Starting phenix.real_space_refine on Tue May 27 13:42:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1a_38829/05_2025/8y1a_38829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1a_38829/05_2025/8y1a_38829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y1a_38829/05_2025/8y1a_38829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1a_38829/05_2025/8y1a_38829.map" model { file = "/net/cci-nas-00/data/ceres_data/8y1a_38829/05_2025/8y1a_38829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1a_38829/05_2025/8y1a_38829.cif" } resolution = 2.8 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= -0.003 sd= 0.114 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: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 18729 2.51 5 N 4734 2.21 5 O 5907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 1.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29541 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "B" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "C" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 16.52, per 1000 atoms: 0.56 Number of scatterers: 29541 At special positions: 0 Unit cell: (166.311, 154.354, 206.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 171 16.00 O 5907 8.00 N 4734 7.00 C 18729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.04 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.04 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.04 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.04 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.02 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.04 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.02 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.04 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.04 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.04 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.02 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.02 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.02 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " MAN N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG I 2 " - " MAN I 3 " " NAG N 2 " - " MAN N 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN I 3 " - " MAN I 4 " " MAN N 3 " - " MAN N 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A2001 " - " ASN A 19 " " NAG A2002 " - " ASN A 29 " " NAG A2003 " - " ASN A 58 " " NAG A2004 " - " ASN A 114 " " NAG A2005 " - " ASN A 171 " " NAG A2006 " - " ASN A 192 " " NAG A2007 " - " ASN A 251 " " NAG A2008 " - " ASN A 433 " " NAG A2009 " - " ASN A 454 " " NAG A2010 " - " ASN A 684 " " NAG A2011 " - " ASN A 703 " " NAG A2012 " - " ASN A 725 " " NAG A2013 " - " ASN A 771 " " NAG A2014 " - " ASN A 776 " " NAG A2015 " - " ASN A 793 " " NAG A2016 " - " ASN A 924 " " NAG A2017 " - " ASN A1211 " " NAG B2001 " - " ASN B 19 " " NAG B2002 " - " ASN B 29 " " NAG B2003 " - " ASN B 58 " " NAG B2004 " - " ASN B 114 " " NAG B2005 " - " ASN B 171 " " NAG B2006 " - " ASN B 192 " " NAG B2007 " - " ASN B 251 " " NAG B2008 " - " ASN B 433 " " NAG B2009 " - " ASN B 454 " " NAG B2010 " - " ASN B 684 " " NAG B2011 " - " ASN B 703 " " NAG B2012 " - " ASN B 725 " " NAG B2013 " - " ASN B 771 " " NAG B2014 " - " ASN B 776 " " NAG B2015 " - " ASN B 793 " " NAG B2016 " - " ASN B 924 " " NAG B2017 " - " ASN B1211 " " NAG C2001 " - " ASN C 19 " " NAG C2002 " - " ASN C 29 " " NAG C2003 " - " ASN C 58 " " NAG C2004 " - " ASN C 114 " " NAG C2005 " - " ASN C 171 " " NAG C2006 " - " ASN C 192 " " NAG C2007 " - " ASN C 251 " " NAG C2008 " - " ASN C 433 " " NAG C2009 " - " ASN C 454 " " NAG C2010 " - " ASN C 684 " " NAG C2011 " - " ASN C 703 " " NAG C2012 " - " ASN C 725 " " NAG C2013 " - " ASN C 771 " " NAG C2014 " - " ASN C 776 " " NAG C2015 " - " ASN C 793 " " NAG C2016 " - " ASN C 924 " " NAG C2017 " - " ASN C1211 " " NAG D 1 " - " ASN A 132 " " NAG E 1 " - " ASN A 188 " " NAG F 1 " - " ASN A 335 " " NAG G 1 " - " ASN A 355 " " NAG H 1 " - " ASN A 664 " " NAG I 1 " - " ASN B 132 " " NAG J 1 " - " ASN B 188 " " NAG K 1 " - " ASN B 335 " " NAG L 1 " - " ASN B 355 " " NAG M 1 " - " ASN B 664 " " NAG N 1 " - " ASN C 132 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 335 " " NAG Q 1 " - " ASN C 355 " " NAG R 1 " - " ASN C 664 " Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 3.4 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6828 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 65 sheets defined 24.3% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 41 through 45 removed outlier: 4.459A pdb=" N LEU A 44 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.660A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.637A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 341 through 344 removed outlier: 3.685A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 377 through 380 removed outlier: 3.628A pdb=" N GLY A 380 " --> pdb=" O LYS A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.936A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.133A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.574A pdb=" N SER A 484 " --> pdb=" O VAL A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 863 removed outlier: 3.541A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 910 removed outlier: 3.877A pdb=" N LYS A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.857A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.515A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.577A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.835A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.701A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1066 through 1113 removed outlier: 3.603A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 4.337A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.767A pdb=" N TYR B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 341 through 344 removed outlier: 3.973A pdb=" N TRP B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.529A pdb=" N LEU B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.659A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.941A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.623A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.886A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.901A pdb=" N GLU B 831 " --> pdb=" O ASP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 863 removed outlier: 3.943A pdb=" N ASN B 838 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 910 removed outlier: 4.099A pdb=" N LYS B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 924 removed outlier: 3.896A pdb=" N ASN B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.512A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 971 through 975 removed outlier: 3.713A pdb=" N ALA B 974 " --> pdb=" O TRP B 971 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B 975 " --> pdb=" O SER B 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 971 through 975' Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.603A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.509A pdb=" N ALA B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.849A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1062 Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.773A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.704A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.545A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.862A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 442 through 447 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.548A pdb=" N VAL C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.836A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 813 through 819 Processing helix chain 'C' and resid 822 through 830 Processing helix chain 'C' and resid 834 through 863 removed outlier: 3.731A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 862 " --> pdb=" O ALA C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.531A pdb=" N LEU C 888 " --> pdb=" O LYS C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 888' Processing helix chain 'C' and resid 901 through 910 removed outlier: 4.216A pdb=" N LYS C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.872A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 removed outlier: 3.614A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.568A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.672A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.701A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.630A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1057 through 1062 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.572A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.137A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 67 removed outlier: 8.074A pdb=" N GLN A 265 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP A 281 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.917A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.548A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 227 removed outlier: 5.384A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 113 Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 306 Processing sheet with id=AA8, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.315A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.510A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 349 Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 466 through 468 removed outlier: 3.959A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB6, first strand: chain 'A' and resid 619 through 624 removed outlier: 4.313A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 724 through 731 removed outlier: 10.566A pdb=" N TYR A 762 " --> pdb=" O ASN A 725 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N THR A 727 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N PHE A 764 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 729 " --> pdb=" O PHE A 764 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.403A pdb=" N SER A 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.805A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.805A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.312A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC4, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AC5, first strand: chain 'A' and resid 1202 through 1205 Processing sheet with id=AC6, first strand: chain 'B' and resid 59 through 67 removed outlier: 4.028A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.208A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 221 through 227 removed outlier: 5.202A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU B 255 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD1, first strand: chain 'B' and resid 185 through 190 Processing sheet with id=AD2, first strand: chain 'B' and resid 302 through 306 Processing sheet with id=AD3, first strand: chain 'B' and resid 316 through 319 removed outlier: 4.223A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.913A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.486A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.486A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AD8, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.424A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 505 through 507 Processing sheet with id=AE1, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.639A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.472A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.114A pdb=" N SER B 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.869A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN B1136 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B1142 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B1134 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B1144 " --> pdb=" O SER B1132 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER B1132 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B1146 " --> pdb=" O ILE B1130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.397A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AE7, first strand: chain 'B' and resid 1202 through 1205 Processing sheet with id=AE8, first strand: chain 'B' and resid 1175 through 1180 Processing sheet with id=AE9, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF1, first strand: chain 'C' and resid 38 through 39 removed outlier: 8.347A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE C 209 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER C 225 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA C 211 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 59 through 67 removed outlier: 7.760A pdb=" N GLN C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP C 281 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.562A pdb=" N GLY C 81 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N THR C 241 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N TRP C 174 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.738A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 109 through 113 Processing sheet with id=AF6, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AF7, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AF8, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.460A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 345 through 349 Processing sheet with id=AG1, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.584A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER C 422 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N CYS C 370 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN C 424 " --> pdb=" O PHE C 368 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE C 368 " --> pdb=" O GLN C 424 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR C 426 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N HIS C 364 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG3, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.548A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 504 through 507 Processing sheet with id=AG5, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.570A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.569A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 786 through 791 removed outlier: 7.173A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 794 through 804 removed outlier: 7.055A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.287A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH2, first strand: chain 'C' and resid 1202 through 1205 1073 hydrogen bonds defined for protein. 2934 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: 14.49 Time building geometry restraints manager: 8.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4697 1.29 - 1.42: 8405 1.42 - 1.56: 16918 1.56 - 1.70: 7 1.70 - 1.83: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" N ARG A 320 " pdb=" CA ARG A 320 " ideal model delta sigma weight residual 1.458 1.363 0.095 9.00e-03 1.23e+04 1.11e+02 bond pdb=" C ARG A 320 " pdb=" O ARG A 320 " ideal model delta sigma weight residual 1.238 1.150 0.088 1.18e-02 7.18e+03 5.53e+01 bond pdb=" CA ARG A 320 " pdb=" C ARG A 320 " ideal model delta sigma weight residual 1.525 1.444 0.081 1.11e-02 8.12e+03 5.26e+01 bond pdb=" C ASN A 323 " pdb=" O ASN A 323 " ideal model delta sigma weight residual 1.236 1.177 0.059 8.80e-03 1.29e+04 4.42e+01 bond pdb=" N PRO A 322 " pdb=" CD PRO A 322 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.95e+01 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 39751 2.45 - 4.89: 1245 4.89 - 7.34: 126 7.34 - 9.78: 26 9.78 - 12.23: 9 Bond angle restraints: 41157 Sorted by residual: angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 120.51 -9.81 1.22e+00 6.72e-01 6.47e+01 angle pdb=" N PRO C 969 " pdb=" CA PRO C 969 " pdb=" C PRO C 969 " ideal model delta sigma weight residual 110.70 118.41 -7.71 1.22e+00 6.72e-01 3.99e+01 angle pdb=" N PRO B 969 " pdb=" CA PRO B 969 " pdb=" C PRO B 969 " ideal model delta sigma weight residual 110.70 118.32 -7.62 1.22e+00 6.72e-01 3.90e+01 angle pdb=" N ASP A 305 " pdb=" CA ASP A 305 " pdb=" C ASP A 305 " ideal model delta sigma weight residual 108.96 99.56 9.40 1.59e+00 3.96e-01 3.50e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 117.67 -6.97 1.22e+00 6.72e-01 3.26e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 17765 23.65 - 47.30: 1119 47.30 - 70.95: 305 70.95 - 94.60: 32 94.60 - 118.25: 6 Dihedral angle restraints: 19227 sinusoidal: 8589 harmonic: 10638 Sorted by residual: dihedral pdb=" CA PRO C 92 " pdb=" C PRO C 92 " pdb=" N PRO C 93 " pdb=" CA PRO C 93 " ideal model delta harmonic sigma weight residual 180.00 129.03 50.97 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA CYS B 819 " pdb=" C CYS B 819 " pdb=" N SER B 820 " pdb=" CA SER B 820 " ideal model delta harmonic sigma weight residual -180.00 -139.92 -40.08 0 5.00e+00 4.00e-02 6.42e+01 dihedral pdb=" CA PRO C 969 " pdb=" C PRO C 969 " pdb=" N PRO C 970 " pdb=" CA PRO C 970 " ideal model delta harmonic sigma weight residual 180.00 141.08 38.92 0 5.00e+00 4.00e-02 6.06e+01 ... (remaining 19224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 4881 0.228 - 0.456: 21 0.456 - 0.685: 4 0.685 - 0.913: 1 0.913 - 1.141: 1 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 132 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.26 -1.14 2.00e-01 2.50e+01 3.26e+01 chirality pdb=" C1 NAG B2005 " pdb=" ND2 ASN B 171 " pdb=" C2 NAG B2005 " pdb=" O5 NAG B2005 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG A2003 " pdb=" ND2 ASN A 58 " pdb=" C2 NAG A2003 " pdb=" O5 NAG A2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.22e+00 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 19 " -0.085 2.00e-02 2.50e+03 1.39e-01 2.40e+02 pdb=" CG ASN B 19 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 19 " -0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN B 19 " 0.245 2.00e-02 2.50e+03 pdb=" C1 NAG B2001 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 132 " -0.113 2.00e-02 2.50e+03 1.37e-01 2.36e+02 pdb=" CG ASN B 132 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 132 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 132 " 0.235 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 171 " 0.053 2.00e-02 2.50e+03 6.73e-02 5.67e+01 pdb=" CG ASN B 171 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 171 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 171 " -0.115 2.00e-02 2.50e+03 pdb=" C1 NAG B2005 " 0.078 2.00e-02 2.50e+03 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 261 2.59 - 3.17: 22205 3.17 - 3.75: 43398 3.75 - 4.32: 63349 4.32 - 4.90: 105284 Nonbonded interactions: 234497 Sorted by model distance: nonbonded pdb=" O ASN A 323 " pdb=" ND2 