Starting phenix.real_space_refine on Mon Dec 30 18:47:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wub_32827/12_2024/7wub_32827_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wub_32827/12_2024/7wub_32827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wub_32827/12_2024/7wub_32827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wub_32827/12_2024/7wub_32827.map" model { file = "/net/cci-nas-00/data/ceres_data/7wub_32827/12_2024/7wub_32827_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wub_32827/12_2024/7wub_32827_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 348 5.16 5 C 39683 2.51 5 N 11169 2.21 5 O 12035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 63259 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "B" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "C" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4490 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "D" Number of atoms: 4487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4487 Classifications: {'peptide': 575} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 544} Chain breaks: 1 Chain: "E" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "F" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "G" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "H" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "I" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "J" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "K" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "L" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.01, per 1000 atoms: 0.43 Number of scatterers: 63259 At special positions: 0 Unit cell: (178.45, 173.47, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 348 16.00 P 24 15.00 O 12035 8.00 N 11169 7.00 C 39683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.40 Conformation dependent library (CDL) restraints added in 6.2 seconds 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14890 Finding SS restraints... Secondary structure from input PDB file: 354 helices and 48 sheets defined 51.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 212 through 226 removed outlier: 5.264A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 4.088A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.197A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.740A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.769A pdb=" N ARG A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.548A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 4.092A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.649A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 716 Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.703A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 760 removed outlier: 3.533A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 5.265A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 removed outlier: 4.087A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.196A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.741A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.770A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.548A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.093A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.647A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 716 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.702A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 760 removed outlier: 3.532A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 5.266A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 233 removed outlier: 4.087A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.196A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.741A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.769A pdb=" N ARG C 358 " --> pdb=" O ASP C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 407 through 426 Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 523 through 536 Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.548A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 4.093A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 587 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.649A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 716 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.703A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 760 removed outlier: 3.532A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 226 removed outlier: 5.265A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 4.087A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.196A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.741A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.769A pdb=" N ARG D 358 " --> pdb=" O ASP D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.547A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.092A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 587 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.648A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.702A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 760 removed outlier: 3.533A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 226 removed outlier: 5.265A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 4.088A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.196A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.742A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.769A pdb=" N ARG E 358 " --> pdb=" O ASP E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 396 through 403 Processing helix chain 'E' and resid 407 through 426 Processing helix chain 'E' and resid 438 through 444 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.548A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 569 removed outlier: 4.092A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 587 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.648A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 716 Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.703A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 760 removed outlier: 3.532A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 226 removed outlier: 5.265A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 233 removed outlier: 4.088A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.196A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.741A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.770A pdb=" N ARG F 358 " --> pdb=" O ASP F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 407 through 426 Processing helix chain 'F' and resid 438 through 444 Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.548A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.092A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 587 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.648A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 713 Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.702A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 760 removed outlier: 3.532A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 93 Processing helix chain 'G' and resid 134 through 140 removed outlier: 3.790A pdb=" N TYR G 138 " --> pdb=" O TYR G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 226 removed outlier: 3.578A pdb=" N ALA G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) Proline residue: G 223 - end of helix Processing helix chain 'G' and resid 226 through 233 removed outlier: 4.366A pdb=" N PHE G 230 " --> pdb=" O HIS G 226 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS G 231 " --> pdb=" O PRO G 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 263 Processing helix chain 'G' and resid 271 through 276 removed outlier: 3.546A pdb=" N MET G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 305 through 310 removed outlier: 3.913A pdb=" N ILE G 309 " --> pdb=" O GLU G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 334 removed outlier: 3.643A pdb=" N ARG G 323 " --> pdb=" O GLU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 359 removed outlier: 3.519A pdb=" N ARG G 359 " --> pdb=" O ALA G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 385 Processing helix chain 'G' and resid 396 through 403 Processing helix chain 'G' and resid 407 through 426 Processing helix chain 'G' and resid 427 through 430 Processing helix chain 'G' and resid 438 through 445 removed outlier: 3.887A pdb=" N MET G 442 " --> pdb=" O ASP G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 458 Processing helix chain 'G' and resid 482 through 499 Proline residue: G 496 - end of helix Processing helix chain 'G' and resid 499 through 506 Processing helix chain 'G' and resid 523 through 535 Processing helix chain 'G' and resid 543 through 553 Processing helix chain 'G' and resid 557 through 569 removed outlier: 3.651A pdb=" N GLU G 561 " --> pdb=" O ALA G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 586 Processing helix chain 'G' and resid 598 through 611 Processing helix chain 'G' and resid 625 through 629 Processing helix chain 'G' and resid 630 through 635 Processing helix chain 'G' and resid 649 through 661 Processing helix chain 'G' and resid 671 through 679 Processing helix chain 'G' and resid 683 through 716 removed outlier: 3.768A pdb=" N THR G 715 " --> pdb=" O ARG G 711 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN G 716 " --> pdb=" O GLU G 712 " (cutoff:3.500A) Processing