Starting phenix.real_space_refine on Mon Aug 25 17:20:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1b_38830/08_2025/8y1b_38830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1b_38830/08_2025/8y1b_38830.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/8y1b_38830/08_2025/8y1b_38830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1b_38830/08_2025/8y1b_38830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y1b_38830/08_2025/8y1b_38830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1b_38830/08_2025/8y1b_38830.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= 0.105 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 42 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: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "B" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "C" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 5.87, per 1000 atoms: 0.20 Number of scatterers: 29541 At special positions: 0 Unit cell: (167.398, 154.354, 204.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 171 16.00 O 5907 8.00 N 4734 7.00 C 18729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.04 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 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=2.04 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=2.04 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 A 132 " " NAG E 1 " - " ASN A 188 " " NAG F 1 " - " ASN A 335 " " NAG G 1 " - " ASN A 355 " " NAG H 1 " - " ASN A 664 " " NAG I 1 " - " ASN B 132 " " NAG J 1 " - " ASN B 188 " " NAG K 1 " - " ASN B 335 " " NAG L 1 " - " ASN B 355 " " NAG M 1 " - " ASN B 664 " " NAG N 1 " - " ASN C 132 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 335 " " NAG Q 1 " - " ASN C 355 " " NAG R 1 " - " ASN C 664 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 86 helices and 66 sheets defined 24.2% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.589A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.170A pdb=" N ILE A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.970A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.082A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.588A pdb=" N CYS A 556 " --> pdb=" O GLU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' 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 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 862 removed outlier: 3.617A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 888 removed outlier: 3.585A pdb=" N LEU A 888 " --> pdb=" O LYS A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 888' Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.968A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.651A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.909A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.846A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1066 through 1113 removed outlier: 3.769A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.585A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.602A pdb=" N LEU B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.506A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.503A pdb=" N ARG B 397 " --> pdb=" O PRO B 394 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.788A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.849A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.935A pdb=" N GLU B 831 " --> pdb=" O ASP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 863 Processing helix chain 'B' and resid 901 through 910 removed outlier: 4.209A pdb=" N LYS B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.753A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) 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 removed outlier: 3.503A pdb=" N ILE B 955 " --> pdb=" O SER B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 975 removed outlier: 3.677A pdb=" N ALA B 974 " --> pdb=" O TRP B 971 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA B 975 " --> pdb=" O SER B 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 971 through 975' Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.648A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.850A pdb=" N ALA B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.548A 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 1063 Processing helix chain 'B' and resid 1070 through 1113 removed outlier: 3.682A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.748A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.760A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 344 removed outlier: 3.961A 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 361 removed outlier: 3.704A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.605A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.956A 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 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 442 through 447 removed outlier: 3.511A pdb=" N ARG C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.535A pdb=" N VAL C 481 " --> pdb=" O ASP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 3.868A pdb=" N THR C 527 " --> pdb=" O PRO C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.743A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' 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 831 through 833 No H-bonds generated for 'chain 'C' and resid 831 through 833' Processing helix chain 'C' and resid 834 through 863 removed outlier: 3.693A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 910 removed outlier: 3.927A pdb=" N LYS C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 923 removed outlier: 4.022A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 926 No H-bonds generated for 'chain 'C' and resid 924 through 926' Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 951 through 965 Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.646A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1048 No H-bonds generated for 'chain 'C' and resid 1046 through 1048' Processing helix chain 'C' and resid 1057 through 1062 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.632A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.831A pdb=" N ASP A 38 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 5.952A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 317 " --> pdb=" O ASP C 623 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 67 removed outlier: 4.163A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.569A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 227 removed outlier: 6.897A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 113 Processing sheet with id=AA7, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.276A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 307 removed outlier: 7.632A pdb=" N ARG A 676 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG A 693 " --> pdb=" O ARG A 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.267A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.415A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.415A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB4, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.633A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AB6, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB7, first strand: chain 'A' and resid 619 through 624 removed outlier: 4.021A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.752A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A 