Starting phenix.real_space_refine on Tue May 27 13:30:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1c_38831/05_2025/8y1c_38831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1c_38831/05_2025/8y1c_38831.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/8y1c_38831/05_2025/8y1c_38831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1c_38831/05_2025/8y1c_38831.map" model { file = "/net/cci-nas-00/data/ceres_data/8y1c_38831/05_2025/8y1c_38831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1c_38831/05_2025/8y1c_38831.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= 0.093 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 68 residue(s): 1.24s 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: "B" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 2, 'PTRANS': 50, '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: "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: "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: "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 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 Time building chain proxies: 18.02, per 1000 atoms: 0.61 Number of scatterers: 29541 At special positions: 0 Unit cell: (159.789, 154.354, 213.052, 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=71, symmetry=0 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 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=2.04 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.04 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 B 132 " " NAG E 1 " - " ASN B 188 " " NAG F 1 " - " ASN B 335 " " NAG G 1 " - " ASN B 355 " " NAG H 1 " - " ASN B 664 " " NAG I 1 " - " ASN C 132 " " NAG J 1 " - " ASN C 188 " " NAG K 1 " - " ASN C 335 " " NAG L 1 " - " ASN C 355 " " NAG M 1 " - " ASN C 664 " " NAG N 1 " - " ASN A 132 " " NAG O 1 " - " ASN A 188 " " NAG P 1 " - " ASN A 335 " " NAG Q 1 " - " ASN A 355 " " NAG R 1 " - " ASN A 664 " Time building additional restraints: 8.10 Conformation dependent library (CDL) restraints added in 3.7 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: 78 helices and 62 sheets defined 23.3% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.628A pdb=" N GLU B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.633A pdb=" N LEU B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.645A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.570A 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 442 through 447 Processing helix chain 'B' and resid 478 through 483 removed outlier: 4.118A pdb=" N VAL B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 478 through 483' Processing helix chain 'B' and resid 552 through 556 removed outlier: 3.601A pdb=" N LYS B 555 " --> pdb=" O ASN B 552 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 556' Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.624A pdb=" N ALA B 571 " --> pdb=" O SER B 568 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE B 572 " --> pdb=" O PRO B 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 568 through 572' 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 830 Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 835 through 862 Processing helix chain 'B' and resid 901 through 910 removed outlier: 4.080A pdb=" N LYS B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 923 Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1024 through 1045 removed outlier: 3.658A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.969A 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 1065 removed outlier: 3.607A pdb=" N LEU B1065 " --> pdb=" O ILE B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1113 removed outlier: 4.131A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.724A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.559A pdb=" N ILE C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.531A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 344 removed outlier: 3.801A pdb=" N TRP C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 341 through 344' Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.882A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.787A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.866A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.653A pdb=" N VAL C 481 " --> pdb=" O ASP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 556 removed outlier: 3.543A pdb=" N LYS C 555 " --> pdb=" O ASN C 552 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 552 through 556' Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.871A pdb=" N PHE C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) 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: 3.724A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 911 removed outlier: 4.180A pdb=" N LYS C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.904A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 940 Processing helix chain 'C' and resid 951 through 965 Processing helix chain 'C' and resid 971 through 975 removed outlier: 3.586A pdb=" N ALA C 974 " --> pdb=" O TRP C 971 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA C 975 " --> pdb=" O SER C 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 971 through 975' Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.819A 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: 3.689A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.817A 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 1069 through 1113 removed outlier: 4.291A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 4.472A pdb=" N LEU A 44 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.724A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.727A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 356 through 363 removed outlier: 3.600A pdb=" N VAL A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' 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 834 through 863 removed outlier: 3.530A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 910 removed outlier: 3.970A pdb=" N LYS A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.946A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.806A pdb=" N ASN A 941 " --> pdb=" O VAL A 937 " (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: 4.213A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1017 removed outlier: 3.583A pdb=" N ILE A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1045 removed outlier: 3.735A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.707A 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 1062 Processing helix chain 'A' and resid 1069 through 1113 removed outlier: 4.094A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 54 through 55 removed outlier: 5.987A pdb=" N VAL B 55 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 68 removed outlier: 4.002A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'B' and resid 221 through 227 removed outlier: 6.950A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 190 Processing sheet with id=AA7, first strand: chain 'B' and resid 155 through 160 removed outlier: 10.852A pdb=" N TYR B 158 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N HIS B 175 " --> pdb=" O TYR B 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 302 through 306 Processing sheet with id=AA9, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.733A pdb=" N ARG B 319 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.890A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.956A pdb=" N PHE B 354 " --> pdb=" O CYS B 603 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.281A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN B 424 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 368 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR B 426 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS B 364 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AB5, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.308A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AB7, first strand: chain 'B' and resid 724 through 731 removed outlier: 10.687A pdb=" N TYR B 762 " --> pdb=" O ASN B 725 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N THR B 727 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N PHE B 764 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR B 729 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 766 " --> pdb=" O TYR B 729 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 773 through 775 Processing sheet with id=AB9, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.834A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASN B1136 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B1142 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL B1134 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE B1144 " --> pdb=" O SER B1132 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B1132 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE B1146 " --> pdb=" O ILE B1130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.834A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B1177 " --> pdb=" O SER B1159 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.293A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 