Starting phenix.real_space_refine on Mon Aug 25 17:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1c_38831/08_2025/8y1c_38831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1c_38831/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y1c_38831/08_2025/8y1c_38831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1c_38831/08_2025/8y1c_38831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y1c_38831/08_2025/8y1c_38831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1c_38831/08_2025/8y1c_38831.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.52, per 1000 atoms: 0.22 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: 2.05 Conformation dependent library (CDL) restraints added in 903.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.08 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: 6.60 Time building geometry restraints manager: 2.65 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: 0.04 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: 4.030 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.780 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.330 ------------------------------------------------------------------------------- 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 : 4.52 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG C 320 TYR 0.025 0.002 TYR B1176 PHE 0.024 0.003 PHE B 794 TRP 0.024 0.002 TRP B 971 HIS 0.010 0.002 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00690 (30225) covalent geometry : angle 0.88256 (41157) SS BOND : bond 0.00315 ( 71) SS BOND : angle 1.02733 ( 142) hydrogen bonds : bond 0.12566 ( 1006) hydrogen bonds : angle 6.93811 ( 2838) link_ALPHA1-3 : bond 0.00418 ( 6) link_ALPHA1-3 : angle 1.92021 ( 18) 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_NAG-ASN : bond 0.00543 ( 66) link_NAG-ASN : angle 3.61749 ( 198) *********************** 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 : 0.852 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: 0.0411 (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: 0.8138 (mm) REVERT: B 102 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6265 (pt) REVERT: B 122 SER cc_start: 0.6682 (OUTLIER) cc_final: 0.5864 (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: 0.3041 (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: 0.7338 (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: 0.8166 (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: 0.3912 time to fit residues: 279.9602 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 : 0.936 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 9.9990 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 26 ASN B 73 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN 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 B1135 GLN C 26 ASN C 108 ASN C 152 GLN C 204 GLN C 248 ASN C 410 GLN C 413 ASN C 605 ASN C 838 ASN C 876 HIS C1091 GLN C1122 ASN 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: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.208051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.148076 restraints weight = 49314.372| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.06 r_work: 0.3629 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30389 Z= 0.137 Angle : 0.649 10.243 41578 Z= 0.332 Chirality : 0.046 0.286 4908 Planarity : 0.006 0.092 5172 Dihedral : 12.314 112.431 6137 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 6.87 % Allowed : 16.14 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.13), residues: 3618 helix: -0.05 (0.18), residues: 765 sheet: -0.79 (0.18), residues: 801 loop : -2.55 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.026 0.001 TYR C 462 PHE 0.020 0.001 PHE B 224 TRP 0.015 0.001 TRP C 644 HIS 0.005 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00296 (30225) covalent geometry : angle 0.61992 (41157) SS BOND : bond 0.00290 ( 71) SS BOND : angle 1.18409 ( 142) hydrogen bonds : bond 0.04588 ( 1006) hydrogen bonds : angle 5.69583 ( 2838) link_ALPHA1-3 : bond 0.00616 ( 6) link_ALPHA1-3 : angle 1.92035 ( 18) link_ALPHA1-4 : bond 0.01633 ( 3) link_ALPHA1-4 : angle 3.41692 ( 9) link_ALPHA1-6 : bond 0.00893 ( 3) link_ALPHA1-6 : angle 1.40662 ( 9) link_BETA1-4 : bond 0.00493 ( 15) link_BETA1-4 : angle 1.60477 ( 45) link_NAG-ASN : bond 0.00406 ( 66) link_NAG-ASN : angle 2.47345 ( 198) *********************** 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 388 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 165 time to evaluate : 0.767 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: -0.1207 (OUTLIER) cc_final: -0.2529 (p0) REVERT: B 34 ARG cc_start: -0.0988 (OUTLIER) cc_final: -0.1239 (ptm160) REVERT: B 46 LEU cc_start: 0.7789 (mm) cc_final: 0.7311 (mp) REVERT: B 122 SER cc_start: 0.6069 (OUTLIER) cc_final: 0.5386 (t) REVERT: B 136 THR cc_start: -0.0987 (OUTLIER) cc_final: -0.1279 (m) REVERT: B 166 LYS cc_start: -0.0813 (OUTLIER) cc_final: -0.1739 (mttt) REVERT: B 264 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6525 (ptm160) REVERT: B 399 ASP cc_start: 0.2554 (OUTLIER) cc_final: 0.2121 (p0) REVERT: B 558 THR cc_start: 0.0117 (OUTLIER) cc_final: -0.0473 (t) REVERT: B 659 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8223 (tttt) REVERT: B 990 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6893 (mt) REVERT: B 1069 GLU cc_start: 0.8435 (tt0) cc_final: 0.7791 (tm-30) REVERT: B 1079 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8247 (m-40) REVERT: B 1185 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6591 (mmm) REVERT: C 53 ASN cc_start: 0.8142 (p0) cc_final: 0.7807 (p0) REVERT: C 69 LYS cc_start: 0.8274 (tttm) cc_final: 0.8028 (tppt) REVERT: C 94 PHE cc_start: 0.5454 (m-80) cc_final: 0.4534 (t80) REVERT: C 97 ASP cc_start: 0.6693 (t0) cc_final: 0.6244 (m-30) REVERT: C 149 THR cc_start: 0.3649 (OUTLIER) cc_final: 0.3090 (p) REVERT: C 187 LYS cc_start: 0.4842 (OUTLIER) cc_final: 0.3762 (mmtt) REVERT: C 213 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6510 (t80) REVERT: C 415 LYS cc_start: 0.7555 (tptt) cc_final: 0.7181 (tptp) REVERT: C 597 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7018 (mt) REVERT: C 659 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7391 (ttpt) REVERT: C 673 TYR cc_start: 0.6397 (OUTLIER) cc_final: 0.5836 (t80) REVERT: C 845 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: C 1026 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8905 (tp) REVERT: A 111 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5628 (mt) REVERT: A 143 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7640 (m-40) REVERT: A 155 MET cc_start: 0.7023 (mmm) cc_final: 0.6365 (mmt) REVERT: A 187 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.6970 (tmtp) REVERT: A 198 LEU cc_start: 0.7465 (mp) cc_final: 0.7210 (mp) REVERT: A 221 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7179 (m) REVERT: A 310 THR cc_start: 0.2962 (OUTLIER) cc_final: 0.2237 (t) REVERT: A 312 LYS cc_start: 0.4706 (OUTLIER) cc_final: 0.4497 (mmmt) REVERT: A 511 TYR cc_start: 0.0998 (OUTLIER) cc_final: 0.0798 (m-80) REVERT: A 573 LEU cc_start: 0.2460 (OUTLIER) cc_final: 0.1278 (pt) REVERT: A 608 LEU cc_start: 0.4936 (OUTLIER) cc_final: 0.4654 (mm) REVERT: A 646 ASN cc_start: 0.7823 (m-40) cc_final: 0.7572 (m-40) REVERT: A 706 PHE cc_start: 0.3495 (OUTLIER) cc_final: 0.2992 (t80) REVERT: A 789 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.6833 (mp10) REVERT: A 1013 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7603 (tt) REVERT: A 1091 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: A 1219 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.5749 (p90) outliers start: 223 outliers final: 114 residues processed: 362 average time/residue: 0.3675 time to fit residues: 172.1522 Evaluate side-chains 276 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 128 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 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 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 399 ASP 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 612 THR Chi-restraints excluded: chain B residue 659 LYS 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 773 SER Chi-restraints excluded: chain B residue 807 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 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 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 149 THR 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 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 732 SER Chi-restraints excluded: chain C residue 743 CYS 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 845 GLU 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 1026 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 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 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 253 THR Chi-restraints excluded: chain A residue 258 VAL 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 447 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 511 TYR 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 661 PHE Chi-restraints excluded: chain A residue 705 SER 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 879 VAL Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1024 SER 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 1132 SER Chi-restraints excluded: chain A residue 1152 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 78 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 341 optimal weight: 0.8980 chunk 301 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 141 optimal weight: 0.0010 chunk 152 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- 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** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 GLN 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 C1016 GLN A 201 HIS A 872 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.206957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.146739 restraints weight = 49129.381| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.07 r_work: 0.3603 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30389 Z= 0.166 Angle : 0.644 10.191 41578 Z= 0.328 Chirality : 0.046 0.243 4908 Planarity : 0.005 0.090 5172 Dihedral : 11.342 107.750 6036 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 7.36 % Allowed : 16.85 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.13), residues: 3618 helix: 0.56 (0.19), residues: 756 sheet: -0.67 (0.18), residues: 813 loop : -2.40 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.018 0.002 TYR A 716 PHE 0.017 0.002 PHE B 202 TRP 0.012 0.001 TRP B 971 HIS 0.008 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00386 (30225) covalent geometry : angle 0.61624 (41157) SS BOND : bond 0.00397 ( 71) SS BOND : angle 1.07202 ( 142) hydrogen bonds : bond 0.04752 ( 1006) hydrogen bonds : angle 5.50454 ( 2838) link_ALPHA1-3 : bond 0.00499 ( 6) link_ALPHA1-3 : angle 1.94181 ( 18) link_ALPHA1-4 : bond 0.01417 ( 3) link_ALPHA1-4 : angle 3.36894 ( 9) link_ALPHA1-6 : bond 0.00756 ( 3) link_ALPHA1-6 : angle 1.46617 ( 9) link_BETA1-4 : bond 0.00401 ( 15) link_BETA1-4 : angle 1.62535 ( 45) link_NAG-ASN : bond 0.00396 ( 66) link_NAG-ASN : angle 2.38559 ( 198) *********************** 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 379 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 140 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1307 (OUTLIER) cc_final: -0.2484 (p0) REVERT: B 30 LYS cc_start: 0.4402 (OUTLIER) cc_final: 0.3554 (tttm) REVERT: B 34 ARG cc_start: -0.1198 (OUTLIER) cc_final: -0.1957 (ptm160) REVERT: B 52 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7344 (tp) REVERT: B 136 THR cc_start: -0.1021 (OUTLIER) cc_final: -0.1313 (m) REVERT: B 166 LYS cc_start: -0.0987 (OUTLIER) cc_final: -0.1884 (mttt) REVERT: B 238 MET cc_start: 0.0585 (mmm) cc_final: 0.0168 (mmm) REVERT: B 264 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6435 (ptm160) REVERT: B 402 GLN cc_start: 0.3796 (OUTLIER) cc_final: 0.3470 (tm-30) REVERT: B 1069 GLU cc_start: 0.8180 (tt0) cc_final: 0.7695 (tm-30) REVERT: B 1185 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6588 (mmp) REVERT: C 25 ILE cc_start: 0.3221 (OUTLIER) cc_final: 0.2623 (tp) REVERT: C 53 ASN cc_start: 0.7949 (p0) cc_final: 0.7507 (p0) REVERT: C 69 LYS cc_start: 0.8269 (tttm) cc_final: 0.7989 (tppt) REVERT: C 74 PHE cc_start: 0.2853 (OUTLIER) cc_final: 0.2162 (p90) REVERT: C 94 PHE cc_start: 0.5428 (OUTLIER) cc_final: 0.4543 (t80) REVERT: C 97 ASP cc_start: 0.6587 (t0) cc_final: 0.6144 (m-30) REVERT: C 149 THR cc_start: 0.3574 (OUTLIER) cc_final: 0.2823 (p) REVERT: C 185 PHE cc_start: 0.2914 (OUTLIER) cc_final: 0.2550 (t80) REVERT: C 187 LYS cc_start: 0.4799 (OUTLIER) cc_final: 0.3384 (mmtm) REVERT: C 213 TYR cc_start: 0.6834 (OUTLIER) cc_final: 0.6446 (t80) REVERT: C 228 LEU cc_start: 0.3409 (OUTLIER) cc_final: 0.3042 (mm) REVERT: C 415 LYS cc_start: 0.7445 (tptt) cc_final: 0.7069 (tptp) REVERT: C 597 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.6957 (mt) REVERT: C 659 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7273 (ttpt) REVERT: C 673 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5925 (t80) REVERT: C 893 SER cc_start: 0.7097 (p) cc_final: 0.6783 (t) REVERT: C 914 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8363 (m) REVERT: A 155 MET cc_start: 0.6920 (mmm) cc_final: 0.6296 (mmt) REVERT: A 198 LEU cc_start: 0.7333 (mp) cc_final: 0.7117 (mp) REVERT: A 310 THR cc_start: 0.2967 (OUTLIER) cc_final: 0.2263 (t) REVERT: A 312 LYS cc_start: 0.4758 (OUTLIER) cc_final: 0.4469 (mmmt) REVERT: A 608 LEU cc_start: 0.4657 (OUTLIER) cc_final: 0.4250 (mm) REVERT: A 630 GLN cc_start: 0.6965 (mt0) cc_final: 0.6293 (pp30) REVERT: A 646 ASN cc_start: 0.7786 (m-40) cc_final: 0.7526 (m-40) REVERT: A 706 PHE cc_start: 0.3413 (OUTLIER) cc_final: 0.2868 (t80) REVERT: A 789 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.6759 (mp10) REVERT: A 1013 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7663 (tt) REVERT: A 1091 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: A 1219 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.5717 (p90) outliers start: 239 outliers final: 146 residues processed: 351 average time/residue: 0.3673 time to fit residues: 165.4747 Evaluate side-chains 306 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 131 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 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 378 ILE Chi-restraints excluded: chain B residue 402 GLN 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 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 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 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 967 MET Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1012 LEU 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 1185 MET Chi-restraints excluded: chain B residue 1189 SER 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 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 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 310 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 356 LEU 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 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 