742 " --> pdb=" O MET A 738 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.358A pdb=" N SER A 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.194A pdb=" N SER A1152 " --> pdb=" O THR A 792 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 794 " --> pdb=" O PRO A1150 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 796 " --> pdb=" O TYR A1148 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR A1148 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY A 798 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE A1146 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A 800 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A1144 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 802 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A1142 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN A 804 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A1140 " --> pdb=" O GLN A 804 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASN A1136 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A1142 " --> pdb=" O VAL A1134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A1134 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A1144 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A1132 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A1146 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.194A pdb=" N SER A1152 " --> pdb=" O THR A 792 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 794 " --> pdb=" O PRO A1150 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 796 " --> pdb=" O TYR A1148 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR A1148 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY A 798 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE A1146 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A 800 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A1144 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 802 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A1142 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN A 804 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A1140 " --> pdb=" O GLN A 804 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.389A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC5, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AC6, first strand: chain 'A' and resid 1202 through 1205 Processing sheet with id=AC7, first strand: chain 'B' and resid 59 through 67 removed outlier: 7.760A pdb=" N GLN B 265 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP B 281 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AC9, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.763A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 221 through 227 removed outlier: 6.744A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD3, first strand: chain 'B' and resid 302 through 306 Processing sheet with id=AD4, first strand: chain 'B' and resid 316 through 319 removed outlier: 6.531A pdb=" N VAL B 317 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 657 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AD6, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.609A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 422 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS B 370 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN B 424 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE B 368 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR B 426 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.609A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AD9, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.253A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AE2, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.835A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.683A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.244A pdb=" N SER B 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.889A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN B1136 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B1142 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B1134 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B1144 " --> pdb=" O SER B1132 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B1132 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE B1146 " --> pdb=" O ILE B1130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.889A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.420A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AE9, first strand: chain 'B' and resid 1202 through 1205 Processing sheet with id=AF1, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF2, first strand: chain 'C' and resid 38 through 39 removed outlier: 8.138A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 59 through 67 removed outlier: 7.929A pdb=" N GLN C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP C 281 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.432A pdb=" N LEU C 146 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 109 through 112 Processing sheet with id=AF6, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.569A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AF8, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AF9, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.566A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.473A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER C 422 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N CYS C 370 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLN C 424 " --> pdb=" O PHE C 368 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE C 368 " --> pdb=" O GLN C 424 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR C 426 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS C 364 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 352 through 354 removed outlier: 3.652A pdb=" N CYS C 603 " --> pdb=" O CYS C 352 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG4, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.162A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 505 through 507 Processing sheet with id=AG6, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.508A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.656A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.793A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.793A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.325A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH3, first strand: chain 'C' and resid 1202 through 1205 1069 hydrogen bonds defined for protein. 