866 through 868 removed outlier: 6.656A pdb=" N LEU B 867 " --> pdb=" O VAL A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 878 through 879 removed outlier: 3.595A pdb=" N VAL B 879 " --> pdb=" O ILE B 882 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.567A pdb=" N CYS B1163 " --> pdb=" O THR B1213 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 59 through 67 removed outlier: 7.602A pdb=" N GLN C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP C 281 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.566A pdb=" N VAL C 258 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE C 209 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 225 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA C 211 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 109 through 112 Processing sheet with id=AC9, first strand: chain 'C' and resid 185 through 190 Processing sheet with id=AD1, first strand: chain 'C' and resid 302 through 306 Processing sheet with id=AD2, first strand: chain 'C' and resid 315 through 319 removed outlier: 3.957A pdb=" N ALA C 315 " --> pdb=" O CYS C 619 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 647 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.573A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.957A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 382 through 383 Processing sheet with id=AD6, first strand: chain 'C' and resid 459 through 462 Processing sheet with id=AD7, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.633A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 505 through 507 Processing sheet with id=AD9, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.735A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 773 through 775 removed outlier: 6.225A pdb=" N SER C 773 " --> pdb=" O LEU A 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.852A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.852A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.409A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AE6, first strand: chain 'C' and resid 1202 through 1205 Processing sheet with id=AE7, first strand: chain 'A' and resid 59 through 67 removed outlier: 4.045A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 80 through 81 removed outlier: 4.164A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'A' and resid 221 through 227 removed outlier: 5.115A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 109 through 112 Processing sheet with id=AF2, first strand: chain 'A' and resid 183 through 190 removed outlier: 3.750A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 302 through 306 Processing sheet with id=AF4, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AF5, first strand: chain 'A' and resid 345 through 349 removed outlier: 7.160A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 382 through 383 Processing sheet with id=AF7, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AF8, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AF9, first strand: chain 'A' and resid 473 through 477 removed outlier: 3.567A pdb=" N CYS A 474 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG A 502 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N CYS A 476 " --> pdb=" O ARG A 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AG2, first strand: chain 'A' and resid 550 through 551 removed outlier: 4.023A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 724 through 731 removed outlier: 10.498A pdb=" N TYR A 762 " --> pdb=" O ASN A 725 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N THR A 727 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N PHE A 764 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR A 729 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A 742 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 736 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.734A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASN A1136 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A1142 " --> pdb=" O VAL A1134 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL A1134 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A1144 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER A1132 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE A1146 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.422A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 878 through 879 removed outlier: 3.592A pdb=" N VAL A 879 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 1202 through 1205 Processing sheet with id=AG8, first strand: chain 'A' and resid 1175 through 1180 1034 hydrogen bonds defined for protein. 2838 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: 14.31 Time building geometry restraints manager: 9.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9160 1.34 - 1.46: 7737 1.46 - 1.58: 13129 1.58 - 1.70: 1 1.70 - 1.83: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" C5 MAN D 3 " pdb=" O5 MAN D 3 " ideal model delta sigma weight residual 1.418 1.495 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 MAN N 3 " pdb=" O5 MAN N 3 " ideal model delta sigma weight residual 1.418 1.485 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 MAN I 3 " pdb=" O5 MAN I 3 " ideal model delta sigma weight residual 1.399 1.459 -0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" C1 MAN N 4 " pdb=" C2 MAN N 4 " ideal model delta sigma weight residual 1.526 1.585 -0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" C3 MAN I 3 " pdb=" C4 MAN I 3 " ideal model delta sigma weight residual 1.524 1.582 -0.058 2.00e-02 2.50e+03 8.31e+00 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 40098 2.41 - 4.82: 958 4.82 - 7.23: 86 7.23 - 9.64: 12 9.64 - 12.05: 3 Bond angle restraints: 41157 Sorted by residual: angle pdb=" N PRO C 969 " pdb=" CA PRO C 969 " pdb=" C PRO C 969 " ideal model delta sigma weight residual 110.70 118.36 -7.66 1.22e+00 6.72e-01 3.94e+01 angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 117.83 -7.13 1.22e+00 6.72e-01 3.42e+01 angle pdb=" C GLY A 928 " pdb=" N SER A 929 " pdb=" CA SER A 929 " ideal model delta sigma weight residual 121.54 130.47 -8.93 1.91e+00 2.74e-01 2.19e+01 angle pdb=" CA PRO C 969 " pdb=" C PRO C 969 " pdb=" N PRO C 970 " ideal model delta sigma weight residual 117.93 123.15 -5.22 1.20e+00 6.94e-01 1.89e+01 angle pdb=" N PRO B1067 " pdb=" CA PRO B1067 " pdb=" C PRO B1067 " ideal model delta sigma weight residual 110.70 115.99 -5.29 1.22e+00 6.72e-01 1.88e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 17698 22.77 - 45.55: 1182 45.55 - 68.32: 292 68.32 - 91.09: 45 91.09 - 113.87: 7 Dihedral angle restraints: 19224 sinusoidal: 8586 harmonic: 10638 Sorted by residual: dihedral pdb=" CA PHE A 968 " pdb=" C PHE A 968 " pdb=" N PRO A 969 " pdb=" CA PRO A 969 " ideal model delta harmonic sigma weight residual -180.00 -135.66 -44.34 0 5.00e+00 4.00e-02 7.86e+01 dihedral pdb=" CA PRO A 969 " pdb=" C PRO A 969 " pdb=" N PRO A 970 " pdb=" CA PRO A 970 " ideal model delta harmonic sigma weight residual 180.00 147.07 32.93 0 5.00e+00 4.00e-02 4.34e+01 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 -147.91 -32.09 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 19221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4572 0.101 - 0.203: 318 0.203 - 0.304: 12 0.304 - 0.406: 3 0.406 - 0.507: 3 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG C2003 " pdb=" ND2 ASN C 58 " pdb=" C2 NAG C2003 " pdb=" O5 NAG C2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.43e+00 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 -1.93 -0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C1 NAG B2003 " pdb=" ND2 ASN B 58 " pdb=" C2 NAG B2003 " pdb=" O5 NAG B2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.02e+00 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 969 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.75e+01 pdb=" N PRO A 970 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 970 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 970 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 92 " -0.067 5.00e-02 4.00e+02 9.95e-02 1.59e+01 pdb=" N PRO A 93 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 969 " -0.066 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO C 970 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO C 970 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 970 " -0.057 5.00e-02 4.00e+02 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6841 2.79 - 3.31: 24079 3.31 - 3.84: 48725 3.84 - 4.37: 55551 4.37 - 4.90: 96836 Nonbonded interactions: 232032 Sorted by model distance: nonbonded pdb=" OH TYR C1148 " pdb=" O SER C1190 " model vdw 2.257 3.040 nonbonded pdb=" O LEU B 990 " pdb=" OG SER B1190 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR C 90 " pdb=" O PRO C 159 " model vdw 2.283 3.040 nonbonded pdb=" O LEU B 849 " pdb=" OG1 THR B 853 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" O GLU B 120 " model vdw 2.291 3.040 ... (remaining 232027 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: 4.950 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: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 70.410 