Starting phenix.real_space_refine on Thu Nov 20 01:58:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1h_38836/11_2025/8y1h_38836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1h_38836/11_2025/8y1h_38836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y1h_38836/11_2025/8y1h_38836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1h_38836/11_2025/8y1h_38836.map" model { file = "/net/cci-nas-00/data/ceres_data/8y1h_38836/11_2025/8y1h_38836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1h_38836/11_2025/8y1h_38836.cif" } resolution = 3.16 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= -0.002 sd= 0.078 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 118 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29541 Number of models: 1 Model: "" Number of chains: 21 Chain: "B" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 1155} Chain: "C" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 6.64, per 1000 atoms: 0.22 Number of scatterers: 29541 At special positions: 0 Unit cell: (160.876, 154.354, 213.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 171 16.00 O 5907 8.00 N 4734 7.00 C 18729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=71, symmetry=0 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.04 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " MAN N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG I 2 " - " MAN I 3 " " NAG N 2 " - " MAN N 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN I 3 " - " MAN I 4 " " MAN N 3 " - " MAN N 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A2001 " - " ASN A 19 " " NAG A2002 " - " ASN A 29 " " NAG A2003 " - " ASN A 58 " " NAG A2004 " - " ASN A 114 " " NAG A2005 " - " ASN A 171 " " NAG A2006 " - " ASN A 192 " " NAG A2007 " - " ASN A 251 " " NAG A2008 " - " ASN A 433 " " NAG A2009 " - " ASN A 454 " " NAG A2010 " - " ASN A 684 " " NAG A2011 " - " ASN A 703 " " NAG A2012 " - " ASN A 725 " " NAG A2013 " - " ASN A 771 " " NAG A2014 " - " ASN A 776 " " NAG A2015 " - " ASN A 793 " " NAG A2016 " - " ASN A 924 " " NAG A2017 " - " ASN A1211 " " NAG B2001 " - " ASN B 19 " " NAG B2002 " - " ASN B 29 " " NAG B2003 " - " ASN B 58 " " NAG B2004 " - " ASN B 114 " " NAG B2005 " - " ASN B 171 " " NAG B2006 " - " ASN B 192 " " NAG B2007 " - " ASN B 251 " " NAG B2008 " - " ASN B 433 " " NAG B2009 " - " ASN B 454 " " NAG B2010 " - " ASN B 684 " " NAG B2011 " - " ASN B 703 " " NAG B2012 " - " ASN B 725 " " NAG B2013 " - " ASN B 771 " " NAG B2014 " - " ASN B 776 " " NAG B2015 " - " ASN B 793 " " NAG B2016 " - " ASN B 924 " " NAG B2017 " - " ASN B1211 " " NAG C2001 " - " ASN C 19 " " NAG C2002 " - " ASN C 29 " " NAG C2003 " - " ASN C 58 " " NAG C2004 " - " ASN C 114 " " NAG C2005 " - " ASN C 171 " " NAG C2006 " - " ASN C 192 " " NAG C2007 " - " ASN C 251 " " NAG C2008 " - " ASN C 433 " " NAG C2009 " - " ASN C 454 " " NAG C2010 " - " ASN C 684 " " NAG C2011 " - " ASN C 703 " " NAG C2012 " - " ASN C 725 " " NAG C2013 " - " ASN C 771 " " NAG C2014 " - " ASN C 776 " " NAG C2015 " - " ASN C 793 " " NAG C2016 " - " ASN C 924 " " NAG C2017 " - " ASN C1211 " " NAG D 1 " - " ASN B 132 " " NAG E 1 " - " ASN B 188 " " NAG F 1 " - " ASN B 335 " " NAG G 1 " - " ASN B 355 " " NAG H 1 " - " ASN B 664 " " NAG I 1 " - " ASN C 132 " " NAG J 1 " - " ASN C 188 " " NAG K 1 " - " ASN C 335 " " NAG L 1 " - " ASN C 355 " " NAG M 1 " - " ASN C 664 " " NAG N 1 " - " ASN A 132 " " NAG O 1 " - " ASN A 188 " " NAG P 1 " - " ASN A 335 " " NAG Q 1 " - " ASN A 355 " " NAG R 1 " - " ASN A 664 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6828 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 71 sheets defined 22.8% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.894A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 355 through 363 removed outlier: 4.325A pdb=" N LEU B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.640A pdb=" N PHE B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.660A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.582A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 485 " --> pdb=" O VAL B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 481 through 485' Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.864A 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 703 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 830 Processing helix chain 'B' and resid 835 through 863 Processing helix chain 'B' and resid 901 through 908 Processing helix chain 'B' and resid 916 through 923 Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 934 through 940 Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 994 through 1000 Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1023 through 1046 removed outlier: 3.784A pdb=" N ALA B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1057 through 1065 removed outlier: 3.707A pdb=" N LEU B1065 " --> pdb=" O ILE B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1113 removed outlier: 4.156A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.972A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.778A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 removed outlier: 3.806A pdb=" N ARG C 398 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 4.043A 