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 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 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 914 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 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 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 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 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 366 ASP 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 608 LEU 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 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 953 THR Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1013 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 1091 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1098 LEU 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 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 258 optimal weight: 6.9990 chunk 224 optimal weight: 0.5980 chunk 167 optimal weight: 0.0370 chunk 278 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.5262 ------------------------------------------------------------------------------- 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** B1135 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 535 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.207054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.143297 restraints weight = 48647.149| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.45 r_work: 0.3664 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30389 Z= 0.158 Angle : 0.626 10.099 41578 Z= 0.319 Chirality : 0.046 0.224 4908 Planarity : 0.005 0.082 5172 Dihedral : 10.832 105.477 6017 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.90 % Allowed : 18.18 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.13), residues: 3618 helix: 0.76 (0.20), residues: 754 sheet: -0.61 (0.18), residues: 808 loop : -2.32 (0.12), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1081 TYR 0.017 0.002 TYR C 667 PHE 0.016 0.002 PHE A 968 TRP 0.013 0.001 TRP C 575 HIS 0.007 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00370 (30225) covalent geometry : angle 0.59857 (41157) SS BOND : bond 0.00298 ( 71) SS BOND : angle 1.11310 ( 142) hydrogen bonds : bond 0.04571 ( 1006) hydrogen bonds : angle 5.41319 ( 2838) link_ALPHA1-3 : bond 0.00446 ( 6) link_ALPHA1-3 : angle 1.95964 ( 18) link_ALPHA1-4 : bond 0.01416 ( 3) link_ALPHA1-4 : angle 3.34029 ( 9) link_ALPHA1-6 : bond 0.00714 ( 3) link_ALPHA1-6 : angle 1.42682 ( 9) link_BETA1-4 : bond 0.00398 ( 15) link_BETA1-4 : angle 1.57265 ( 45) link_NAG-ASN : bond 0.00365 ( 66) link_NAG-ASN : angle 2.30291 ( 198) *********************** 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 358 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 134 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1127 (OUTLIER) cc_final: -0.2614 (p0) REVERT: B 34 ARG cc_start: -0.0799 (OUTLIER) cc_final: -0.1183 (ptm160) REVERT: B 52 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7363 (tp) REVERT: B 136 THR cc_start: -0.0647 (OUTLIER) cc_final: -0.0974 (m) REVERT: B 166 LYS cc_start: -0.0985 (OUTLIER) cc_final: -0.1552 (pttm) REVERT: B 185 PHE cc_start: 0.4213 (OUTLIER) cc_final: 0.3198 (m-10) REVERT: B 218 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6612 (mpp) REVERT: B 264 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5488 (ptp90) REVERT: B 402 GLN cc_start: 0.3777 (OUTLIER) cc_final: 0.3438 (tm-30) REVERT: B 558 THR cc_start: -0.0539 (OUTLIER) cc_final: -0.0829 (m) REVERT: B 990 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6852 (mt) REVERT: B 1069 GLU cc_start: 0.8277 (tt0) cc_final: 0.7741 (tm-30) REVERT: B 1185 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6605 (mmm) REVERT: C 53 ASN cc_start: 0.8047 (p0) cc_final: 0.7603 (p0) REVERT: C 74 PHE cc_start: 0.2992 (OUTLIER) cc_final: 0.2297 (p90) REVERT: C 94 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.4575 (t80) REVERT: C 97 ASP cc_start: 0.6587 (t0) cc_final: 0.6111 (m-30) REVERT: C 149 THR cc_start: 0.3047 (OUTLIER) cc_final: 0.2790 (p) REVERT: C 185 PHE cc_start: 0.3076 (OUTLIER) cc_final: 0.2587 (t80) REVERT: C 187 LYS cc_start: 0.4734 (OUTLIER) cc_final: 0.3233 (mmtm) REVERT: C 213 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6434 (t80) REVERT: C 228 LEU cc_start: 0.3500 (OUTLIER) cc_final: 0.3100 (mm) REVERT: C 415 LYS cc_start: 0.7544 (tptt) cc_final: 0.7176 (tptp) REVERT: C 588 ILE cc_start: 0.5944 (OUTLIER) cc_final: 0.5688 (tt) REVERT: C 597 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7005 (mt) REVERT: C 659 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7346 (ttpt) REVERT: C 673 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.5941 (t80) REVERT: C 893 SER cc_start: 0.7276 (p) cc_final: 0.6954 (t) REVERT: A 198 LEU cc_start: 0.7265 (mp) cc_final: 0.7049 (mp) REVERT: A 310 THR cc_start: 0.3087 (OUTLIER) cc_final: 0.2345 (t) REVERT: A 312 LYS cc_start: 0.4685 (OUTLIER) cc_final: 0.4417 (mmmt) REVERT: A 573 LEU cc_start: 0.2741 (OUTLIER) cc_final: 0.1633 (pt) REVERT: A 608 LEU cc_start: 0.5087 (OUTLIER) cc_final: 0.4732 (mm) REVERT: A 646 ASN cc_start: 0.7858 (m-40) cc_final: 0.7631 (m-40) REVERT: A 706 PHE cc_start: 0.3335 (OUTLIER) cc_final: 0.2778 (t80) REVERT: A 777 ASP cc_start: 0.7181 (m-30) cc_final: 0.6283 (m-30) REVERT: A 789 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: A 972 SER cc_start: 0.7410 (OUTLIER) cc_final: 0.7028 (t) REVERT: A 1013 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7683 (tt) REVERT: A 1091 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: A 1185 MET cc_start: 0.7501 (tpp) cc_final: 0.7290 (tpp) outliers start: 224 outliers final: 141 residues processed: 333 average time/residue: 0.3510 time to fit residues: 151.6826 Evaluate side-chains 298 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 125 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 185 PHE Chi-restraints excluded: chain B residue 218 MET 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 348 ILE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 402 GLN 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 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 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 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 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 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 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 330 ASP Chi-restraints excluded: chain C residue 356 LEU 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 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 588 ILE 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 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 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 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 1038 GLN Chi-restraints excluded: chain C residue 1042 SER 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 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 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 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 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 615 SER 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 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 902 LEU 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 1013 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 1091 GLN Chi-restraints excluded: chain A residue 1098 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 96 optimal weight: 0.8980 chunk 310 optimal weight: 0.8980 chunk 302 optimal