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 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 : 0.007 0.086 30389 Z= 0.318 Angle : 0.921 15.900 41578 Z= 0.495 Chirality : 0.057 0.507 4908 Planarity : 0.007 0.104 5172 Dihedral : 15.954 113.866 12183 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 11.49 % Allowed : 11.40 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.06 % 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: -3.39 (0.11), residues: 3618 helix: -2.04 (0.14), residues: 761 sheet: -1.20 (0.17), residues: 815 loop : -2.89 (0.11), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 971 HIS 0.010 0.002 HIS C1129 PHE 0.024 0.003 PHE B 794 TYR 0.025 0.002 TYR B1176 ARG 0.004 0.001 ARG C 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 66) link_NAG-ASN : angle 3.61749 ( 198) link_ALPHA1-4 : bond 0.01461 ( 3) link_ALPHA1-4 : angle 3.53688 ( 9) link_ALPHA1-6 : bond 0.00653 ( 3) link_ALPHA1-6 : angle 1.38016 ( 9) link_BETA1-4 : bond 0.00936 ( 15) link_BETA1-4 : angle 2.54544 ( 45) link_ALPHA1-3 : bond 0.00418 ( 6) link_ALPHA1-3 : angle 1.92021 ( 18) hydrogen bonds : bond 0.12566 ( 1006) hydrogen bonds : angle 6.93811 ( 2838) SS BOND : bond 0.00315 ( 71) SS BOND : angle 1.02733 ( 142) covalent geometry : bond 0.00690 (30225) covalent geometry : angle 0.88256 (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 601 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 373 poor density : 228 time to evaluate : 3.108 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: B 29 ASN cc_start: 0.0411 (OUTLIER) cc_final: -0.0529 (p0) REVERT: B 30 LYS cc_start: 0.4467 (OUTLIER) cc_final: 0.4082 (tttm) REVERT: B 34 ARG cc_start: 0.0031 (OUTLIER) cc_final: -0.1495 (ptp90) REVERT: B 57 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8137 (mm) REVERT: B 102 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6264 (pt) REVERT: B 122 SER cc_start: 0.6682 (OUTLIER) cc_final: 0.5866 (t) REVERT: B 136 THR cc_start: 0.0625 (OUTLIER) cc_final: 0.0192 (m) REVERT: B 166 LYS cc_start: -0.0492 (OUTLIER) cc_final: -0.1303 (mttt) REVERT: B 399 ASP cc_start: 0.1666 (OUTLIER) cc_final: 0.0767 (p0) REVERT: B 597 ILE cc_start: 0.0169 (OUTLIER) cc_final: -0.0441 (mp) REVERT: B 849 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7388 (mp) REVERT: B 851 ASP cc_start: 0.7438 (m-30) cc_final: 0.7154 (m-30) REVERT: B 990 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6259 (mt) REVERT: B 1180 GLN cc_start: 0.4769 (OUTLIER) cc_final: 0.4567 (pt0) REVERT: B 1185 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.6154 (mmp) REVERT: C 74 PHE cc_start: 0.3825 (OUTLIER) cc_final: 0.3394 (p90) REVERT: C 97 ASP cc_start: 0.6393 (t0) cc_final: 0.6001 (m-30) REVERT: C 99 ASN cc_start: 0.5634 (OUTLIER) cc_final: 0.5129 (m-40) REVERT: C 143 ASN cc_start: 0.3621 (OUTLIER) cc_final: 0.3042 (t0) REVERT: C 187 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4110 (mmtt) REVERT: C 213 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.6180 (t80) REVERT: C 365 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7615 (p) REVERT: C 374 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6300 (m-30) REVERT: C 415 LYS cc_start: 0.7511 (tptt) cc_final: 0.7170 (tptp) REVERT: C 655 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8553 (mp) REVERT: C 659 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6972 (ttpt) REVERT: C 845 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: C 851 ASP cc_start: 0.7049 (m-30) cc_final: 0.6724 (m-30) REVERT: C 1026 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8167 (tp) REVERT: C 1147 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.7710 (t) REVERT: A 105 LYS cc_start: 0.7191 (tttt) cc_final: 0.6796 (ttpt) REVERT: A 198 LEU cc_start: 0.7411 (mp) cc_final: 0.7132 (mp) REVERT: A 245 ILE cc_start: 0.4275 (OUTLIER) cc_final: 0.4031 (mt) REVERT: A 310 THR cc_start: 0.3503 (OUTLIER) cc_final: 0.2733 (t) REVERT: A 312 LYS cc_start: 0.4876 (OUTLIER) cc_final: 0.4494 (mmmt) REVERT: A 378 ILE cc_start: 0.0798 (OUTLIER) cc_final: 0.0538 (mt) REVERT: A 511 TYR cc_start: 0.2328 (OUTLIER) cc_final: 0.2061 (m-80) REVERT: A 630 GLN cc_start: 0.6618 (mt0) cc_final: 0.6340 (pp30) REVERT: A 646 ASN cc_start: 0.7748 (m-40) cc_final: 0.7512 (m-40) REVERT: A 712 TYR cc_start: 0.7949 (p90) cc_final: 0.7703 (p90) REVERT: A 737 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7616 (mtm180) REVERT: A 863 GLN cc_start: 0.7839 (tt0) cc_final: 0.7547 (tt0) REVERT: A 1002 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6871 (tptm) REVERT: A 1095 ASP cc_start: 0.6802 (m-30) cc_final: 0.6495 (m-30) REVERT: A 1108 GLU cc_start: 0.7169 (tt0) cc_final: 0.6718 (tp30) REVERT: A 1124 CYS cc_start: 0.5387 (OUTLIER) cc_final: 0.5073 (m) REVERT: A 1132 SER cc_start: 0.8018 (OUTLIER) cc_final: 0.7807 (m) REVERT: A 1219 TYR cc_start: 0.5774 (OUTLIER) cc_final: 0.5342 (p90) outliers start: 373 outliers final: 141 residues processed: 567 average time/residue: 0.8846 time to fit residues: 636.4009 Evaluate side-chains 318 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 141 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 THR 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 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1180 GLN Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1096 ILE 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 1203 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 VAL 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 245 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1219 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 chunk 326 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 73 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 ASN B 654 ASN B 694 ASN B 799 HIS B 863 GLN B 876 HIS B 984 GLN B1001 GLN B1016 GLN B1049 ASN B1079 ASN B1091 GLN B1135 GLN C 26 ASN C 108 ASN C 152 GLN C 204 GLN C 248 ASN C 410 GLN C 413 ASN C 535 GLN C 605 ASN C 621 ASN C 838 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 GLN C1091 GLN A 204 GLN A 351 ASN A 605 ASN A 630 GLN A 876 HIS A 894 GLN A1091 GLN A1122 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.206451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.146141 restraints weight = 48976.567| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.09 r_work: 0.3597 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30389 Z= 0.210 Angle : 0.718 10.588 41578 Z= 0.366 Chirality : 0.048 0.232 4908 Planarity : 0.006 0.095 5172 Dihedral : 12.715 112.861 6137 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 8.23 % Allowed : 15.53 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.54 (0.13), residues: 3618 helix: -0.39 (0.18), residues: 766 sheet: -0.90 (0.18), residues: 797 loop : -2.64 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 971 HIS 0.009 0.001 HIS C1129 PHE 0.021 0.002 PHE A 786 TYR 0.027 0.002 TYR C 462 ARG 0.007 0.001 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 66) link_NAG-ASN : angle 2.66945 ( 198) link_ALPHA1-4 : bond 0.01495 ( 3) link_ALPHA1-4 : angle 3.49322 ( 9) link_ALPHA1-6 : bond 0.00999 ( 3) link_ALPHA1-6 : angle 1.39681 ( 9) link_BETA1-4 : bond 0.00472 ( 15) link_BETA1-4 : angle 1.71588 ( 45) link_ALPHA1-3 : bond 0.00506 ( 6) link_ALPHA1-3 : angle 1.92329 ( 18) hydrogen bonds : bond 0.05461 ( 1006) hydrogen bonds : angle 5.92580 ( 2838) SS BOND : bond 0.00354 ( 71) SS BOND : angle 1.24360 ( 142) covalent geometry : bond 0.00489 (30225) covalent geometry : angle 0.68777 (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 422 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 155 time to evaluate : 3.126 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: B 29 ASN cc_start: -0.1197 (OUTLIER) cc_final: -0.2183 (p0) REVERT: B 30 LYS cc_start: 0.4147 (OUTLIER) cc_final: 0.3265 (tttm) REVERT: B 34 ARG cc_start: -0.0798 (OUTLIER) cc_final: -0.1143 (ptm160) REVERT: B 46 LEU cc_start: 0.7918 (mm) cc_final: 0.7457 (mp) REVERT: B 122 SER cc_start: 0.6019 (OUTLIER) cc_final: 0.5170 (t) REVERT: B 136 THR cc_start: -0.1179 (OUTLIER) cc_final: -0.1469 (m) REVERT: B 145 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6361 (tt) REVERT: B 166 LYS cc_start: -0.0886 (OUTLIER) cc_final: -0.1781 (mttt) REVERT: B 264 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6623 (ptp-110) REVERT: B 399 ASP cc_start: 0.2669 (OUTLIER) cc_final: 0.2165 (p0) REVERT: B 402 GLN cc_start: 0.3426 (OUTLIER) cc_final: 0.3155 (tm-30) REVERT: B 990 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6852 (mt) REVERT: B 1079 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8269 (m-40) REVERT: B 1185 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6664 (mmp) REVERT: C 53 ASN cc_start: 0.8115 (p0) cc_final: 0.7699 (p0) REVERT: C 69 LYS cc_start: 0.8334 (tttm) cc_final: 0.8060 (tppt) REVERT: C 94 PHE cc_start: 0.5477 (m-80) cc_final: 0.4481 (t80) REVERT: C 97 ASP cc_start: 0.6662 (t0) cc_final: 0.6227 (m-30) REVERT: C 187 LYS cc_start: 0.4889 (OUTLIER) cc_final: 0.3764 (mmtt) REVERT: C 213 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.6520 (t80) REVERT: C 374 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6481 (m-30) REVERT: C 415 LYS