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 442 through 447 Processing helix chain 'C' and resid 552 through 556 removed outlier: 3.691A pdb=" N LYS C 555 " --> pdb=" O ASN C 552 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 552 through 556' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 813 through 819 Processing helix chain 'C' and resid 822 through 830 Processing helix chain 'C' and resid 834 through 862 Processing helix chain 'C' and resid 902 through 911 removed outlier: 3.703A pdb=" N LYS C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.915A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.539A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 965 Processing helix chain 'C' and resid 971 through 975 removed outlier: 3.710A pdb=" N ALA C 975 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 990 removed outlier: 3.623A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1000 Processing helix chain 'C' and resid 1000 through 1017 removed outlier: 3.769A pdb=" N ILE C1004 " --> pdb=" O ASN C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1046 Processing helix chain 'C' and resid 1057 through 1062 removed outlier: 3.621A pdb=" N LEU C1062 " --> pdb=" O LEU C1058 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1113 removed outlier: 4.319A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 1198 through 1202 removed outlier: 3.507A pdb=" N ASN C1201 " --> pdb=" O SER C1198 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C1202 " --> pdb=" O ASP C1199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1198 through 1202' Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.541A 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 356 through 362 Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.612A pdb=" N GLY A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.809A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 400 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.717A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.714A pdb=" N THR A 532 " --> pdb=" O SER A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 863 Processing helix chain 'A' and resid 901 through 911 removed outlier: 3.653A pdb=" N ASN A 909 " --> pdb=" O ASP A 905 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.663A pdb=" N PHE A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 940 Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 994 through 1017 removed outlier: 7.523A pdb=" N LYS A1002 " --> pdb=" O ASN A 998 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN A1017 " --> pdb=" O LEU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1045 Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.750A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1068 through 1113 removed outlier: 4.214A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.704A pdb=" N TYR A 649 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 648 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 634 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 670 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 624 " --> pdb=" O ILE A 627 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 61 removed outlier: 4.610A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 81 removed outlier: 3.558A pdb=" N LEU B 240 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.694A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 148 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 187 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 150 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 197 through 201 removed outlier: 3.616A pdb=" N THR B 259 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 257 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.643A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 160 removed outlier: 10.768A pdb=" N TYR B 158 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N HIS B 175 " --> pdb=" O TYR B 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 205 removed outlier: 7.321A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 307 removed outlier: 3.755A pdb=" N PHE B 681 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA B 679 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.590A pdb=" N GLY B 631 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 634 " --> pdb=" O THR B 668 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 658 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 657 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 337 through 339 removed outlier: 7.888A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 349 removed outlier: 4.108A pdb=" N THR B 387 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 593 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP B 389 " --> pdb=" O ASN B 591 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 429 " --> pdb=" O CYS B 586 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 588 " --> pdb=" O TYR B 427 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 427 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AB6, first strand: chain 'B' and resid 460 through 463 Processing sheet with id=AB7, first strand: chain 'B' and resid 466 through 468 removed outlier: 