weight: 8.9990 chunk 332 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 303 optimal weight: 1.9990 chunk 343 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 chunk 327 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** B1135 GLN C 108 ASN C 201 HIS A 73 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 = 0.4572 r_free = 0.4572 target = 0.207967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148102 restraints weight = 49068.229| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.97 r_work: 0.3622 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30389 Z= 0.126 Angle : 0.592 9.581 41578 Z= 0.301 Chirality : 0.045 0.217 4908 Planarity : 0.005 0.077 5172 Dihedral : 10.264 103.656 6011 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.78 % Allowed : 18.33 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.14), residues: 3618 helix: 1.02 (0.20), residues: 764 sheet: -0.48 (0.18), residues: 812 loop : -2.21 (0.12), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 932 TYR 0.031 0.001 TYR B 427 PHE 0.015 0.001 PHE B 202 TRP 0.010 0.001 TRP B 971 HIS 0.006 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00286 (30225) covalent geometry : angle 0.56664 (41157) SS BOND : bond 0.00268 ( 71) SS BOND : angle 0.88685 ( 142) hydrogen bonds : bond 0.04142 ( 1006) hydrogen bonds : angle 5.23077 ( 2838) link_ALPHA1-3 : bond 0.00447 ( 6) link_ALPHA1-3 : angle 1.97904 ( 18) link_ALPHA1-4 : bond 0.01545 ( 3) link_ALPHA1-4 : angle 3.34532 ( 9) link_ALPHA1-6 : bond 0.00704 ( 3) link_ALPHA1-6 : angle 1.40671 ( 9) link_BETA1-4 : bond 0.00408 ( 15) link_BETA1-4 : angle 1.50687 ( 45) link_NAG-ASN : bond 0.00343 ( 66) link_NAG-ASN : angle 2.17928 ( 198) *********************** 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 359 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 139 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1260 (OUTLIER) cc_final: -0.2734 (p0) REVERT: B 34 ARG cc_start: -0.0899 (OUTLIER) cc_final: -0.1542 (ptm160) REVERT: B 52 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7314 (tp) REVERT: B 136 THR cc_start: -0.0861 (OUTLIER) cc_final: -0.1161 (m) REVERT: B 166 LYS cc_start: -0.0909 (OUTLIER) cc_final: -0.1491 (pttm) REVERT: B 185 PHE cc_start: 0.4099 (OUTLIER) cc_final: 0.3166 (m-10) REVERT: B 238 MET cc_start: 0.0705 (mmm) cc_final: 0.0373 (mmm) REVERT: B 558 THR cc_start: -0.0533 (OUTLIER) cc_final: -0.0784 (m) REVERT: B 920 GLU cc_start: 0.8344 (pt0) cc_final: 0.8128 (pt0) REVERT: B 1069 GLU cc_start: 0.8134 (tt0) cc_final: 0.7714 (tm-30) REVERT: B 1185 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6513 (mmm) REVERT: C 25 ILE cc_start: 0.3111 (OUTLIER) cc_final: 0.2461 (tp) REVERT: C 53 ASN cc_start: 0.7948 (p0) cc_final: 0.7489 (p0) REVERT: C 74 PHE cc_start: 0.2958 (OUTLIER) cc_final: 0.2308 (p90) REVERT: C 94 PHE cc_start: 0.5519 (OUTLIER) cc_final: 0.4627 (t80) REVERT: C 97 ASP cc_start: 0.6697 (t0) cc_final: 0.6166 (m-30) REVERT: C 149 THR cc_start: 0.2912 (OUTLIER) cc_final: 0.2643 (p) REVERT: C 185 PHE cc_start: 0.2740 (OUTLIER) cc_final: 0.2257 (t80) REVERT: C 187 LYS cc_start: 0.4655 (OUTLIER) cc_final: 0.3205 (mmtm) REVERT: C 213 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6418 (t80) REVERT: C 216 VAL cc_start: 0.5195 (OUTLIER) cc_final: 0.4440 (m) REVERT: C 228 LEU cc_start: 0.3331 (OUTLIER) cc_final: 0.2940 (mm) REVERT: C 403 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6341 (tt) REVERT: C 415 LYS cc_start: 0.7433 (tptt) cc_final: 0.7121 (tptp) REVERT: C 535 GLN cc_start: 0.5905 (OUTLIER) cc_final: 0.5681 (mp10) REVERT: C 588 ILE cc_start: 0.5875 (OUTLIER) cc_final: 0.5634 (tt) REVERT: C 597 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7013 (mt) REVERT: C 673 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.5965 (t80) REVERT: A 155 MET cc_start: 0.7068 (mmm) cc_final: 0.6701 (mmt) REVERT: A 198 LEU cc_start: 0.7276 (mp) cc_final: 0.7056 (mp) REVERT: A 310 THR cc_start: 0.2952 (OUTLIER) cc_final: 0.2242 (t) REVERT: A 447 ARG cc_start: 0.4009 (OUTLIER) cc_final: 0.3266 (tpt170) REVERT: A 573 LEU cc_start: 0.2800 (OUTLIER) cc_final: 0.1690 (pt) REVERT: A 608 LEU cc_start: 0.5062 (OUTLIER) cc_final: 0.4736 (mm) REVERT: A 646 ASN cc_start: 0.7775 (m-40) cc_final: 0.7493 (m-40) REVERT: A 706 PHE cc_start: 0.3179 (OUTLIER) cc_final: 0.2626 (t80) REVERT: A 777 ASP cc_start: 0.7007 (m-30) cc_final: 0.6332 (m-30) REVERT: A 789 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.6832 (mp10) REVERT: A 972 SER cc_start: 0.7264 (OUTLIER) cc_final: 0.6988 (t) REVERT: A 1013 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7605 (tt) REVERT: A 1091 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: A 1219 TYR cc_start: 0.5900 (OUTLIER) cc_final: 0.5543 (p90) outliers start: 220 outliers final: 140 residues processed: 333 average time/residue: 0.3493 time to fit residues: 152.5586 Evaluate side-chains 303 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 131 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 218 MET 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 378 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 499 THR 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 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 1012 LEU 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 1156 VAL 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 136 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 216 VAL Chi-restraints excluded: chain C residue 228 LEU 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 369 SER Chi-restraints excluded: chain C residue 378 ILE 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 573 LEU Chi-restraints excluded: chain C residue 588 ILE 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 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 849 LEU Chi-restraints excluded: chain C residue 866 THR 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 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 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 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 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 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 706 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 731 VAL 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 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 1013 LEU 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 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 1189 SER Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL 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 353 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** 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 C 201 HIS C 413 ASN C 465 HIS C 535 GLN A 160 HIS A 295 GLN A 587 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.204103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143574 restraints weight = 48662.016| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.09 r_work: 0.3550 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2192 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= 0.354 Angle : 0.815 11.973 41578 Z= 0.413 Chirality : 0.053 0.300 4908 Planarity : 0.006 0.104 5172 Dihedral : 10.947 105.514 5994 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 7.98 % Allowed : 18.08 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.13), residues: 3618 helix: 0.00 (0.18), residues: 758 sheet: -0.74 (0.18), residues: 822 loop : -2.42 (0.12), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1081 TYR 0.035 0.003 TYR B 622 PHE 0.029 0.003 PHE A 786 TRP 0.021 0.002 TRP B 971 HIS 0.014 