cc_start: 0.7533 (tptt) cc_final: 0.7150 (tptp) REVERT: C 597 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7230 (mt) REVERT: C 659 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7310 (ttpt) REVERT: C 673 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5793 (t80) REVERT: C 914 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8386 (m) REVERT: C 1026 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8906 (tp) REVERT: A 111 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5631 (mt) REVERT: A 143 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7690 (m-40) REVERT: A 187 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.6953 (tmtp) REVERT: A 198 LEU cc_start: 0.7480 (mp) cc_final: 0.7223 (mp) REVERT: A 245 ILE cc_start: 0.3086 (OUTLIER) cc_final: 0.2881 (mt) REVERT: A 255 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7137 (mm-30) REVERT: A 310 THR cc_start: 0.2874 (OUTLIER) cc_final: 0.2145 (t) REVERT: A 312 LYS cc_start: 0.4838 (OUTLIER) cc_final: 0.4453 (mmmt) REVERT: A 608 LEU cc_start: 0.4618 (OUTLIER) cc_final: 0.4338 (mm) REVERT: A 630 GLN cc_start: 0.7107 (mt0) cc_final: 0.6423 (pp30) REVERT: A 646 ASN cc_start: 0.7972 (m-40) cc_final: 0.7623 (m-40) REVERT: A 706 PHE cc_start: 0.3557 (OUTLIER) cc_final: 0.3027 (t80) REVERT: A 789 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: A 1091 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: A 1108 GLU cc_start: 0.8782 (tt0) cc_final: 0.8343 (mm-30) REVERT: A 1124 CYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5900 (m) REVERT: A 1219 TYR cc_start: 0.6101 (OUTLIER) cc_final: 0.5871 (p90) outliers start: 267 outliers final: 152 residues processed: 395 average time/residue: 0.8156 time to fit residues: 420.0363 Evaluate side-chains 317 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 132 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 THR 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 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER 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 1210 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 35 ILE 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 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER 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 245 ILE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A 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: 7.9990 chunk 207 optimal weight: 0.6980 chunk 323 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 269 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 356 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B1122 ASN B1135 GLN C 99 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 440 ASN C 535 GLN C 876 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.207949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148538 restraints weight = 48915.778| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.98 r_work: 0.3626 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30389 Z= 0.124 Angle : 0.612 10.033 41578 Z= 0.312 Chirality : 0.045 0.218 4908 Planarity : 0.005 0.089 5172 Dihedral : 11.417 107.282 6073 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.59 % Allowed : 17.59 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.95 (0.13), residues: 3618 helix: 0.52 (0.19), residues: 774 sheet: -0.67 (0.18), residues: 812 loop : -2.42 (0.12), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 575 HIS 0.005 0.001 HIS C1129 PHE 0.017 0.001 PHE B 202 TYR 0.015 0.001 TYR B1148 ARG 0.003 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 66) link_NAG-ASN : angle 2.31057 ( 198) link_ALPHA1-4 : bond 0.01564 ( 3) link_ALPHA1-4 : angle 3.29308 ( 9) link_ALPHA1-6 : bond 0.00756 ( 3) link_ALPHA1-6 : angle 1.46653 ( 9) link_BETA1-4 : bond 0.00414 ( 15) link_BETA1-4 : angle 1.56439 ( 45) link_ALPHA1-3 : bond 0.00526 ( 6) link_ALPHA1-3 : angle 1.94954 ( 18) hydrogen bonds : bond 0.04273 ( 1006) hydrogen bonds : angle 5.44312 ( 2838) SS BOND : bond 0.00325 ( 71) SS BOND : angle 0.98956 ( 142) covalent geometry : bond 0.00273 (30225) covalent geometry : angle 0.58485 (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 363 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 149 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1375 (OUTLIER) cc_final: -0.2721 (p0) REVERT: B 34 ARG cc_start: -0.1110 (OUTLIER) cc_final: -0.1872 (ptm160) REVERT: B 52 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7315 (tp) REVERT: B 136 THR cc_start: -0.1077 (OUTLIER) cc_final: -0.1370 (m) REVERT: B 166 LYS cc_start: -0.1195 (OUTLIER) cc_final: -0.2086 (mttt) REVERT: B 238 MET cc_start: 0.0568 (mmm) cc_final: 0.0142 (mmm) REVERT: B 264 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5406 (ptp90) REVERT: B 558 THR cc_start: -0.0388 (OUTLIER) cc_final: -0.0940 (t) REVERT: B 1001 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6413 (mt0) REVERT: B 1069 GLU cc_start: 0.8160 (tt0) cc_final: 0.7683 (tm-30) REVERT: B 1185 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6537 (mmm) REVERT: C 25 ILE cc_start: 0.3193 (OUTLIER) cc_final: 0.2604 (tp) REVERT: C 52 LEU cc_start: 0.7838 (mp) cc_final: 0.7576 (mt) REVERT: C 53 ASN cc_start: 0.7998 (p0) cc_final: 0.7547 (p0) REVERT: C 69 LYS cc_start: 0.8239 (tttm) cc_final: 0.7991 (tppt) REVERT: C 74 PHE cc_start: 0.2984 (OUTLIER) cc_final: 0.2259 (p90) REVERT: C 94 PHE cc_start: 0.5507 (OUTLIER) cc_final: 0.4627 (t80) REVERT: C 97 ASP cc_start: 0.6508 (t0) cc_final: 0.6085 (m-30) REVERT: C 185 PHE cc_start: 0.2884 (OUTLIER) cc_final: 0.2527 (t80) REVERT: C 187 LYS cc_start: 0.4730 (OUTLIER) cc_final: 0.3344 (mmtm) REVERT: C 213 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6443 (t80) REVERT: C 228 LEU cc_start: 0.3401 (OUTLIER) cc_final: 0.3022 (mm) REVERT: C 415 LYS cc_start: 0.7408 (tptt) cc_final: 0.7028 (tptp) REVERT: C 659 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7323 (ttpt) REVERT: C 673 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5884 (t80) REVERT: C 893 SER cc_start: 0.7175 (p) cc_final: 0.6819 (t) REVERT: A 155 MET cc_start: 0.6940 (mmm) cc_final: 0.6536 (mmt) REVERT: A 198 LEU cc_start: 0.7309 (mp) cc_final: 0.7090 (mp) REVERT: A 310 THR cc_start: 0.3178 (OUTLIER) cc_final: 0.2427 (t) REVERT: A 608 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4389 (mm) REVERT: A 646 ASN cc_start: 0.7755 (m-40) cc_final: 0.7510 (m-40) REVERT: A 706 PHE cc_start: 0.3360 (OUTLIER) cc_final: 0.2809 (t80) REVERT: A 777 ASP cc_start: 0.7083 (m-30) cc_final: 0.6216 (m-30) REVERT: A 789 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.6749 (mp10) REVERT: A 828 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8829 (tt) REVERT: A 848 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: A 1091 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: A 1108 GLU cc_start: 0.8453 (tt0) cc_final: 0.8145 (mm-30) REVERT: A 1219 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5667 (p90) outliers start: 214 outliers final: 120 residues processed: 334 average time/residue: 0.7983 time to fit residues: 347.7522 Evaluate side-chains 278 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 132 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 830 SER 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 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 667 TYR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain A residue 35 ILE 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 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain A 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: 4.9990 chunk 284 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 245 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN B1135 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 GLN A 73 ASN A 160 HIS A 201 HIS A 295 GLN A 587 ASN A 872 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.204470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.144004 restraints weight = 48927.669| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.12 r_work: 0.3548 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 30389 Z= 0.323 Angle : 0.790 11.861 41578 Z= 0.401 Chirality : 0.052 0.298 4908 Planarity : 0.006 0.095 5172 Dihedral : 11.469 107.035 6012 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 8.29 % Allowed : 17.74 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.06 % 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: -2.31 (0.13), residues: 3618 helix: -0.06 (0.18), residues: 764 sheet: -0.85 (0.18), residues: 810 loop : -2.52 (0.12), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 971 HIS 0.020 0.002 HIS B 142 PHE 0.030 0.003 PHE A 786 TYR 0.027 0.003 TYR B 622 ARG 0.006 0.001 ARG B1120 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 66) link_NAG-ASN : angle 2.69053 ( 198) link_ALPHA1-4 : bond 0.01367 ( 3) link_ALPHA1-4 : angle 3.53792 ( 9) link_ALPHA1-6 : bond 0.00863 ( 3) link_ALPHA1-6 : angle 1.40363 ( 9) link_BETA1-4 : bond 0.00439 ( 15) link_BETA1-4 : angle 1.84568 ( 45) link_ALPHA1-3 : bond 0.00440 ( 6) link_ALPHA1-3 : angle 1.99149 ( 18) hydrogen bonds : bond 0.06210 ( 1006) hydrogen bonds : angle 5.92301 ( 2838) SS BOND : bond 0.00496 ( 71) SS