3.903A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER B 468 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AB9, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC1, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.775A pdb=" N PHE B 713 " --> pdb=" O VAL B 720 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 724 through 731 removed outlier: 7.059A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 773 through 775 removed outlier: 4.011A pdb=" N LEU C 867 " --> pdb=" O SER B 773 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 786 through 791 removed outlier: 3.600A pdb=" N VAL B1158 " --> pdb=" O PHE B 786 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 788 " --> pdb=" O VAL B1156 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B1177 " --> pdb=" O SER B1159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 794 through 797 removed outlier: 3.622A pdb=" N SER B1147 " --> pdb=" O ALA B 797 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE B1146 " --> pdb=" O ILE B1130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 800 through 803 removed outlier: 3.543A pdb=" N GLY B1140 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B1137 " --> pdb=" O GLY B1140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.360A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 866 through 868 removed outlier: 6.732A pdb=" N LEU B 867 " --> pdb=" O VAL A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 1162 through 1164 removed outlier: 3.570A pdb=" N ALA B1171 " --> pdb=" O VAL B1203 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 64 through 67 Processing sheet with id=AD2, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.779A pdb=" N GLU C 255 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 109 through 112 removed outlier: 3.860A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 183 through 190 removed outlier: 4.856A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA C 150 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS C 187 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE C 148 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE C 189 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 146 " --> pdb=" O PHE C 189 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 149 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 138 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 123 " --> pdb=" O MET C 238 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS C 234 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 212 through 213 Processing sheet with id=AD6, first strand: chain 'C' and resid 302 through 306 removed outlier: 3.689A pdb=" N GLY C 302 " --> pdb=" O PHE C 681 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.790A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 345 through 348 removed outlier: 3.923A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 388 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER C 422 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N CYS C 370 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLN C 424 " --> pdb=" O PHE C 368 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE C 368 " --> pdb=" O GLN C 424 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR C 426 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS C 364 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 345 through 348 removed outlier: 3.923A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 388 " --> pdb=" O ARG C 347 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AE2, first strand: chain 'C' and resid 460 through 462 removed outlier: 3.628A pdb=" N TYR C 462 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 467 through 468 Processing sheet with id=AE4, first strand: chain 'C' and resid 505 through 507 removed outlier: 3.788A pdb=" N TRP C 515 " --> pdb=" O ASP C 507 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 620 through 621 removed outlier: 3.522A pdb=" N LYS C 634 " --> pdb=" O THR C 668 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 648 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 690 through 693 removed outlier: 3.809A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 724 through 731 removed outlier: 3.656A pdb=" N LEU C 726 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR C 766 " --> pdb=" O LEU C 726 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER C 728 " --> pdb=" O THR C 766 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 773 through 775 Processing sheet with id=AE9, first strand: chain 'C' and resid 786 through 791 removed outlier: 3.685A pdb=" N ILE C 788 " --> pdb=" O VAL C1156 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL C1156 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 790 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 794 through 796 removed outlier: 3.575A pdb=" N LYS C1149 " --> pdb=" O THR C 795 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 803 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS C 799 " --> pdb=" O HIS C1145 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 794 through 796 removed outlier: 3.575A pdb=" N LYS C1149 " --> pdb=" O THR C 795 