0.002 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00846 (30225) covalent geometry : angle 0.78874 (41157) SS BOND : bond 0.00541 ( 71) SS BOND : angle 1.27688 ( 142) hydrogen bonds : bond 0.06396 ( 1006) hydrogen bonds : angle 5.86008 ( 2838) link_ALPHA1-3 : bond 0.00464 ( 6) link_ALPHA1-3 : angle 2.11207 ( 18) link_ALPHA1-4 : bond 0.01191 ( 3) link_ALPHA1-4 : angle 3.60163 ( 9) link_ALPHA1-6 : bond 0.00923 ( 3) link_ALPHA1-6 : angle 1.36216 ( 9) link_BETA1-4 : bond 0.00490 ( 15) link_BETA1-4 : angle 1.87600 ( 45) link_NAG-ASN : bond 0.00474 ( 66) link_NAG-ASN : angle 2.68845 ( 198) *********************** 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 380 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 259 poor density : 121 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1138 (OUTLIER) cc_final: -0.2859 (p0) REVERT: B 34 ARG cc_start: -0.0130 (OUTLIER) cc_final: -0.0893 (ptm160) REVERT: B 136 THR cc_start: -0.0828 (OUTLIER) cc_final: -0.1160 (m) REVERT: B 166 LYS cc_start: -0.0774 (OUTLIER) cc_final: -0.1370 (pttm) REVERT: B 185 PHE cc_start: 0.4392 (OUTLIER) cc_final: 0.3336 (m-10) REVERT: B 402 GLN cc_start: 0.3939 (OUTLIER) cc_final: 0.3584 (tm-30) REVERT: B 558 THR cc_start: -0.0416 (OUTLIER) cc_final: -0.0638 (m) REVERT: B 990 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6892 (mt) REVERT: B 1069 GLU cc_start: 0.8533 (tt0) cc_final: 0.7860 (tm-30) REVERT: B 1079 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8306 (m110) REVERT: B 1163 CYS cc_start: 0.7451 (t) cc_final: 0.7216 (t) REVERT: B 1185 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6648 (mmp) REVERT: C 25 ILE cc_start: 0.3092 (OUTLIER) cc_final: 0.2456 (tp) REVERT: C 74 PHE cc_start: 0.3284 (OUTLIER) cc_final: 0.2641 (p90) REVERT: C 94 PHE cc_start: 0.5707 (OUTLIER) cc_final: 0.4662 (t80) REVERT: C 97 ASP cc_start: 0.6773 (t0) cc_final: 0.6265 (m-30) REVERT: C 149 THR cc_start: 0.3237 (OUTLIER) cc_final: 0.2986 (p) REVERT: C 185 PHE cc_start: 0.2721 (OUTLIER) cc_final: 0.2311 (t80) REVERT: C 187 LYS cc_start: 0.4966 (OUTLIER) cc_final: 0.4644 (tmtt) REVERT: C 213 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.6488 (t80) REVERT: C 228 LEU cc_start: 0.3453 (OUTLIER) cc_final: 0.3039 (mm) REVERT: C 348 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8169 (mt) REVERT: C 403 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6392 (tt) REVERT: C 415 LYS cc_start: 0.7517 (tptt) cc_final: 0.7228 (tptp) REVERT: C 588 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5951 (tt) REVERT: C 673 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.6191 (t80) REVERT: C 893 SER cc_start: 0.7488 (p) cc_final: 0.7175 (t) REVERT: A 198 LEU cc_start: 0.7329 (mp) cc_final: 0.7094 (mp) REVERT: A 310 THR cc_start: 0.3034 (OUTLIER) cc_final: 0.2260 (t) REVERT: A 312 LYS cc_start: 0.4958 (OUTLIER) cc_final: 0.4688 (mmmt) REVERT: A 573 LEU cc_start: 0.3067 (OUTLIER) cc_final: 0.1975 (pt) REVERT: A 608 LEU cc_start: 0.5099 (OUTLIER) cc_final: 0.4821 (mm) REVERT: A 630 GLN cc_start: 0.7223 (mt0) cc_final: 0.6376 (pp30) REVERT: A 646 ASN cc_start: 0.7969 (m-40) cc_final: 0.7700 (m-40) REVERT: A 706 PHE cc_start: 0.3541 (OUTLIER) cc_final: 0.2905 (t80) REVERT: A 748 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7890 (pp) REVERT: A 946 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (tp) REVERT: A 1091 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8367 (tm-30) outliers start: 259 outliers final: 175 residues processed: 354 average time/residue: 0.3246 time to fit residues: 154.0331 Evaluate side-chains 323 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 118 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 277 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 378 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 609 TYR 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 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 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 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 25 ILE 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 348 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 369 SER 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 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 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 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 886 SER Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 914 SER 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 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 A residue 14 VAL 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 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 312 LYS 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 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 573 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 744 ILE 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 233 optimal weight: 0.5980 chunk 310 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 253 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 328 optimal weight: 0.6980 chunk 199 optimal weight: 0.9980 chunk 249 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** C 201 HIS ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** 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 = 0.4564 r_free = 0.4564 target = 0.207355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.147162 restraints weight = 48704.168| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.18 r_work: 0.3603 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30389 Z= 0.119 Angle : 0.602 10.395 41578 Z= 0.306 Chirality : 0.045 0.268 4908 Planarity : 0.005 0.078 5172 Dihedral : 9.968 103.084 5989 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.88 % Allowed : 20.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.14), residues: 3618 helix: 0.89 (0.19), residues: 764 sheet: -0.49 (0.18), residues: 829 loop : -2.22 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 517 TYR 0.017 0.001 TYR B 427 PHE 0.014 0.001 PHE B 200 TRP 0.020 0.001 TRP C 971 HIS 0.005 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00262 (30225) covalent geometry : angle 0.57832 (41157) SS BOND : bond 0.00253 ( 71) SS BOND : angle 0.74633 ( 142) hydrogen bonds : bond 0.04184 ( 1006) hydrogen bonds : angle 5.27171 ( 2838) link_ALPHA1-3 : bond 0.00436 ( 6) link_ALPHA1-3 : angle 2.00204 ( 18) link_ALPHA1-4 : bond 0.01545 ( 3) link_ALPHA1-4 : angle 3.41810 ( 9) link_ALPHA1-6 : bond 0.00685 ( 3) link_ALPHA1-6 : angle 1.38851 ( 9) link_BETA1-4 : bond 0.00423 ( 15) link_BETA1-4 : angle 1.46653 ( 45) link_NAG-ASN : bond 0.00341 ( 66) link_NAG-ASN : angle 2.19368 ( 198) *********************** 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 324 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 133 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1235 (OUTLIER) cc_final: -0.2934 (p0) REVERT: B 34 ARG cc_start: -0.0335 (OUTLIER) cc_final: -0.1136 (ptm160) REVERT: B 52 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7273 (tp) REVERT: B 136 THR cc_start: -0.0628 (OUTLIER) cc_final: -0.0946 (m) REVERT: B 166 LYS cc_start: -0.0826 (OUTLIER) cc_final: -0.1355 (pttm) REVERT: B 204 GLN cc_start: 0.5229 (OUTLIER) cc_final: 0.4953 (tm-30) REVERT: B 238 MET cc_start: -0.0359 (mmm) cc_final: -0.0662 (mmm) REVERT: B 558 THR cc_start: -0.0285 (OUTLIER) cc_final: -0.0489 (m) REVERT: B 1069 GLU cc_start: 0.8200 (tt0) cc_final: 0.7745 (tm-30) REVERT: B 1185 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6496 (mmm) REVERT: C 25 ILE cc_start: 0.3357 (OUTLIER) cc_final: 0.2769 (tp) REVERT: C 53 ASN cc_start: 