2934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.53 Time building geometry restraints manager: 3.21 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: 9106 1.34 - 1.46: 7837 1.46 - 1.59: 13084 1.59 - 1.71: 0 1.71 - 1.83: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" CA TYR A 28 " pdb=" CB TYR A 28 " ideal model delta sigma weight residual 1.524 1.576 -0.053 1.62e-02 3.81e+03 1.05e+01 bond pdb=" C5 MAN I 3 " pdb=" O5 MAN I 3 " ideal model delta sigma weight residual 1.418 1.482 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 NAG A2014 " pdb=" O5 NAG A2014 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" C1 MAN N 6 " pdb=" O5 MAN N 6 " ideal model delta sigma weight residual 1.399 1.456 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" CA ASP C 250 " pdb=" C ASP C 250 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.34e-02 5.57e+03 7.98e+00 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 39447 1.92 - 3.83: 1498 3.83 - 5.75: 157 5.75 - 7.66: 38 7.66 - 9.58: 17 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 110.70 118.55 -7.85 1.22e+00 6.72e-01 4.14e+01 angle pdb=" N PRO B 969 " pdb=" CA PRO B 969 " pdb=" C PRO B 969 " ideal model delta sigma weight residual 110.70 118.43 -7.73 1.22e+00 6.72e-01 4.02e+01 angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 118.12 -7.42 1.22e+00 6.72e-01 3.70e+01 angle pdb=" N ASN B 132 " pdb=" CA ASN B 132 " pdb=" C ASN B 132 " ideal model delta sigma weight residual 113.37 120.91 -7.54 1.38e+00 5.25e-01 2.99e+01 angle pdb=" N GLU B 37 " pdb=" CA GLU B 37 " pdb=" C GLU B 37 " ideal model delta sigma weight residual 112.54 104.52 8.02 1.51e+00 4.39e-01 2.82e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.61: 17916 24.61 - 49.23: 1035 49.23 - 73.84: 242 73.84 - 98.46: 27 98.46 - 123.07: 7 Dihedral angle restraints: 19227 sinusoidal: 8589 harmonic: 10638 Sorted by residual: dihedral pdb=" CA PRO C 92 " pdb=" C PRO C 92 " pdb=" N PRO C 93 " pdb=" CA PRO C 93 " ideal model delta harmonic sigma weight residual 180.00 130.80 49.20 0 5.00e+00 4.00e-02 9.68e+01 dihedral pdb=" CA PRO C 969 " pdb=" C PRO C 969 " pdb=" N PRO C 970 " pdb=" CA PRO C 970 " ideal model delta harmonic sigma weight residual 180.00 144.59 35.41 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA PHE B 968 " pdb=" C PHE B 968 " pdb=" N PRO B 969 " pdb=" CA PRO B 969 " ideal model delta harmonic sigma weight residual -180.00 -144.71 -35.29 0 5.00e+00 4.00e-02 4.98e+01 ... (remaining 19224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 4899 0.331 - 0.662: 5 0.662 - 0.993: 1 0.993 - 1.323: 2 1.323 - 1.654: 1 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 19 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 132 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.11 -1.29 2.00e-01 2.50e+01 4.17e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 188 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.73e+01 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 19 " -0.085 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CG ASN B 19 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 19 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN B 19 " 0.230 2.00e-02 2.50e+03 pdb=" C1 NAG B2001 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 132 " -0.068 2.00e-02 2.50e+03 8.88e-02 9.85e+01 pdb=" CG ASN B 132 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 132 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 132 " 0.152 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 188 " -0.038 2.00e-02 2.50e+03 5.30e-02 3.51e+01 pdb=" CG ASN B 188 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B 188 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 188 " 0.093 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.060 2.00e-02 2.50e+03 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7711 2.80 - 3.32: 23407 3.32 - 3.85: 47986 3.85 - 4.37: 55957 4.37 - 4.90: 97987 Nonbonded interactions: 233048 Sorted by model distance: nonbonded pdb=" O TRP B 89 " pdb=" OH TYR B 236 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP B 523 " pdb=" OG SER B 526 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" O PHE A 473 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR C 625 " pdb=" OD1 ASP C 660 " model vdw 2.292 3.040 nonbonded pdb=" O VAL A 636 " pdb=" OG1 THR A 666 " model vdw 2.296 3.040 ... (remaining 233043 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: 3.640 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.330 Find NCS groups from input model: 0.780 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: 0.000 Load rotamer database and sin/cos tables:5.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 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 0.137 30390 Z= 0.311 Angle : 0.961 39.392 41580 Z= 0.489 Chirality : 0.068 1.654 4908 Planarity : 0.008 0.115 5172 Dihedral : 15.653 123.072 12183 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 9.92 % Allowed : 8.81 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -3.12 (0.12), residues: 3618 helix: -2.07 (0.14), residues: 790 sheet: -1.00 (0.17), residues: 853 loop : -2.63 (0.11), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 737 TYR 0.030 0.002 TYR A 622 PHE 0.025 0.002 PHE A 968 TRP 0.020 0.002 TRP C 174 HIS 0.009 0.002 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00685 (30225) covalent geometry : angle 0.85357 (41157) SS BOND : bond 0.00347 ( 72) SS BOND : angle 1.08418 ( 144) hydrogen bonds : bond 0.14646 ( 1016) hydrogen bonds : angle 6.68087 ( 2934) link_ALPHA1-3 : bond 0.00533 ( 6) link_ALPHA1-3 : angle 2.10665 ( 18) link_ALPHA1-4 : bond 0.01006 ( 3) link_ALPHA1-4 : angle 3.10174 ( 9) link_ALPHA1-6 : bond 0.00505 ( 3) link_ALPHA1-6 : angle 2.08287 ( 9) link_BETA1-4 : bond 0.00727 ( 15) link_BETA1-4 : angle 2.30321 ( 45) link_NAG-ASN : bond 0.02020 ( 66) link_NAG-ASN : angle 6.27948 ( 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 572 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 322 poor density : 250 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.6772 (mp) REVERT: A 120 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5884 (tt0) REVERT: A 124 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6911 (tp) REVERT: A 186 LYS cc_start: 0.8463 (ttmp) cc_final: 0.8030 (ttpt) REVERT: A 187 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6934 (tptp) REVERT: A 351 ASN cc_start: 0.5357 (m-40) cc_final: 0.5150 (m-40) REVERT: A 560 LEU cc_start: -0.0685 (OUTLIER) cc_final: -0.1095 (pp) REVERT: A 606 ASP cc_start: 0.1726 (OUTLIER) cc_final: 0.1239 (t0) REVERT: A 643 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7292 (m110) REVERT: A 659 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7858 (ttpm) REVERT: A 831 GLU cc_start: 0.7993 (pt0) cc_final: 0.7781 (pp20) REVERT: A 845 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: A 885 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8000 (tptp) REVERT: A 902 LEU cc_start: 0.7716 (tp) cc_final: 0.7485 (tt) REVERT: A 906 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7620 (mp) REVERT: A 981 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7759 (mt) REVERT: A 1038 GLN cc_start: 0.7231 (mm110) cc_final: 0.6974 (mm-40) REVERT: A 1091 GLN cc_start: 0.7353 (tt0) cc_final: 0.7001 (tt0) REVERT: B 97 ASP cc_start: 0.6869 (m-30) cc_final: 0.6579 (t0) REVERT: B 234 HIS cc_start: 0.6649 (m90) cc_final: 0.6199 (m90) REVERT: B 289 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7423 (tt0) REVERT: B 544 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 655 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 711 PHE cc_start: 0.6900 (m-80) cc_final: 0.6638 (m-10) REVERT: B 837 ASP cc_start: 0.7686 (m-30) cc_final: 0.7396 (m-30) REVERT: B 848 ASP cc_start: 0.7706 (m-30) cc_final: 0.7455 (m-30) REVERT: B 930 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.5580 (mp0) REVERT: B 1149 LYS cc_start: 0.7818 (tttt) cc_final: 0.7458 (tttm) REVERT: C 187 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7229 (ttmm) REVERT: C 213 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.6924 (p90) REVERT: C 373 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (tp) REVERT: C 464 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6518 (m-30) REVERT: C 511 TYR cc_start: 0.1864 (OUTLIER) cc_final: 