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.495A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AF5, first strand: chain 'C' and resid 1179 through 1180 Processing sheet with id=AF6, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.503A pdb=" N LEU A 268 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 65 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.503A pdb=" N LEU A 268 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN A 265 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP A 281 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 80 through 81 removed outlier: 4.210A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.536A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 139 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS A 151 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 187 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.523A pdb=" N LYS A 105 " --> pdb=" O TRP A 257 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 257 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AG3, first strand: chain 'A' and resid 302 through 307 Processing sheet with id=AG4, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AG5, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.710A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 391 " --> pdb=" O PHE A 589 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 421 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AG7, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AG8, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AG9, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.822A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 573 " --> pdb=" O GLY A 550 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'A' and resid 690 through 693 Processing sheet with id=AH2, first strand: chain 'A' and resid 724 through 731 removed outlier: 10.034A pdb=" N TYR A 762 " --> pdb=" O ASN A 725 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N THR A 727 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N PHE A 764 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A 729 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 766 " --> pdb=" O TYR A 729 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 786 through 790 removed outlier: 3.848A pdb=" N VAL A1156 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 794 through 803 removed outlier: 3.526A pdb=" N SER A1147 " --> pdb=" O ALA A 797 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A1144 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A1132 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE A1146 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.318A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 878 through 879 removed outlier: 4.048A pdb=" N VAL A 879 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'A' and resid 1203 through 1204 removed outlier: 3.565A pdb=" N VAL A1203 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1162 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'A' and resid 1176 through 1177 871 hydrogen bonds defined for protein. 2367 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: 6.22 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9224 1.35 - 1.47: 8095 1.47 - 1.60: 12708 1.60 - 1.72: 0 1.72 - 1.85: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" C VAL A 945 " pdb=" N LEU A 946 " ideal model delta sigma weight residual 1.329 1.238 0.091 1.60e-02 3.91e+03 3.23e+01 bond pdb=" C5 MAN D 3 " pdb=" O5 MAN D 3 " ideal model delta sigma weight residual 1.418 1.498 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C5 MAN N 3 " pdb=" O5 MAN N 3 " ideal model delta sigma weight residual 1.418 1.497 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C SER C1159 " pdb=" N PRO C1160 " ideal model delta sigma weight residual 1.333 1.363 -0.030 7.80e-03 1.64e+04 1.50e+01 bond pdb=" C PRO C 969 " pdb=" N PRO C 970 " ideal model delta sigma weight residual 1.337 1.377 -0.041 1.06e-02 8.90e+03 1.47e+01 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 39255 2.03 - 4.06: 1692 4.06 - 6.09: 162 6.09 - 8.12: 37 8.12 - 10.16: 11 Bond angle restraints: 41157 Sorted by residual: angle pdb=" N ILE A 245 " pdb=" CA ILE A 245 " pdb=" C ILE A 245 " ideal model delta sigma weight residual 113.20 106.73 6.47 9.60e-01 1.09e+00 4.54e+01 angle pdb=" N ILE B 329 " pdb=" CA ILE B 329 " pdb=" C ILE B 329 " ideal model delta sigma weight residual 113.53 107.12 6.41 9.80e-01 1.04e+00 4.28e+01 angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 116.99 -6.29 1.22e+00 6.72e-01 2.66e+01 angle pdb=" CA TYR B1148 " pdb=" CB TYR B1148 " pdb=" CG TYR B1148 " ideal model delta sigma weight residual 113.90 123.10 -9.20 1.80e+00 3.09e-01 2.61e+01 angle pdb=" N SER B 820 " pdb=" CA SER B 820 " pdb=" C SER B 820 " ideal model delta sigma weight residual 111.02 117.25 -6.23 1.22e+00 6.72e-01 2.61e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 17366 22.61 - 45.22: 1430 45.22 - 67.84: 373 67.84 - 90.45: 49 90.45 - 113.06: 6 Dihedral angle restraints: 19224 sinusoidal: 8586 harmonic: 10638 Sorted by residual: dihedral pdb=" CA PHE A 968 " pdb=" C PHE A 968 " pdb=" N PRO A 969 " pdb=" CA PRO A 969 " ideal model delta harmonic sigma weight residual -180.00 -127.63 -52.37 