0.7927 (p0) cc_final: 0.7539 (p0) REVERT: C 54 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7854 (mtt-85) REVERT: C 74 PHE cc_start: 0.3131 (OUTLIER) cc_final: 0.2445 (p90) REVERT: C 94 PHE cc_start: 0.5663 (OUTLIER) cc_final: 0.5000 (t80) REVERT: C 97 ASP cc_start: 0.6648 (t0) cc_final: 0.6171 (m-30) REVERT: C 149 THR cc_start: 0.3249 (OUTLIER) cc_final: 0.2990 (p) REVERT: C 185 PHE cc_start: 0.2653 (OUTLIER) cc_final: 0.2216 (t80) REVERT: C 187 LYS cc_start: 0.4635 (OUTLIER) cc_final: 0.3225 (mmtm) REVERT: C 213 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.6394 (t80) REVERT: C 228 LEU cc_start: 0.3415 (OUTLIER) cc_final: 0.3019 (mm) REVERT: C 415 LYS cc_start: 0.7452 (tptt) cc_final: 0.7134 (tptp) REVERT: C 503 HIS cc_start: 0.2053 (t70) cc_final: 0.0644 (p-80) REVERT: C 505 ASP cc_start: 0.6332 (OUTLIER) cc_final: 0.5303 (t70) REVERT: C 673 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5927 (t80) REVERT: C 893 SER cc_start: 0.7305 (p) cc_final: 0.6924 (t) REVERT: C 920 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: A 147 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6823 (pp20) REVERT: A 155 MET cc_start: 0.7000 (mmm) cc_final: 0.6709 (mmt) REVERT: A 187 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7628 (tmtt) REVERT: A 198 LEU cc_start: 0.7292 (mp) cc_final: 0.7064 (mp) REVERT: A 310 THR cc_start: 0.3008 (OUTLIER) cc_final: 0.2206 (t) REVERT: A 573 LEU cc_start: 0.2725 (OUTLIER) cc_final: 0.1516 (pt) REVERT: A 608 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4654 (mm) REVERT: A 646 ASN cc_start: 0.7791 (m-40) cc_final: 0.7576 (m-40) REVERT: A 706 PHE cc_start: 0.3248 (OUTLIER) cc_final: 0.2654 (t80) REVERT: A 789 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6167 (mp10) REVERT: A 848 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8215 (m-30) REVERT: A 972 SER cc_start: 0.7322 (OUTLIER) cc_final: 0.6903 (t) REVERT: A 1091 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: A 1108 GLU cc_start: 0.8265 (tp30) cc_final: 0.7876 (mm-30) outliers start: 191 outliers final: 127 residues processed: 302 average time/residue: 0.3586 time to fit residues: 142.1090 Evaluate side-chains 288 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 132 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 204 GLN 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 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 609 TYR 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 731 VAL Chi-restraints excluded: chain B residue 740 SER 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 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 1075 ASP 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 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 136 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 330 ASP Chi-restraints excluded: chain C residue 369 SER 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 618 VAL Chi-restraints excluded: chain C residue 628 THR 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 920 GLU 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 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 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 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 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 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 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 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 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 222 optimal weight: 2.9990 chunk 69 optimal weight: 0.0000 chunk 77 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 chunk 295 optimal weight: 20.0000 chunk 181 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 201 HIS A 143 ASN ** 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 = 0.4560 r_free = 0.4560 target = 0.206952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.146416 restraints weight = 48848.373| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.99 r_work: 0.3619 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30389 Z= 0.139 Angle : 0.614 10.458 41578 Z= 0.309 Chirality : 0.045 0.315 4908 Planarity : 0.005 0.081 5172 Dihedral : 9.623 103.258 5987 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 6.04 % Allowed : 20.12 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.14), residues: 3618 helix: 1.03 (0.19), residues: 771 sheet: -0.43 (0.18), residues: 834 loop : -2.19 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 932 TYR 0.020 0.001 TYR A 712 PHE 0.014 0.001 PHE B 202 TRP 0.047 0.002 TRP C 971 HIS 0.007 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00323 (30225) covalent geometry : angle 0.58982 (41157) SS BOND : bond 0.00267 ( 71) SS BOND : angle 0.73997 ( 142) hydrogen bonds : bond 0.04283 ( 1006) hydrogen bonds : angle 5.20604 ( 2838) link_ALPHA1-3 : bond 0.00430 ( 6) link_ALPHA1-3 : angle 2.00722 ( 18) link_ALPHA1-4 : bond 0.01476 ( 3) link_ALPHA1-4 : angle 3.45675 ( 9) link_ALPHA1-6 : bond 0.00702 ( 3) link_ALPHA1-6 : angle 1.33849 ( 9) link_BETA1-4 : bond 0.00425 ( 15) link_BETA1-4 : angle 1.50736 ( 45) link_NAG-ASN : bond 0.00342 ( 66) link_NAG-ASN : angle 2.24751 ( 198) *********************** 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 329 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 133 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1221 (OUTLIER) cc_final: -0.2929 (p0) REVERT: B 34 ARG cc_start: -0.0060 (OUTLIER) cc_final: -0.0871 (ptm160) REVERT: B 52 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7362 (tp) REVERT: B 136 THR cc_start: -0.0799 (OUTLIER) cc_final: -0.1115 (m) REVERT: B 166 LYS cc_start: -0.0768 (OUTLIER) cc_final: -0.1324 (pttm) REVERT: B 185 PHE cc_start: 0.4339 (OUTLIER) cc_final: 0.3340 (m-10) REVERT: B 204 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.5117 (tm-30) REVERT: B 238 MET cc_start: 0.0080 (mmm) cc_final: -0.0188 (mmm) REVERT: B 920 GLU cc_start: 0.8605 (pt0) cc_final: 0.8389 (pt0) REVERT: B 1015 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8422 (tp) REVERT: B 1069 GLU cc_start: 0.8389 (tt0) cc_final: 0.7836 (tm-30) REVERT: B 1185 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6559 (mmm) REVERT: C 25 ILE cc_start: 0.3362 (OUTLIER) cc_final: 0.2764 (tp) REVERT: C 53 ASN cc_start: 0.8043 (p0) cc_final: 0.7680 (p0) REVERT: C 54 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.8037 (mtt-85) REVERT: C 74 PHE cc_start: 0.3410 (OUTLIER) cc_final: 0.2703 (p90) REVERT: C 94 PHE cc_start: 0.5731 (OUTLIER) cc_final: 0.5048 (t80) REVERT: C 97 ASP cc_start: 0.6844 (t0) cc_final: 0.6286 (m-30) REVERT: C 149 THR cc_start: 0.3041 (OUTLIER) cc_final: 0.2775 (p) REVERT: C 185 PHE cc_start: 0.2696 (OUTLIER) cc_final: 0.2202 (t80) REVERT: C 187 LYS cc_start: 0.4814 (OUTLIER) cc_final: 0.3271 (mmtm) REVERT: C 213 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6433 (t80) REVERT: C 228 LEU cc_start: 0.3467 (OUTLIER) cc_final: 0.3055 (mm) REVERT: C 236 TYR cc_start: 0.4258 (t80) cc_final: 0.3987 (t80) REVERT: C 403 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6357 (tt) REVERT: C 415 LYS cc_start: 0.7526 (tptt) cc_final: 0.7197 (tptp) REVERT: C 420 SER cc_start: 0.7528 (m) cc_final: 0.7232 (p) REVERT: C 503 HIS cc_start: 0.1795 (t70) cc_final: 0.0610 (p-80) REVERT: C 673 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.5969 (t80) REVERT: C 920 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: C 1002 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7853 (mmmt) REVERT: A 143 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8080 (m110) REVERT: A 147 