helix chain 'G' and resid 732 through 742 removed outlier: 3.995A pdb=" N PHE G 742 " --> pdb=" O GLU G 738 " (cutoff:3.500A) Processing helix chain 'G' and resid 748 through 762 Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'H' and resid 134 through 140 removed outlier: 3.790A pdb=" N TYR H 138 " --> pdb=" O TYR H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 226 removed outlier: 3.578A pdb=" N ALA H 214 " --> pdb=" O ARG H 210 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) Proline residue: H 223 - end of helix Processing helix chain 'H' and resid 226 through 233 removed outlier: 4.367A pdb=" N PHE H 230 " --> pdb=" O HIS H 226 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS H 231 " --> pdb=" O PRO H 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 232 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 263 Processing helix chain 'H' and resid 271 through 276 removed outlier: 3.546A pdb=" N MET H 275 " --> pdb=" O GLY H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 296 Processing helix chain 'H' and resid 305 through 310 removed outlier: 3.913A pdb=" N ILE H 309 " --> pdb=" O GLU H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 334 removed outlier: 3.643A pdb=" N ARG H 323 " --> pdb=" O GLU H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 359 removed outlier: 3.519A pdb=" N ARG H 359 " --> pdb=" O ALA H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 385 Processing helix chain 'H' and resid 396 through 403 Processing helix chain 'H' and resid 407 through 426 Processing helix chain 'H' and resid 427 through 430 Processing helix chain 'H' and resid 438 through 445 removed outlier: 3.888A pdb=" N MET H 442 " --> pdb=" O ASP H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 458 Processing helix chain 'H' and resid 482 through 499 Proline residue: H 496 - end of helix Processing helix chain 'H' and resid 499 through 506 Processing helix chain 'H' and resid 523 through 535 Processing helix chain 'H' and resid 543 through 553 Processing helix chain 'H' and resid 557 through 569 removed outlier: 3.650A pdb=" N GLU H 561 " --> pdb=" O ALA H 557 " (cutoff:3.500A) Processing helix chain 'H' and resid 580 through 586 Processing helix chain 'H' and resid 598 through 611 Processing helix chain 'H' and resid 625 through 629 Processing helix chain 'H' and resid 630 through 635 Processing helix chain 'H' and resid 649 through 661 Processing helix chain 'H' and resid 671 through 679 Processing helix chain 'H' and resid 683 through 716 removed outlier: 3.769A pdb=" N THR H 715 " --> pdb=" O ARG H 711 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN H 716 " --> pdb=" O GLU H 712 " (cutoff:3.500A) Processing helix chain 'H' and resid 732 through 742 removed outlier: 3.995A pdb=" N PHE H 742 " --> pdb=" O GLU H 738 " (cutoff:3.500A) Processing helix chain 'H' and resid 748 through 762 Processing helix chain 'I' and resid 85 through 93 Processing helix chain 'I' and resid 134 through 140 removed outlier: 3.790A pdb=" N TYR I 138 " --> pdb=" O TYR I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 removed outlier: 3.578A pdb=" N ALA I 214 " --> pdb=" O ARG I 210 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) Proline residue: I 223 - end of helix Processing helix chain 'I' and resid 226 through 233 removed outlier: 4.367A pdb=" N PHE I 230 " --> pdb=" O HIS I 226 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 232 " --> pdb=" O ALA I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 263 Processing helix chain 'I' and resid 271 through 276 removed outlier: 3.548A pdb=" N MET I 275 " --> pdb=" O GLY I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 296 Processing helix chain 'I' and resid 305 through 310 removed outlier: 3.912A pdb=" N ILE I 309 " --> pdb=" O GLU I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 334 removed outlier: 3.643A pdb=" N ARG I 323 " --> pdb=" O GLU I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 359 removed outlier: 3.519A pdb=" N ARG I 359 " --> pdb=" O ALA I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 385 Processing helix chain 'I' and resid 396 through 403 Processing helix chain 'I' and resid 407 through 426 Processing helix chain 'I' and resid 427 through 430 Processing helix chain 'I' and resid 438 through 445 removed outlier: 3.887A pdb=" N MET I 442 " --> pdb=" O ASP I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 458 Processing helix chain 'I' and resid 482 through 499 Proline residue: I 496 - end of helix Processing helix chain 'I' and resid 499 through 506 Processing helix chain 'I' and resid 523 through 535 Processing helix chain 'I' and resid 543 through 553 Processing helix chain 'I' and resid 557 through 569 removed outlier: 3.651A pdb=" N GLU I 561 " --> pdb=" O ALA I 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 586 Processing helix chain 'I' and resid 598 through 611 Processing helix chain 'I' and resid 625 through 629 Processing helix chain 'I' and resid 630 through 635 Processing helix chain 'I' and resid 649 through 661 Processing helix chain 'I' and resid 671 through 679 Processing helix chain 'I' and resid 683 through 716 removed outlier: 3.769A pdb=" N THR I 715 " --> pdb=" O ARG I 711 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN I 716 " --> pdb=" O GLU I 712 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 742 removed outlier: 3.995A pdb=" N PHE I 742 " --> pdb=" O GLU I 738 " (cutoff:3.500A) Processing helix chain 'I' and resid 748 through 762 Processing helix chain 'J' and resid 85 through 93 Processing helix chain 'J' and resid 134 through 140 removed outlier: 3.789A pdb=" N TYR J 138 " --> pdb=" O TYR J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 226 removed outlier: 3.577A pdb=" N ALA J 214 " --> pdb=" O ARG J 210 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN J 215 " --> pdb=" O LYS J 211 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU J 222 " --> pdb=" O GLU J 218 " (cutoff:3.500A) Proline residue: J 223 - end of helix Processing helix chain 'J' and resid 226 through 233 removed outlier: 4.367A pdb=" N PHE J 230 " --> pdb=" O HIS J 226 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS J 231 " --> pdb=" O PRO J 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA J 232 " --> pdb=" O ALA J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 263 Processing helix chain 'J' and resid 271 through 276 removed outlier: 3.547A pdb=" N MET J 275 " --> pdb=" O GLY J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 296 Processing helix chain 'J' and resid 305 through 310 removed outlier: 3.913A pdb=" N ILE J 309 " --> pdb=" O GLU J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 334 removed outlier: 3.643A pdb=" N ARG J 323 " --> pdb=" O GLU J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 359 removed outlier: 3.520A pdb=" N ARG J 359 " --> pdb=" O ALA J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 385 Processing helix chain 'J' and resid 396 through 403 Processing helix chain 'J' and resid 407 through 426 Processing helix chain 'J' and resid 427 through 430 Processing helix chain 'J' and resid 438 through 445 removed outlier: 3.887A pdb=" N MET J 442 " --> pdb=" O ASP J 438 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 458 Processing helix chain 'J' and resid 482 through 499 Proline residue: J 496 - end of helix Processing helix chain 'J' and resid 499 through 506 Processing helix chain 'J' and resid 523 through 535 Processing helix chain 'J' and resid 543 through 553 Processing helix chain 'J' and resid 557 through 569 removed outlier: 3.651A pdb=" N GLU J 561 " --> pdb=" O ALA J 557 " (cutoff:3.500A) Processing helix chain 'J' and resid 580 through 586 Processing helix chain 'J' and resid 598 through 611 Processing helix chain 'J' and resid 625 through 629 Processing helix chain 'J' and resid 630 through 635 Processing helix chain 'J' and resid 649 through 661 Processing helix chain 'J' and resid 671 through 679 Processing helix chain 'J' and resid 683 through 716 removed outlier: 3.768A pdb=" N THR J 715 " --> pdb=" O ARG J 711 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN J 716 " --> pdb=" O GLU J 712 " (cutoff:3.500A) Processing helix chain 'J' and resid 732 through 742 removed outlier: 3.996A pdb=" N PHE J 742 " --> pdb=" O GLU J 738 " (cutoff:3.500A) Processing helix chain 'J' and resid 748 through 762 Processing helix chain 'K' and resid 85 through 93 Processing helix chain 'K' and resid 134 through 140 removed outlier: 3.789A pdb=" N TYR K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 226 removed outlier: 3.578A pdb=" N ALA K 214 " --> pdb=" O ARG K 210 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN K 215 " --> pdb=" O LYS K 211 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) Proline residue: K 223 - end of helix Processing helix chain 'K' and resid 226 through 233 removed outlier: 4.366A pdb=" N PHE K 230 " --> pdb=" O HIS K 226 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS K 231 " --> pdb=" O PRO K 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 263 Processing helix chain 'K' and resid 271 through 276 removed outlier: 3.547A pdb=" N MET K 275 " --> pdb=" O GLY K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 296 Processing helix chain 'K' and resid 305 through 310 removed outlier: 3.913A pdb=" N ILE K 309 " --> pdb=" O GLU