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA PHE C 968 " pdb=" C PHE C 968 " pdb=" N PRO C 969 " pdb=" CA PRO C 969 " ideal model delta harmonic sigma weight residual 180.00 -128.81 -51.19 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA PRO A 969 " pdb=" C PRO A 969 " pdb=" N PRO A 970 " pdb=" CA PRO A 970 " ideal model delta harmonic sigma weight residual 180.00 138.74 41.26 0 5.00e+00 4.00e-02 6.81e+01 ... (remaining 19221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4413 0.090 - 0.181: 473 0.181 - 0.271: 15 0.271 - 0.362: 4 0.362 - 0.452: 3 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.78e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.51e+00 chirality pdb=" C1 NAG B2003 " pdb=" ND2 ASN B 58 " pdb=" C2 NAG B2003 " pdb=" O5 NAG B2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 92 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 93 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B1067 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO B1068 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO B1068 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1068 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1067 " -0.062 5.00e-02 4.00e+02 9.27e-02 1.37e+01 pdb=" N PRO A1068 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO A1068 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A1068 " -0.052 5.00e-02 4.00e+02 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4394 2.76 - 3.29: 25963 3.29 - 3.83: 49850 3.83 - 4.36: 55560 4.36 - 4.90: 95806 Nonbonded interactions: 231573 Sorted by model distance: nonbonded pdb=" O SER C 886 " pdb=" OG SER C 901 " model vdw 2.224 3.040 nonbonded pdb=" O THR C 959 " pdb=" OG1 THR C 963 " model vdw 2.239 3.040 nonbonded pdb=" O LEU C1047 " pdb=" OG SER C1056 " model vdw 2.256 3.040 nonbonded pdb=" O THR B 959 " pdb=" OG1 THR B 963 " model vdw 2.276 3.040 nonbonded pdb=" O SER A 886 " pdb=" OG SER A 901 " model vdw 2.278 3.040 ... (remaining 231568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.680 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 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 : 0.006 0.091 30389 Z= 0.303 Angle : 0.975 18.375 41578 Z= 0.536 Chirality : 0.055 0.452 4908 Planarity : 0.007 0.108 5172 Dihedral : 17.119 113.060 12183 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 15.19 % Allowed : 13.28 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.56 (0.11), residues: 3618 helix: -2.73 (0.13), residues: 761 sheet: -2.88 (0.18), residues: 657 loop : -3.34 (0.10), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 346 TYR 0.027 0.002 TYR B 203 PHE 0.029 0.002 PHE C 713 TRP 0.025 0.002 TRP C 971 HIS 0.011 0.001 HIS B1129 Details of bonding type rmsd covalent geometry : bond 0.00605 (30225) covalent geometry : angle 0.93631 (41157) SS BOND : bond 0.00429 ( 71) SS BOND : angle 1.23336 ( 142) hydrogen bonds : bond 0.23001 ( 859) hydrogen bonds : angle 9.42790 ( 2367) link_ALPHA1-3 : bond 0.00920 ( 6) link_ALPHA1-3 : angle 2.12669 ( 18) link_ALPHA1-4 : bond 0.01403 ( 3) link_ALPHA1-4 : angle 4.42520 ( 9) link_ALPHA1-6 : bond 0.00591 ( 3) link_ALPHA1-6 : angle 1.81183 ( 9) link_BETA1-4 : bond 0.01041 ( 15) link_BETA1-4 : angle 2.43325 ( 45) link_NAG-ASN : bond 0.00720 ( 66) link_NAG-ASN : angle 3.67681 ( 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 822 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 493 poor density : 329 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ILE cc_start: 0.4503 (OUTLIER) cc_final: 0.4225 (mt) REVERT: B 73 ASN cc_start: 0.3069 (OUTLIER) cc_final: 0.2756 (t0) REVERT: B 117 LEU cc_start: 0.2511 (OUTLIER) cc_final: 0.1839 (tp) REVERT: B 145 ILE cc_start: 0.3962 (OUTLIER) cc_final: 0.3406 (mt) REVERT: B 177 ASP cc_start: 0.2705 (OUTLIER) cc_final: 0.2203 (m-30) REVERT: B 238 MET cc_start: 0.1334 (mtt) cc_final: 0.0909 (tpp) REVERT: B 266 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.5699 (t80) REVERT: B 280 VAL cc_start: 0.4955 (OUTLIER) cc_final: 0.4432 (t) REVERT: B 331 ASN cc_start: 0.1612 (OUTLIER) cc_final: 0.0864 (t0) REVERT: B 503 HIS cc_start: 0.2511 (OUTLIER) cc_final: 0.2264 (t-90) REVERT: B 737 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6959 (mtm180) REVERT: B 740 SER cc_start: 0.6597 (OUTLIER) cc_final: 0.6373 (p) REVERT: B 801 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7480 (pp20) REVERT: B 835 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.6848 (t80) REVERT: B 952 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5092 (tp30) REVERT: B 1015 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6957 (mp) REVERT: B 1017 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.5976 (m-40) REVERT: B 1075 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: B 1129 HIS cc_start: 0.5734 (OUTLIER) cc_final: 0.4805 (t-90) REVERT: B 1178 ILE cc_start: 0.2458 (OUTLIER) cc_final: 0.2128 (pp) REVERT: B 1182 ASP cc_start: 0.6951 (m-30) cc_final: 0.6547 (m-30) REVERT: B 1193 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6784 (m-80) REVERT: B 1197 ILE cc_start: 0.7263 (mt) cc_final: 0.6819 (mm) REVERT: C 34 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6147 (ppt-90) REVERT: C 52 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7033 (mp) REVERT: C 69 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6386 (ttpt) REVERT: C 112 TYR cc_start: 0.5536 (OUTLIER) cc_final: 0.4488 (m-10) REVERT: C 132 ASN cc_start: 0.1704 (OUTLIER) cc_final: 0.0959 (m-40) REVERT: C 187 LYS cc_start: 0.2357 (OUTLIER) cc_final: 0.2082 (tptt) REVERT: C 202 PHE cc_start: 0.5372 (m-10) cc_final: 0.5044 (m-10) REVERT: C 248 ASN cc_start: 0.3292 (OUTLIER) cc_final: 0.2762 (m110) REVERT: C 262 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7727 (p) REVERT: C 309 PHE cc_start: 0.4179 (OUTLIER) cc_final: 0.3441 (p90) REVERT: C 373 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7604 (tt) REVERT: C 396 ARG cc_start: 0.5714 (ptt-90) cc_final: 0.5212 (ptt90) REVERT: C 577 PHE cc_start: 0.5398 (p90) cc_final: 0.5143 (p90) REVERT: C 621 ASN cc_start: 0.6705 (OUTLIER) cc_final: 0.5753 (t0) REVERT: C 661 PHE cc_start: 0.6358 (OUTLIER) cc_final: 0.6083 (t80) REVERT: C 748 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.5857 (tp) REVERT: C 811 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7419 (p) REVERT: C 822 TYR cc_start: 0.8385 (m-80) cc_final: 0.8142 (m-80) REVERT: C 828 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7759 (mm) REVERT: C 1115 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6996 (mptm) REVERT: C 1121 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7207 (mm) REVERT: A 18 PHE cc_start: 0.2153 (OUTLIER) cc_final: 0.0855 (t80) REVERT: A 34 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.5790 (mmm160) REVERT: A 213 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6545 (t80) REVERT: A 503 HIS cc_start: 0.1941 (OUTLIER) cc_final: 0.1478 (t70) REVERT: A 525 ILE cc_start: -0.0614 (OUTLIER) cc_final: -0.0932 (mt) REVERT: A 528 TYR cc_start: 0.1294 (OUTLIER) cc_final: 0.0825 (t80) REVERT: A 644 TRP cc_start: 0.6759 (OUTLIER) cc_final: 0.6491 (p-90) REVERT: A 714 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: A 737 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7575 (mmt-90) REVERT: A 745 ASP cc_start: 0.6513 (t0) cc_final: 0.5971 (p0) REVERT: A 835 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7259 (t80) REVERT: A 888 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6096 (pp) REVERT: A 1057 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.7945 (p) outliers start: 493 outliers final: 189 residues processed: 762 average time/residue: 0.1829 time to fit residues: 227.7467 Evaluate side-chains 445 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 207 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 760 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 870 ASN Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 995 ASP Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1075 ASP Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 794 PHE Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 811 THR Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 880 ASP Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 899 SER Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1115 LYS Chi-restraints excluded: chain C residue 1121 ILE Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain C residue 1209 SER Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 644 TRP Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1210 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN B 99 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 265 GLN B 291 GLN B 371 ASN B 545 HIS B 694 ASN B 799 HIS B 998 ASN B1000 ASN B1001 GLN B1017 ASN B1045 GLN B1091 GLN B1122 ASN C 22 ASN C 26 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN C 351 ASN C 561 ASN C 583 ASN C 694 ASN C 923 ASN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 GLN C1071 GLN C1091 GLN C1122 ASN C1136 ASN A 73 ASN A 115 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 295 GLN A 371 ASN A 465 HIS A 605 ASN A 872 ASN A 894 GLN A1038 GLN A1059 GLN A1091 GLN ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.193387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.154302 restraints weight = 71762.533| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 3.94 r_work: 0.4114 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 30389 Z= 0.140 Angle : 0.715 24.160 41578 Z= 0.360 Chirality : 0.048 0.371 4908 Planarity : 0.006 0.093 5172 Dihedral : 12.498 111.338 6251 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 8.01 % Allowed : 18.18 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -3.53 (0.12), residues: 3618 helix: -0.99 (0.17), residues: 759 sheet: -2.43 (0.17), residues: 700 loop : -2.95 (0.11), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 34 TYR 0.027 0.001 TYR C1219 PHE 0.017 0.001 PHE C1153 TRP 0.022 0.002 TRP B 174 HIS 0.004 0.001 HIS A1129 Details of bonding type rmsd covalent geometry : bond 0.00304 (30225) covalent geometry : angle 0.67368 (41157) SS BOND : bond 0.00359 ( 71) SS BOND : angle 1.68968 ( 142) hydrogen bonds : bond 0.04455 ( 859) hydrogen bonds : angle 6.82986 ( 2367) link_ALPHA1-3 : bond 0.00948 ( 6) link_ALPHA1-3 : angle 2.24996 ( 18) link_ALPHA1-4 : bond 0.01447 ( 3) link_ALPHA1-4 : angle 3.95255 ( 9) link_ALPHA1-6 : bond 0.01082 ( 3) link_ALPHA1-6 : angle 1.72879 ( 9) link_BETA1-4 : bond 