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6976 (pp20) REVERT: A 198 LEU cc_start: 0.7358 (mp) cc_final: 0.7125 (mp) REVERT: A 310 THR cc_start: 0.3037 (OUTLIER) cc_final: 0.2260 (t) REVERT: A 457 SER cc_start: -0.0261 (OUTLIER) cc_final: -0.0495 (t) REVERT: A 573 LEU cc_start: 0.2476 (OUTLIER) cc_final: 0.1299 (pt) REVERT: A 608 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4813 (mm) REVERT: A 706 PHE cc_start: 0.3346 (OUTLIER) cc_final: 0.2770 (t80) REVERT: A 748 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7857 (pp) REVERT: A 789 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6349 (mp10) REVERT: A 972 SER cc_start: 0.7467 (OUTLIER) cc_final: 0.7141 (t) REVERT: A 1108 GLU cc_start: 0.8502 (tp30) cc_final: 0.8083 (mm-30) outliers start: 196 outliers final: 138 residues processed: 309 average time/residue: 0.3372 time to fit residues: 137.5800 Evaluate side-chains 296 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 127 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 204 GLN 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 538 VAL Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 609 TYR 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 731 VAL Chi-restraints excluded: chain B residue 740 SER 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 811 THR Chi-restraints excluded: chain B residue 820 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 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 1012 LEU Chi-restraints excluded: chain B residue 1015 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 B residue 1151 THR 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 136 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 403 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 573 LEU Chi-restraints excluded: chain C residue 628 THR 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 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 1002 LYS 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 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 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 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 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 329 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 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 720 VAL Chi-restraints excluded: chain A residue 724 VAL 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 241 optimal weight: 0.9990 chunk 345 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 344 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 287 optimal weight: 0.0870 chunk 211 optimal weight: 0.0470 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 799 HIS A 587 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.209365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147927 restraints weight = 48957.649| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.72 r_work: 0.3693 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 30389 Z= 0.097 Angle : 0.573 11.625 41578 Z= 0.287 Chirality : 0.044 0.296 4908 Planarity : 0.004 0.072 5172 Dihedral : 8.917 102.410 5976 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.04 % Allowed : 22.18 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.14), residues: 3618 helix: 1.48 (0.20), residues: 782 sheet: -0.28 (0.18), residues: 793 loop : -2.00 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 932 TYR 0.015 0.001 TYR C 462 PHE 0.014 0.001 PHE B 224 TRP 0.041 0.001 TRP C 971 HIS 0.006 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00204 (30225) covalent geometry : angle 0.54713 (41157) SS BOND : bond 0.00220 ( 71) SS BOND : angle 0.63360 ( 142) hydrogen bonds : bond 0.03512 ( 1006) hydrogen bonds : angle 4.93311 ( 2838) link_ALPHA1-3 : bond 0.00447 ( 6) link_ALPHA1-3 : angle 2.00818 ( 18) link_ALPHA1-4 : bond 0.01597 ( 3) link_ALPHA1-4 : angle 3.33542 ( 9) link_ALPHA1-6 : bond 0.00632 ( 3) link_ALPHA1-6 : angle 1.36874 ( 9) link_BETA1-4 : bond 0.00419 ( 15) link_BETA1-4 : angle 1.38754 ( 45) link_NAG-ASN : bond 0.00432 ( 66) link_NAG-ASN : angle 2.21829 ( 198) *********************** 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 272 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 141 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1064 (OUTLIER) cc_final: -0.2808 (p0) REVERT: B 34 ARG cc_start: -0.0187 (OUTLIER) cc_final: -0.1060 (ptm160) REVERT: B 52 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7314 (tp) REVERT: B 136 THR cc_start: -0.0658 (OUTLIER) cc_final: -0.0962 (m) REVERT: B 166 LYS cc_start: -0.0779 (OUTLIER) cc_final: -0.1357 (pttm) REVERT: B 185 PHE cc_start: 0.4300 (OUTLIER) cc_final: 0.3276 (m-10) REVERT: B 238 MET cc_start: 0.0219 (mmm) cc_final: -0.0006 (mmm) REVERT: B 1069 GLU cc_start: 0.8256 (tt0) cc_final: 0.7727 (tm-30) REVERT: B 1185 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6457 (mmm) REVERT: C 25 ILE cc_start: 0.3502 (OUTLIER) cc_final: 0.3004 (tp) REVERT: C 54 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7848 (mtt-85) REVERT: C 74 PHE cc_start: 0.3465 (OUTLIER) cc_final: 0.2844 (p90) REVERT: C 94 PHE cc_start: 0.5692 (OUTLIER) cc_final: 0.5048 (t80) REVERT: C 97 ASP cc_start: 0.6874 (t0) cc_final: 0.6369 (m-30) REVERT: C 149 THR cc_start: 0.3094 (OUTLIER) cc_final: 0.2796 (p) REVERT: C 185 PHE cc_start: 0.2785 (OUTLIER) cc_final: 0.2261 (t80) REVERT: C 187 LYS cc_start: 0.4604 (OUTLIER) cc_final: 0.3198 (mmtm) REVERT: C 213 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6426 (t80) REVERT: C 228 LEU cc_start: 0.3506 (OUTLIER) cc_final: 0.3102 (mm) REVERT: C 236 TYR cc_start: 0.4371 (t80) cc_final: 0.4138 (t80) REVERT: C 415 LYS cc_start: 0.7523 (tptt) cc_final: 0.7104 (tptp) REVERT: C 503 HIS cc_start: 0.1804 (t70) cc_final: 0.0783 (p-80) REVERT: C 920 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: A 147 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6946 (pp20) REVERT: A 187 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7735 (tmtt) REVERT: A 198 LEU cc_start: 0.7264 (mp) cc_final: 0.7046 (mp) REVERT: A 310 THR cc_start: 0.2889 (OUTLIER) cc_final: 0.2148 (t) REVERT: A 573 LEU cc_start: 0.2594 (OUTLIER) cc_final: 0.1452 (pt) REVERT: A 608 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4755 (mm) REVERT: A 706 PHE cc_start: 0.3265 (OUTLIER) cc_final: 0.2764 (t80) REVERT: A 748 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7774 (pp) REVERT: A 789 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.5913 (mp10) REVERT: A 848 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: A 1205 MET cc_start: 0.7609 (ptp) cc_final: 0.7317 (ptp) outliers start: 131 outliers final: 79 residues processed: 257 average time/residue: 0.3469 time to fit residues: 117.4474 Evaluate side-chains 229 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 125 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN 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 499 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 772 VAL 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 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 B residue 1185 MET 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 136 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 330 ASP Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 512 VAL 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 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 52 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR 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 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 455 VAL 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 