start: 0.8403 (m-40) cc_final: 0.8118 (m110) REVERT: B 329 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8249 (tptt) REVERT: B 430 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7870 (m-40) REVERT: B 554 GLU cc_start: 0.7968 (tt0) cc_final: 0.7710 (tt0) REVERT: C 152 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: C 303 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7434 (tp) REVERT: C 306 ARG cc_start: 0.7329 (mtm-85) cc_final: 0.7069 (mtm-85) REVERT: C 554 GLU cc_start: 0.7958 (tt0) cc_final: 0.7702 (tt0) REVERT: D 225 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7999 (mmt90) REVERT: D 476 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7661 (mtm180) REVERT: D 554 GLU cc_start: 0.7967 (tt0) cc_final: 0.7696 (tt0) REVERT: E 225 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.8040 (mmt90) REVERT: E 265 GLU cc_start: 0.8585 (pt0) cc_final: 0.8154 (pp20) REVERT: E 303 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7454 (tp) REVERT: E 406 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8877 (tmt90) REVERT: E 554 GLU cc_start: 0.8028 (tt0) cc_final: 0.7619 (tt0) REVERT: F 152 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: F 309 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8499 (pt) REVERT: F 329 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8255 (tptt) REVERT: F 554 GLU cc_start: 0.8018 (tt0) cc_final: 0.7630 (tt0) REVERT: G 220 ASP cc_start: 0.8408 (m-30) cc_final: 0.8186 (m-30) REVERT: G 225 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7994 (mmt90) REVERT: G 309 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8513 (pt) REVERT: G 476 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8083 (mmm160) REVERT: G 554 GLU cc_start: 0.8016 (tt0) cc_final: 0.7626 (tt0) outliers start: 107 outliers final: 45 residues processed: 393 average time/residue: 0.8469 time to fit residues: 371.6445 Evaluate side-chains 363 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 476 ARG Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 472 ASP Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 481 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 227 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 292 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 chunk 280 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS B 311 GLN B 426 HIS E 311 GLN E 426 HIS F 311 GLN F 426 HIS G 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109155 restraints weight = 22189.897| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.36 r_work: 0.3174 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 25585 Z= 0.261 Angle : 0.605 7.341 34797 Z= 0.336 Chirality : 0.047 0.152 3787 Planarity : 0.005 0.049 4564 Dihedral : 5.410 21.339 3494 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.03 % Allowed : 16.12 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.15), residues: 3122 helix: -5.01 (0.15), residues: 84 sheet: 0.78 (0.13), residues: 1435 loop : 0.20 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 204 TYR 0.013 0.002 TYR F 499 PHE 0.027 0.003 PHE E 252 TRP 0.010 0.002 TRP E 530 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00569 (25571) covalent geometry : angle 0.59805 (34769) SS BOND : bond 0.00328 ( 14) SS BOND : angle 3.32181 ( 28) hydrogen bonds : bond 0.04398 ( 994) hydrogen bonds : angle 5.75307 ( 2871) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 312 time to evaluate : 1.002 Fit side-chains REVERT: A 303 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7443 (tp) REVERT: A 309 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8431 (pt) REVERT: A 476 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7462 (mtm180) REVERT: A 554 GLU cc_start: 0.7953 (tt0) cc_final: 0.7664 (tt0) REVERT: B 152 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: B 329 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8225 (tptt) REVERT: B 554 GLU cc_start: 0.7930 (tt0) cc_final: 0.7652 (tt0) REVERT: C 152 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: C 303 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7453 (tp) REVERT: C 366 VAL cc_start: 0.8461 (m) cc_final: 0.8239 (p) REVERT: C 554 GLU cc_start: 0.7957 (tt0) cc_final: 0.7676 (tt0) REVERT: D 554 GLU cc_start: 0.7933 (tt0) cc_final: 0.7660 (tt0) REVERT: E 152 