K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 334 removed outlier: 3.643A pdb=" N ARG K 323 " --> pdb=" O GLU K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 359 removed outlier: 3.520A pdb=" N ARG K 359 " --> pdb=" O ALA K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 373 through 385 Processing helix chain 'K' and resid 396 through 403 Processing helix chain 'K' and resid 407 through 426 Processing helix chain 'K' and resid 427 through 430 Processing helix chain 'K' and resid 438 through 445 removed outlier: 3.886A pdb=" N MET K 442 " --> pdb=" O ASP K 438 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 458 Processing helix chain 'K' and resid 482 through 499 Proline residue: K 496 - end of helix Processing helix chain 'K' and resid 499 through 506 Processing helix chain 'K' and resid 523 through 535 Processing helix chain 'K' and resid 543 through 553 Processing helix chain 'K' and resid 557 through 569 removed outlier: 3.652A pdb=" N GLU K 561 " --> pdb=" O ALA K 557 " (cutoff:3.500A) Processing helix chain 'K' and resid 580 through 586 Processing helix chain 'K' and resid 598 through 611 Processing helix chain 'K' and resid 625 through 629 Processing helix chain 'K' and resid 630 through 635 Processing helix chain 'K' and resid 649 through 661 Processing helix chain 'K' and resid 671 through 679 Processing helix chain 'K' and resid 683 through 716 removed outlier: 3.769A pdb=" N THR K 715 " --> pdb=" O ARG K 711 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN K 716 " --> pdb=" O GLU K 712 " (cutoff:3.500A) Processing helix chain 'K' and resid 732 through 742 removed outlier: 3.995A pdb=" N PHE K 742 " --> pdb=" O GLU K 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 748 through 762 Processing helix chain 'L' and resid 85 through 93 Processing helix chain 'L' and resid 134 through 140 removed outlier: 3.790A pdb=" N TYR L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 226 removed outlier: 3.578A pdb=" N ALA L 214 " --> pdb=" O ARG L 210 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN L 215 " --> pdb=" O LYS L 211 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 226 through 233 removed outlier: 4.366A pdb=" N PHE L 230 " --> pdb=" O HIS L 226 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS L 231 " --> pdb=" O PRO L 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 263 Processing helix chain 'L' and resid 271 through 276 removed outlier: 3.547A pdb=" N MET L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 296 Processing helix chain 'L' and resid 305 through 310 removed outlier: 3.913A pdb=" N ILE L 309 " --> pdb=" O GLU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 334 removed outlier: 3.643A pdb=" N ARG L 323 " --> pdb=" O GLU L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 359 removed outlier: 3.519A pdb=" N ARG L 359 " --> pdb=" O ALA L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 385 Processing helix chain 'L' and resid 396 through 403 Processing helix chain 'L' and resid 407 through 426 Processing helix chain 'L' and resid 427 through 430 Processing helix chain 'L' and resid 438 through 445 removed outlier: 3.887A pdb=" N MET L 442 " --> pdb=" O ASP L 438 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 458 Processing helix chain 'L' and resid 482 through 499 Proline residue: L 496 - end of helix Processing helix chain 'L' and resid 499 through 506 Processing helix chain 'L' and resid 523 through 535 Processing helix chain 'L' and resid 543 through 553 Processing helix chain 'L' and resid 557 through 569 removed outlier: 3.652A pdb=" N GLU L 561 " --> pdb=" O ALA L 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 586 Processing helix chain 'L' and resid 598 through 611 Processing helix chain 'L' and resid 625 through 629 Processing helix chain 'L' and resid 630 through 635 Processing helix chain 'L' and resid 649 through 661 Processing helix chain 'L' and resid 671 through 679 Processing helix chain 'L' and resid 683 through 716 removed outlier: 3.769A pdb=" N THR L 715 " --> pdb=" O ARG L 711 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN L 716 " --> pdb=" O GLU L 712 " (cutoff:3.500A) Processing helix chain 'L' and resid 732 through 742 removed outlier: 3.995A pdb=" N PHE L 742 " --> pdb=" O GLU L 738 " (cutoff:3.500A) Processing helix chain 'L' and resid 748 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.051A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 541 removed outlier: 7.127A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.051A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 541 removed outlier: 7.127A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.051A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 541 removed outlier: 7.126A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.051A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 541 removed outlier: 7.127A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.051A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 541 removed outlier: 7.127A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.051A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 541 removed outlier: 7.127A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 38 through 42 removed outlier: 3.738A pdb=" N LEU G 26 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE G 82 " --> pdb=" O ARG G 25 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE G 27 " --> pdb=" O ILE G 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 114 through 115 removed outlier: 7.076A pdb=" N ILE G 114 " --> pdb=" O HIS G 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 117 through 118 Processing sheet with id=AB7, first strand: chain 'G' and resid 145 through 147 Processing sheet with id=AB8, first strand: chain 'G' and resid 265 through 270 removed outlier: 3.877A pdb=" N ARG G 365 " --> pdb=" O GLY G 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 538 through 541 removed outlier: 6.855A pdb=" N ASN G 538 " --> pdb=" O VAL G 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE G 575 " --> pdb=" O ASN G 538 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE G 540 " --> pdb=" O PHE G 575 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU G 515 " --> pdb=" O ILE G 643 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 38 through 42 removed outlier: 3.738A pdb=" N LEU H 26 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE H 82 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE H 27 " --> pdb=" O ILE H 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 114 through 115 removed outlier: 7.077A pdb=" N ILE H 114 " --> pdb=" O HIS H 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'H' and resid 117 through 118 Processing sheet with id=AC4, first strand: chain 'H' and resid 145 through 147 Processing sheet with id=AC5, first strand: chain 'H' and resid 265 through 270 removed outlier: 3.877A pdb=" N ARG H 365 " --> pdb=" O GLY H 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 538 through 541 removed outlier: 6.856A pdb=" N ASN H 538 " --> pdb=" O VAL H 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE H 575 " --> pdb=" O ASN H 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE H 540 " --> pdb=" O PHE H 575 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU H 515 " --> pdb=" O ILE H 643 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 38 through 42 removed outlier: 3.737A pdb=" N LEU I 26 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE I 82 " --> pdb=" O ARG I 25 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE I 27 " --> pdb=" O ILE I 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 114 through 115 removed outlier: 7.076A pdb=" N ILE I 114 " --> pdb=" O HIS I 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 117 through 118 Processing sheet with id=AD1, first strand: chain 'I' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'I' and resid 265 through 270 removed outlier: 3.877A pdb=" N ARG I 365 " --> pdb=" O GLY I 240 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 538 through 541 removed outlier: 6.856A pdb=" N ASN I 538 " --> pdb=" O VAL I 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE I 575 " --> pdb=" O ASN I 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE I 540 " --> pdb=" O PHE I 575 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU I 515 " --> pdb=" O ILE I 643 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 38 through 42 removed outlier: 3.738A pdb=" N LEU J 26 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE J 82 " --> pdb=" O ARG J 25 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE J 27 " --> pdb=" O ILE J 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 114 through 115 removed outlier: 7.076A pdb=" N ILE J 114 " --> pdb=" O HIS J 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 117 through 118 Processing sheet with id=AD7, first strand: chain 'J' and resid 145 through 147 Processing sheet with id=AD8, first strand: chain 'J' and resid 265 through 270 removed outlier: 3.877A pdb=" N ARG J 365 " --> pdb=" O GLY J 240 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 538 through 541 removed outlier: 6.856A pdb=" N ASN J 538 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE J 575 " --> pdb=" O ASN J 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE J 540 " --> pdb=" O PHE J 575 