BOND : angle 1.26970 ( 142) covalent geometry : bond 0.00771 (30225) covalent geometry : angle 0.76230 (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 395 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 126 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1140 (OUTLIER) cc_final: -0.2521 (p0) REVERT: B 34 ARG cc_start: -0.0719 (OUTLIER) cc_final: -0.1113 (ptm160) REVERT: B 136 THR cc_start: -0.1078 (OUTLIER) cc_final: -0.1374 (m) REVERT: B 145 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.6035 (pp) REVERT: B 166 LYS cc_start: -0.0910 (OUTLIER) cc_final: -0.1831 (mttt) REVERT: B 185 PHE cc_start: 0.4419 (OUTLIER) cc_final: 0.3456 (m-10) REVERT: B 402 GLN cc_start: 0.3588 (OUTLIER) cc_final: 0.3273 (tm-30) REVERT: B 990 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6784 (mt) REVERT: B 1079 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7974 (m-40) REVERT: B 1185 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6546 (mmp) REVERT: C 53 ASN cc_start: 0.8129 (p0) cc_final: 0.7639 (p0) REVERT: C 74 PHE cc_start: 0.2944 (OUTLIER) cc_final: 0.2299 (p90) REVERT: C 94 PHE cc_start: 0.5603 (OUTLIER) cc_final: 0.4579 (t80) REVERT: C 97 ASP cc_start: 0.6669 (t0) cc_final: 0.6139 (m-30) REVERT: C 185 PHE cc_start: 0.2921 (OUTLIER) cc_final: 0.2539 (t80) REVERT: C 187 LYS cc_start: 0.4869 (OUTLIER) cc_final: 0.3299 (mmtm) REVERT: C 213 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.6483 (t80) REVERT: C 228 LEU cc_start: 0.3285 (OUTLIER) cc_final: 0.2929 (mm) REVERT: C 415 LYS cc_start: 0.7478 (tptt) cc_final: 0.7193 (tptp) REVERT: C 588 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5902 (tt) REVERT: C 673 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.6056 (t80) REVERT: C 893 SER cc_start: 0.7398 (p) cc_final: 0.7077 (t) REVERT: C 899 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.7469 (t) REVERT: A 198 LEU cc_start: 0.7365 (mp) cc_final: 0.7129 (mp) REVERT: A 310 THR cc_start: 0.3094 (OUTLIER) cc_final: 0.2333 (t) REVERT: A 312 LYS cc_start: 0.4814 (OUTLIER) cc_final: 0.4561 (mmmt) REVERT: A 608 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4790 (mm) REVERT: A 630 GLN cc_start: 0.7094 (mt0) cc_final: 0.6373 (pp30) REVERT: A 646 ASN cc_start: 0.7861 (m-40) cc_final: 0.7584 (m-40) REVERT: A 706 PHE cc_start: 0.3309 (OUTLIER) cc_final: 0.2691 (t80) REVERT: A 737 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8550 (mtm180) REVERT: A 946 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8563 (tp) REVERT: A 1091 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: A 1108 GLU cc_start: 0.8647 (tt0) cc_final: 0.8269 (mm-30) REVERT: A 1219 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.5643 (p90) outliers start: 269 outliers final: 186 residues processed: 372 average time/residue: 0.7922 time to fit residues: 388.2000 Evaluate side-chains 332 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 119 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 830 SER 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 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1090 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 535 GLN Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 667 TYR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 899 SER Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1096 ILE 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 1185 MET Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A 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: 20.0000 chunk 333 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 338 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 266 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN B1135 GLN C 108 ASN C 351 ASN C 535 GLN A 295 GLN A 587 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.207361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145476 restraints weight = 48828.366| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.70 r_work: 0.3643 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 30389 Z= 0.130 Angle : 0.610 10.443 41578 Z= 0.311 Chirality : 0.045 0.230 4908 Planarity : 0.005 0.088 5172 Dihedral : 10.554 103.456 6000 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.47 % Allowed : 19.56 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.82 (0.13), residues: 3618 helix: 0.71 (0.19), residues: 768 sheet: -0.61 (0.18), residues: 811 loop : -2.34 (0.12), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 971 HIS 0.006 0.001 HIS C1129 PHE 0.015 0.001 PHE B 794 TYR 0.030 0.001 TYR B 427 ARG 0.003 0.000 ARG B 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 66) link_NAG-ASN : angle 2.26635 ( 198) link_ALPHA1-4 : bond 0.01531 ( 3) link_ALPHA1-4 : angle 3.39269 ( 9) link_ALPHA1-6 : bond 0.00724 ( 3) link_ALPHA1-6 : angle 1.43273 ( 9) link_BETA1-4 : bond 0.00401 ( 15) link_BETA1-4 : angle 1.50657 ( 45) link_ALPHA1-3 : bond 0.00443 ( 6) link_ALPHA1-3 : angle 1.97962 ( 18) hydrogen bonds : bond 0.04355 ( 1006) hydrogen bonds : angle 5.41619 ( 2838) SS BOND : bond 0.00297 ( 71) SS BOND : angle 0.86452 ( 142) covalent geometry : bond 0.00290 (30225) covalent geometry : angle 0.58462 (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 339 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 129 time to evaluate : 3.034 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: B 29 ASN cc_start: -0.1118 (OUTLIER) cc_final: -0.2690 (p0) REVERT: B 34 ARG cc_start: -0.0535 (OUTLIER) cc_final: -0.1246 (ptm160) REVERT: B 52 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7276 (tp) REVERT: B 136 THR cc_start: -0.0743 (OUTLIER) cc_final: -0.1061 (m) REVERT: B 166 LYS cc_start: -0.0915 (OUTLIER) cc_final: -0.1434 (pttm) REVERT: B 558 THR cc_start: -0.0809 (OUTLIER) cc_final: -0.1080 (m) REVERT: B 670 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6659 (mt) REVERT: B 1079 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8142 (m-40) REVERT: B 1135 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8663 (mm110) REVERT: B 1185 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6551 (mmm) REVERT: C 25 ILE cc_start: 0.3132 (OUTLIER) cc_final: 0.2482 (tp) REVERT: C 52 LEU cc_start: 0.7857 (mp) cc_final: 0.7563 (mt) REVERT: C 53 ASN cc_start: 0.8079 (p0) cc_final: 0.7672 (p0) REVERT: C 74 PHE cc_start: 0.3320 (OUTLIER) cc_final: 0.2601 (p90) REVERT: C 94 PHE cc_start: 0.5639 (OUTLIER) cc_final: 0.4653 (t80) REVERT: C 97 ASP cc_start: 0.6493 (t0) cc_final: 0.5956 (m-30) REVERT: C 149 THR cc_start: 0.3035 (OUTLIER) cc_final: 0.2789 (p) REVERT: C 185 PHE cc_start: 0.2733 (OUTLIER) cc_final: 0.2196 (t80) REVERT: C 187 LYS cc_start: 0.4713 (OUTLIER) cc_final: 0.3190 (mmtm) REVERT: C 213 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.6443 (t80) REVERT: C 415 LYS cc_start: 0.7487 (tptt) cc_final: 0.7162 (tptp) REVERT: C 588 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5865 (tt) REVERT: C 673 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5979 (t80) REVERT: C 893 SER cc_start: 0.7474 (p) cc_final: 0.7178 (t) REVERT: C 920 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: A 155 MET cc_start: 0.6895 (mmm) cc_final: 0.6685 (mmt) REVERT: A 187 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.6979 (tmtp) REVERT: A 198 LEU cc_start: 0.7324 (mp) cc_final: 0.7085 (mp) REVERT: A 310 THR cc_start: 0.2955 (OUTLIER) cc_final: 0.2255 (t) REVERT: A 608 LEU cc_start: 0.5050 (OUTLIER) cc_final: 0.4728 (mm) REVERT: A 646 ASN cc_start: 0.7825 (m-40) cc_final: 0.7501 (m-40) REVERT: A 706 PHE cc_start: 0.3286 (OUTLIER) cc_final: 0.2729 (t80) REVERT: A 748 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7831 (pp) REVERT: A 789 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6360 (mp10) REVERT: A 848 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: A 1091 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: A 1108 GLU cc_start: 0.8699 (tt0) cc_final: 0.8217 (mm-30) REVERT: A 1219 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.5590 (p90) outliers start: 210 outliers final: 128 residues processed: 316 average time/residue: 0.7924 time to fit residues: 332.1533 Evaluate side-chains 282 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 125 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 830 SER 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 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1135 GLN Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 667 TYR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1096 ILE 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 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A 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: 0.8980 chunk 297 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 343 optimal weight: 2.9990 chunk 281 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 345 optimal weight: 0.0270 chunk 199 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN B1135 GLN C 413 ASN C 535 GLN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.207832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.147631 restraints weight = 48579.641| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.04 r_work: 0.3629 