0.0176 (m-10) REVERT: C 652 ASN cc_start: 0.8659 (m-40) cc_final: 0.8257 (m-40) REVERT: C 698 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7681 (p) REVERT: C 780 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: C 827 ASP cc_start: 0.8085 (m-30) cc_final: 0.7740 (m-30) REVERT: C 1026 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8259 (tp) REVERT: C 1124 CYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6716 (m) REVERT: C 1205 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8653 (ptp) outliers start: 322 outliers final: 122 residues processed: 537 average time/residue: 0.4052 time to fit residues: 271.6333 Evaluate side-chains 308 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 162 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 ASN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 930 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 1001 GLN Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1063 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 278 ASN A 353 ASN A 559 GLN A 595 ASN A 611 ASN A 621 ASN A 630 GLN A 876 HIS A 881 ASN A 984 GLN A1001 GLN A1091 GLN B 22 ASN B 26 ASN B 204 GLN B 630 GLN B 876 HIS B 894 GLN B1001 GLN B1086 ASN B1091 GLN B1122 ASN C 73 ASN C 204 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 ASN C 630 GLN C 872 ASN C 894 GLN C1001 GLN C1023 ASN C1045 GLN C1079 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.162099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108369 restraints weight = 44241.323| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.78 r_work: 0.3184 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30390 Z= 0.131 Angle : 0.660 21.000 41580 Z= 0.329 Chirality : 0.050 0.794 4908 Planarity : 0.006 0.103 5172 Dihedral : 11.423 106.148 6089 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.76 % Allowed : 13.25 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.93 (0.13), residues: 3618 helix: 0.08 (0.19), residues: 760 sheet: -0.55 (0.17), residues: 855 loop : -2.25 (0.12), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1064 TYR 0.014 0.001 TYR A 191 PHE 0.021 0.001 PHE A 968 TRP 0.016 0.001 TRP C 174 HIS 0.004 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00288 (30225) covalent geometry : angle 0.60404 (41157) SS BOND : bond 0.00281 ( 72) SS BOND : angle 0.96402 ( 144) hydrogen bonds : bond 0.05096 ( 1016) hydrogen bonds : angle 5.25000 ( 2934) link_ALPHA1-3 : bond 0.00632 ( 6) link_ALPHA1-3 : angle 1.95667 ( 18) link_ALPHA1-4 : bond 0.01621 ( 3) link_ALPHA1-4 : angle 3.34031 ( 9) link_ALPHA1-6 : bond 0.00764 ( 3) link_ALPHA1-6 : angle 1.65454 ( 9) link_BETA1-4 : bond 0.00495 ( 15) link_BETA1-4 : angle 1.70382 ( 45) link_NAG-ASN : bond 0.00575 ( 66) link_NAG-ASN : angle 3.63154 ( 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 380 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 193 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9006 (mp) cc_final: 0.8783 (mm) REVERT: A 124 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7143 (tp) REVERT: A 182 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 263 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8158 (tpt-90) REVERT: A 659 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7749 (tttm) REVERT: A 885 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8439 (tptp) REVERT: A 906 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 1003 LEU cc_start: 0.8563 (mm) cc_final: 0.8202 (tp) REVERT: A 1069 GLU cc_start: 0.7661 (tp30) cc_final: 0.7193 (tm-30) REVERT: A 1091 GLN cc_start: 0.8678 (tt0) cc_final: 0.8471 (tt0) REVERT: B 97 ASP cc_start: 0.7545 (m-30) cc_final: 0.6812 (t0) REVERT: B 234 HIS cc_start: 0.6346 (m90) cc_final: 0.5843 (m90) REVERT: B 236 TYR cc_start: 0.7435 (t80) cc_final: 0.6612 (t80) REVERT: B 289 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8258 (tt0) REVERT: B 655 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8834 (mt) REVERT: B 711 PHE cc_start: 0.7912 (m-80) cc_final: 0.7548 (m-10) REVERT: B 894 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7095 (pp30) REVERT: C 213 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8152 (p90) REVERT: C 400 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.5764 (t0) REVERT: C 464 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: C 511 TYR cc_start: -0.0965 (OUTLIER) cc_final: -0.1783 (m-10) REVERT: C 652 ASN cc_start: 0.8720 (m-40) cc_final: 0.8428 (m-40) REVERT: C 827 ASP cc_start: 0.8689 (m-30) cc_final: 0.8409 (m-30) REVERT: C 894 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5804 (pp30) REVERT: C 1066 ASP cc_start: 0.8197 (p0) cc_final: 0.7650 (p0) REVERT: C 1069 GLU cc_start: 0.8355 (tt0) cc_final: 0.7902 (pt0) REVERT: C 1071 GLN cc_start: 0.8368 (mt0) cc_final: 0.7973 (mp-120) REVERT: C 1075 ASP cc_start: 0.8626 (t70) cc_final: 0.8280 (t0) REVERT: C 1096 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8935 (tp) REVERT: C 1124 CYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7483 (m) REVERT: C 1205 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8742 (ptp) outliers start: 187 outliers final: 105 residues processed: 359 average time/residue: 0.4236 time to fit residues: 189.2518 Evaluate side-chains 282 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 162 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 894 GLN Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 894 GLN Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 78 optimal weight: 4.9990 chunk 292 optimal weight: 8.9990 chunk 149 optimal weight: 0.0870 chunk 341 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 142 HIS B 353 ASN B 583 ASN B 826 HIS B1059 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 ASN C 876 HIS C 894 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.160382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105950 restraints weight = 44186.958| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.73 r_work: 0.3151 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 30390 Z= 0.198 Angle : 0.698 18.862 41580 Z= 0.346 Chirality : 0.052 0.937 4908 Planarity : 0.006 0.108 5172 Dihedral : 10.564 108.638 5992 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.79 % Allowed : 14.48 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.21 % 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: -1.59 (0.13), residues: 3618 helix: 0.65 (0.19), residues: 759 sheet: -0.49 (0.17), residues: 856 loop : -2.08 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 206 TYR 0.025 0.002 TYR A 191 PHE 0.020 0.002 PHE B 968 TRP 0.016 0.001 TRP C 174 HIS 0.008 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00473 (30225) covalent geometry : angle 0.63535 (41157) SS BOND : bond 0.00346 ( 72) SS BOND : angle 1.53530 ( 144) hydrogen bonds : bond 0.05605 ( 1016) hydrogen bonds : angle 5.18048 ( 2934) link_ALPHA1-3 : bond 0.00605 ( 6) link_ALPHA1-3 : angle 2.06783 ( 18) link_ALPHA1-4 : bond 0.01424 ( 3) link_ALPHA1-4 : angle 3.33068 ( 9) link_ALPHA1-6 : bond 0.00651 ( 3) link_ALPHA1-6 : angle 1.72164 ( 9) link_BETA1-4 : bond 0.00371 ( 15) link_BETA1-4 : angle 1.65687 ( 45) link_NAG-ASN : bond 0.00560 ( 66) link_NAG-ASN : angle 3.89270 ( 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 355 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 167 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7253 (tp) REVERT: A 233 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8510 (t) REVERT: A 447 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5661 (ptp90) REVERT: A 659 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7784 (tttm) REVERT: A 885 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8389 (tptp) REVERT: A 906 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 1003 LEU cc_start: 0.8622 (mm) cc_final: 0.8257 (tp) REVERT: A 1069 GLU cc_start: 0.7745 (tp30) cc_final: 0.7266 (tm-30) REVERT: A 1091 GLN cc_start: 0.8684 (tt0) cc_final: 0.8481 (tt0) REVERT: B 97 ASP cc_start: 0.7525 (m-30) cc_final: 0.6853 (t0) REVERT: B 234 HIS cc_start: 0.6383 (m90) cc_final: 0.5921 (m90) REVERT: B 289 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8189 (tt0) REVERT: B 655 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8861 (mt) REVERT: B 711 PHE cc_start: 0.7941 (m-80) cc_final: 0.7582 (m-10) REVERT: C 213 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8113 (p90) REVERT: C 400 ASP cc_start: 0.6394 (OUTLIER) cc_final: 0.5843 (t0) REVERT: C 433 ASN cc_start: 0.6168 (m-40) cc_final: 0.5641 (OUTLIER) REVERT: C 511 TYR cc_start: -0.0963 (OUTLIER) cc_final: -0.1774 (m-10) REVERT: C 652 ASN cc_start: 0.8737 (m-40) cc_final: 0.8417 (m-40) REVERT: C 800 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8314 (pt0) REVERT: C 827 ASP cc_start: 0.8687 (m-30) cc_final: 0.8430 (m-30) REVERT: C 863 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: C 1066 ASP cc_start: 0.8183 (p0) cc_final: 0.7738 (p0) REVERT: C 1069 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: C 1071 GLN cc_start: 0.8437 (mt0) cc_final: 0.8026 (mp-120) REVERT: C 1096 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8971 (tp) REVERT: C 1205 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8814 (ptp) outliers start: 188 outliers final: 120 residues processed: 329 average time/residue: 0.4245 time to fit residues: 173.9362 Evaluate side-chains 290 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 157 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU 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 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1205 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 258 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 595 ASN B 402 GLN B 583 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.159212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105681 restraints weight = 43751.270| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.84 r_work: 0.3124 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 30390 Z= 0.258 Angle : 0.730 17.343 41580 Z= 0.362 Chirality : 0.053 0.762 4908 Planarity : 0.006 0.106 5172 Dihedral : 10.354 108.437 5978 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.16 % Allowed : 14.94 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.57 (0.13), residues: 3618 helix: 0.64 (0.19), residues: 760 sheet: -0.51 (0.17), residues: 865 loop : -2.05 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 206 TYR 0.021 0.002 TYR A 191 PHE 0.019 0.002 PHE B 968 TRP 0.016 0.002 TRP C 174 HIS 0.009 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00625 (30225) covalent geometry : angle 0.66902 (41157) SS BOND : bond 0.00381 ( 72) SS BOND : angle 1.40499 ( 144) hydrogen bonds : bond 0.06094 ( 1016) hydrogen bonds : angle 5.22465 ( 2934) link_ALPHA1-3 : bond 0.00550 ( 6) link_ALPHA1-3 : angle 2.14876 ( 18) link_ALPHA1-4 : bond 0.01588 ( 3) link_ALPHA1-4 : angle 3.34273 ( 9) link_ALPHA1-6 : bond 0.00606 ( 3) link_ALPHA1-6 : angle 1.76764 ( 9) link_BETA1-4 : bond 0.00371 ( 15) link_BETA1-4 : angle 1.70238 ( 45) link_NAG-ASN : bond 0.00535 ( 66) link_NAG-ASN : angle 3.96259 ( 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 363 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 163 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9103 (mp) cc_final: 0.8840 (mm) REVERT: A 124 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7303 (tp) REVERT: A 233 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8568 (t) REVERT: A 659 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7819 (ttpm) REVERT: A 885 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8427 (tptp) REVERT: A 906 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8395 (mp) REVERT: A 1003 LEU cc_start: 0.8607 (mm) cc_final: 0.8248 (tp) REVERT: A 1069 GLU cc_start: 0.7704 (tp30) cc_final: 0.7240 (tm-30) REVERT: A 1091 GLN cc_start: 0.8737 (tt0) cc_final: 0.8483 (tt0) REVERT: B 97 ASP cc_start: 0.7560 (m-30) cc_final: 0.6901 (t0) REVERT: B 126 ILE cc_start: 0.6081 (OUTLIER) cc_final: 0.5771 (mp) REVERT: B 289 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8201 (tt0) REVERT: B 655 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8847 (mt) REVERT: B 711 PHE cc_start: 0.7943 (m-80) cc_final: 0.7579 (m-10) REVERT: B 952 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: C 213 TYR cc_start: 0.9265 (OUTLIER) cc_final: 0.8078 (p90) REVERT: C 511 TYR cc_start: -0.0812 (OUTLIER) cc_final: -0.1701 (m-10) REVERT: C 652 ASN cc_start: 0.8739 (m-40) cc_final: 0.8454 (m-40) REVERT: C 780 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: C 800 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: C 827 ASP cc_start: 0.8778 (m-30) cc_final: 0.8519 (m-30) REVERT: C 845 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: C 1066 ASP cc_start: 0.8009 (p0) cc_final: 0.7534 (p0) REVERT: C 1069 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: C 1071 GLN cc_start: 0.8440 (mt0) cc_final: 0.8045 (mp-120) REVERT: C 1096 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9035 (tp) REVERT: C 1205 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8782 (ptp) outliers start: 200 outliers final: 135 residues processed: 339 average time/residue: 0.4020 time to fit residues: 172.2010 Evaluate side-chains 303 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 153 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU 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 952 GLU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1038 GLN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1205 MET Chi-restraints excluded: chain B residue 1207 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 841 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 96 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 302 optimal weight: 6.9990 chunk 332 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 303 optimal weight: 0.9990 chunk 343 optimal weight: 0.7980 chunk 354 optimal weight: 0.8980 chunk 327 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN B1059 GLN ** C 413 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 = 0.4089 r_free = 0.4089 target = 0.161829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108110 restraints weight = 44119.577| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.76 r_work: 0.3175 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30390 Z= 0.124 Angle : 0.631 17.048 41580 Z= 0.314 Chirality : 0.049 0.715 4908 Planarity : 0.005 0.102 5172 Dihedral : 9.653 106.869 5971 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 4.87 % Allowed : 16.27 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.21 (0.14), residues: 3618 helix: 1.18 (0.20), residues: 760 sheet: -0.36 (0.17), residues: 855 loop : -1.87 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 206 TYR 0.022 0.001 TYR A 191 PHE 0.017 0.001 PHE A 968 TRP 0.015 0.001 TRP B 257 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00278 (30225) covalent geometry : angle 0.57085 (41157) SS BOND : bond 0.00230 ( 72) SS BOND : angle 0.98978 ( 144) hydrogen bonds : bond 0.04693 ( 1016) hydrogen bonds : angle 4.93861 ( 2934) link_ALPHA1-3 : bond 0.00605 ( 6) link_ALPHA1-3 : angle 2.00476 ( 18) link_ALPHA1-4 : bond 0.01405 ( 3) link_ALPHA1-4 : angle 3.20021 ( 9) link_ALPHA1-6 : bond 0.00629 ( 3) link_ALPHA1-6 : angle 1.66894 ( 9) link_BETA1-4 : bond 0.00343 ( 15) link_BETA1-4 : angle 1.54169 ( 45) link_NAG-ASN : bond 0.00523 ( 66) link_NAG-ASN : angle 3.70005 ( 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 324 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 166 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7208 (tp) REVERT: A 659 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7748 (tttm) REVERT: A 885 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8438 (tptp) REVERT: A 906 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8448 (mp) REVERT: A 1003 LEU cc_start: 0.8629 (mm) cc_final: 0.8282 (tp) REVERT: A 1091 GLN cc_start: 0.8661 (tt0) cc_final: 0.8445 (tt0) REVERT: B 126 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5728 (mp) REVERT: B 289 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8201 (tt0) REVERT: B 711 PHE cc_start: 0.7964 (m-80) cc_final: 0.7604 (m-10) REVERT: C 213 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8096 (p90) REVERT: C 511 TYR cc_start: -0.0979 (OUTLIER) cc_final: -0.1783 (m-10) REVERT: C 636 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.8033 (m) REVERT: C 652 ASN cc_start: 0.8664 (m-40) cc_final: 0.8380 (m-40) REVERT: C 827 ASP cc_start: 0.8777 (m-30) cc_final: 0.8552 (m-30) REVERT: C 1066 ASP cc_start: 0.8026 (p0) cc_final: 0.7695 (p0) REVERT: C 1069 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: C 1071 GLN cc_start: 0.8409 (mt0) cc_final: 0.7999 (mp10) REVERT: C 1096 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8964 (tp) REVERT: C 1205 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8714 (ptp) outliers start: 158 outliers final: 104 residues processed: 305 average time/residue: 0.4142 time to fit residues: 158.8175 Evaluate side-chains 270 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 156 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU 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 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 353 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 0.0030 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 0.0970 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN B 583 ASN B 998 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 HIS C 894 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.163557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110570 restraints weight = 44095.705| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.79 r_work: 0.3209 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30390 Z= 0.102 Angle : 0.588 16.717 41580 Z= 0.293 Chirality : 0.047 0.699 4908 Planarity : 0.005 0.105 5172 Dihedral : 8.964 105.993 5953 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.00 % Allowed : 17.47 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.94 (0.14), residues: 3618 helix: 1.58 (0.21), residues: 758 sheet: -0.27 (0.17), residues: 864 loop : -1.75 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 932 TYR 0.027 0.001 TYR A 191 PHE 0.024 0.001 PHE C 391 TRP 0.015 0.001 TRP B 971 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00214 (30225) covalent geometry : angle 0.53767 (41157) SS BOND : bond 0.00299 ( 72) SS BOND : angle 0.99787 ( 144) hydrogen bonds : bond 0.04015 ( 1016) hydrogen bonds : angle 4.70937 ( 2934) link_ALPHA1-3 : bond 0.00623 ( 6) link_ALPHA1-3 : angle 2.00720 ( 18) link_ALPHA1-4 : bond 0.01613 ( 3) link_ALPHA1-4 : angle 3.27353 ( 9) link_ALPHA1-6 : bond 0.00638 ( 3) link_ALPHA1-6 : angle 1.64387 ( 9) link_BETA1-4 : bond 0.00358 ( 15) link_BETA1-4 : angle 1.47977 ( 45) link_NAG-ASN : bond 0.00532 ( 66) link_NAG-ASN : angle 3.20546 ( 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 294 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 164 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7125 (tp) REVERT: A 447 ARG cc_start: 0.5004 (OUTLIER) cc_final: 0.4562 (tmm-80) REVERT: A 659 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7781 (tttm) REVERT: A 885 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8410 (tptp) REVERT: A 1003 LEU cc_start: 0.8594 (mm) cc_final: 0.8230 (tp) REVERT: B 51 VAL cc_start: 0.6780 (OUTLIER) cc_final: 0.6573 (t) REVERT: B 289 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8193 (tt0) REVERT: B 711 PHE cc_start: 0.7932 (m-80) cc_final: 0.7562 (m-10) REVERT: C 213 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8144 (p90) REVERT: C 511 TYR cc_start: -0.0839 (OUTLIER) cc_final: -0.1632 (m-10) REVERT: C 827 ASP cc_start: 0.8772 (m-30) cc_final: 0.8549 (m-30) REVERT: C 863 GLN cc_start: 0.8033 (tt0) cc_final: 0.7573 (pt0) REVERT: C 1066 ASP cc_start: 0.8009 (p0) cc_final: 0.7754 (p0) REVERT: C 1069 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: C 1071 GLN cc_start: 0.8300 (mt0) cc_final: 0.7955 (mp-120) REVERT: C 1096 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8959 (tp) outliers start: 130 outliers final: 84 residues processed: 276 average time/residue: 0.4393 time to fit residues: 151.4915 Evaluate side-chains 243 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 151 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 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 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 233 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 328 optimal weight: 0.1980 chunk 199 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN B 894 GLN ** C 413 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 = 0.4085 r_free = 0.4085 target = 0.161418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107560 restraints weight = 43907.891| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.79 r_work: 0.3156 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30390 Z= 0.164 Angle : 0.625 16.597 41580 Z= 0.313 Chirality : 0.049 0.675 4908 Planarity : 0.005 0.105 5172 Dihedral : 8.766 106.154 5930 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.41 % Allowed : 17.07 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % 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: -0.96 (0.14), residues: 3618 helix: 1.43 (0.20), residues: 761 sheet: -0.23 (0.17), residues: 869 loop : -1.74 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 932 TYR 0.021 0.001 TYR A 191 PHE 0.017 0.001 PHE B 222 TRP 0.014 0.001 TRP B 257 HIS 0.007 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00388 (30225) covalent geometry : angle 0.57789 (41157) SS BOND : bond 0.00326 ( 72) SS BOND : angle 1.00501 ( 144) hydrogen bonds : bond 0.04929 ( 1016) hydrogen bonds : angle 4.81372 ( 2934) link_ALPHA1-3 : bond 0.00567 ( 6) link_ALPHA1-3 : angle 2.11734 ( 18) link_ALPHA1-4 : bond 0.01603 ( 3) link_ALPHA1-4 : angle 3.31042 ( 9) link_ALPHA1-6 : bond 0.00580 ( 3) link_ALPHA1-6 : angle 1.69742 ( 9) link_BETA1-4 : bond 0.00356 ( 15) link_BETA1-4 : angle 1.56254 ( 45) link_NAG-ASN : bond 0.00516 ( 66) link_NAG-ASN : angle 3.22642 ( 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 299 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 156 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7158 (tp) REVERT: A 659 