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: E 265 GLU cc_start: 0.8590 (pt0) cc_final: 0.8133 (pp20) REVERT: E 303 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7445 (tp) REVERT: E 406 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8853 (tmt90) REVERT: E 554 GLU cc_start: 0.7966 (tt0) cc_final: 0.7630 (tt0) REVERT: E 560 SER cc_start: 0.8180 (p) cc_final: 0.7922 (t) REVERT: F 309 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8491 (pt) REVERT: F 329 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8222 (tptt) REVERT: F 476 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7598 (mtm180) REVERT: F 554 GLU cc_start: 0.8031 (tt0) cc_final: 0.7613 (tt0) REVERT: G 220 ASP cc_start: 0.8383 (m-30) cc_final: 0.8141 (m-30) REVERT: G 309 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8506 (pt) REVERT: G 476 ARG cc_start: 0.8305 (mtp85) cc_final: 0.8105 (mmm160) REVERT: G 554 GLU cc_start: 0.7971 (tt0) cc_final: 0.7589 (tt0) outliers start: 110 outliers final: 60 residues processed: 386 average time/residue: 0.8434 time to fit residues: 365.1097 Evaluate side-chains 374 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 302 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 503 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 16 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 23 optimal weight: 0.0020 chunk 305 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS B 311 GLN B 426 HIS E 426 HIS F 311 GLN F 426 HIS G 426 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108956 restraints weight = 21826.053| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.43 r_work: 0.3178 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25585 Z= 0.212 Angle : 0.559 5.533 34797 Z= 0.312 Chirality : 0.046 0.145 3787 Planarity : 0.004 0.046 4564 Dihedral : 5.260 20.800 3493 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.18 % Allowed : 15.93 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.36 (0.15), residues: 3122 helix: -5.01 (0.15), residues: 84 sheet: 0.73 (0.13), residues: 1435 loop : 0.20 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 204 TYR 0.012 0.002 TYR G 385 PHE 0.023 0.003 PHE G 284 TRP 0.010 0.002 TRP E 530 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00459 (25571) covalent geometry : angle 0.55618 (34769) SS BOND : bond 0.00253 ( 14) SS BOND : angle 2.12715 ( 28) hydrogen bonds : bond 0.04108 ( 994) hydrogen bonds : angle 5.59300 ( 2871) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 314 time to evaluate : 0.995 Fit side-chains REVERT: A 303 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7429 (tp) REVERT: A 309 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8441 (pt) REVERT: A 554 GLU cc_start: 0.7974 (tt0) cc_final: 0.7685 (tt0) REVERT: B 152 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: B 329 LYS cc_start: 0.8562 (mtpp) cc_final: 0.8240 (tptt) REVERT: B 430 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7860 (m-40) REVERT: B 554 GLU cc_start: 0.7927 (tt0) cc_final: 0.7650 (tt0) REVERT: C 152 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: C 303 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7424 (tp) REVERT: C 366 VAL cc_start: 0.8465 (m) cc_final: 0.8246 (p) REVERT: C 554 GLU cc_start: 0.7959 (tt0) cc_final: 0.7670 (tt0) REVERT: D 554 GLU cc_start: 0.7969 (tt0) cc_final: 0.7691 (tt0) REVERT: E 152 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: E 265 GLU cc_start: 0.8588 (pt0) cc_final: 0.8122 (pp20) REVERT: E 303 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7437 (tp) REVERT: E 554 GLU cc_start: 0.7974 (tt0) cc_final: 0.7590 (tt0) REVERT: F 152 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: F 272 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8456 (mp) REVERT: F 309 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8513 (pt) REVERT: F 329 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8231 (tptt) REVERT: F 554 GLU cc_start: 0.8043 (tt0) cc_final: 0.7625 (tt0) REVERT: G 220 ASP cc_start: 0.8393 (m-30) cc_final: 0.8156 (m-30) REVERT: G 309 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8509 (pt) REVERT: G 554 GLU cc_start: 0.8001 (tt0) cc_final: 0.7621 (tt0) outliers start: 114 outliers final: 64 residues processed: 398 average time/residue: 0.8279 time to fit residues: 