ASN A 323 " model vdw 2.013 3.120 nonbonded pdb=" O GLY B 407 " pdb=" OG SER B 411 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" O GLU B 120 " model vdw 2.270 3.040 nonbonded pdb=" N ASP A 326 " pdb=" OD1 ASP A 326 " model vdw 2.270 3.120 nonbonded pdb=" O GLY A 407 " pdb=" OG SER A 411 " model vdw 2.272 3.040 ... (remaining 234492 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 67.650 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 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 : 0.010 0.118 30390 Z= 0.460 Angle : 1.089 31.027 41580 Z= 0.576 Chirality : 0.067 1.141 4908 Planarity : 0.009 0.111 5172 Dihedral : 16.233 118.250 12183 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.61 % Favored : 93.20 % Rotamer: Outliers : 11.34 % Allowed : 10.38 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.21 % Twisted General : 0.14 % 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: -3.08 (0.12), residues: 3618 helix: -1.91 (0.15), residues: 772 sheet: -1.00 (0.16), residues: 870 loop : -2.67 (0.11), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 174 HIS 0.013 0.002 HIS B1129 PHE 0.027 0.004 PHE B 592 TYR 0.032 0.003 TYR A 49 ARG 0.006 0.001 ARG C 585 Details of bonding type rmsd link_NAG-ASN : bond 0.01660 ( 66) link_NAG-ASN : angle 5.49026 ( 198) link_ALPHA1-4 : bond 0.00856 ( 3) link_ALPHA1-4 : angle 3.93941 ( 9) link_ALPHA1-6 : bond 0.00358 ( 3) link_ALPHA1-6 : angle 2.30177 ( 9) link_BETA1-4 : bond 0.00770 ( 15) link_BETA1-4 : angle 3.01969 ( 45) link_ALPHA1-3 : bond 0.00446 ( 6) link_ALPHA1-3 : angle 2.17050 ( 18) hydrogen bonds : bond 0.14395 ( 1042) hydrogen bonds : angle 6.93434 ( 2934) SS BOND : bond 0.00559 ( 72) SS BOND : angle 1.54638 ( 144) covalent geometry : bond 0.01044 (30225) covalent geometry : angle 1.01361 (41157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 368 poor density : 297 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8742 (mt) REVERT: A 221 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7622 (t) REVERT: A 264 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7601 (ptp-110) REVERT: A 273 HIS cc_start: 0.7995 (m-70) cc_final: 0.7770 (m90) REVERT: A 310 THR cc_start: 0.4450 (OUTLIER) cc_final: 0.4040 (t) REVERT: A 371 ASN cc_start: 0.3235 (OUTLIER) cc_final: 0.2370 (p0) REVERT: A 384 ASN cc_start: 0.7101 (m-40) cc_final: 0.6836 (t0) REVERT: A 590 SER cc_start: 0.4538 (OUTLIER) cc_final: 0.3576 (p) REVERT: A 863 GLN cc_start: 0.7587 (tp40) cc_final: 0.7061 (tm-30) REVERT: A 891 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7998 (tt) REVERT: A 1002 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7651 (tppt) REVERT: A 1071 GLN cc_start: 0.7750 (mt0) cc_final: 0.6978 (mm-40) REVERT: A 1108 GLU cc_start: 0.7056 (tt0) cc_final: 0.6673 (tt0) REVERT: A 1126 ASN cc_start: 0.7383 (p0) cc_final: 0.7154 (p0) REVERT: B 34 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6365 (ptt180) REVERT: B 135 TYR cc_start: 0.6146 (m-80) cc_final: 0.5666 (m-80) REVERT: B 155 MET cc_start: 0.5124 (mmm) cc_final: 0.4470 (pmm) REVERT: B 204 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: B 205 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6465 (tt0) REVERT: B 258 VAL cc_start: 0.7218 (OUTLIER) cc_final: 0.6977 (t) REVERT: B 468 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7554 (p) REVERT: B 515 TRP cc_start: 0.6397 (p-90) cc_final: 0.5992 (p-90) REVERT: B 573 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8212 (mt) REVERT: B 636 VAL cc_start: 0.7917 (p) cc_final: 0.7587 (m) REVERT: B 637 SER cc_start: 0.8522 (t) cc_final: 0.8288 (t) REVERT: B 835 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.6842 (t80) REVERT: B 863 GLN cc_start: 0.7735 (tp40) cc_final: 0.7385 (tm130) REVERT: B 885 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7724 (tptt) REVERT: B 986 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6315 (mmt180) REVERT: B 1012 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7538 (tt) REVERT: B 1095 ASP cc_start: 0.7797 (m-30) cc_final: 0.7553 (m-30) REVERT: B 1096 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7811 (mm) REVERT: B 1117 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: B 1124 CYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6792 (m) REVERT: B 1167 ASP cc_start: 0.6904 (m-30) cc_final: 0.6620 (m-30) REVERT: B 1200 LYS cc_start: 0.7691 (mttt) cc_final: 0.7318 (mmtp) REVERT: B 1219 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.5509 (p90) REVERT: C 88 LEU cc_start: 0.7948 (mt) cc_final: 0.7717 (mp) REVERT: C 158 TYR cc_start: 0.8308 (m-80) cc_final: 0.7454 (m-80) REVERT: C 187 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7411 (tptt) REVERT: C 206 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7407 (mtt180) REVERT: C 255 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: C 305 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: C 330 ASP cc_start: 0.6937 (p0) cc_final: 0.6703 (p0) REVERT: C 500 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8148 (ptmt) REVERT: C 577 PHE cc_start: 0.7590 (p90) cc_final: 0.7383 (p90) REVERT: C 644 TRP cc_start: 0.7264 (p-90) cc_final: 0.6859 (p-90) REVERT: C 655 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8585 (mt) REVERT: C 659 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6701 (ttpt) REVERT: C 737 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7409 (mpp80) REVERT: C 848 ASP cc_start: 0.6953 (m-30) cc_final: 0.6448 (m-30) REVERT: C 851 ASP cc_start: 0.7395 (m-30) cc_final: 0.7117 (m-30) REVERT: C 862 MET cc_start: 0.7762 (mmm) cc_final: 0.7279 (mmm) REVERT: C 885 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8147 (tptp) REVERT: C 894 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: C 994 MET cc_start: 0.8791 (tpp) cc_final: 0.8343 (mmt) REVERT: C 1010 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7319 (tttm) REVERT: C 1030 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.6670 (mp10) REVERT: C 1075 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7203 (t70) REVERT: C 1219 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5041 (p90) outliers start: 368 outliers final: 171 residues processed: 618 average time/residue: 0.9479 time to fit residues: 734.8157 Evaluate side-chains 402 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 197 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 PRO Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1117 GLN Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 737 ARG Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 894 GLN Chi-restraints excluded: chain C residue 895 CYS Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1182 ASP Chi-restraints excluded: chain C residue 1185 MET Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.8980 chunk 272 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 282 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 326 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 331 ASN A 353 ASN A 371 ASN A 384 ASN A 413 ASN A 440 ASN A 838 ASN A 876 HIS A 984 GLN A1001 GLN A1091 GLN A1180 GLN B 204 GLN B 248 ASN B 605 ASN B 630 GLN B 799 HIS B 863 GLN B 872 ASN B 874 ASN B 876 HIS B 998 ASN B1001 GLN B1091 GLN B1136 ASN B1201 ASN C 73 ASN C 204 GLN C 561 ASN C 598 ASN C 630 GLN C 799 HIS C 854 GLN C 872 ASN C 876 HIS C 894 GLN C 984 GLN C1079 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.159981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.118744 restraints weight = 42393.659| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.63 r_work: 0.3258 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30390 Z= 0.131 Angle : 0.733 25.951 41580 Z= 0.353 Chirality : 0.052 1.133 4908 Planarity : 0.006 0.097 5172 Dihedral : 12.233 102.737 6189 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.72 % Allowed : 14.73 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -2.02 (0.13), residues: 3618 helix: 0.01 (0.18), residues: 772 sheet: -0.71 (0.16), residues: 871 loop : -2.28 (0.12), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 197 HIS 0.011 0.001 HIS B 175 PHE 0.017 0.001 PHE B 968 TYR 0.018 0.001 TYR A 414 ARG 0.008 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 66) link_NAG-ASN : angle 4.89085 ( 198) link_ALPHA1-4 : bond 0.01326 ( 3) link_ALPHA1-4 : angle 3.66223 ( 9) link_ALPHA1-6 : bond 0.00725 ( 3) link_ALPHA1-6 : angle 1.72685 ( 9) link_BETA1-4 : bond 0.00418 ( 15) link_BETA1-4 : angle 1.54913 ( 45) link_ALPHA1-3 : bond 0.00633 ( 6) link_ALPHA1-3 : angle 2.20585 ( 18) hydrogen bonds : bond 0.04898 ( 1042) hydrogen bonds : angle 5.44954 ( 2934) SS BOND : bond 0.00249 ( 72) SS BOND : angle 1.16120 ( 144) covalent geometry : bond 0.00279 (30225) covalent geometry : angle 0.64437 (41157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 230 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8684 (m) REVERT: A 264 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8443 (ptp-110) REVERT: A 273 HIS cc_start: 0.8401 (m-70) cc_final: 0.8186 (m-70) REVERT: A 289 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8243 (tt0) REVERT: A 310 THR cc_start: 0.4961 (OUTLIER) cc_final: 0.4398 (t) REVERT: A 590 SER cc_start: 0.5176 (OUTLIER) cc_final: 0.4483 (p) REVERT: A 903 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8176 (tt) REVERT: A 1002 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8147 (tppt) REVERT: A 1010 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8471 (ttmm) REVERT: A 1066 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6755 (m-30) REVERT: A 1071 GLN cc_start: 0.8254 (mt0) cc_final: 0.7907 (mm110) REVERT: B 34 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6628 (ptp90) REVERT: B 85 LEU cc_start: 0.4095 (OUTLIER) cc_final: 0.3735 (tt) REVERT: B 90 TYR cc_start: 0.5017 (m-80) cc_final: 0.4730 (m-80) REVERT: B 135 TYR cc_start: 0.5957 (m-80) cc_final: 0.5362 (m-80) REVERT: B 140 GLN cc_start: 0.7552 (mp-120) cc_final: 0.6814 (tt0) REVERT: B 155 MET cc_start: 0.4635 (mmm) cc_final: 0.3858 (pmm) REVERT: B 205 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: B 206 ARG cc_start: 0.7547 (tpp80) cc_final: 0.7068 (tpp-160) REVERT: B 324 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6904 (mp) REVERT: B 447 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8172 (ttt180) REVERT: B 515 TRP cc_start: 0.5439 (p-90) cc_final: 0.4726 (p-90) REVERT: B 523 ASP cc_start: 0.7436 (p0) cc_final: 0.6996 (p0) REVERT: B 573 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8588 (mt) REVERT: B 636 VAL cc_start: 0.8498 (p) cc_final: 0.8266 (m) REVERT: B 655 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8560 (mt) REVERT: B 800 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7413 (pp20) REVERT: B 849 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8945 (mp) REVERT: B 885 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8216 (tptt) REVERT: B 931 ILE cc_start: 0.5557 (OUTLIER) cc_final: 0.5354 (tp) REVERT: B 1012 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8499 (tt) REVERT: B 1091 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8329 (mp-120) REVERT: B 1115 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.7841 (mptm) REVERT: B 1124 CYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7720 (m) REVERT: B 1167 ASP cc_start: 0.7683 (m-30) cc_final: 0.7454 (m-30) REVERT: B 1219 TYR cc_start: 0.5818 (OUTLIER) cc_final: 0.5361 (p90) REVERT: C 164 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7349 (mtmt) REVERT: C 176 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8375 (mt) REVERT: C 255 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8471 (mt-10) REVERT: C 369 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7976 (p) REVERT: C 491 LEU cc_start: 0.6949 (mp) cc_final: 0.6626 (mt) REVERT: C 500 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8160 (pmtt) REVERT: C 644 TRP cc_start: 0.7331 (p-90) cc_final: 0.7035 (p-90) REVERT: C 659 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7715 (ttpt) REVERT: C 828 LEU cc_start: 0.9086 (mt) cc_final: 0.8783 (mm) REVERT: C 848 ASP cc_start: 0.8340 (m-30) cc_final: 0.8083 (m-30) REVERT: C 862 MET cc_start: 0.8637 (mmm) cc_final: 0.8275 (mmm) REVERT: C 885 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8467 (tptp) REVERT: C 894 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: C 1003 LEU cc_start: 0.8566 (mt) cc_final: 0.8365 (tt) REVERT: C 1010 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8355 (tttm) REVERT: C 1030 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: C 1165 SER cc_start: 0.7818 (m) cc_final: 0.7572 (p) REVERT: C 1214 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8212 (mtpp) REVERT: C 1219 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.5154 (p90) outliers start: 218 outliers final: 108 residues processed: 420 average time/residue: 0.9004 time to fit residues: 481.8257 Evaluate side-chains 326 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 186 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 894 GLN Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 251 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 269 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 356 optimal weight: 0.8980 chunk 253 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 364 HIS A 643 ASN A1091 GLN B 143 ASN B1136 ASN C 854 GLN C1023 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117055 restraints weight = 42284.557| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.68 r_work: 0.3234 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30390 Z= 0.167 Angle : 0.699 16.581 41580 Z= 0.347 Chirality : 0.050 0.788 4908 Planarity : 0.006 0.106 5172 Dihedral : 10.797 100.548 6027 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.32 % Allowed : 16.27 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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: -1.64 (0.13), residues: 3618 helix: 0.59 (0.19), residues: 780 sheet: -0.59 (0.17), residues: 864 loop : -2.11 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 197 HIS 0.007 0.001 HIS B1129 PHE 0.021 0.002 PHE B 453 TYR 0.018 0.002 TYR C 203 ARG 0.008 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00771 ( 66) link_NAG-ASN : angle 3.83696 ( 198) link_ALPHA1-4 : bond 0.01357 ( 3) link_ALPHA1-4 : angle 3.51638 ( 9) link_ALPHA1-6 : bond 0.00682 ( 3) link_ALPHA1-6 : angle 1.96597 ( 9) link_BETA1-4 : bond 0.00413 ( 15) link_BETA1-4 : angle 1.64430 ( 45) link_ALPHA1-3 : bond 0.00736 ( 6) link_ALPHA1-3 : angle 2.03148 ( 18) hydrogen bonds : bond 0.05036 ( 1042) hydrogen bonds : angle 5.24427 ( 2934) SS BOND : bond 0.00313 ( 72) SS BOND : angle 1.49507 ( 144) covalent geometry : bond 0.00389 (30225) covalent geometry : angle 0.63771 (41157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 212 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.9315 (t) cc_final: 0.9001 (m) REVERT: A 289 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8198 (tt0) REVERT: A 310 THR cc_start: 0.5108 (OUTLIER) cc_final: 0.4558 (t) REVERT: A 590 SER cc_start: 0.5395 (OUTLIER) cc_final: 0.4642 (p) REVERT: A 891 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7889 (tt) REVERT: A 903 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 1002 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8200 (tppt) REVERT: A 1071 GLN cc_start: 0.8288 (mt0) cc_final: 0.7943 (mm-40) REVERT: B 34 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6315 (ptt180) REVERT: B 85 LEU cc_start: 0.3854 (OUTLIER) cc_final: 0.3429 (tt) REVERT: B 90 TYR cc_start: 0.5167 (m-80) cc_final: 0.4901 (m-80) REVERT: B 155 MET cc_start: 0.4650 (mmm) cc_final: 0.3842 (pmm) REVERT: B 218 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7066 (ppp) REVERT: B 324 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6947 (mp) REVERT: B 447 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7978 (ttt180) REVERT: B 573 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8861 (mt) REVERT: B 636 VAL cc_start: 0.8486 (p) cc_final: 0.8266 (m) REVERT: B 800 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7477 (pp20) REVERT: B 849 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8998 (mp) REVERT: B 885 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8205 (tptt) REVERT: B 931 ILE cc_start: 0.5551 (OUTLIER) cc_final: 0.5338 (tp) REVERT: B 986 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7296 (mmt180) REVERT: B 1012 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8479 (tt) REVERT: B 1117 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.6650 (mt0) REVERT: B 1124 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7775 (m) REVERT: B 1167 ASP cc_start: 0.7848 (m-30) cc_final: 0.7627 (m-30) REVERT: B 1200 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7799 (mmtp) REVERT: B 1219 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.5343 (p90) REVERT: C 255 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8498 (mt-10) REVERT: C 289 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: C 500 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8151 (pmtt) REVERT: C 644 TRP cc_start: 0.7399 (p-90) cc_final: 0.7068 (p-90) REVERT: C 828 LEU cc_start: 0.9125 (mt) cc_final: 0.8799 (mm) REVERT: C 845 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: C 848 ASP cc_start: 0.8342 (m-30) cc_final: 0.8093 (m-30) REVERT: C 862 MET cc_start: 0.8636 (mmm) cc_final: 0.8317 (mmm) REVERT: C 894 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: C 994 MET cc_start: 0.8829 (mmt) cc_final: 0.8408 (mmt) REVERT: C 1010 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8374 (tttm) REVERT: C 1030 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: C 1050 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9106 (mttp) REVERT: C 1165 SER cc_start: 0.7782 (m) cc_final: 0.7544 (p) REVERT: C 1219 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5242 (p90) outliers start: 205 outliers final: 114 residues processed: 392 average time/residue: 0.9097 time to fit residues: 454.6788 Evaluate side-chains 334 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 193 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1117 GLN Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1200 LYS Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 854 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 894 GLN Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 272 optimal weight: 5.9990 chunk 284 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 326 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN C 160 HIS C 854 GLN C1001 GLN C1023 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118132 restraints weight = 42597.793| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.63 r_work: 0.3255 