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7812 (ttpm) REVERT: A 788 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8723 (tp) REVERT: A 885 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8394 (tptp) REVERT: A 1003 LEU cc_start: 0.8560 (mm) cc_final: 0.8202 (tp) REVERT: A 1038 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: A 1066 ASP cc_start: 0.6327 (OUTLIER) cc_final: 0.5901 (m-30) REVERT: B 236 TYR cc_start: 0.7371 (t80) cc_final: 0.6584 (t80) REVERT: B 289 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8212 (tt0) REVERT: B 711 PHE cc_start: 0.7915 (m-80) cc_final: 0.7544 (m-10) REVERT: B 894 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7096 (pp30) REVERT: B 916 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8528 (t) REVERT: C 213 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8126 (p90) REVERT: C 511 TYR cc_start: -0.0725 (OUTLIER) cc_final: -0.1561 (m-10) REVERT: C 780 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8331 (pm20) REVERT: C 827 ASP cc_start: 0.8787 (m-30) cc_final: 0.8567 (m-30) REVERT: C 845 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: C 1066 ASP cc_start: 0.8073 (p0) cc_final: 0.7784 (p0) REVERT: C 1069 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: C 1071 GLN cc_start: 0.8404 (mt0) cc_final: 0.7996 (mp-120) REVERT: C 1096 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9028 (tp) outliers start: 143 outliers final: 104 residues processed: 280 average time/residue: 0.4316 time to fit residues: 153.1642 Evaluate side-chains 267 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 150 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 894 GLN Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1207 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1118 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 1213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 222 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 356 optimal weight: 2.9990 chunk 295 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 413 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 = 0.4076 r_free = 0.4076 target = 0.160603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106948 restraints weight = 44050.322| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.86 r_work: 0.3151 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30390 Z= 0.191 Angle : 0.650 16.369 41580 Z= 0.326 Chirality : 0.050 0.661 4908 Planarity : 0.005 0.104 5172 Dihedral : 8.804 106.026 5926 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.68 % Allowed : 16.97 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.06 (0.14), residues: 3618 helix: 1.24 (0.20), residues: 768 sheet: -0.30 (0.17), residues: 859 loop : -1.74 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 932 TYR 0.021 0.002 TYR A 191 PHE 0.025 0.002 PHE C 391 TRP 0.016 0.001 TRP B 257 HIS 0.008 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00460 (30225) covalent geometry : angle 0.60503 (41157) SS BOND : bond 0.00338 ( 72) SS BOND : angle 1.10711 ( 144) hydrogen bonds : bond 0.05279 ( 1016) hydrogen bonds : angle 4.89025 ( 2934) link_ALPHA1-3 : bond 0.00552 ( 6) link_ALPHA1-3 : angle 2.13643 ( 18) link_ALPHA1-4 : bond 0.01557 ( 3) link_ALPHA1-4 : angle 3.33316 ( 9) link_ALPHA1-6 : bond 0.00571 ( 3) link_ALPHA1-6 : angle 1.71377 ( 9) link_BETA1-4 : bond 0.00343 ( 15) link_BETA1-4 : angle 1.60372 ( 45) link_NAG-ASN : bond 0.00492 ( 66) link_NAG-ASN : angle 3.18828 ( 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 300 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 148 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 SER cc_start: 0.6978 (OUTLIER) cc_final: 0.6778 (t) REVERT: A 124 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7192 (tp) REVERT: A 659 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7811 (ttpm) REVERT: A 788 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8707 (tp) REVERT: A 885 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8388 (tptp) REVERT: A 1003 LEU cc_start: 0.8562 (mm) cc_final: 0.8203 (tp) REVERT: A 1038 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: A 1066 ASP cc_start: 0.6310 (OUTLIER) cc_final: 0.5729 (m-30) REVERT: B 83 LYS cc_start: 0.4392 (OUTLIER) cc_final: 0.3954 (pptt) REVERT: B 236 TYR cc_start: 0.7278 (t80) cc_final: 0.6515 (t80) REVERT: B 289 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8206 (tt0) REVERT: B 711 PHE cc_start: 0.7921 (m-80) cc_final: 0.7542 (m-10) REVERT: C 34 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6768 (ppt170) REVERT: C 213 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8157 (p90) REVERT: C 511 TYR cc_start: -0.0709 (OUTLIER) cc_final: -0.1553 (m-10) REVERT: C 652 ASN cc_start: 0.8673 (m-40) cc_final: 0.8401 (m-40) REVERT: C 780 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: C 800 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8311 (pt0) REVERT: C 827 ASP cc_start: 0.8753 (m-30) cc_final: 0.8527 (m-30) REVERT: C 845 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: C 1066 ASP cc_start: 0.8048 (p0) cc_final: 0.7523 (p0) REVERT: C 1069 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: C 1071 GLN cc_start: 0.8436 (mt0) cc_final: 0.8001 (mp-120) REVERT: C 1096 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9020 (tp) outliers start: 152 outliers final: 114 residues processed: 277 average time/residue: 0.4056 time to fit residues: 143.1055 Evaluate side-chains 274 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 145 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 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 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1205 MET Chi-restraints excluded: chain B residue 1207 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1118 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 1213 THR Chi-restraints excluded: chain C residue 1218 ILE 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: 3.9990 chunk 200 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 344 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN A 371 ASN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.162957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109460 restraints weight = 44047.735| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.73 r_work: 0.3192 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30390 Z= 0.111 Angle : 0.585 16.406 41580 Z= 0.292 Chirality : 0.047 0.652 4908 Planarity : 0.005 0.102 5172 Dihedral : 8.347 104.348 5926 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.85 % Allowed : 17.81 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.82 (0.14), residues: 3618 helix: 1.58 (0.20), residues: 767 sheet: -0.20 (0.17), residues: 864 loop : -1.63 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 932 TYR 0.023 0.001 TYR A 191 PHE 0.015 0.001 PHE B 222 TRP 0.016 0.001 TRP B 971 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00245 (30225) covalent geometry : angle 0.53902 (41157) SS BOND : bond 0.00249 ( 72) SS BOND : angle 0.80061 ( 144) hydrogen bonds : bond 0.04190 ( 1016) hydrogen bonds : angle 4.67297 ( 2934) link_ALPHA1-3 : bond 0.00611 ( 6) link_ALPHA1-3 : angle 2.00287 ( 18) link_ALPHA1-4 : bond 0.01562 ( 3) link_ALPHA1-4 : angle 3.23830 ( 9) link_ALPHA1-6 : bond 0.00597 ( 3) link_ALPHA1-6 : angle 1.64511 ( 9) link_BETA1-4 : bond 0.00349 ( 15) link_BETA1-4 : angle 1.46123 ( 45) link_NAG-ASN : bond 0.00542 ( 66) link_NAG-ASN : angle 3.07824 ( 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 278 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 153 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7115 (tp) REVERT: A 659 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7708 (tttm) REVERT: A 771 ASN cc_start: 0.7095 (OUTLIER) cc_final: 0.6431 (p0) REVERT: A 885 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8371 (tptp) REVERT: A 1003 LEU cc_start: 0.8590 (mm) cc_final: 0.8219 (tp) REVERT: A 1066 ASP cc_start: 0.6272 (OUTLIER) cc_final: 0.5860 (m-30) REVERT: B 34 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6205 (ptp90) REVERT: B 51 VAL cc_start: 0.6527 (OUTLIER) cc_final: 0.6316 (t) REVERT: B 289 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8168 (tt0) REVERT: B 711 PHE cc_start: 0.7907 (m-80) cc_final: 0.7528 (m-10) REVERT: B 890 CYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7610 (t) REVERT: C 34 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6792 (ppt170) REVERT: C 213 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8167 (p90) REVERT: C 511 TYR cc_start: -0.0732 (OUTLIER) cc_final: -0.1563 (m-10) REVERT: C 652 ASN cc_start: 0.8651 (m-40) cc_final: 0.8375 (m-40) REVERT: C 780 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: C 827 ASP cc_start: 0.8751 (m-30) cc_final: 0.8539 (m-30) REVERT: C 967 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8506 (mtp) REVERT: C 1066 ASP cc_start: 0.8077 (p0) cc_final: 0.7830 (p0) REVERT: C 1069 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: C 1071 GLN cc_start: 0.8368 (mt0) cc_final: 0.7972 (mp-120) outliers start: 125 outliers final: 93 residues processed: 262 average time/residue: 0.4056 time to fit residues: 135.8740 Evaluate side-chains 252 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 146 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 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 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 967 MET Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1118 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 123 optimal weight: 2.9990 chunk 296 optimal weight: 0.0270 chunk 235 optimal weight: 0.9990 chunk 358 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 315 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.163589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110726 restraints weight = 44008.669| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.82 r_work: 0.3195 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30390 Z= 0.106 Angle : 0.580 16.160 41580 Z= 0.289 Chirality : 0.047 0.641 4908 Planarity : 0.005 0.105 5172 Dihedral : 8.044 103.664 5920 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.42 % Allowed : 18.27 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.68 (0.14), residues: 3618 helix: 1.71 (0.20), residues: 767 sheet: -0.10 (0.17), residues: 869 loop : -1.56 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 932 TYR 0.027 0.001 TYR A 191 PHE 0.027 0.001 PHE C 391 TRP 0.025 0.001 TRP B 971 HIS 0.005 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00234 (30225) covalent geometry : angle 0.53596 (41157) SS BOND : bond 0.00252 ( 72) SS BOND : angle 0.77749 ( 144) hydrogen bonds : bond 0.04055 ( 1016) hydrogen bonds : angle 4.58266 ( 2934) link_ALPHA1-3 : bond 0.00577 ( 6) link_ALPHA1-3 : angle 2.05332 ( 18) link_ALPHA1-4 : bond 0.01665 ( 3) link_ALPHA1-4 : angle 3.26872 ( 9) link_ALPHA1-6 : bond 0.00587 ( 3) link_ALPHA1-6 : angle 1.64937 ( 9) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 1.45033 ( 45) link_NAG-ASN : bond 0.00511 ( 66) link_NAG-ASN : angle 3.00046 ( 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 260 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 149 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7102 (tp) REVERT: A 659 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7726 (tttm) REVERT: A 885 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8322 (tptp) REVERT: A 1003 LEU cc_start: 0.8612 (mm) cc_final: 0.8237 (tp) REVERT: A 1066 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5834 (m-30) REVERT: B 34 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6087 (ptp-170) REVERT: B 289 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8188 (tt0) REVERT: B 711 PHE cc_start: 0.7922 (m-80) cc_final: 0.7546 (m-10) REVERT: B 953 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8549 (m) REVERT: C 34 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6905 (ppt170) REVERT: C 213 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8248 (p90) REVERT: C 511 TYR cc_start: -0.0756 (OUTLIER) cc_final: -0.1571 (m-10) REVERT: C 780 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: C 827 ASP cc_start: 0.8715 (m-30) cc_final: 0.8501 (m-30) REVERT: C 967 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8441 (ptm) REVERT: C 1066 ASP cc_start: 0.8095 (p0) cc_final: 0.7856 (p0) REVERT: C 1069 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: C 1071 GLN cc_start: 0.8324 (mt0) cc_final: 0.7934 (mp-120) REVERT: C 1104 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8916 (m) outliers start: 111 outliers final: 84 residues processed: 245 average time/residue: 0.3968 time to fit residues: 124.5723 Evaluate side-chains 244 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 148 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU 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 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 967 MET Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1104 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 182 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 278 optimal weight: 10.0000 chunk 303 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 353 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 413 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 = 0.4070 r_free = 0.4070 target = 0.160103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106534 restraints weight = 44070.989| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.82 r_work: 0.3129 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30390 Z= 0.240 Angle : 0.694 15.836 41580 Z= 0.348 Chirality : 0.051 0.624 4908 Planarity : 0.005 0.109 5172 Dihedral : 8.484 104.298 5911 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.73 % Allowed : 18.21 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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: -0.99 (0.14), residues: 3618 helix: 1.21 (0.20), residues: 768 sheet: -0.26 (0.17), residues: 860 loop : -1.66 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 932 TYR 0.025 0.002 TYR A 191 PHE 0.018 0.002 PHE C 592 TRP 0.016 0.002 TRP B 257 HIS 0.009 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00584 (30225) covalent geometry : angle 0.65028 (41157) SS BOND : bond 0.00388 ( 72) SS BOND : angle 1.16674 ( 144) hydrogen bonds : bond 0.05807 ( 1016) hydrogen bonds : angle 4.93615 ( 2934) link_ALPHA1-3 : bond 0.00536 ( 6) link_ALPHA1-3 : angle 2.27049 ( 18) link_ALPHA1-4 : bond 0.01712 ( 3) link_ALPHA1-4 : angle 3.38619 ( 9) link_ALPHA1-6 : bond 0.00546 ( 3) link_ALPHA1-6 : angle 1.77568 ( 9) link_BETA1-4 : bond 0.00361 ( 15) link_BETA1-4 : angle 1.63244 ( 45) link_NAG-ASN : bond 0.00517 ( 66) link_NAG-ASN : angle 3.22108 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11352.37 seconds wall clock time: 193 minutes 30.58 seconds (11610.58 seconds total)