370.7885 Evaluate side-chains 384 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 308 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 503 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 250 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 208 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS B 426 HIS ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN E 426 HIS F 426 HIS G 426 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112655 restraints weight = 22005.744| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.44 r_work: 0.3235 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25585 Z= 0.117 Angle : 0.466 5.615 34797 Z= 0.262 Chirality : 0.043 0.141 3787 Planarity : 0.003 0.045 4564 Dihedral : 4.772 18.540 3493 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.59 % Allowed : 16.63 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.39 (0.15), residues: 3122 helix: -5.01 (0.15), residues: 84 sheet: 0.71 (0.13), residues: 1435 loop : 0.26 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 204 TYR 0.009 0.001 TYR B 499 PHE 0.027 0.002 PHE G 284 TRP 0.010 0.001 TRP E 314 HIS 0.002 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00249 (25571) covalent geometry : angle 0.46290 (34769) SS BOND : bond 0.00081 ( 14) SS BOND : angle 2.05439 ( 28) hydrogen bonds : bond 0.03317 ( 994) hydrogen bonds : angle 5.16439 ( 2871) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 328 time to evaluate : 1.018 Fit side-chains REVERT: A 303 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7381 (tp) REVERT: A 309 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8480 (pt) REVERT: A 554 GLU cc_start: 0.7923 (tt0) cc_final: 0.7615 (tt0) REVERT: B 152 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: B 329 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8173 (tptt) REVERT: B 554 GLU cc_start: 0.7890 (tt0) cc_final: 0.7603 (tt0) REVERT: C 303 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7378 (tp) REVERT: C 304 GLU cc_start: 0.6629 (tt0) cc_final: 0.6316 (tt0) REVERT: C 366 VAL cc_start: 0.8402 (m) cc_final: 0.8143 (p) REVERT: C 470 GLN cc_start: 0.9010 (tt0) cc_final: 0.8781 (tt0) REVERT: C 554 GLU cc_start: 0.7914 (tt0) cc_final: 0.7629 (tt0) REVERT: D 225 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.7860 (mmt90) REVERT: D 554 GLU cc_start: 0.7929 (tt0) cc_final: 0.7652 (tt0) REVERT: E 152 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: E 265 GLU cc_start: 0.8530 (pt0) cc_final: 0.8036 (pp20) REVERT: E 303 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7391 (tp) REVERT: E 554 GLU cc_start: 0.7955 (tt0) cc_final: 0.7567 (tt0) REVERT: F 309 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8498 (pt) REVERT: F 329 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8202 (tptt) REVERT: F 554 GLU cc_start: 0.7996 (tt0) cc_final: 0.7670 (tt0) REVERT: G 309 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8484 (pt) REVERT: G 311 GLN cc_start: 0.8662 (mt0) cc_final: 0.8437 (mt0) REVERT: G 554 GLU cc_start: 0.7951 (tt0) cc_final: 0.7555 (tt0) outliers start: 98 outliers final: 58 residues processed: 395 average time/residue: 0.8274 time to fit residues: 367.3687 Evaluate side-chains 377 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 311 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 481 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 159 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 244 optimal weight: 0.0770 chunk 39 optimal weight: 10.0000 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS B 311 GLN C 311 GLN E 311 GLN E 426 HIS F 426 HIS G 426 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110464 restraints weight = 21788.959| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.42 r_work: 0.3188 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25585 Z= 0.159 Angle : 0.512 7.296 34797 Z= 0.285 Chirality : 0.044 0.145 3787 Planarity : 0.004 0.074 4564 Dihedral : 4.938 19.344 3493 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.41 % Allowed : 16.85 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.36 (0.15), residues: 3122 helix: -5.01 (0.15), residues: 84 sheet: 0.67 (0.13), residues: 1435 loop : 0.26 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 204 TYR 0.010 0.001 TYR A 385 PHE 0.019 0.002 