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30389 Z= 0.114 Angle : 0.586 10.014 41578 Z= 0.297 Chirality : 0.045 0.218 4908 Planarity : 0.005 0.079 5172 Dihedral : 9.927 102.942 5995 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 6.19 % Allowed : 19.81 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.58 (0.14), residues: 3618 helix: 1.07 (0.20), residues: 776 sheet: -0.47 (0.18), residues: 806 loop : -2.26 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 575 HIS 0.008 0.001 HIS B 142 PHE 0.014 0.001 PHE B 200 TYR 0.021 0.001 TYR B 427 ARG 0.003 0.000 ARG C 932 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 66) link_NAG-ASN : angle 2.16281 ( 198) link_ALPHA1-4 : bond 0.01552 ( 3) link_ALPHA1-4 : angle 3.40547 ( 9) link_ALPHA1-6 : bond 0.00689 ( 3) link_ALPHA1-6 : angle 1.38900 ( 9) link_BETA1-4 : bond 0.00415 ( 15) link_BETA1-4 : angle 1.48927 ( 45) link_ALPHA1-3 : bond 0.00446 ( 6) link_ALPHA1-3 : angle 1.99027 ( 18) hydrogen bonds : bond 0.04001 ( 1006) hydrogen bonds : angle 5.21428 ( 2838) SS BOND : bond 0.00262 ( 71) SS BOND : angle 0.78949 ( 142) covalent geometry : bond 0.00255 (30225) covalent geometry : angle 0.56153 (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 337 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 136 time to evaluate : 3.303 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: B 29 ASN cc_start: -0.1137 (OUTLIER) cc_final: -0.2887 (p0) REVERT: B 34 ARG cc_start: -0.0555 (OUTLIER) cc_final: -0.1347 (ptm160) REVERT: B 52 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7348 (tp) REVERT: B 136 THR cc_start: -0.0739 (OUTLIER) cc_final: -0.1040 (m) REVERT: B 166 LYS cc_start: -0.0914 (OUTLIER) cc_final: -0.1486 (pttm) REVERT: B 185 PHE cc_start: 0.4300 (OUTLIER) cc_final: 0.3404 (m-10) REVERT: B 224 PHE cc_start: 0.5469 (p90) cc_final: 0.5142 (p90) REVERT: B 238 MET cc_start: 0.0199 (mmm) cc_final: -0.0118 (mmm) REVERT: B 558 THR cc_start: -0.0442 (OUTLIER) cc_final: -0.0706 (m) REVERT: B 990 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6848 (mt) REVERT: B 1079 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7946 (m-40) REVERT: B 1185 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6479 (mmm) REVERT: C 25 ILE cc_start: 0.3095 (OUTLIER) cc_final: 0.2466 (tp) REVERT: C 52 LEU cc_start: 0.7759 (mp) cc_final: 0.7487 (mt) REVERT: C 53 ASN cc_start: 0.8035 (p0) cc_final: 0.7649 (p0) REVERT: C 74 PHE cc_start: 0.3108 (OUTLIER) cc_final: 0.2472 (p90) REVERT: C 94 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.4584 (t80) REVERT: C 97 ASP cc_start: 0.6702 (t0) cc_final: 0.6233 (m-30) REVERT: C 149 THR cc_start: 0.3168 (OUTLIER) cc_final: 0.2819 (p) REVERT: C 185 PHE cc_start: 0.2783 (OUTLIER) cc_final: 0.2304 (t80) REVERT: C 187 LYS cc_start: 0.4584 (OUTLIER) cc_final: 0.3151 (mmtm) REVERT: C 213 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6425 (t80) REVERT: C 228 LEU cc_start: 0.3512 (OUTLIER) cc_final: 0.3101 (mm) REVERT: C 415 LYS cc_start: 0.7431 (tptt) cc_final: 0.7110 (tptp) REVERT: C 673 TYR cc_start: 0.6360 (OUTLIER) cc_final: 0.5979 (t80) REVERT: C 893 SER cc_start: 0.7357 (p) cc_final: 0.6963 (t) REVERT: C 920 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: A 147 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6807 (pp20) REVERT: A 198 LEU cc_start: 0.7298 (mp) cc_final: 0.7064 (mp) REVERT: A 310 THR cc_start: 0.3128 (OUTLIER) cc_final: 0.2451 (t) REVERT: A 573 LEU cc_start: 0.2921 (OUTLIER) cc_final: 0.1803 (pt) REVERT: A 608 LEU cc_start: 0.5025 (OUTLIER) cc_final: 0.4686 (mm) REVERT: A 646 ASN cc_start: 0.7757 (m-40) cc_final: 0.7436 (m-40) REVERT: A 706 PHE cc_start: 0.3212 (OUTLIER) cc_final: 0.2660 (t80) REVERT: A 748 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7893 (pp) REVERT: A 789 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.6103 (mp10) REVERT: A 972 SER cc_start: 0.7268 (OUTLIER) cc_final: 0.6958 (t) REVERT: A 1091 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 1108 GLU cc_start: 0.8506 (tt0) cc_final: 0.8136 (mm-30) outliers start: 201 outliers final: 138 residues processed: 312 average time/residue: 0.7796 time to fit residues: 324.5589 Evaluate side-chains 294 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 127 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 830 SER 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 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 667 TYR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1096 ILE 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 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain A residue 35 ILE 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 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 351 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 535 GLN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.207058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.146126 restraints weight = 48662.921| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.23 r_work: 0.3588 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30389 Z= 0.152 Angle : 0.613 10.172 41578 Z= 0.310 Chirality : 0.046 0.274 4908 Planarity : 0.005 0.075 5172 Dihedral : 9.771 103.341 5987 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 6.72 % Allowed : 19.65 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.56 (0.14), residues: 3618 helix: 1.02 (0.20), residues: 770 sheet: -0.46 (0.18), residues: 829 loop : -2.23 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 174 HIS 0.007 0.001 HIS C1129 PHE 0.016 0.001 PHE A 968 TYR 0.018 0.001 TYR B 427 ARG 0.003 0.000 ARG C 932 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 66) link_NAG-ASN : angle 2.20519 ( 198) link_ALPHA1-4 : bond 0.01484 ( 3) link_ALPHA1-4 : angle 3.39033 ( 9) link_ALPHA1-6 : bond 0.00683 ( 3) link_ALPHA1-6 : angle 1.34009 ( 9) link_BETA1-4 : bond 0.00421 ( 15) link_BETA1-4 : angle 1.52753 ( 45) link_ALPHA1-3 : bond 0.00411 ( 6) link_ALPHA1-3 : angle 1.99514 ( 18) hydrogen bonds : bond 0.04377 ( 1006) hydrogen bonds : angle 5.23386 ( 2838) SS BOND : bond 0.00297 ( 71) SS BOND : angle 0.82408 ( 142) covalent geometry : bond 0.00354 (30225) covalent geometry : angle 0.58881 (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 350 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 132 time to evaluate : 2.879 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: B 29 ASN cc_start: -0.1253 (OUTLIER) cc_final: -0.2964 (p0) REVERT: B 34 ARG cc_start: -0.0376 (OUTLIER) cc_final: -0.1187 (ptm160) REVERT: B 52 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7337 (tp) REVERT: B 136 THR cc_start: -0.0773 (OUTLIER) cc_final: -0.1079 (m) REVERT: B 166 LYS cc_start: -0.0903 (OUTLIER) cc_final: -0.1483 (pttm) REVERT: B 185 PHE cc_start: 0.4203 (OUTLIER) cc_final: 0.3308 (m-10) REVERT: B 238 MET cc_start: -0.0277 (mmm) cc_final: -0.0565 (mmm) REVERT: B 558 THR cc_start: -0.0290 (OUTLIER) cc_final: -0.0509 (m) REVERT: B 920 GLU cc_start: 0.8411 (pt0) cc_final: 0.8197 (pt0) REVERT: B 990 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6819 (mt) REVERT: B 1015 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8422 (tp) REVERT: B 1069 GLU cc_start: 0.8190 (tt0) cc_final: 0.7694 (tm-30) REVERT: B 1079 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7991 (m-40) REVERT: B 1185 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6506 (mmm) REVERT: C 25 ILE cc_start: 0.3370 (OUTLIER) cc_final: 0.2768 (tp) REVERT: C 52 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7472 (mt) REVERT: C 53 ASN cc_start: 0.8017 (p0) cc_final: 0.7649 (p0) REVERT: C 54 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7943 (mtt-85) REVERT: C 74 PHE cc_start: 0.3238 (OUTLIER) cc_final: 0.2584 (p90) REVERT: C 94 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.4670 (t80) REVERT: C 97 ASP cc_start: 0.6731 (t0) cc_final: 0.6215 (m-30) REVERT: C 149 THR cc_start: 0.3154 (OUTLIER) cc_final: 0.2885 (p) REVERT: C 185 PHE cc_start: 0.2578 (OUTLIER) cc_final: 0.2152 (t80) REVERT: C 187 LYS cc_start: 0.4562 (OUTLIER) cc_final: 0.3142 (mmtm) REVERT: C 213 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6425 (t80) REVERT: C 228 LEU cc_start: 0.3386 (OUTLIER) cc_final: 0.2978 (mm) REVERT: C 415 LYS cc_start: 0.7421 (tptt) cc_final: 0.7084 (tptp) REVERT: C 420 SER cc_start: 0.7487 (m) cc_final: 0.7192 (p) REVERT: C 673 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.6023 (t80) REVERT: C 893 SER cc_start: 0.7381 (p) cc_final: 0.7013 (t) REVERT: C 920 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: A 147 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6794 (pp20) REVERT: A 198 LEU cc_start: 0.7309 (mp) cc_final: 0.7078 (mp) REVERT: A 310 THR cc_start: 0.3156 (OUTLIER) cc_final: 0.2500 (t) REVERT: A 573 LEU cc_start: 0.2959 (OUTLIER) cc_final: 0.1804 (pt) REVERT: A 608 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4797 (mm) REVERT: A 646 ASN cc_start: 0.7774 (m-40) cc_final: 0.7441 (m-40) REVERT: A 706 PHE cc_start: 0.3220 (OUTLIER) cc_final: 0.2653 (t80) REVERT: A 748 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7883 (pp) REVERT: A 789 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6166 (mp10) REVERT: A 972 SER