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30390 Z= 0.151 Angle : 0.697 21.884 41580 Z= 0.340 Chirality : 0.049 0.745 4908 Planarity : 0.006 0.100 5172 Dihedral : 10.038 103.603 5984 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.82 % Allowed : 17.78 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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: -1.42 (0.13), residues: 3618 helix: 0.99 (0.20), residues: 772 sheet: -0.53 (0.17), residues: 858 loop : -2.00 (0.12), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 197 HIS 0.007 0.001 HIS B1129 PHE 0.017 0.001 PHE B 453 TYR 0.017 0.001 TYR C 203 ARG 0.008 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 66) link_NAG-ASN : angle 4.39894 ( 198) link_ALPHA1-4 : bond 0.01409 ( 3) link_ALPHA1-4 : angle 3.57162 ( 9) link_ALPHA1-6 : bond 0.00625 ( 3) link_ALPHA1-6 : angle 1.93595 ( 9) link_BETA1-4 : bond 0.00389 ( 15) link_BETA1-4 : angle 1.54823 ( 45) link_ALPHA1-3 : bond 0.00629 ( 6) link_ALPHA1-3 : angle 2.01135 ( 18) hydrogen bonds : bond 0.04718 ( 1042) hydrogen bonds : angle 5.07485 ( 2934) SS BOND : bond 0.00325 ( 72) SS BOND : angle 1.48501 ( 144) covalent geometry : bond 0.00351 (30225) covalent geometry : angle 0.61757 (41157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 205 time to evaluate : 3.416 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 64 THR cc_start: 0.9297 (t) cc_final: 0.8987 (m) REVERT: A 243 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6903 (mttt) REVERT: A 289 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8205 (tt0) REVERT: A 310 THR cc_start: 0.5141 (OUTLIER) cc_final: 0.4700 (t) REVERT: A 590 SER cc_start: 0.5354 (OUTLIER) cc_final: 0.4603 (p) REVERT: A 903 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 1002 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8183 (tppt) REVERT: A 1071 GLN cc_start: 0.8261 (mt0) cc_final: 0.7959 (mm-40) REVERT: B 34 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6800 (ptp90) REVERT: B 85 LEU cc_start: 0.3762 (OUTLIER) cc_final: 0.3354 (tt) REVERT: B 90 TYR cc_start: 0.5125 (m-80) cc_final: 0.4777 (m-80) REVERT: B 155 MET cc_start: 0.4706 (mmm) cc_final: 0.3848 (pmm) REVERT: B 218 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7026 (ppp) REVERT: B 289 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7960 (mt-10) REVERT: B 324 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6806 (mp) REVERT: B 447 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8026 (ttt180) REVERT: B 636 VAL cc_start: 0.8484 (p) cc_final: 0.8265 (m) REVERT: B 655 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8564 (mt) REVERT: B 776 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.6669 (t0) REVERT: B 800 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7504 (pp20) REVERT: B 849 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9037 (mp) REVERT: B 885 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8216 (tptt) REVERT: B 986 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7323 (mmt180) REVERT: B 1012 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8485 (tt) REVERT: B 1124 CYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7745 (m) REVERT: B 1200 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7783 (mmtp) REVERT: B 1219 TYR cc_start: 0.5674 (OUTLIER) cc_final: 0.5342 (p90) REVERT: C 164 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7243 (mtmt) REVERT: C 176 ILE cc_start: 0.8450 (tt) cc_final: 0.8048 (mt) REVERT: C 289 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: C 491 LEU cc_start: 0.6869 (mp) cc_final: 0.6592 (mt) REVERT: C 500 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8153 (pmtt) REVERT: C 644 TRP cc_start: 0.7370 (p-90) cc_final: 0.7033 (p-90) REVERT: C 779 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8338 (t) REVERT: C 828 LEU cc_start: 0.9110 (mt) cc_final: 0.8803 (mm) REVERT: C 845 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: C 848 ASP cc_start: 0.8346 (m-30) cc_final: 0.8112 (m-30) REVERT: C 862 MET cc_start: 0.8588 (mmm) cc_final: 0.8368 (mmm) REVERT: C 994 MET cc_start: 0.8827 (mmt) cc_final: 0.8347 (mmt) REVERT: C 1010 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8371 (tttm) REVERT: C 1030 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: C 1050 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9043 (mttp) REVERT: C 1165 SER cc_start: 0.7799 (m) cc_final: 0.7575 (p) REVERT: C 1211 ASN cc_start: 0.7441 (m-40) cc_final: 0.7179 (m-40) REVERT: C 1219 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5268 (p90) outliers start: 189 outliers final: 118 residues processed: 373 average time/residue: 0.9404 time to fit residues: 445.2621 Evaluate side-chains 339 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 194 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 776 ASN Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1200 LYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 120 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 338 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN C1023 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.160369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119464 restraints weight = 42364.759| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.59 r_work: 0.3287 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30390 Z= 0.126 Angle : 0.650 15.205 41580 Z= 0.321 Chirality : 0.048 0.696 4908 Planarity : 0.005 0.105 5172 Dihedral : 9.614 104.214 5967 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.27 % Allowed : 18.64 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.20 (0.13), residues: 3618 helix: 1.31 (0.20), residues: 774 sheet: -0.48 (0.17), residues: 863 loop : -1.88 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 197 HIS 0.009 0.001 HIS B 175 PHE 0.017 0.001 PHE C 577 TYR 0.017 0.001 TYR C 203 ARG 0.010 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 66) link_NAG-ASN : angle 3.33976 ( 198) link_ALPHA1-4 : bond 0.01462 ( 3) link_ALPHA1-4 : angle 3.58466 ( 9) link_ALPHA1-6 : bond 0.00637 ( 3) link_ALPHA1-6 : angle 1.93260 ( 9) link_BETA1-4 : bond 0.00397 ( 15) link_BETA1-4 : angle 1.49203 ( 45) link_ALPHA1-3 : bond 0.00626 ( 6) link_ALPHA1-3 : angle 1.95215 ( 18) hydrogen bonds : bond 0.04242 ( 1042) hydrogen bonds : angle 4.88807 ( 2934) SS BOND : bond 0.00322 ( 72) SS BOND : angle 1.27931 ( 144) covalent geometry : bond 0.00280 (30225) covalent geometry : angle 0.59942 (41157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 208 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.9291 (t) cc_final: 0.8996 (m) REVERT: A 136 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 243 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6907 (mttt) REVERT: A 289 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8248 (tt0) REVERT: A 310 THR cc_start: 0.5099 (OUTLIER) cc_final: 0.4692 (t) REVERT: A 590 SER cc_start: 0.5203 (OUTLIER) cc_final: 0.4442 (p) REVERT: A 737 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8572 (mtp180) REVERT: A 771 ASN cc_start: 0.6342 (t0) cc_final: 0.5887 (p0) REVERT: A 890 CYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7613 (t) REVERT: A 1002 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8182 (tppt) REVERT: B 34 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6733 (ptp90) REVERT: B 85 LEU cc_start: 0.3995 (OUTLIER) cc_final: 0.3565 (tt) REVERT: B 90 TYR cc_start: 0.5070 (m-80) cc_final: 0.4710 (m-80) REVERT: B 155 MET cc_start: 0.4778 (mmm) cc_final: 0.3855 (pmm) REVERT: B 205 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: B 218 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7156 (ppp) REVERT: B 258 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7287 (t) REVERT: B 289 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7966 (mt-10) REVERT: B 324 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6753 (mp) REVERT: B 447 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8493 (ttt180) REVERT: B 636 VAL cc_start: 0.8475 (p) cc_final: 0.8266 (m) REVERT: B 644 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.7577 (p90) REVERT: B 655 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8586 (mt) REVERT: B 776 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6863 (t0) REVERT: B 885 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8200 (tptt) REVERT: B 986 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7321 (mmt180) REVERT: B 1012 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8462 (tt) REVERT: B 1200 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7786 (mmtp) REVERT: B 1219 TYR cc_start: 0.5647 (OUTLIER) cc_final: 0.5359 (p90) REVERT: C 164 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7231 (mtmt) REVERT: C 289 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: C 500 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8162 (pmtt) REVERT: C 644 TRP cc_start: 0.7321 (p-90) cc_final: 0.7004 (p-90) REVERT: C 779 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8321 (t) REVERT: C 828 LEU cc_start: 0.9055 (mt) cc_final: 0.8768 (mm) REVERT: C 845 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: C 848 ASP cc_start: 0.8295 (m-30) cc_final: 0.8058 (m-30) REVERT: C 994 MET cc_start: 0.8843 (mmt) cc_final: 0.8409 (mmt) REVERT: C 1010 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8363 (tttm) REVERT: C 1030 