PHE E 252 TRP 0.011 0.001 TRP G 314 HIS 0.002 0.001 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00345 (25571) covalent geometry : angle 0.50710 (34769) SS BOND : bond 0.00158 ( 14) SS BOND : angle 2.42364 ( 28) hydrogen bonds : bond 0.03620 ( 994) hydrogen bonds : angle 5.27662 ( 2871) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 318 time to evaluate : 0.908 Fit side-chains REVERT: A 303 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7384 (tp) REVERT: A 309 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8460 (pt) REVERT: A 554 GLU cc_start: 0.7872 (tt0) cc_final: 0.7563 (tt0) REVERT: B 152 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: B 329 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8177 (tptt) REVERT: B 554 GLU cc_start: 0.7871 (tt0) cc_final: 0.7577 (tt0) REVERT: C 303 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7377 (tp) REVERT: C 304 GLU cc_start: 0.6629 (tt0) cc_final: 0.6303 (tt0) REVERT: C 366 VAL cc_start: 0.8406 (m) cc_final: 0.8157 (p) REVERT: C 554 GLU cc_start: 0.7911 (tt0) cc_final: 0.7622 (tt0) REVERT: D 554 GLU cc_start: 0.7882 (tt0) cc_final: 0.7602 (tt0) REVERT: E 265 GLU cc_start: 0.8566 (pt0) cc_final: 0.8056 (pp20) REVERT: E 303 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7377 (tp) REVERT: E 554 GLU cc_start: 0.7911 (tt0) cc_final: 0.7511 (tt0) REVERT: F 152 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: F 272 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8379 (mp) REVERT: F 309 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8480 (pt) REVERT: F 329 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8177 (tptt) REVERT: F 554 GLU cc_start: 0.7968 (tt0) cc_final: 0.7527 (tt0) REVERT: G 309 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8476 (pt) REVERT: G 311 GLN cc_start: 0.8678 (mt0) cc_final: 0.8444 (mt0) REVERT: G 554 GLU cc_start: 0.7884 (tt0) cc_final: 0.7480 (tt0) outliers start: 93 outliers final: 64 residues processed: 379 average time/residue: 0.8273 time to fit residues: 352.3778 Evaluate side-chains 384 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 311 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 481 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 229 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 23 optimal weight: 0.2980 chunk 266 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS B 311 GLN C 311 GLN E 311 GLN E 426 HIS F 311 GLN F 426 HIS G 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108852 restraints weight = 21814.440| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.39 r_work: 0.3159 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25585 Z= 0.217 Angle : 0.574 8.218 34797 Z= 0.318 Chirality : 0.046 0.147 3787 Planarity : 0.005 0.076 4564 Dihedral : 5.222 20.471 3493 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.52 % Allowed : 16.89 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3122 helix: -5.01 (0.15), residues: 84 sheet: 0.63 (0.13), residues: 1435 loop : 0.24 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 204 TYR 0.011 0.002 TYR G 385 PHE 0.027 0.003 PHE G 284 TRP 0.011 0.002 TRP D 314 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00471 (25571) covalent geometry : angle 0.56607 (34769) SS BOND : bond 0.00233 ( 14) SS BOND : angle 3.38936 ( 28) hydrogen bonds : bond 0.04023 ( 994) hydrogen bonds : angle 5.48722 ( 2871) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 313 time to evaluate : 0.952 Fit side-chains REVERT: A 303 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7396 (tp) REVERT: A 309 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8482 (pt) REVERT: A 554 GLU cc_start: 0.7892 (tt0) cc_final: 0.7586 (tt0) REVERT: B 152 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: B 329 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8215 (tptt) REVERT: B 554 GLU cc_start: 0.7918 (tt0) cc_final: 0.7621 (tt0) REVERT: C 303 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7386 (tp) REVERT: C 304 GLU cc_start: 0.6663 (tt0) cc_final: 0.6344 (tt0) REVERT: C 366 VAL cc_start: 0.8432 (m) cc_final: 0.8207 (p) REVERT: C 554 GLU cc_start: 0.7930 (tt0) cc_final: 0.7644 (tt0) REVERT: D 366 VAL cc_start: 0.8386 (m) cc_final: 0.8167 (p) REVERT: D 554 GLU cc_start: 0.7893 (tt0) cc_final: 0.7611 (tt0) REVERT: E 265 GLU