cc_start: 0.7265 (OUTLIER) cc_final: 0.6918 (t) REVERT: A 1091 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: A 1108 GLU cc_start: 0.8591 (tt0) cc_final: 0.8181 (mm-30) REVERT: A 1219 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5667 (p90) outliers start: 218 outliers final: 153 residues processed: 329 average time/residue: 0.7959 time to fit residues: 349.1679 Evaluate side-chains 314 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 129 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 830 SER 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 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1090 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1221 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 535 GLN Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 667 TYR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1096 ILE 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 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 35 ILE 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 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A 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: 2.9990 chunk 51 optimal weight: 0.0030 chunk 205 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 259 optimal weight: 0.5980 chunk 250 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN C 108 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.207589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.147323 restraints weight = 49105.782| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.96 r_work: 0.3628 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30389 Z= 0.130 Angle : 0.601 9.884 41578 Z= 0.304 Chirality : 0.045 0.225 4908 Planarity : 0.005 0.072 5172 Dihedral : 9.507 103.139 5986 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.35 % Allowed : 20.09 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.46 (0.14), residues: 3618 helix: 1.16 (0.20), residues: 769 sheet: -0.41 (0.18), residues: 809 loop : -2.16 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 174 HIS 0.006 0.001 HIS C1129 PHE 0.015 0.001 PHE A 968 TYR 0.016 0.001 TYR B 427 ARG 0.003 0.000 ARG C 932 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 66) link_NAG-ASN : angle 2.20391 ( 198) link_ALPHA1-4 : bond 0.01499 ( 3) link_ALPHA1-4 : angle 3.40228 ( 9) link_ALPHA1-6 : bond 0.00680 ( 3) link_ALPHA1-6 : angle 1.35089 ( 9) link_BETA1-4 : bond 0.00417 ( 15) link_BETA1-4 : angle 1.49569 ( 45) link_ALPHA1-3 : bond 0.00422 ( 6) link_ALPHA1-3 : angle 1.99891 ( 18) hydrogen bonds : bond 0.04156 ( 1006) hydrogen bonds : angle 5.13871 ( 2838) SS BOND : bond 0.00266 ( 71) SS BOND : angle 0.74245 ( 142) covalent geometry : bond 0.00297 (30225) covalent geometry : angle 0.57699 (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 343 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 137 time to evaluate : 3.213 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: B 29 ASN cc_start: -0.1022 (OUTLIER) cc_final: -0.2842 (p0) REVERT: B 34 ARG cc_start: -0.0270 (OUTLIER) cc_final: -0.1066 (ptm160) REVERT: B 52 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7360 (tp) REVERT: B 136 THR cc_start: -0.0722 (OUTLIER) cc_final: -0.1039 (m) REVERT: B 166 LYS cc_start: -0.0848 (OUTLIER) cc_final: -0.1426 (pttm) REVERT: B 185 PHE cc_start: 0.4169 (OUTLIER) cc_final: 0.3253 (m-10) REVERT: B 238 MET cc_start: -0.0322 (mmm) cc_final: -0.0618 (mmm) REVERT: B 558 THR cc_start: -0.0335 (OUTLIER) cc_final: -0.0536 (m) REVERT: B 990 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6899 (mt) REVERT: B 1069 GLU cc_start: 0.8337 (tt0) cc_final: 0.7745 (tm-30) REVERT: B 1079 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8184 (m-40) REVERT: B 1185 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6574 (mmm) REVERT: C 25 ILE cc_start: 0.3355 (OUTLIER) cc_final: 0.2762 (tp) REVERT: C 52 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7409 (mt) REVERT: C 53 ASN cc_start: 0.8171 (p0) cc_final: 0.7808 (p0) REVERT: C 54 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.8032 (mtt-85) REVERT: C 74 PHE cc_start: 0.3202 (OUTLIER) cc_final: 0.2539 (p90) REVERT: C 94 PHE cc_start: 0.5643 (OUTLIER) cc_final: 0.4712 (t80) REVERT: C 97 ASP cc_start: 0.6744 (t0) cc_final: 0.6217 (m-30) REVERT: C 149 THR cc_start: 0.3347 (OUTLIER) cc_final: 0.2993 (p) REVERT: C 185 PHE cc_start: 0.2738 (OUTLIER) cc_final: 0.2293 (t80) REVERT: C 187 LYS cc_start: 0.4715 (OUTLIER) cc_final: 0.3205 (mmtm) REVERT: C 213 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6465 (t80) REVERT: C 218 MET cc_start: 0.7269 (ttp) cc_final: 0.7069 (ppp) REVERT: C 228 LEU cc_start: 0.3459 (OUTLIER) cc_final: 0.3051 (mm) REVERT: C 415 LYS cc_start: 0.7546 (tptt) cc_final: 0.7227 (tptp) REVERT: C 673 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.6009 (t80) REVERT: C 920 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8566 (mp0) REVERT: A 147 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6982 (pp20) REVERT: A 187 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7665 (tmtt) REVERT: A 198 LEU cc_start: 0.7352 (mp) cc_final: 0.7126 (mp) REVERT: A 310 THR cc_start: 0.2897 (OUTLIER) cc_final: 0.2270 (t) REVERT: A 457 SER cc_start: -0.0270 (OUTLIER) cc_final: -0.0514 (t) REVERT: A 573 LEU cc_start: 0.2808 (OUTLIER) cc_final: 0.1612 (pt) REVERT: A 608 LEU cc_start: 0.5059 (OUTLIER) cc_final: 0.4796 (mm) REVERT: A 646 ASN cc_start: 0.7867 (m-40) cc_final: 0.7588 (m-40) REVERT: A 706 PHE cc_start: 0.3368 (OUTLIER) cc_final: 0.2823 (t80) REVERT: A 737 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8906 (mtt180) REVERT: A 789 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.6187 (mp10) REVERT: A 972 SER cc_start: 0.7399 (OUTLIER) cc_final: 0.7119 (t) REVERT: A 1108 GLU cc_start: 0.8790 (tt0) cc_final: 0.8313 (mm-30) REVERT: A 1205 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7173 (ptp) REVERT: A 1219 TYR cc_start: 0.6065 (OUTLIER) cc_final: 0.5702 (p90) outliers start: 206 outliers final: 144 residues processed: 318 average time/residue: 0.8103 time to fit residues: 338.9522 Evaluate side-chains 306 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 129 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 830 SER 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 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1221 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 667 TYR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 967 MET Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1096 ILE 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 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain A residue 35 ILE 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 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A 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: 0.0000 chunk 355 optimal weight: 0.7980 chunk 307 optimal weight: 0.2980 chunk 183 optimal weight: 0.0370 chunk 290 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN C 535 GLN C 799 HIS C1009 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.209442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147751 restraints weight = 48911.688| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.80 r_work: 0.3687 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30389 Z= 0.097 Angle : 0.567 12.333 41578 Z= 0.285 Chirality : 0.044 0.264 4908 Planarity : 0.004 0.072 5172 Dihedral : 8.804 102.400 5977 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.65 % Allowed : 21.75 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.16 (0.14), residues: 3618 helix: 1.56 (0.20), residues: 773 sheet: -0.28 (0.18), residues: 791 loop : -2.01 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 971 HIS 0.003 0.001 HIS A 799 PHE 0.016 0.001 PHE B 202 TYR 0.015 0.001 TYR B1148 ARG 0.007 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 66) link_NAG-ASN : angle 2.15627 ( 198) link_ALPHA1-4 : bond 0.01554 ( 3) link_ALPHA1-4 : angle 3.30307 ( 9) link_ALPHA1-6 : bond 0.00741 ( 3) link_ALPHA1-6 : angle 1.40366 ( 9) link_BETA1-4 : bond 0.00424 ( 15) link_BETA1-4 : angle 1.40395 ( 45) link_ALPHA1-3 : bond 0.00434 ( 6) link_ALPHA1-3 : angle 1.97654 ( 18) hydrogen bonds : bond 0.03488 ( 1006) hydrogen bonds : angle 4.90215 ( 2838) SS BOND : bond 0.00213 ( 71) SS BOND : angle 0.64419 ( 142) covalent geometry : bond 0.00204 (30225) covalent geometry : angle 0.54203 (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 289 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 138 time to evaluate : 3.322 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: B 29 ASN cc_start: -0.1025 (OUTLIER) cc_final: -0.2800 (p0) REVERT: B 34 ARG cc_start: -0.0392 (OUTLIER) cc_final: -0.1248 (ptm160) REVERT: B 52 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7347 (tp) REVERT: B 136 THR cc_start: -0.0731 (OUTLIER) cc_final: -0.1037 (m) REVERT: B 166 LYS cc_start: -0.0798 (OUTLIER) cc_final: -0.1358 (pttm) REVERT: B 185 PHE cc_start: 0.4293 (OUTLIER) cc_final: 0.3341 (m-10) REVERT: B 238 MET cc_start: 0.0046 (mmm) cc_final: -0.0228 (mmm) REVERT: B 1069 GLU cc_start: 0.8278 (tt0) cc_final: 0.7717 (tm-30) REVERT: B 1079 