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: C 1211 ASN cc_start: 0.7505 (m-40) cc_final: 0.7237 (m-40) REVERT: C 1219 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5305 (p90) outliers start: 171 outliers final: 100 residues processed: 357 average time/residue: 0.8965 time to fit residues: 409.8234 Evaluate side-chains 319 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 192 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 776 ASN Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1200 LYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 287 optimal weight: 0.0570 chunk 297 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 343 optimal weight: 0.5980 chunk 281 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 345 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1091 GLN B 26 ASN C 854 GLN C1023 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.161813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121432 restraints weight = 42393.282| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.53 r_work: 0.3307 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 30390 Z= 0.115 Angle : 0.645 19.146 41580 Z= 0.315 Chirality : 0.046 0.407 4908 Planarity : 0.005 0.101 5172 Dihedral : 9.099 103.662 5938 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.65 % Allowed : 19.16 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.02 (0.14), residues: 3618 helix: 1.54 (0.20), residues: 772 sheet: -0.43 (0.17), residues: 863 loop : -1.77 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 197 HIS 0.009 0.001 HIS B 175 PHE 0.018 0.001 PHE C 577 TYR 0.017 0.001 TYR A 118 ARG 0.011 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00682 ( 66) link_NAG-ASN : angle 3.47658 ( 198) link_ALPHA1-4 : bond 0.01609 ( 3) link_ALPHA1-4 : angle 3.70529 ( 9) link_ALPHA1-6 : bond 0.00599 ( 3) link_ALPHA1-6 : angle 1.90403 ( 9) link_BETA1-4 : bond 0.00417 ( 15) link_BETA1-4 : angle 1.45688 ( 45) link_ALPHA1-3 : bond 0.00662 ( 6) link_ALPHA1-3 : angle 1.90163 ( 18) hydrogen bonds : bond 0.03975 ( 1042) hydrogen bonds : angle 4.78631 ( 2934) SS BOND : bond 0.00373 ( 72) SS BOND : angle 1.20957 ( 144) covalent geometry : bond 0.00254 (30225) covalent geometry : angle 0.59147 (41157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 212 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.9270 (t) cc_final: 0.8994 (m) REVERT: A 221 THR cc_start: 0.8880 (t) cc_final: 0.8557 (m) REVERT: A 243 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6880 (mttt) REVERT: A 289 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8244 (tt0) REVERT: A 306 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8524 (pp) REVERT: A 310 THR cc_start: 0.5154 (OUTLIER) cc_final: 0.4724 (t) REVERT: A 590 SER cc_start: 0.5408 (OUTLIER) cc_final: 0.4743 (p) REVERT: A 737 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8558 (mtp180) REVERT: A 1002 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8158 (tppt) REVERT: B 34 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6710 (ptp90) REVERT: B 85 LEU cc_start: 0.3690 (OUTLIER) cc_final: 0.3307 (tt) REVERT: B 90 TYR cc_start: 0.4958 (m-80) cc_final: 0.4635 (m-80) REVERT: B 155 MET cc_start: 0.4803 (mmm) cc_final: 0.3908 (pmm) REVERT: B 218 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7075 (ppp) REVERT: B 289 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7828 (mt-10) REVERT: B 324 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6773 (mp) REVERT: B 356 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.6937 (tp) REVERT: B 395 ASN cc_start: 0.8389 (m-40) cc_final: 0.8186 (m110) REVERT: B 636 VAL cc_start: 0.8478 (p) cc_final: 0.8268 (m) REVERT: B 655 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8596 (mt) REVERT: B 776 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6587 (t0) REVERT: B 800 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: B 1012 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8474 (tt) REVERT: B 1200 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7758 (mttp) REVERT: B 1219 TYR cc_start: 0.5611 (OUTLIER) cc_final: 0.5355 (p90) REVERT: C 164 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7248 (mtmt) REVERT: C 176 ILE cc_start: 0.8504 (tt) cc_final: 0.8230 (mt) REVERT: C 289 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: C 319 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8282 (mmm160) REVERT: C 491 LEU cc_start: 0.6922 (mp) cc_final: 0.6570 (mt) REVERT: C 644 TRP cc_start: 0.7288 (p-90) cc_final: 0.7006 (p-90) REVERT: C 779 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8320 (t) REVERT: C 780 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: C 828 LEU cc_start: 0.9042 (mt) cc_final: 0.8748 (mm) REVERT: C 848 ASP cc_start: 0.8296 (m-30) cc_final: 0.7988 (m-30) REVERT: C 994 MET cc_start: 0.8826 (mmt) cc_final: 0.8415 (mmt) REVERT: C 1010 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8317 (tttm) REVERT: C 1030 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8761 (mm110) REVERT: C 1050 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9023 (mttp) REVERT: C 1211 ASN cc_start: 0.7481 (m-40) cc_final: 0.7225 (m-40) REVERT: C 1219 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5318 (p90) outliers start: 151 outliers final: 96 residues processed: 346 average time/residue: 0.9263 time to fit residues: 408.1203 Evaluate side-chains 313 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 192 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 776 ASN Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1200 LYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 351 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 255 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 172 optimal weight: 0.0970 chunk 200 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 GLN C 854 GLN C1023 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118559 restraints weight = 42361.358| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.55 r_work: 0.3270 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30390 Z= 0.170 Angle : 0.674 16.165 41580 Z= 0.335 Chirality : 0.047 0.402 4908 Planarity : 0.005 0.108 5172 Dihedral : 8.902 104.111 5920 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.99 % Allowed : 19.41 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % 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: -1.08 (0.13), residues: 3618 helix: 1.45 (0.20), residues: 767 sheet: -0.47 (0.17), residues: 855 loop : -1.78 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 971 HIS 0.008 0.001 HIS B 175 PHE 0.020 0.002 PHE C 577 TYR 0.018 0.002 TYR C 203 ARG 0.012 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 66) link_NAG-ASN : angle 3.11900 ( 198) link_ALPHA1-4 : bond 0.01598 ( 3) link_ALPHA1-4 : angle 3.53427 ( 9) link_ALPHA1-6 : bond 0.00569 ( 3) link_ALPHA1-6 : angle 1.98745 ( 9) link_BETA1-4 : bond 0.00490 ( 15) link_BETA1-4 : angle 1.48887 ( 45) link_ALPHA1-3 : bond 0.00601 ( 6) link_ALPHA1-3 : angle 1.92043 ( 18) hydrogen bonds : bond 0.04690 ( 1042) hydrogen bonds : angle 4.93351 ( 2934) SS BOND : bond 0.00456 ( 72) SS BOND : angle 1.93289 ( 144) covalent geometry : bond 0.00405 (30225) covalent geometry : angle 0.62606 (41157) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 202 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.9300 (t) cc_final: 0.8966 (m) REVERT: A 253 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 289 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8243 (tt0) REVERT: A 306 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8554 (pp) REVERT: A 310 THR cc_start: 0.5027 (OUTLIER) cc_final: 0.4622 (t) REVERT: A 383 PHE cc_start: 0.4350 (m-80) cc_final: 0.4010 (m-80) REVERT: A 590 SER cc_start: 0.5177 (OUTLIER) cc_final: 0.4438 (p) REVERT: A 737 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.8678 (mtp180) REVERT: A 851 ASP cc_start: 0.8368 (m-30) cc_final: 0.8120 (m-30) REVERT: A 903 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8190 (tt) REVERT: A 1002 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8302 (tppt) REVERT: B 34 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6612 (ptp90) REVERT: B 85 LEU cc_start: 0.3790 (OUTLIER) cc_final: 0.3385 (tt) REVERT: B 90 TYR cc_start: 0.5021 (m-80) cc_final: 0.4702 (m-80) REVERT: B 155 MET cc_start: 0.4841 (mmm) cc_final: 0.3957 (pmm) REVERT: B 218 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7123 (ppp) REVERT: B 289 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7834 (mt-10) REVERT: B 324 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6653 (mp) REVERT: B 481 VAL cc_start: 0.8748 (m) cc_final: 0.8423 (p) REVERT: B 636 VAL cc_start: 0.8476 (p) cc_final: 0.8256 (m) REVERT: B 655 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8551 (mt) REVERT: B 776 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6951 (t0) REVERT: B 800 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7403 (pp20) REVERT: B 885 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8222 (tptt) REVERT: B 1012 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8465 (tt) REVERT: B 1124 CYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7729 (m) REVERT: B 1219 TYR cc_start: 0.5556 (OUTLIER) cc_final: 0.5323 (p90) REVERT: C 164 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7304 (mtmt) REVERT: C 289 