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU J 515 " --> pdb=" O ILE J 643 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 38 through 42 removed outlier: 3.738A pdb=" N LEU K 26 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE K 82 " --> pdb=" O ARG K 25 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE K 27 " --> pdb=" O ILE K 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 114 through 115 removed outlier: 7.075A pdb=" N ILE K 114 " --> pdb=" O HIS K 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 117 through 118 Processing sheet with id=AE4, first strand: chain 'K' and resid 145 through 147 Processing sheet with id=AE5, first strand: chain 'K' and resid 265 through 270 removed outlier: 3.878A pdb=" N ARG K 365 " --> pdb=" O GLY K 240 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 538 through 541 removed outlier: 6.855A pdb=" N ASN K 538 " --> pdb=" O VAL K 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE K 575 " --> pdb=" O ASN K 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE K 540 " --> pdb=" O PHE K 575 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU K 515 " --> pdb=" O ILE K 643 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 38 through 42 removed outlier: 3.737A pdb=" N LEU L 26 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE L 82 " --> pdb=" O ARG L 25 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE L 27 " --> pdb=" O ILE L 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 114 through 115 removed outlier: 7.076A pdb=" N ILE L 114 " --> pdb=" O HIS L 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AF1, first strand: chain 'L' and resid 145 through 147 Processing sheet with id=AF2, first strand: chain 'L' and resid 265 through 270 removed outlier: 3.877A pdb=" N ARG L 365 " --> pdb=" O GLY L 240 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 538 through 541 removed outlier: 6.855A pdb=" N ASN L 538 " --> pdb=" O VAL L 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE L 575 " --> pdb=" O ASN L 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE L 540 " --> pdb=" O PHE L 575 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU L 515 " --> pdb=" O ILE L 643 " (cutoff:3.500A) 2841 hydrogen bonds defined for protein. 8127 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: 25.34 Time building geometry restraints manager: 14.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 21782 1.35 - 1.48: 13346 1.48 - 1.61: 28609 1.61 - 1.74: 60 1.74 - 1.87: 582 Bond restraints: 64379 Sorted by residual: bond pdb=" C3' ADP L 801 " pdb=" C4' ADP L 801 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3' ADP G 801 " pdb=" C4' ADP G 801 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3' ADP H 801 " pdb=" C4' ADP H 801 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3' ADP I 801 " pdb=" C4' ADP I 801 " ideal model delta sigma weight residual 1.524 1.303 0.221 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3' ADP J 801 " pdb=" C4' ADP J 801 " ideal model delta sigma weight residual 1.524 1.303 0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 64374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 86604 4.91 - 9.83: 304 9.83 - 14.74: 61 14.74 - 19.66: 30 19.66 - 24.57: 12 Bond angle restraints: 87011 Sorted by residual: angle pdb=" C ARG C 711 " pdb=" CA ARG C 711 " pdb=" CB ARG C 711 " ideal model delta sigma weight residual 110.79 95.53 15.26 1.66e+00 3.63e-01 8.45e+01 angle pdb=" C ARG E 711 " pdb=" CA ARG E 711 " pdb=" CB ARG E 711 " ideal model delta sigma weight residual 110.79 95.53 15.26 1.66e+00 3.63e-01 8.45e+01 angle pdb=" C ARG A 711 " pdb=" CA ARG A 711 " pdb=" CB ARG A 711 " ideal model delta sigma weight residual 110.79 95.53 15.26 1.66e+00 3.63e-01 8.45e+01 angle pdb=" C ARG D 711 " pdb=" CA ARG D 711 " pdb=" CB ARG D 711 " ideal model delta sigma weight residual 110.79 95.53 15.26 1.66e+00 3.63e-01 8.45e+01 angle pdb=" C ARG B 711 " pdb=" CA ARG B 711 " pdb=" CB ARG B 711 " ideal model delta sigma weight residual 110.79 95.56 15.23 1.66e+00 3.63e-01 8.42e+01 ... (remaining 87006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 38502 30.39 - 60.77: 1240 60.77 - 91.15: 207 91.15 - 121.54: 30 121.54 - 151.92: 6 Dihedral angle restraints: 39985 sinusoidal: 17021 harmonic: 22964 Sorted by residual: dihedral pdb=" CD ARG G 741 " pdb=" NE ARG G 741 " pdb=" CZ ARG G 741 " pdb=" NH1 ARG G 741 " ideal model delta sinusoidal sigma weight residual 0.00 85.62 -85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CD ARG H 741 " pdb=" NE ARG H 741 " pdb=" CZ ARG H 741 " pdb=" NH1 ARG H 741 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CD ARG K 741 " pdb=" NE ARG K 741 " pdb=" CZ ARG K 741 " pdb=" NH1 ARG K 741 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 1.00e+01 1.00e-02 8.86e+01 ... (remaining 39982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 7428 0.049 - 0.098: 1579 0.098 - 0.148: 545 0.148 - 0.197: 66 0.197 - 0.246: 18 Chirality restraints: 9636 Sorted by residual: chirality pdb=" C17 Y6Y I 802 " pdb=" C18 Y6Y I 802 " pdb=" C21 Y6Y I 802 " pdb=" S1 Y6Y I 802 " both_signs ideal model delta sigma weight residual False 3.51 3.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C17 Y6Y G 802 " pdb=" C18 Y6Y G 802 " pdb=" C21 Y6Y G 802 " pdb=" S1 Y6Y G 802 " both_signs ideal model delta sigma weight residual False 3.51 3.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C17 Y6Y J 802 " pdb=" C18 Y6Y J 802 " pdb=" C21 Y6Y J 802 " pdb=" S1 Y6Y J 802 " both_signs ideal model delta sigma weight residual False 3.51 3.26 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 9633 not shown) Planarity restraints: 11498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 741 " -0.992 9.50e-02 1.11e+02 4.45e-01 1.22e+02 pdb=" NE ARG K 741 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG K 741 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 741 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 741 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 741 " -0.992 9.50e-02 1.11e+02 4.45e-01 1.22e+02 pdb=" NE ARG H 741 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG H 741 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 741 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 741 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 741 " -0.992 9.50e-02 1.11e+02 4.45e-01 1.22e+02 pdb=" NE ARG G 741 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG G 741 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 741 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 741 " -0.009 2.00e-02 2.50e+03 ... (remaining 11495 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 544 2.47 - 3.08: 47806 3.08 - 3.68: 95824 3.68 - 4.29: 141211 4.29 - 4.90: 233155 Nonbonded interactions: 518540 Sorted by model distance: nonbonded pdb=" O VAL A 399 " pdb=" OG1 THR A 403 " model vdw 1.859 3.040 nonbonded pdb=" O VAL E 399 " pdb=" OG1 THR E 403 " model vdw 1.859 3.040 nonbonded pdb=" O VAL F 399 " pdb=" OG1 THR F 403 " model vdw 1.859 3.040 nonbonded pdb=" O VAL D 399 " pdb=" OG1 THR D 403 " model vdw 1.859 3.040 nonbonded pdb=" O VAL C 399 " pdb=" OG1 THR C 403 " model vdw 1.860 3.040 ... (remaining 518535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) selection = (chain 'B' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) selection = (chain 'C' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) selection = (chain 'D' and (resid 200 through 711 or resid 714 through 775 or resid 801 thro \ ugh 802)) selection = (chain 'E' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) selection = (chain 'F' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.510 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 115.600 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.012 0.222 64379 Z= 0.797 Angle : 0.948 24.573 87011 Z= 0.476 Chirality : 0.047 0.246 9636 Planarity : 0.013 0.445 11498 Dihedral : 15.238 151.925 25095 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 45.64 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.42 % Favored : 94.21 % Rotamer: Outliers : 1.96 % Allowed : 1.69 % Favored : 96.35 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.08 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 7959 helix: 2.23 (0.09), residues: 3456 sheet: -0.63 (0.18), residues: 894 loop : -0.53 (0.11), residues: 3609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 454 HIS 0.008 0.001 HIS A 406 PHE 0.062 0.002 PHE K 360 TYR 0.026 0.001 TYR D 495 ARG 0.073 0.002 ARG B 732 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1313 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1181 time to evaluate : 5.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.8022 (mm) REVERT: A 709 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6968 (ttm170) REVERT: C 678 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: D 359 ARG cc_start: 0.7401 (ttt-90) cc_final: 0.6936 (ttm170) REVERT: D 678 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7964 (mmm) REVERT: F 709 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.6260 (ttm170) REVERT: G 723 GLU cc_start: 0.3484 (OUTLIER) cc_final: 0.3144 (tm-30) REVERT: H 723 GLU cc_start: 0.3175 (OUTLIER) cc_final: 0.2785 (tm-30) REVERT: I 669 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7590 (OUTLIER) REVERT: I 723 GLU cc_start: 0.3098 (OUTLIER) cc_final: 0.2655 (tm-30) REVERT: K 598 ASP cc_start: 0.7478 (p0) cc_final: 0.7256 (p0) REVERT: L 194 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: L 723 GLU cc_start: 0.2986 (OUTLIER) cc_final: 0.2617 (tm-30) outliers start: 132 outliers final: 33 residues processed: 1228 average time/residue: 1.5291 time to fit residues: 2379.4766 Evaluate side-chains 737 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 694 time to evaluate : 5.