0.00744 ( 15) link_BETA1-4 : angle 1.40037 ( 45) link_NAG-ASN : bond 0.00520 ( 66) link_NAG-ASN : angle 3.05757 ( 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 515 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 255 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.1728 (OUTLIER) cc_final: 0.1320 (tp) REVERT: B 177 ASP cc_start: 0.3290 (OUTLIER) cc_final: 0.2248 (m-30) REVERT: B 212 TYR cc_start: 0.2294 (m-80) cc_final: 0.2049 (m-80) REVERT: B 266 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.5788 (t80) REVERT: B 835 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6887 (t80) REVERT: B 1017 ASN cc_start: 0.6567 (OUTLIER) cc_final: 0.6210 (m110) REVERT: B 1120 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6562 (mtt180) REVERT: B 1129 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.5372 (t-90) REVERT: B 1131 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6284 (pp) REVERT: B 1135 GLN cc_start: 0.6259 (OUTLIER) cc_final: 0.6045 (mt0) REVERT: B 1197 ILE cc_start: 0.7221 (mt) cc_final: 0.6685 (mm) REVERT: C 52 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7019 (mt) REVERT: C 112 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6977 (m-10) REVERT: C 132 ASN cc_start: 0.2220 (OUTLIER) cc_final: 0.1035 (t0) REVERT: C 187 LYS cc_start: 0.3161 (OUTLIER) cc_final: 0.2649 (tptt) REVERT: C 202 PHE cc_start: 0.5292 (m-10) cc_final: 0.4738 (m-10) REVERT: C 238 MET cc_start: 0.0679 (mtp) cc_final: 0.0428 (mtp) REVERT: C 248 ASN cc_start: 0.5391 (OUTLIER) cc_final: 0.4841 (m110) REVERT: C 309 PHE cc_start: 0.4607 (OUTLIER) cc_final: 0.3786 (p90) REVERT: C 577 PHE cc_start: 0.7373 (p90) cc_final: 0.6564 (p90) REVERT: C 621 ASN cc_start: 0.6814 (OUTLIER) cc_final: 0.5870 (t0) REVERT: C 661 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.6263 (t80) REVERT: C 748 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6173 (tp) REVERT: C 828 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7890 (mm) REVERT: C 1002 LYS cc_start: 0.7230 (tptt) cc_final: 0.6680 (ptmm) REVERT: C 1068 PRO cc_start: 0.8200 (Cg_exo) cc_final: 0.7976 (Cg_endo) REVERT: C 1159 SER cc_start: 0.0947 (OUTLIER) cc_final: 0.0270 (p) REVERT: C 1178 ILE cc_start: 0.5188 (OUTLIER) cc_final: 0.4708 (pt) REVERT: A 18 PHE cc_start: 0.2998 (OUTLIER) cc_final: 0.1653 (t80) REVERT: A 34 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.5836 (mmm160) REVERT: A 69 LYS cc_start: 0.7072 (tttm) cc_final: 0.6848 (mtpp) REVERT: A 213 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7441 (t80) REVERT: A 528 TYR cc_start: 0.0050 (OUTLIER) cc_final: -0.0254 (t80) REVERT: A 644 TRP cc_start: 0.7293 (OUTLIER) cc_final: 0.7060 (p-90) REVERT: A 835 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.6989 (t80) REVERT: A 848 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: A 872 ASN cc_start: 0.5375 (OUTLIER) cc_final: 0.5173 (m110) REVERT: A 888 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6005 (pp) outliers start: 260 outliers final: 150 residues processed: 489 average time/residue: 0.1698 time to fit residues: 138.7239 Evaluate side-chains 385 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 205 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1135 GLN Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 706 PHE Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 794 PHE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1115 LYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1136 ASN Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1209 SER Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 644 TRP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 872 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1210 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 78 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 341 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 chunk 141 optimal weight: 0.0670 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 132 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 847 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN A 465 HIS A 561 ASN A 605 ASN A1038 GLN A1071 GLN ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.209565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.180739 restraints weight = 79802.370| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 3.50 r_work: 0.4200 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30389 Z= 0.119 Angle : 0.653 17.170 41578 Z= 0.326 Chirality : 0.046 0.345 4908 Planarity : 0.005 0.085 5172 Dihedral : 10.844 111.335 6086 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 6.56 % Allowed : 19.69 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -2.94 (0.13), residues: 3618 helix: -0.08 (0.18), residues: 770 sheet: -2.10 (0.17), residues: 705 loop : -2.75 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 264 TYR 0.021 0.001 TYR C 958 PHE 0.023 0.001 PHE A1217 TRP 0.039 0.001 TRP B 174 HIS 0.004 0.001 HIS A1129 Details of bonding type rmsd covalent geometry : bond 0.00251 (30225) covalent geometry : angle 0.60990 (41157) SS BOND : bond 0.00681 ( 71) SS BOND : angle 1.63647 ( 142) hydrogen bonds : bond 0.03838 ( 859) hydrogen bonds : angle 6.20659 ( 2367) link_ALPHA1-3 : bond 0.01037 ( 