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 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 848 ASP 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 1079 ASN Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1152 SER 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 123 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 358 optimal weight: 0.0270 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 315 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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** C 108 ASN C 201 HIS C 351 ASN ** 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 = 0.4581 r_free = 0.4581 target = 0.208789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146903 restraints weight = 48744.982| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.77 r_work: 0.3668 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 30389 Z= 0.111 Angle : 0.584 13.527 41578 Z= 0.294 Chirality : 0.044 0.237 4908 Planarity : 0.004 0.071 5172 Dihedral : 8.460 103.031 5944 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.67 % Allowed : 22.67 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.14), residues: 3618 helix: 1.60 (0.20), residues: 776 sheet: -0.23 (0.18), residues: 795 loop : -1.95 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1064 TYR 0.015 0.001 TYR C 235 PHE 0.020 0.001 PHE C 98 TRP 0.034 0.001 TRP C 971 HIS 0.005 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00251 (30225) covalent geometry : angle 0.55749 (41157) SS BOND : bond 0.00415 ( 71) SS BOND : angle 1.39694 ( 142) hydrogen bonds : bond 0.03704 ( 1006) hydrogen bonds : angle 4.90804 ( 2838) link_ALPHA1-3 : bond 0.00422 ( 6) link_ALPHA1-3 : angle 1.98924 ( 18) link_ALPHA1-4 : bond 0.01500 ( 3) link_ALPHA1-4 : angle 3.39713 ( 9) link_ALPHA1-6 : bond 0.00648 ( 3) link_ALPHA1-6 : angle 1.32530 ( 9) link_BETA1-4 : bond 0.00417 ( 15) link_BETA1-4 : angle 1.42070 ( 45) link_NAG-ASN : bond 0.00324 ( 66) link_NAG-ASN : angle 2.06709 ( 198) ********************** 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 250 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 131 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ASN cc_start: -0.1186 (OUTLIER) cc_final: -0.2885 (p0) REVERT: B 34 ARG cc_start: -0.0184 (OUTLIER) cc_final: -0.1048 (ptm160) REVERT: B 136 THR cc_start: -0.0753 (OUTLIER) cc_final: -0.1025 (m) REVERT: B 166 LYS cc_start: -0.0639 (OUTLIER) cc_final: -0.1262 (pttm) REVERT: B 185 PHE cc_start: 0.4230 (OUTLIER) cc_final: 0.3194 (m-10) REVERT: B 1069 GLU cc_start: 0.8378 (tt0) cc_final: 0.7796 (tm-30) REVERT: B 1185 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6478 (mmm) REVERT: C 25 ILE cc_start: 0.3680 (OUTLIER) cc_final: 0.3195 (tp) REVERT: C 74 PHE cc_start: 0.3717 (OUTLIER) cc_final: 0.3098 (p90) REVERT: C 94 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.5222 (t80) REVERT: C 97 ASP cc_start: 0.7009 (t0) cc_final: 0.6380 (m-30) REVERT: C 149 THR cc_start: 0.3126 (OUTLIER) cc_final: 0.2851 (p) REVERT: C 185 PHE cc_start: 0.2750 (OUTLIER) cc_final: 0.2234 (t80) REVERT: C 187 LYS cc_start: 0.4585 (OUTLIER) cc_final: 0.3183 (mmtm) REVERT: C 213 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6467 (t80) REVERT: C 228 LEU cc_start: 0.3490 (OUTLIER) cc_final: 0.3079 (mm) REVERT: C 356 LEU cc_start: 0.7997 (mt) cc_final: 0.7784 (mt) REVERT: C 415 LYS cc_start: 0.7482 (tptt) cc_final: 0.7066 (tptp) REVERT: C 503 HIS cc_start: 0.1955 (t70) cc_final: 0.0874 (p-80) REVERT: C 920 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: C 1205 MET cc_start: 0.7013 (mtm) cc_final: 0.6789 (mtt) REVERT: A 147 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6968 (pp20) REVERT: A 187 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7510 (tmtt) REVERT: A 198 LEU cc_start: 0.7365 (mp) cc_final: 0.7160 (mp) REVERT: A 310 THR cc_start: 0.2975 (OUTLIER) cc_final: 0.2284 (t) REVERT: A 573 LEU cc_start: 0.2617 (OUTLIER) cc_final: 0.1518 (pt) REVERT: A 608 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4877 (mm) REVERT: A 789 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.5893 (mp10) REVERT: A 1095 ASP cc_start: 0.8343 (t0) cc_final: 0.8008 (m-30) REVERT: A 1205 MET cc_start: 0.7512 (ptp) cc_final: 0.7222 (ptp) outliers start: 119 outliers final: 81 residues processed: 240 average time/residue: 0.3543 time to fit residues: 110.9899 Evaluate side-chains 232 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 130 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN 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 499 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 772 VAL 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 964 VAL 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 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 116 THR Chi-restraints excluded: chain C residue 136 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 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 512 VAL Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 964 VAL 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 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1147 SER 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 52 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR 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 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 455 VAL 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 661 PHE Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 724 VAL 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 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 1028 LYS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1202 VAL 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 182 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 339 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 266 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 353 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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** B 826 HIS C 73 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS A 295 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 = 0.4553 r_free = 0.4553 target = 0.206002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.145591 restraints weight = 48796.176| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.99 r_work: 0.3591 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 30389 Z= 0.230 Angle : 0.695 14.144 41578 Z= 0.353 Chirality : 0.048 0.328 4908 Planarity : 0.005 0.092 5172 Dihedral : 8.917 104.202 5936 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.47 % Allowed : 22.27 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.14), residues: 3618 helix: 0.85 (0.19), residues: 774 sheet: -0.41 (0.18), residues: 822 loop : -2.05 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 54 TYR 0.023 0.002 TYR B 622 PHE 0.023 0.002 PHE A 786 TRP 0.022 0.002 TRP C 971 HIS 0.011 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00549 (30225) covalent geometry : angle 0.66736 (41157) SS BOND : bond 0.00456 ( 71) SS BOND : angle 1.70633 ( 142) hydrogen bonds : bond 0.05170 ( 1006) hydrogen bonds : angle 5.36403 ( 2838) link_ALPHA1-3 : bond 0.00385 ( 6) link_ALPHA1-3 : angle 2.11462 ( 18) link_ALPHA1-4 : bond 0.01440 ( 3) link_ALPHA1-4 : angle 3.61465 ( 9) link_ALPHA1-6 : bond 0.00734 ( 3) link_ALPHA1-6 : angle 1.29961 ( 9) link_BETA1-4 : bond 0.00448 ( 15) link_BETA1-4 : angle 1.61587 ( 45) link_NAG-ASN : bond 0.00351 ( 66) link_NAG-ASN : angle 2.28019 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12321.08 seconds wall clock time: 209 minutes 31.84 seconds (12571.84 seconds total)