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 706 GLU Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 706 GLU Chi-restraints excluded: chain F residue 709 ARG Chi-restraints excluded: chain F residue 749 ASP Chi-restraints excluded: chain G residue 706 GLU Chi-restraints excluded: chain G residue 723 GLU Chi-restraints excluded: chain G residue 738 GLU Chi-restraints excluded: chain H residue 706 GLU Chi-restraints excluded: chain H residue 707 ILE Chi-restraints excluded: chain H residue 723 GLU Chi-restraints excluded: chain H residue 738 GLU Chi-restraints excluded: chain I residue 669 ASP Chi-restraints excluded: chain I residue 706 GLU Chi-restraints excluded: chain I residue 723 GLU Chi-restraints excluded: chain I residue 738 GLU Chi-restraints excluded: chain J residue 706 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 738 GLU Chi-restraints excluded: chain K residue 706 GLU Chi-restraints excluded: chain K residue 707 ILE Chi-restraints excluded: chain K residue 738 GLU Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 706 GLU Chi-restraints excluded: chain L residue 723 GLU Chi-restraints excluded: chain L residue 738 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 668 optimal weight: 0.5980 chunk 600 optimal weight: 3.9990 chunk 333 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 404 optimal weight: 0.9990 chunk 320 optimal weight: 0.0980 chunk 620 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 462 optimal weight: 2.9990 chunk 719 optimal weight: 6.9990 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 285 ASN B 285 ASN C 285 ASN D 285 ASN D 538 ASN E 285 ASN F 285 ASN G 212 GLN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 602 ASN ** I 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 ASN ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 ASN ** L 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 602 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 64379 Z= 0.292 Angle : 0.768 10.381 87011 Z= 0.381 Chirality : 0.047 0.204 9636 Planarity : 0.006 0.075 11498 Dihedral : 9.534 127.619 9283 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.94 % Favored : 93.60 % Rotamer: Outliers : 3.60 % Allowed : 9.71 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 7959 helix: 1.50 (0.09), residues: 3626 sheet: -0.24 (0.17), residues: 960 loop : -0.59 (0.11), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 454 HIS 0.010 0.002 HIS G 317 PHE 0.017 0.002 PHE J 139 TYR 0.023 0.002 TYR C 755 ARG 0.010 0.001 ARG B 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 803 time to evaluate : 5.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8505 (tt) cc_final: 0.8264 (mt) REVERT: A 564 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: A 706 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: B 401 ASN cc_start: 0.7677 (m-40) cc_final: 0.7438 (m110) REVERT: B 564 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: C 504 LEU cc_start: 0.8485 (tt) cc_final: 0.8283 (mt) REVERT: D 359 ARG cc_start: 0.7185 (ttt-90) cc_final: 0.6664 (ttm110) REVERT: D 561 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: E 401 ASN cc_start: 0.7625 (m-40) cc_final: 0.7393 (m110) REVERT: E 508 MET cc_start: 0.8781 (ttt) cc_final: 0.8337 (ttt) REVERT: E 706 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: F 427 MET cc_start: 0.3939 (tmt) cc_final: 0.3270 (ttm) REVERT: F 564 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: F 706 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: G 672 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8340 (mp) REVERT: H 378 LEU cc_start: 0.8512 (tm) cc_final: 0.8293 (tt) REVERT: H 423 ILE cc_start: 0.7800 (mt) cc_final: 0.7582 (mt) REVERT: H 427 MET cc_start: 0.6289 (tpt) cc_final: 0.6070 (ttt) REVERT: H 672 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8200 (mp) REVERT: I 427 MET cc_start: 0.6130 (tpt) cc_final: 0.5897 (ttt) REVERT: I 713 ARG cc_start: 0.7923 (tmm160) cc_final: 0.7601 (ttp80) REVERT: J 278 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8078 (mp) REVERT: J 713 ARG cc_start: 0.7945 (tmm160) cc_final: 0.7544 (ttp80) REVERT: K 278 LEU cc_start: 0.8258 (tt) cc_final: 0.8048 (tp) REVERT: K 378 LEU cc_start: 0.8599 (tm) cc_final: 0.8360 (tt) REVERT: K 427 MET cc_start: 0.6322 (tpt) cc_final: 0.5948 (ttt) REVERT: L 198 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7644 (tt) REVERT: L 278 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8094 (tp) outliers start: 243 outliers final: 61 residues processed: 942 average time/residue: 1.3501 time to fit residues: 1663.2130 Evaluate side-chains 732 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 659 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 285 ASN Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 709 ARG Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 706 GLU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 365 ARG Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 669 ASP Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 707 ILE Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 218 GLU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 633 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 399 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 598 optimal weight: 0.0370 chunk 489 optimal weight: 0.6980 chunk 198 optimal weight: 0.0470 chunk 720 optimal weight: 0.5980 chunk 778 optimal weight: 0.5980 chunk 641 optimal weight: 6.9990 chunk 714 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 578 optimal weight: 4.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN B 538 ASN C 285 ASN C 401 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN C 760 GLN D 285 ASN D 401 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN F 285 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN F 760 GLN G 24 ASN ** G 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 ASN ** I 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN ** L 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 602 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 64379 Z= 0.198 Angle : 0.669 12.296 87011 Z= 0.332 Chirality : 0.044 0.176 9636 Planarity : 0.005 0.071 11498 Dihedral : 7.841 117.972 9180 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.06 % Favored : 93.57 % Rotamer: Outliers : 3.19 % Allowed : 11.89 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.10), residues: 7959 helix: 1.45 (0.09), residues: 3704 sheet: -0.14 (0.17), residues: 960 loop : -0.63 (0.11), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.007 0.001 HIS J 317 PHE 0.014 0.001 PHE I 139 TYR 0.022 0.001 TYR L 244 ARG 0.009 0.001 ARG J 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 732 time to evaluate : 5.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6668 (mm-30) REVERT: A 349 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7640 (mtp-110) REVERT: A 365 ARG cc_start: 0.7638 (ptp-110) cc_final: 0.7329 (ptp-110) REVERT: A 564 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: C 294 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: C 349 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7672 (mtp-110) REVERT: C 449 MET cc_start: 0.7541 (tpt) cc_final: 0.7277 (tpt) REVERT: C 564 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: D 218 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6695 (mt-10) REVERT: D 294 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6555 (tt0) REVERT: D 561 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: D 564 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: E 349 ARG cc_start: 0.7820 (mtp-110) cc_final: 0.7615 (mtp-110) REVERT: E 470 GLU cc_start: 0.7170 (pp20) cc_final: 0.6926 (pm20) REVERT: E 508 MET cc_start: 0.8807 (ttt) cc_final: 0.8425 (ttt) REVERT: E 564 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: E 706 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: F 564 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: F 706 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: H 198 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7322 (tt) REVERT: H 672 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8224 (mp) REVERT: I 420 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7665 (mt) REVERT: I 713 ARG cc_start: 0.7969 (tmm160) cc_final: 0.7729 (ttp80) REVERT: J 423 ILE cc_start: 0.7910 (mt) cc_final: 0.7653 (mt) REVERT: J 427 MET cc_start: 0.6212 (tpt) cc_final: 0.5992 (ttt) REVERT: J 713 ARG cc_start: 0.7880 (tmm160) cc_final: 0.7645 (ttp80) REVERT: K 158 MET cc_start: 0.7900 (mtt) cc_final: 0.7538 (mtt) REVERT: K 198 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7338 (tt) REVERT: K 672 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8281 (mp) REVERT: K 713 ARG cc_start: 0.7979 (tmm160) cc_final: 0.7774 (tmm-80) REVERT: L 198 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7609 (tt) REVERT: L 427 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5986 (ttt) outliers start: 215 outliers final: 72 residues processed: 856 average time/residue: 1.3117 time to fit residues: 1473.9897 Evaluate side-chains 737 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 647 time to evaluate : 5.