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: C 295 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: C 491 LEU cc_start: 0.6928 (mp) cc_final: 0.6535 (mt) REVERT: C 494 ILE cc_start: 0.7426 (mp) cc_final: 0.6871 (tp) REVERT: C 500 LYS cc_start: 0.8177 (pmtt) cc_final: 0.7894 (pmtt) REVERT: C 644 TRP cc_start: 0.7331 (p-90) cc_final: 0.6990 (p-90) REVERT: C 670 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8294 (mp) REVERT: C 779 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8340 (t) REVERT: C 780 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: C 828 LEU cc_start: 0.9104 (mt) cc_final: 0.8793 (mm) REVERT: C 848 ASP cc_start: 0.8321 (m-30) cc_final: 0.8056 (m-30) REVERT: C 994 MET cc_start: 0.8860 (mmt) cc_final: 0.8401 (mmt) REVERT: C 1010 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8353 (tttm) REVERT: C 1030 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: C 1050 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9051 (mttp) REVERT: C 1211 ASN cc_start: 0.7626 (m-40) cc_final: 0.7355 (m-40) REVERT: C 1219 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5313 (p90) outliers start: 162 outliers final: 116 residues processed: 349 average time/residue: 0.9093 time to fit residues: 408.2995 Evaluate side-chains 331 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 188 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 776 ASN Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 814 CYS Chi-restraints excluded: chain C residue 854 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN C 424 GLN C 826 HIS C 854 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.117493 restraints weight = 42705.748| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.60 r_work: 0.3258 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 30390 Z= 0.215 Angle : 0.730 18.881 41580 Z= 0.362 Chirality : 0.049 0.410 4908 Planarity : 0.006 0.106 5172 Dihedral : 9.396 120.219 5918 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.21 % Allowed : 19.38 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.03 % 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: -1.21 (0.13), residues: 3618 helix: 1.26 (0.20), residues: 767 sheet: -0.51 (0.17), residues: 853 loop : -1.84 (0.12), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 197 HIS 0.009 0.001 HIS B 175 PHE 0.020 0.002 PHE C 577 TYR 0.020 0.002 TYR C 458 ARG 0.013 0.001 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 66) link_NAG-ASN : angle 3.66118 ( 198) link_ALPHA1-4 : bond 0.01556 ( 3) link_ALPHA1-4 : angle 3.50552 ( 9) link_ALPHA1-6 : bond 0.00532 ( 3) link_ALPHA1-6 : angle 2.07047 ( 9) link_BETA1-4 : bond 0.00455 ( 15) link_BETA1-4 : angle 1.57319 ( 45) link_ALPHA1-3 : bond 0.00582 ( 6) link_ALPHA1-3 : angle 1.95379 ( 18) hydrogen bonds : bond 0.05200 ( 1042) hydrogen bonds : angle 5.10221 ( 2934) SS BOND : bond 0.00510 ( 72) SS BOND : angle 1.83858 ( 144) covalent geometry : bond 0.00520 (30225) covalent geometry : angle 0.67436 (41157) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 191 time to evaluate : 2.972 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 64 THR cc_start: 0.9315 (t) cc_final: 0.8952 (m) REVERT: A 253 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8361 (p) REVERT: A 289 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8186 (tt0) REVERT: A 306 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8581 (pp) REVERT: A 310 THR cc_start: 0.5111 (OUTLIER) cc_final: 0.4678 (t) REVERT: A 326 ASP cc_start: 0.5358 (OUTLIER) cc_final: 0.4927 (t70) REVERT: A 737 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.8681 (mtp180) REVERT: A 851 ASP cc_start: 0.8258 (m-30) cc_final: 0.7986 (m-30) REVERT: A 891 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7810 (tt) REVERT: A 903 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 1002 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8347 (tppt) REVERT: A 1071 GLN cc_start: 0.8237 (mt0) cc_final: 0.7962 (mm-40) REVERT: B 34 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6645 (ptp90) REVERT: B 85 LEU cc_start: 0.3908 (OUTLIER) cc_final: 0.3475 (tt) REVERT: B 90 TYR cc_start: 0.5151 (m-80) cc_final: 0.4850 (m-80) REVERT: B 155 MET cc_start: 0.4943 (mmm) cc_final: 0.3912 (pmm) REVERT: B 289 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7915 (mt-10) REVERT: B 324 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6724 (mp) REVERT: B 481 VAL cc_start: 0.8781 (m) cc_final: 0.8456 (p) REVERT: B 636 VAL cc_start: 0.8512 (p) cc_final: 0.8290 (m) REVERT: B 776 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.7114 (t0) REVERT: B 800 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7412 (pp20) REVERT: B 885 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8281 (tptt) REVERT: B 1012 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8555 (tt) REVERT: B 1028 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8261 (tttt) REVERT: B 1124 CYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7764 (m) REVERT: B 1219 TYR cc_start: 0.5637 (OUTLIER) cc_final: 0.5347 (p90) REVERT: C 164 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7310 (mtmt) REVERT: C 176 ILE cc_start: 0.8563 (tt) cc_final: 0.8279 (mt) REVERT: C 289 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: C 295 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: C 494 ILE cc_start: 0.7437 (mp) cc_final: 0.6972 (tp) REVERT: C 500 LYS cc_start: 0.8241 (pmtt) cc_final: 0.7952 (pmtt) REVERT: C 644 TRP cc_start: 0.7326 (p-90) cc_final: 0.6932 (p-90) REVERT: C 779 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8355 (t) REVERT: C 780 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: C 828 LEU cc_start: 0.9124 (mt) cc_final: 0.8818 (mm) REVERT: C 848 ASP cc_start: 0.8332 (m-30) cc_final: 0.8038 (m-30) REVERT: C 994 MET cc_start: 0.8861 (mmt) cc_final: 0.8445 (mmt) REVERT: C 1010 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8387 (tttm) REVERT: C 1030 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: C 1050 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9081 (mttp) REVERT: C 1211 ASN cc_start: 0.7639 (m-40) cc_final: 0.7381 (m-40) REVERT: C 1219 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5386 (p90) outliers start: 169 outliers final: 122 residues processed: 343 average time/residue: 0.8711 time to fit residues: 383.0558 Evaluate side-chains 339 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 191 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 776 ASN Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 273 optimal weight: 0.8980 chunk 355 optimal weight: 3.9990 chunk 307 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 224 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN A 998 ASN C 854 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119566 restraints weight = 42525.403| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.54 r_work: 0.3274 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 30390 Z= 0.135 Angle : 0.651 15.627 41580 Z= 0.324 Chirality : 0.046 0.410 4908 Planarity : 0.005 0.104 5172 Dihedral : 9.124 125.027 5918 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.71 % Allowed : 19.96 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % 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: -1.01 (0.13), residues: 3618 helix: 1.51 (0.20), residues: 765 sheet: -0.43 (0.17), residues: 858 loop : -1.73 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 197 HIS 0.009 0.001 HIS B 175 PHE 0.021 0.001 PHE C 577 TYR 0.017 0.001 TYR C 203 ARG 0.015 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 66) link_NAG-ASN : angle 3.33930 ( 198) link_ALPHA1-4 : bond 0.01630 ( 3) link_ALPHA1-4 : angle 3.50915 ( 9) link_ALPHA1-6 : bond 0.00552 ( 3) link_ALPHA1-6 : angle 1.99920 ( 9) link_BETA1-4 : bond 0.00426 ( 15) link_BETA1-4 : angle 1.43658 ( 45) link_ALPHA1-3 : bond 0.00635 ( 6) link_ALPHA1-3 : angle 1.88538 ( 18) hydrogen bonds : bond 0.04358 ( 1042) hydrogen bonds : angle 4.92218 ( 2934) SS BOND : bond 0.00384 ( 72) SS BOND : angle 1.54456 ( 144) covalent geometry : bond 0.00314 (30225) covalent geometry : angle 0.59932 (41157) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 205 time to evaluate : 3.225 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 64 THR cc_start: 0.9322 (t) cc_final: 0.8992 (m) REVERT: A 253 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8338 (p) REVERT: A 289 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8238 (tt0) REVERT: A 306 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8496 (pp) REVERT: A 310 THR cc_start: 0.5150 (OUTLIER) cc_final: 0.4758 (t) REVERT: A 326 ASP cc_start: 0.5090 (OUTLIER) cc_final: 0.4737 (t70) REVERT: A 737 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.8628 (mtp180) REVERT: A 891 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7802 (tt) REVERT: A 903 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8187 (tt) REVERT: A 1002 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8305 (tppt) REVERT: A 1071 GLN cc_start: 0.8186 (mt0) cc_final: 0.7885 (mm-40) REVERT: B 34 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6627 (ptp90) REVERT: B 85 LEU cc_start: 0.3767 (OUTLIER) cc_final: 0.3364 (tt) REVERT: B 90 TYR cc_start: 0.5023 (m-80) cc_final: 0.4730 (m-80) REVERT: B 140 GLN cc_start: 0.7357 (mp10) cc_final: 0.6830 (tt0) REVERT: B 155 MET cc_start: 0.4922 (mmm) cc_final: 