cc_start: 0.8586 (pt0) cc_final: 0.8080 (pp20) REVERT: E 303 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7401 (tp) REVERT: E 554 GLU cc_start: 0.7919 (tt0) cc_final: 0.7571 (tt0) REVERT: F 152 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: F 272 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8375 (mp) REVERT: F 329 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8204 (tptt) REVERT: F 476 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7641 (mtm180) REVERT: F 554 GLU cc_start: 0.7969 (tt0) cc_final: 0.7647 (tt0) REVERT: G 309 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8475 (pt) REVERT: G 554 GLU cc_start: 0.7914 (tt0) cc_final: 0.7517 (tt0) outliers start: 96 outliers final: 70 residues processed: 378 average time/residue: 0.8639 time to fit residues: 366.0166 Evaluate side-chains 391 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 312 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 503 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 256 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS C 311 GLN E 311 GLN E 426 HIS F 426 HIS G 426 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111175 restraints weight = 21958.760| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.43 r_work: 0.3195 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25585 Z= 0.144 Angle : 0.504 6.699 34797 Z= 0.281 Chirality : 0.044 0.143 3787 Planarity : 0.004 0.083 4564 Dihedral : 4.929 19.161 3493 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.11 % Allowed : 17.58 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.34 (0.15), residues: 3122 helix: -5.01 (0.15), residues: 84 sheet: 0.62 (0.13), residues: 1435 loop : 0.29 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 204 TYR 0.010 0.001 TYR B 250 PHE 0.031 0.002 PHE G 284 TRP 0.011 0.001 TRP D 314 HIS 0.002 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00311 (25571) covalent geometry : angle 0.50035 (34769) SS BOND : bond 0.00085 ( 14) SS BOND : angle 2.32363 ( 28) hydrogen bonds : bond 0.03524 ( 994) hydrogen bonds : angle 5.23831 ( 2871) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 319 time to evaluate : 1.095 Fit side-chains REVERT: A 303 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7352 (tp) REVERT: A 309 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8441 (pt) REVERT: A 554 GLU cc_start: 0.7874 (tt0) cc_final: 0.7569 (tt0) REVERT: B 152 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: B 185 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: B 329 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8163 (tptt) REVERT: B 554 GLU cc_start: 0.7875 (tt0) cc_final: 0.7582 (tt0) REVERT: C 303 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7380 (tp) REVERT: C 304 GLU cc_start: 0.6615 (tt0) cc_final: 0.6296 (tt0) REVERT: C 366 VAL cc_start: 0.8409 (m) cc_final: 0.8161 (p) REVERT: C 554 GLU cc_start: 0.7905 (tt0) cc_final: 0.7619 (tt0) REVERT: D 311 GLN cc_start: 0.8657 (mt0) cc_final: 0.8454 (mt0) REVERT: D 366 VAL cc_start: 0.8352 (m) cc_final: 0.8113 (p) REVERT: D 554 GLU cc_start: 0.7884 (tt0) cc_final: 0.7603 (tt0) REVERT: E 265 GLU cc_start: 0.8557 (pt0) cc_final: 0.8048 (pp20) REVERT: E 303 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7356 (tp) REVERT: E 304 GLU cc_start: 0.6547 (tt0) cc_final: 0.6196 (tt0) REVERT: E 554 GLU cc_start: 0.7913 (tt0) cc_final: 0.7573 (tt0) REVERT: F 152 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: F 272 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8383 (mp) REVERT: F 329 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8176 (tptt) REVERT: F 554 GLU cc_start: 0.7949 (tt0) cc_final: 0.7627 (tt0) REVERT: G 309 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8439 (pt) REVERT: G 311 GLN cc_start: 0.8670 (mt0) cc_final: 0.8439 (mt0) REVERT: G 554 GLU cc_start: 0.7908 (tt0) cc_final: 0.7509 (tt0) outliers start: 85 outliers final: 62 residues processed: 379 average time/residue: 0.8302 time to fit residues: 352.6904 Evaluate side-chains 385 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 314 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 481 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 67 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 82 optimal weight: 0.0040 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS B 311 GLN C 311 GLN E 311 GLN E 426 HIS F 426 HIS G 426 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111223 restraints weight = 21981.833| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.42 r_work: 0.3196 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25585 Z= 0.146 Angle : 0.512 7.153 34797 Z= 0.284 Chirality : 0.044 0.144 3787 Planarity : 0.004 0.087 4564 Dihedral : 4.903 18.992 3493 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.89 % Allowed : 17.99 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.32 (0.15), residues: 3122 helix: -5.01 (0.15), residues: 84 sheet: 0.60 (0.13), residues: 1435 loop : 0.29 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 204 TYR 0.010 0.001 TYR A 385 PHE 0.034 0.002 PHE G 284 TRP 0.011 0.001 TRP G 314 HIS 0.002 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00316 (25571) covalent geometry : angle 0.50878 (34769) SS BOND : bond 0.00089 ( 14) SS BOND : angle 2.19826 ( 28) hydrogen bonds : bond 0.03504 ( 994) hydrogen bonds : angle 5.21905 ( 2871) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 319 time to evaluate : 1.061 Fit side-chains REVERT: A 303 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7367 (tp) REVERT: A 309 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8452 (pt) REVERT: A 554 GLU cc_start: 0.7879 (tt0) cc_final: 0.7568 (tt0) REVERT: B 329 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8190 (tptt) REVERT: B 554 GLU cc_start: 0.7890 (tt0) cc_final: 0.7601 (tt0) REVERT: C 303 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7373 (tp) REVERT: C 304 GLU cc_start: 0.6607 (tt0) cc_final: 0.6292 (tt0) REVERT: C 366 VAL cc_start: 0.8412 (m) cc_final: 0.8159 (p) REVERT: C 554 GLU cc_start: 0.7915 (tt0) cc_final: 0.7630 (tt0) REVERT: D 311 GLN cc_start: 0.8668 (mt0) cc_final: 0.8464 (mt0) REVERT: D 554 GLU cc_start: 0.7892 (tt0) cc_final: 0.7612 (tt0) REVERT: E 265 GLU cc_start: 0.8555 (pt0) cc_final: 0.8055 (pp20) REVERT: E 303 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7361 (tp) REVERT: E 304 GLU cc_start: 0.6540 (tt0) cc_final: 0.6203 (tt0) REVERT: E 554 GLU cc_start: 0.7926 (tt0) cc_final: 0.7532 (tt0) REVERT: F 152 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: F 272 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8394 (mp) REVERT: F 329 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8191 (tptt) REVERT: F 554 GLU cc_start: 0.7972 (tt0) cc_final: 0.7639 (tt0) REVERT: G 309 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8447 (pt) REVERT: G 311 GLN cc_start: 0.8664 (mt0) cc_final: 0.8443 (mt0) REVERT: G 554 GLU cc_start: 0.7914 (tt0) cc_final: 0.7514 (tt0) outliers start: 79 outliers final: 61 residues processed: 372 average time/residue: 0.8583 time to fit residues: 357.7388 Evaluate side-chains 381 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 313 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 503 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 59 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 248 optimal weight: 0.0370 chunk 140 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS B 311 GLN C 311 GLN E 311 GLN E 426 HIS F 426 HIS G 426 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108556 restraints weight = 21706.173| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.40 r_work: 0.3156 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25585 Z= 0.238 Angle : 0.602 7.591 34797 Z= 0.332 Chirality : 0.047 0.146 3787 Planarity : 0.005 0.085 4564 Dihedral : 5.286 20.607 3493 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.04 % Allowed : 17.66 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.15), residues: 3122 helix: -5.01 (0.15), residues: 84 sheet: 0.58 (0.13), residues: 1435 loop : 0.25 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 204 TYR 0.012 0.002 TYR G 385 PHE 0.032 0.003 PHE G 284 TRP 0.012 0.002 TRP G 314 HIS 0.003 0.001 HIS G 426 Details of bonding type rmsd covalent geometry : bond 0.00521 (25571) covalent geometry : angle 0.59554 (34769) SS BOND : bond 0.00284 ( 14) SS BOND : angle 3.10320 ( 28) hydrogen bonds : bond 0.04123 ( 994) hydrogen bonds : angle 5.53533 ( 2871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14272.74 seconds wall clock time: 242 minutes 47.14 seconds (14567.14 seconds total)