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 706 GLU Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 728 VAL Chi-restraints excluded: chain G residue 752 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 680 ASN Chi-restraints excluded: chain I residue 757 MET Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 672 LEU Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 427 MET Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 680 ASN Chi-restraints excluded: chain L residue 757 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 711 optimal weight: 0.0060 chunk 541 optimal weight: 0.0270 chunk 373 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 343 optimal weight: 9.9990 chunk 483 optimal weight: 0.9980 chunk 723 optimal weight: 0.8980 chunk 765 optimal weight: 0.8980 chunk 377 optimal weight: 2.9990 chunk 685 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 401 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN C 401 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN E 401 ASN F 285 ASN F 401 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 760 GLN ** G 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 ASN ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 64379 Z= 0.186 Angle : 0.635 10.365 87011 Z= 0.315 Chirality : 0.044 0.207 9636 Planarity : 0.004 0.071 11498 Dihedral : 7.267 108.354 9171 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.87 % Favored : 93.76 % Rotamer: Outliers : 3.16 % Allowed : 13.84 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.10), residues: 7959 helix: 1.46 (0.09), residues: 3711 sheet: -0.06 (0.17), residues: 978 loop : -0.61 (0.11), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.024 0.001 HIS H 317 PHE 0.012 0.001 PHE B 363 TYR 0.020 0.001 TYR I 244 ARG 0.009 0.001 ARG C 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 723 time to evaluate : 5.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.7209 (pp20) cc_final: 0.6987 (pm20) REVERT: B 401 ASN cc_start: 0.7498 (m-40) cc_final: 0.7251 (m110) REVERT: B 470 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: B 754 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7720 (tttt) REVERT: C 294 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6728 (tt0) REVERT: C 304 ASP cc_start: 0.8015 (t0) cc_final: 0.7619 (t0) REVERT: D 294 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6680 (mt-10) REVERT: D 470 GLU cc_start: 0.7278 (pt0) cc_final: 0.6804 (pm20) REVERT: E 470 GLU cc_start: 0.7160 (pp20) cc_final: 0.6941 (pm20) REVERT: E 508 MET cc_start: 0.8862 (ttt) cc_final: 0.8561 (ttt) REVERT: E 706 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: F 706 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: G 278 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8133 (mp) REVERT: G 423 ILE cc_start: 0.7760 (mt) cc_final: 0.7551 (mt) REVERT: H 198 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7342 (tt) REVERT: H 278 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8078 (tt) REVERT: I 382 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: I 672 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8332 (mp) REVERT: I 713 ARG cc_start: 0.7897 (tmm160) cc_final: 0.7648 (ttp80) REVERT: J 427 MET cc_start: 0.6104 (tpt) cc_final: 0.5818 (ttt) REVERT: K 158 MET cc_start: 0.7752 (mtt) cc_final: 0.7455 (mtt) REVERT: K 198 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7290 (tt) REVERT: K 713 ARG cc_start: 0.7957 (tmm160) cc_final: 0.7697 (ttp80) REVERT: L 198 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7587 (tt) REVERT: L 388 MET cc_start: 0.5584 (mtm) cc_final: 0.5355 (ptp) REVERT: L 479 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8360 (mm) outliers start: 213 outliers final: 77 residues processed: 847 average time/residue: 1.3420 time to fit residues: 1500.9929 Evaluate side-chains 738 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 647 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 285 ASN Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 706 GLU Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 550 MET Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain H residue 278 LEU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 382 GLN Chi-restraints excluded: chain I residue 442 MET Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 672 LEU Chi-restraints excluded: chain I residue 680 ASN Chi-restraints excluded: chain J residue 307 ASP Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 218 GLU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 218 GLU Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 680 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 637 optimal weight: 0.0870 chunk 434 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 570 optimal weight: 0.0970 chunk 315 optimal weight: 0.9990 chunk 653 optimal weight: 0.9990 chunk 529 optimal weight: 0.0470 chunk 0 optimal weight: 8.9990 chunk 390 optimal weight: 2.9990 chunk 687 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 401 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 401 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN D 401 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN F 226 HIS F 285 ASN F 401 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 760 GLN ** G 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 348 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** L 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 64379 Z= 0.176 Angle : 0.619 11.901 87011 Z= 0.305 Chirality : 0.043 0.202 9636 Planarity : 0.004 0.070 11498 Dihedral : 6.981 97.456 9171 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.84 % Favored : 93.81 % Rotamer: Outliers : 3.11 % Allowed : 15.51 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 7959 helix: 1.48 (0.09), residues: 3727 sheet: -0.00 (0.17), residues: 978 loop : -0.56 (0.11), residues: 3254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 454 HIS 0.015 0.001 HIS G 317 PHE 0.016 0.001 PHE B 363 TYR 0.014 0.001 TYR J 244 ARG 0.008 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 708 time to evaluate : 5.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.7237 (pp20) cc_final: 0.7004 (pm20) REVERT: B 401 ASN cc_start: 0.7611 (m-40) cc_final: 0.7350 (m110) REVERT: B 470 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: B 754 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7754 (tttt) REVERT: C 294 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6744 (tt0) REVERT: C 304 ASP cc_start: 0.7990 (t0) cc_final: 0.7602 (t0) REVERT: D 211 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.6267 (pptt) REVERT: D 294 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: D 470 GLU cc_start: 0.7322 (pt0) cc_final: 0.6843 (pm20) REVERT: D 720 MET cc_start: 0.5265 (ppp) cc_final: 0.2963 (tpt) REVERT: E 470 GLU cc_start: 0.7165 (pp20) cc_final: 0.6911 (pm20) REVERT: F 294 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6688 (tt0) REVERT: F 706 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: G 278 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8186 (mp) REVERT: H 198 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7355 (tt) REVERT: H 278 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8106 (tt) REVERT: I 504 LEU cc_start: 0.9024 (tp) cc_final: 0.8802 (mt) REVERT: I 672 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8335 (mp) REVERT: I 713 ARG cc_start: 0.7879 (tmm160) cc_final: 0.7656 (ttp80) REVERT: J 427 MET cc_start: 0.5926 (tpt) cc_final: 0.5643 (ttt) REVERT: K 198 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7317 (tt) REVERT: K 672 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8191 (mp) REVERT: L 198 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7501 (tt) outliers start: 210 outliers final: 71 residues processed: 840 average time/residue: 1.3189 time to fit residues: 1455.4647 Evaluate side-chains 734 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 649 time to evaluate : 5.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 203 TYR Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 706 GLU Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain H residue 278 LEU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 442 MET Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 672 LEU Chi-restraints excluded: chain I residue 680 ASN Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 307 ASP Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 218 GLU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 672 LEU Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 442 MET Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 680 ASN Chi-restraints excluded: chain L residue 752 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 257 optimal weight: 0.7980 chunk 689 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 449 optimal weight: 2.9990 chunk 188 optimal weight: 0.0570 chunk 766 optimal weight: 0.4980 chunk 636 optimal weight: 5.9990 chunk 354 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 253 optimal weight: 0.9980 chunk 402 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 401 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS F 285 ASN F 401 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 HIS ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 64379 Z= 0.199 Angle : 0.620 9.610 87011 Z= 0.304 Chirality : 0.044 0.255 9636 Planarity : 0.004 0.070 11498 Dihedral : 6.775 90.744 9168 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.93 % Favored : 93.77 % Rotamer: Outliers : 2.97 % Allowed : 16.59 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 7959 helix: 1.49 (0.09), residues: 3724 sheet: 0.06 (0.17), residues: 978 loop : -0.61 (0.11), residues: 3257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 454 HIS 0.007 0.001 HIS F 406 PHE 0.016 0.001 PHE F 363 TYR 0.014 0.001 TYR I 244 ARG 0.009 0.000 ARG D 753 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 691 time to evaluate : 5.