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8132 (m-40) REVERT: B 1185 MET cc_start: 0.6785 (mtp) cc_final: 0.6436 (mmm) REVERT: C 25 ILE cc_start: 0.3322 (OUTLIER) cc_final: 0.2745 (tp) REVERT: C 52 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7228 (mt) REVERT: C 53 ASN cc_start: 0.7996 (p0) cc_final: 0.7721 (p0) REVERT: C 54 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7925 (mtt-85) REVERT: C 74 PHE cc_start: 0.3434 (OUTLIER) cc_final: 0.2830 (p90) REVERT: C 94 PHE cc_start: 0.5637 (OUTLIER) cc_final: 0.5124 (t80) REVERT: C 97 ASP cc_start: 0.6865 (t0) cc_final: 0.6299 (m-30) REVERT: C 149 THR cc_start: 0.3181 (OUTLIER) cc_final: 0.2872 (p) REVERT: C 185 PHE cc_start: 0.2750 (OUTLIER) cc_final: 0.2214 (t80) REVERT: C 187 LYS cc_start: 0.4522 (OUTLIER) cc_final: 0.3138 (mmtm) REVERT: C 213 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.6458 (t80) REVERT: C 228 LEU cc_start: 0.3527 (OUTLIER) cc_final: 0.3119 (mm) REVERT: C 356 LEU cc_start: 0.7977 (mt) cc_final: 0.7760 (mt) REVERT: C 415 LYS cc_start: 0.7505 (tptt) cc_final: 0.7185 (tptp) REVERT: C 503 HIS cc_start: 0.1960 (t-90) cc_final: 0.0739 (p-80) REVERT: C 920 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: A 36 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7453 (m) REVERT: A 147 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6914 (pp20) REVERT: A 187 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7694 (tmtt) REVERT: A 310 THR cc_start: 0.2909 (OUTLIER) cc_final: 0.2294 (t) REVERT: A 457 SER cc_start: -0.0274 (OUTLIER) cc_final: -0.0542 (t) REVERT: A 573 LEU cc_start: 0.2522 (OUTLIER) cc_final: 0.1462 (pt) REVERT: A 608 LEU cc_start: 0.5136 (OUTLIER) cc_final: 0.4872 (mm) REVERT: A 737 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8899 (mtt180) REVERT: A 789 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.5785 (mp10) REVERT: A 862 MET cc_start: 0.7500 (mmm) cc_final: 0.7197 (tpt) REVERT: A 1091 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: A 1108 GLU cc_start: 0.8714 (tt0) cc_final: 0.8193 (mm-30) outliers start: 151 outliers final: 89 residues processed: 275 average time/residue: 0.8536 time to fit residues: 308.3967 Evaluate side-chains 246 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 130 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 811 THR 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 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 967 MET Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 237 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 354 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 269 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.207109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.146886 restraints weight = 48767.916| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.04 r_work: 0.3607 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 30389 Z= 0.198 Angle : 0.662 15.675 41578 Z= 0.334 Chirality : 0.047 0.255 4908 Planarity : 0.005 0.078 5172 Dihedral : 8.829 103.831 5948 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.25 % Allowed : 22.24 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.39 (0.14), residues: 3618 helix: 1.09 (0.19), residues: 774 sheet: -0.41 (0.18), residues: 814 loop : -2.06 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 971 HIS 0.010 0.001 HIS C1129 PHE 0.030 0.002 PHE B 224 TYR 0.021 0.002 TYR A 318 ARG 0.010 0.001 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 66) link_NAG-ASN : angle 2.26597 ( 198) link_ALPHA1-4 : bond 0.01462 ( 3) link_ALPHA1-4 : angle 3.53828 ( 9) link_ALPHA1-6 : bond 0.00741 ( 3) link_ALPHA1-6 : angle 1.29436 ( 9) link_BETA1-4 : bond 0.00433 ( 15) link_BETA1-4 : angle 1.54481 ( 45) link_ALPHA1-3 : bond 0.00386 ( 6) link_ALPHA1-3 : angle 2.05575 ( 18) hydrogen bonds : bond 0.04687 ( 1006) hydrogen bonds : angle 5.17388 ( 2838) SS BOND : bond 0.00331 ( 71) SS BOND : angle 1.68712 ( 142) covalent geometry : bond 0.00468 (30225) covalent geometry : angle 0.63291 (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 267 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 129 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1193 (OUTLIER) cc_final: -0.2874 (p0) REVERT: B 34 ARG cc_start: -0.0226 (OUTLIER) cc_final: -0.1094 (ptm160) REVERT: B 52 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7431 (tp) REVERT: B 136 THR cc_start: -0.0720 (OUTLIER) cc_final: -0.1042 (m) REVERT: B 166 LYS cc_start: -0.0542 (OUTLIER) cc_final: -0.1168 (pttm) REVERT: B 185 PHE cc_start: 0.4182 (OUTLIER) cc_final: 0.3129 (m-10) REVERT: B 238 MET cc_start: 0.0259 (mmm) cc_final: 0.0031 (mmm) REVERT: B 1069 GLU cc_start: 0.8315 (tt0) cc_final: 0.7747 (tm-30) REVERT: B 1185 MET cc_start: 0.6851 (mtp) cc_final: 0.6524 (mmm) REVERT: C 25 ILE cc_start: 0.3509 (OUTLIER) cc_final: 0.3006 (tp) REVERT: C 52 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7151 (mt) REVERT: C 53 ASN cc_start: 0.8175 (p0) cc_final: 0.7726 (p0) REVERT: C 54 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8099 (mtt-85) REVERT: C 74 PHE cc_start: 0.3264 (OUTLIER) cc_final: 0.2645 (p90) REVERT: C 94 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.4782 (t80) REVERT: C 97 ASP cc_start: 0.6928 (t0) cc_final: 0.6427 (m-30) REVERT: C 149 THR cc_start: 0.3064 (OUTLIER) cc_final: 0.2794 (p) REVERT: C 185 PHE cc_start: 0.2824 (OUTLIER) cc_final: 0.2257 (t80) REVERT: C 187 LYS cc_start: 0.4703 (OUTLIER) cc_final: 0.3251 (mmtm) REVERT: C 213 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6490 (t80) REVERT: C 228 LEU cc_start: 0.3487 (OUTLIER) cc_final: 0.3065 (mm) REVERT: C 415 LYS cc_start: 0.7544 (tptt) cc_final: 0.7223 (tptp) REVERT: C 920 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: A 36 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7596 (m) REVERT: A 147 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6949 (pp20) REVERT: A 187 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7737 (tmtt) REVERT: A 198 LEU cc_start: 0.7361 (mp) cc_final: 0.7132 (mp) REVERT: A 310 THR cc_start: 0.2872 (OUTLIER) cc_final: 0.2254 (t) REVERT: A 457 SER cc_start: -0.0255 (OUTLIER) cc_final: -0.0484 (t) REVERT: A 573 LEU cc_start: 0.2649 (OUTLIER) cc_final: 0.1524 (pt) REVERT: A 608 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4941 (mm) REVERT: A 646 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7291 (t0) REVERT: A 706 PHE cc_start: 0.3593 (OUTLIER) cc_final: 0.3003 (t80) REVERT: A 737 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8941 (mtt180) REVERT: A 789 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.6171 (mp10) REVERT: A 862 MET cc_start: 0.7939 (mmm) cc_final: 0.7734 (tpt) REVERT: A 1095 ASP cc_start: 0.8413 (t0) cc_final: 0.8083 (m-30) REVERT: A 1108 GLU cc_start: 0.8807 (tt0) cc_final: 0.8305 (mm-30) REVERT: A 1219 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.5682 (p90) outliers start: 138 outliers final: 98 residues processed: 251 average time/residue: 0.8358 time to fit residues: 275.0407 Evaluate side-chains 252 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 126 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 830 SER 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 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 667 TYR Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 967 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1096 ILE 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 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A 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: 0.9980 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 316 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 308 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.208200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146664 restraints weight = 48731.392| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.87 r_work: 0.3653 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30389 Z= 0.133 Angle : 0.604 11.574 41578 Z= 0.306 Chirality : 0.045 0.237 4908 Planarity : 0.005 0.074 5172 Dihedral : 8.605 103.113 5941 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.28 % Allowed : 22.24 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.29 (0.14), residues: 3618 helix: 1.22 (0.19), residues: 780 sheet: -0.37 (0.18), residues: 805 loop : -2.00 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 971 HIS 0.006 0.001 HIS C1129 PHE 0.032 0.001 PHE B 224 TYR 0.016 0.001 TYR A 318 ARG 0.010 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 66) link_NAG-ASN : angle 2.12836 ( 198) link_ALPHA1-4 : bond 0.01512 ( 3) link_ALPHA1-4 : angle 3.45472 ( 9) link_ALPHA1-6 : bond 0.00674 ( 3) link_ALPHA1-6 : angle 1.33160 ( 9) link_BETA1-4 : bond 0.00421 ( 15) link_BETA1-4 : angle 1.47367 ( 45) link_ALPHA1-3 : bond 0.00412 ( 6) link_ALPHA1-3 : angle 2.02952 ( 18) hydrogen bonds : bond 0.04125 ( 1006) hydrogen bonds : angle 5.06879 ( 2838) SS BOND : bond 0.00286 ( 71) SS BOND : angle 1.34723 ( 142) covalent geometry : bond 0.00306 (30225) covalent geometry : angle 0.57778 (41157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25801.14 seconds wall clock time: 444 minutes 14.29 seconds (26654.29 seconds total)