0.3890 (pmm) REVERT: B 289 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7809 (mt-10) REVERT: B 324 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6659 (mp) REVERT: B 481 VAL cc_start: 0.8740 (m) cc_final: 0.8406 (p) REVERT: B 636 VAL cc_start: 0.8460 (p) cc_final: 0.8245 (m) REVERT: B 644 TRP cc_start: 0.7907 (OUTLIER) cc_final: 0.7611 (p90) REVERT: B 655 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8590 (mt) REVERT: B 776 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.7083 (t0) REVERT: B 800 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7427 (pp20) REVERT: B 885 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8202 (tptt) REVERT: B 1012 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8451 (tt) REVERT: B 1124 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7710 (m) REVERT: B 1219 TYR cc_start: 0.5519 (OUTLIER) cc_final: 0.5266 (p90) REVERT: C 158 TYR cc_start: 0.8705 (m-80) cc_final: 0.8177 (m-80) REVERT: C 164 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7290 (mtmt) REVERT: C 289 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7976 (mm-30) REVERT: C 295 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: C 491 LEU cc_start: 0.6858 (mp) cc_final: 0.6568 (mt) REVERT: C 494 ILE cc_start: 0.7288 (mp) cc_final: 0.6870 (tp) REVERT: C 500 LYS cc_start: 0.8191 (pmtt) cc_final: 0.7907 (pmtt) REVERT: C 644 TRP cc_start: 0.7297 (p-90) cc_final: 0.6965 (p-90) REVERT: C 779 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8342 (t) REVERT: C 780 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: C 828 LEU cc_start: 0.9058 (mt) cc_final: 0.8752 (mm) REVERT: C 848 ASP cc_start: 0.8321 (m-30) cc_final: 0.8068 (m-30) REVERT: C 994 MET cc_start: 0.8846 (mmt) cc_final: 0.8388 (mmt) REVERT: C 1010 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8350 (tttm) REVERT: C 1030 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8767 (mm110) REVERT: C 1050 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9041 (mttp) REVERT: C 1211 ASN cc_start: 0.7644 (m-40) cc_final: 0.7375 (m-40) REVERT: C 1219 TYR cc_start: 0.6259 (OUTLIER) cc_final: 0.5365 (p90) outliers start: 153 outliers final: 111 residues processed: 342 average time/residue: 0.9410 time to fit residues: 413.4911 Evaluate side-chains 334 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 196 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 776 ASN Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 237 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 354 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.160566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119830 restraints weight = 42565.205| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.53 r_work: 0.3285 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30390 Z= 0.129 Angle : 0.642 15.403 41580 Z= 0.319 Chirality : 0.045 0.401 4908 Planarity : 0.005 0.106 5172 Dihedral : 8.850 121.258 5916 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.37 % Allowed : 20.33 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % 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: -0.91 (0.14), residues: 3618 helix: 1.64 (0.20), residues: 759 sheet: -0.38 (0.17), residues: 858 loop : -1.67 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 971 HIS 0.010 0.001 HIS B 175 PHE 0.021 0.001 PHE C1217 TYR 0.017 0.001 TYR B 609 ARG 0.010 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 66) link_NAG-ASN : angle 3.26709 ( 198) link_ALPHA1-4 : bond 0.01615 ( 3) link_ALPHA1-4 : angle 3.51812 ( 9) link_ALPHA1-6 : bond 0.00547 ( 3) link_ALPHA1-6 : angle 2.00077 ( 9) link_BETA1-4 : bond 0.00420 ( 15) link_BETA1-4 : angle 1.41584 ( 45) link_ALPHA1-3 : bond 0.00693 ( 6) link_ALPHA1-3 : angle 1.89169 ( 18) hydrogen bonds : bond 0.04230 ( 1042) hydrogen bonds : angle 4.87106 ( 2934) SS BOND : bond 0.00375 ( 72) SS BOND : angle 1.41951 ( 144) covalent geometry : bond 0.00296 (30225) covalent geometry : angle 0.59163 (41157) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 199 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.9321 (t) cc_final: 0.8988 (m) REVERT: A 253 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (p) REVERT: A 289 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8250 (tt0) REVERT: A 306 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8476 (pp) REVERT: A 310 THR cc_start: 0.5170 (OUTLIER) cc_final: 0.4823 (t) REVERT: A 737 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.8602 (mtp180) REVERT: A 891 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7716 (tt) REVERT: A 903 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8171 (tt) REVERT: A 1002 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8288 (tppt) REVERT: B 34 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6652 (ptp90) REVERT: B 85 LEU cc_start: 0.3748 (OUTLIER) cc_final: 0.3355 (tt) REVERT: B 90 TYR cc_start: 0.4990 (m-80) cc_final: 0.4691 (m-80) REVERT: B 140 GLN cc_start: 0.7382 (mp10) cc_final: 0.6867 (tt0) REVERT: B 155 MET cc_start: 0.4847 (mmm) cc_final: 0.3933 (pmm) REVERT: B 218 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6741 (ppp) REVERT: B 289 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7846 (mt-10) REVERT: B 324 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6633 (mp) REVERT: B 481 VAL cc_start: 0.8724 (m) cc_final: 0.8390 (p) REVERT: B 636 VAL cc_start: 0.8464 (p) cc_final: 0.8247 (m) REVERT: B 644 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.7622 (p90) REVERT: B 655 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8613 (mt) REVERT: B 776 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.7059 (t0) REVERT: B 800 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7392 (pp20) REVERT: B 885 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8209 (tptt) REVERT: B 1012 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8477 (tt) REVERT: B 1200 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7735 (mmtp) REVERT: B 1219 TYR cc_start: 0.5489 (OUTLIER) cc_final: 0.5247 (p90) REVERT: C 164 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7285 (mtmt) REVERT: C 176 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8080 (mt) REVERT: C 289 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: C 295 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: C 491 LEU cc_start: 0.6869 (mp) cc_final: 0.6558 (mt) REVERT: C 494 ILE cc_start: 0.7401 (mp) cc_final: 0.6954 (tp) REVERT: C 500 LYS cc_start: 0.8207 (pmtt) cc_final: 0.7907 (pmtt) REVERT: C 644 TRP cc_start: 0.7301 (p-90) cc_final: 0.6998 (p-90) REVERT: C 779 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8348 (t) REVERT: C 780 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: C 828 LEU cc_start: 0.9056 (mt) cc_final: 0.8757 (mm) REVERT: C 848 ASP cc_start: 0.8320 (m-30) cc_final: 0.7958 (m-30) REVERT: C 994 MET cc_start: 0.8841 (mmt) cc_final: 0.8381 (mmt) REVERT: C 1010 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8358 (tttm) REVERT: C 1030 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8750 (mm110) REVERT: C 1050 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9053 (mttp) REVERT: C 1211 ASN cc_start: 0.7645 (m-40) cc_final: 0.7386 (m-40) REVERT: C 1219 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5347 (p90) outliers start: 142 outliers final: 106 residues processed: 325 average time/residue: 0.9131 time to fit residues: 379.7549 Evaluate side-chains 325 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 191 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 644 TRP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 776 ASN Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1200 LYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1050 LYS Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 316 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 308 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118274 restraints weight = 42368.812| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.52 r_work: 0.3259 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 30390 Z= 0.171 Angle : 0.696 25.892 41580 Z= 0.341 Chirality : 0.048 0.769 4908 Planarity : 0.005 0.106 5172 Dihedral : 8.848 117.715 5915 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.50 % Allowed : 20.39 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % 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: -1.03 (0.13), residues: 3618 helix: 1.47 (0.20), residues: 760 sheet: -0.45 (0.17), residues: 851 loop : -1.71 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 197 HIS 0.010 0.001 HIS B 175 PHE 0.022 0.002 PHE C1217 TYR 0.032 0.002 TYR C 458 ARG 0.015 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 66) link_NAG-ASN : angle 4.01961 ( 198) link_ALPHA1-4 : bond 0.01811 ( 3) link_ALPHA1-4 : angle 3.55444 ( 9) link_ALPHA1-6 : bond 0.00498 ( 3) link_ALPHA1-6 : angle 2.07888 ( 9) link_BETA1-4 : bond 0.00437 ( 15) link_BETA1-4 : angle 1.49011 ( 45) link_ALPHA1-3 : bond 0.00658 ( 6) link_ALPHA1-3 : angle 1.92615 ( 18) hydrogen bonds : bond 0.04785 ( 1042) hydrogen bonds : angle 4.97337 ( 2934) SS BOND : bond 0.00451 ( 72) SS BOND : angle 1.46596 ( 144) covalent geometry : bond 0.00407 (30225) covalent geometry : angle 0.62970 (41157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24423.10 seconds wall clock time: 420 minutes 18.52 seconds (25218.52 seconds total)