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.3835 (tmm) cc_final: 0.3447 (ttt) REVERT: A 470 GLU cc_start: 0.7167 (pp20) cc_final: 0.6882 (pm20) REVERT: B 401 ASN cc_start: 0.7663 (m-40) cc_final: 0.7424 (m110) REVERT: B 470 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: B 611 MET cc_start: 0.8051 (tpp) cc_final: 0.7661 (tpt) REVERT: B 754 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7818 (tttt) REVERT: C 294 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: C 304 ASP cc_start: 0.8098 (t0) cc_final: 0.7703 (t0) REVERT: D 211 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6238 (pptt) REVERT: D 294 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: D 470 GLU cc_start: 0.7377 (pt0) cc_final: 0.6891 (pm20) REVERT: D 720 MET cc_start: 0.5091 (ppp) cc_final: 0.2915 (tpt) REVERT: F 285 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8508 (t160) REVERT: F 294 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6731 (tt0) REVERT: H 158 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7477 (mtt) REVERT: H 198 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7330 (tt) REVERT: H 278 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8087 (tt) REVERT: I 672 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8331 (mp) REVERT: J 82 ILE cc_start: 0.5658 (OUTLIER) cc_final: 0.5425 (tt) REVERT: K 198 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7279 (tt) REVERT: K 672 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8258 (mp) REVERT: L 198 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7491 (tt) outliers start: 200 outliers final: 91 residues processed: 825 average time/residue: 1.3580 time to fit residues: 1465.4483 Evaluate side-chains 760 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 654 time to evaluate : 5.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 550 MET Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 752 ILE Chi-restraints excluded: chain H residue 158 MET Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain H residue 278 LEU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 627 ASP Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 442 MET Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 672 LEU Chi-restraints excluded: chain I residue 680 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 307 ASP Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 757 MET Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 218 GLU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 627 ASP Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 672 LEU Chi-restraints excluded: chain K residue 680 ASN Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain L residue 442 MET Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 680 ASN Chi-restraints excluded: chain L residue 752 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 738 optimal weight: 0.0070 chunk 86 optimal weight: 0.8980 chunk 436 optimal weight: 2.9990 chunk 559 optimal weight: 0.9990 chunk 433 optimal weight: 7.9990 chunk 645 optimal weight: 9.9990 chunk 427 optimal weight: 0.0040 chunk 763 optimal weight: 0.1980 chunk 477 optimal weight: 1.9990 chunk 465 optimal weight: 0.6980 chunk 352 optimal weight: 10.0000 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 226 HIS F 401 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 24 ASN ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN K 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 64379 Z= 0.168 Angle : 0.610 10.676 87011 Z= 0.298 Chirality : 0.044 0.220 9636 Planarity : 0.004 0.069 11498 Dihedral : 6.594 97.423 9165 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.80 % Favored : 93.89 % Rotamer: Outliers : 2.76 % Allowed : 17.31 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 7959 helix: 1.48 (0.09), residues: 3760 sheet: 0.09 (0.16), residues: 1074 loop : -0.65 (0.11), residues: 3125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 454 HIS 0.008 0.001 HIS F 406 PHE 0.014 0.001 PHE A 266 TYR 0.018 0.001 TYR I 244 ARG 0.012 0.000 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 703 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 ASN cc_start: 0.7696 (m-40) cc_final: 0.7480 (m110) REVERT: B 754 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7805 (tttt) REVERT: C 304 ASP cc_start: 0.8099 (t0) cc_final: 0.7695 (t0) REVERT: C 720 MET cc_start: 0.5297 (ppp) cc_final: 0.4867 (pmm) REVERT: D 211 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.6219 (pptt) REVERT: D 294 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: D 470 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: D 720 MET cc_start: 0.4745 (ppp) cc_final: 0.2812 (tpt) REVERT: E 218 GLU cc_start: 0.7833 (pp20) cc_final: 0.7602 (mt-10) REVERT: E 373 ASP cc_start: 0.6689 (p0) cc_final: 0.6397 (p0) REVERT: H 198 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7263 (tt) REVERT: H 278 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8082 (tt) REVERT: J 427 MET cc_start: 0.5717 (tpt) cc_final: 0.5380 (ttt) REVERT: K 198 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7233 (tt) REVERT: K 672 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8354 (mp) REVERT: L 198 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7385 (tt) REVERT: L 427 MET cc_start: 0.5983 (ttt) cc_final: 0.5687 (mtp) outliers start: 186 outliers final: 76 residues processed: 827 average time/residue: 1.3691 time to fit residues: 1475.8813 Evaluate side-chains 735 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 650 time to evaluate : 5.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain H residue 278 LEU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 680 ASN Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 442 MET Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 307 ASP Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 317 HIS Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 672 LEU Chi-restraints excluded: chain K residue 680 ASN Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 678 MET Chi-restraints excluded: chain L residue 680 ASN Chi-restraints excluded: chain L residue 752 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 472 optimal weight: 1.9990 chunk 304 optimal weight: 0.6980 chunk 455 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 485 optimal weight: 1.9990 chunk 520 optimal weight: 0.7980 chunk 377 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 600 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS E 760 GLN F 226 HIS F 285 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 760 GLN ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 64379 Z= 0.288 Angle : 0.658 12.613 87011 Z= 0.321 Chirality : 0.046 0.264 9636 Planarity : 0.005 0.072 11498 Dihedral : 6.581 108.643 9165 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.98 % Favored : 93.78 % Rotamer: Outliers : 2.70 % Allowed : 17.87 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 7959 helix: 1.40 (0.09), residues: 3729 sheet: 0.05 (0.16), residues: 1080 loop : -0.65 (0.11), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 454 HIS 0.012 0.001 HIS D 406 PHE 0.015 0.001 PHE F 363 TYR 0.015 0.002 TYR L 244 ARG 0.009 0.001 ARG G 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 658 time to evaluate : 5.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 ASN cc_start: 0.7875 (m-40) cc_final: 0.7622 (m110) REVERT: B 754 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7886 (tttt) REVERT: C 304 ASP cc_start: 0.8134 (t0) cc_final: 0.7751 (t0) REVERT: C 427 MET cc_start: 0.4001 (tmm) cc_final: 0.3200 (tmm) REVERT: C 720 MET cc_start: 0.5257 (ppp) cc_final: 0.4697 (pmm) REVERT: D 211 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.6233 (pptt) REVERT: D 294 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: D 720 MET cc_start: 0.4737 (ppp) cc_final: 0.2831 (tpt) REVERT: E 283 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6194 (mm-30) REVERT: F 304 ASP cc_start: 0.8158 (t0) cc_final: 0.7918 (t0) REVERT: G 757 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6652 (mpp) REVERT: H 198 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7365 (tt) REVERT: H 278 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8096 (tt) REVERT: J 427 MET cc_start: 0.5829 (tpt) cc_final: 0.5442 (ttt) REVERT: J 757 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6731 (mpp) REVERT: K 198 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7341 (tt) REVERT: L 198 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7546 (tt) REVERT: L 323 ARG cc_start: 0.7651 (mtp180) cc_final: 0.7372 (ttm-80) outliers start: 182 outliers final: 92 residues processed: 788 average time/residue: 1.3573 time to fit residues: 1406.7720 Evaluate side-chains 724 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 622 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 680 ASN Chi-restraints excluded: chain G residue 757 MET Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain H residue 278 LEU Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 629 ILE Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 680 ASN Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 442 MET Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 680 ASN Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 274 ILE Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 757 MET Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 680 ASN Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 442 MET Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 678 MET Chi-restraints excluded: chain L residue 680 ASN Chi-restraints excluded: chain L residue 752 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 694 optimal weight: 0.6980 chunk 731 optimal weight: 3.9990 chunk 667 optimal weight: 2.9990 chunk 711 optimal weight: 0.5980 chunk 428 optimal weight: 5.9990 chunk 309 optimal weight: 0.2980 chunk 558 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 642 optimal weight: 6.9990 chunk 672 optimal weight: 3.9990 chunk 708 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS E 760 GLN F 226 HIS F 285 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 64379 Z= 0.192 Angle : 0.630 14.288 87011 Z= 0.307 Chirality : 0.044 0.231 9636 Planarity : 0.004 0.070 11498 Dihedral : 6.403 115.659 9165 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.98 % Favored : 93.82 % Rotamer: Outliers : 2.00 % Allowed : 18.75 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.10), residues: 7959 helix: 1.45 (0.09), residues: 3725 sheet: 0.09 (0.16), residues: 1080 loop : -0.66 (0.11), residues: 3154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 454 HIS 0.013 0.001 HIS F 406 PHE 0.013 0.001 PHE A 266 TYR 0.014 0.001 TYR L 244 ARG 0.010 0.001 ARG I 713 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 651 time to evaluate : 5.521 Fit side-chains revert: symmetry clash REVERT: B 401 ASN cc_start: 0.7815 (m-40) cc_final: 0.7557 (m110) REVERT: B 722 VAL cc_start: 0.4689 (OUTLIER) cc_final: 0.4422 (m) REVERT: B 754 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7850 (tttt) REVERT: C 203 TYR cc_start: 0.5589 (OUTLIER) cc_final: 0.5339 (p90) REVERT: C 304 ASP cc_start: 0.8141 (t0) cc_final: 0.7747 (t0) REVERT: C 720 MET cc_start: 0.5205 (ppp) cc_final: 0.4705 (pmm) REVERT: D 211 LYS cc_start: 0.6412 (OUTLIER) cc_final: 0.6148 (pptt) REVERT: D 720 MET cc_start: 0.4720 (ppp) cc_final: 0.2818 (tpt) REVERT: E 283 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6129 (mm-30) REVERT: E 720 MET cc_start: 0.5018 (ppp) cc_final: 0.2957 (tpt) REVERT: F 304 ASP cc_start: 0.8148 (t0) cc_final: 0.7810 (t0) REVERT: F 708 ARG cc_start: 0.7300 (ttp-110) cc_final: 0.7049 (ttm110) REVERT: H 198 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7217 (tt) REVERT: H 278 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8096 (tt) REVERT: J 427 MET cc_start: 0.5755 (tpt) cc_final: 0.5394 (ttt) REVERT: J 720 MET cc_start: 0.4133 (ptt) cc_final: 0.3833 (ptt) REVERT: K 198 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7241 (tt) REVERT: L 198 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7424 (tt) REVERT: L 323 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7300 (ttm-80) outliers start: 135 outliers final: 77 residues processed: 754 average time/residue: 1.4484 time to fit residues: 1418.6283 Evaluate side-chains 708 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 622 time to evaluate : 5.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 203 TYR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 680 ASN Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 278 LEU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 680 ASN Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 680 ASN Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 274 ILE Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 680 ASN Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 680 ASN Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 680 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 467 optimal weight: 0.0980 chunk 752 optimal weight: 1.9990 chunk 459 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 chunk 522 optimal weight: 3.9990 chunk 789 optimal weight: 1.9990 chunk 726 optimal weight: 1.9990 chunk 628 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 485 optimal weight: 0.9980 chunk 385 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS E 760 GLN F 226 HIS F 285 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** I 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 64379 Z= 0.246 Angle : 0.658 14.889 87011 Z= 0.319 Chirality : 0.045 0.253 9636 Planarity : 0.005 0.071 11498 Dihedral : 6.393 116.812 9165 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.98 % Favored : 93.82 % Rotamer: Outliers : 1.72 % Allowed : 19.35 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.10), residues: 7959 helix: 1.39 (0.09), residues: 3733 sheet: 0.03 (0.16), residues: 1080 loop : -0.66 (0.11), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 454 HIS 0.021 0.001 HIS F 406 PHE 0.018 0.001 PHE A 363 TYR 0.022 0.001 TYR I 244 ARG 0.014 0.001 ARG I 713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 639 time to evaluate : 5.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.3959 (tmm) cc_final: 0.3153 (tmm) REVERT: B 401 ASN cc_start: 0.7854 (m-40) cc_final: 0.7575 (m110) REVERT: B 722 VAL cc_start: 0.4576 (OUTLIER) cc_final: 0.4324 (m) REVERT: B 740 MET cc_start: 0.8530 (tpt) cc_final: 0.8098 (tpt) REVERT: B 754 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7858 (tttt) REVERT: C 203 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.5310 (p90) REVERT: C 304 ASP cc_start: 0.8155 (t0) cc_final: 0.7860 (t0) REVERT: C 720 MET cc_start: 0.5131 (ppp) cc_final: 0.4901 (pmm) REVERT: D 720 MET cc_start: 0.4604 (ppp) cc_final: 0.2759 (tpt) REVERT: E 283 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6169 (mm-30) REVERT: E 720 MET cc_start: 0.5086 (ppp) cc_final: 0.3030 (tpt) REVERT: F 304 ASP cc_start: 0.8175 (t0) cc_final: 0.7939 (t0) REVERT: H 198 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7228 (tt) REVERT: H 278 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8080 (tt) REVERT: H 504 LEU cc_start: 0.9094 (tp) cc_final: 0.8815 (mt) REVERT: J 427 MET cc_start: 0.5802 (tpt) cc_final: 0.5443 (ttt) REVERT: J 720 MET cc_start: 0.4146 (ptt) cc_final: 0.3853 (ptt) REVERT: K 198 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7267 (tt) REVERT: L 198 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7479 (tt) REVERT: L 323 ARG cc_start: 0.7607 (mtp180) cc_final: 0.7355 (ttm-80) REVERT: L 487 ARG cc_start: 0.7388 (mtp85) cc_final: 0.7129 (ttp-110) outliers start: 116 outliers final: 84 residues processed: 734 average time/residue: 1.4020 time to fit residues: 1335.3008 Evaluate side-chains 703 residues out of total 6743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 611 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 203 TYR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 680 ASN Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 278 LEU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 680 ASN Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 680 ASN Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 274 ILE Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 680 ASN Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 680 ASN Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 453 ARG Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 680 ASN Chi-restraints excluded: chain L residue 707 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 499 optimal weight: 8.9990 chunk 669 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 579 optimal weight: 0.1980 chunk 92 optimal weight: 0.0980 chunk 174 optimal weight: 0.9980 chunk 629 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 646 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS E 760 GLN F 226 HIS F 285 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 24 ASN H 337 GLN ** I 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.176995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132482 restraints weight = 73627.532| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.53 r_work: 0.3302 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 64379 Z= 0.196 Angle : 0.638 14.545 87011 Z= 0.310 Chirality : 0.044 0.232 9636 Planarity : 0.004 0.071 11498 Dihedral : 6.320 118.072 9165 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.04 % Favored : 93.76 % Rotamer: Outliers : 1.81 % Allowed : 19.35 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.10), residues: 7959 helix: 1.45 (0.09), residues: 3725 sheet: 0.04 (0.16), residues: 1086 loop : -0.65 (0.11), residues: 3148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 454 HIS 0.015 0.001 HIS A 406 PHE 0.014 0.001 PHE B 363 TYR 0.019 0.001 TYR I 244 ARG 0.021 0.001 ARG I 713 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22312.20 seconds wall clock time: 387 minutes 31.58 seconds (23251.58 seconds total)