6) link_ALPHA1-3 : angle 2.00370 ( 18) link_ALPHA1-4 : bond 0.01662 ( 3) link_ALPHA1-4 : angle 3.56588 ( 9) link_ALPHA1-6 : bond 0.00725 ( 3) link_ALPHA1-6 : angle 1.85167 ( 9) link_BETA1-4 : bond 0.00497 ( 15) link_BETA1-4 : angle 1.31404 ( 45) link_NAG-ASN : bond 0.00672 ( 66) link_NAG-ASN : angle 2.95772 ( 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 455 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 242 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.1707 (OUTLIER) cc_final: 0.1280 (tp) REVERT: B 176 ILE cc_start: 0.3299 (OUTLIER) cc_final: 0.3073 (mt) REVERT: B 213 TYR cc_start: 0.2653 (p90) cc_final: 0.2417 (p90) REVERT: B 266 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.5700 (t80) REVERT: B 1120 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6482 (mtt180) REVERT: B 1129 HIS cc_start: 0.6437 (OUTLIER) cc_final: 0.5419 (t-90) REVERT: B 1197 ILE cc_start: 0.7077 (mt) cc_final: 0.6660 (mm) REVERT: C 52 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6999 (mt) REVERT: C 112 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.7016 (m-10) REVERT: C 132 ASN cc_start: 0.2575 (OUTLIER) cc_final: 0.1614 (m-40) REVERT: C 187 LYS cc_start: 0.3049 (OUTLIER) cc_final: 0.2759 (tptt) REVERT: C 202 PHE cc_start: 0.5467 (m-10) cc_final: 0.4951 (m-10) REVERT: C 238 MET cc_start: 0.0734 (mtp) cc_final: 0.0377 (mtp) REVERT: C 240 LEU cc_start: 0.7361 (tp) cc_final: 0.7023 (mt) REVERT: C 248 ASN cc_start: 0.5224 (OUTLIER) cc_final: 0.4404 (m110) REVERT: C 309 PHE cc_start: 0.4574 (OUTLIER) cc_final: 0.3811 (p90) REVERT: C 500 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.4418 (ttpt) REVERT: C 511 TYR cc_start: 0.3838 (OUTLIER) cc_final: 0.3251 (m-80) REVERT: C 577 PHE cc_start: 0.7401 (p90) cc_final: 0.6737 (p90) REVERT: C 748 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6251 (tp) REVERT: C 828 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7978 (mm) REVERT: C 1002 LYS cc_start: 0.7234 (tptt) cc_final: 0.6687 (ptmm) REVERT: A 18 PHE cc_start: 0.2981 (OUTLIER) cc_final: 0.1768 (t80) REVERT: A 34 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.5998 (mmm160) REVERT: A 69 LYS cc_start: 0.7166 (tttm) cc_final: 0.6861 (mtpp) REVERT: A 121 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6589 (p90) REVERT: A 213 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7531 (t80) REVERT: A 309 PHE cc_start: 0.5721 (OUTLIER) cc_final: 0.4529 (p90) REVERT: A 528 TYR cc_start: 0.0055 (OUTLIER) cc_final: -0.0246 (t80) REVERT: A 644 TRP cc_start: 0.7336 (OUTLIER) cc_final: 0.7051 (p-90) REVERT: A 737 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7752 (mmt-90) REVERT: A 777 ASP cc_start: 0.4104 (p0) cc_final: 0.3819 (p0) REVERT: A 788 ILE cc_start: 0.6092 (tt) cc_final: 0.5775 (tp) REVERT: A 835 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7003 (t80) REVERT: A 848 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7403 (m-30) outliers start: 213 outliers final: 132 residues processed: 427 average time/residue: 0.1736 time to fit residues: 123.8775 Evaluate side-chains 359 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 202 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 794 PHE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 993 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain C residue 1209 SER Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 644 TRP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1210 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 258 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 chunk 167 optimal weight: 0.0770 chunk 278 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 175 optimal weight: 0.0970 chunk 43 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.6336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1117 GLN A 204 GLN A 465 HIS A 605 ASN A1023 ASN A1038 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.209862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.4712 r_free = 0.4712 target = 0.180694 restraints weight = 79334.392| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 3.64 r_work: 0.4201 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 30389 Z= 0.115 Angle : 0.625 13.457 41578 Z= 0.313 Chirality : 0.045 0.343 4908 Planarity : 0.004 0.079 5172 Dihedral : 9.859 111.670 6031 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 6.38 % Allowed : 20.24 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.13), residues: 3618 helix: 0.39 (0.19), residues: 768 sheet: -1.87 (0.18), residues: 706 loop : -2.60 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 264 TYR 0.028 0.001 TYR C 528 PHE 0.021 0.001 PHE A1217 TRP 0.020 0.001 TRP B 174 HIS 0.004 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00253 (30225) covalent geometry : angle 0.58665 (41157) SS BOND : bond 0.00263 ( 71) SS BOND : angle 1.60275 ( 142) hydrogen bonds : bond 0.03549 ( 859) hydrogen bonds : angle 5.89105 ( 2367) link_ALPHA1-3 : bond 0.00989 ( 6) link_ALPHA1-3 : angle 1.90723 ( 18) link_ALPHA1-4 : bond 0.01535 ( 3) link_ALPHA1-4 : angle 3.37186 ( 9) link_ALPHA1-6 : bond 0.00673 ( 3) link_ALPHA1-6 : angle 1.90109 ( 9) link_BETA1-4 : bond 0.00458 ( 15) link_BETA1-4 : angle 1.26696 ( 45) link_NAG-ASN : bond 0.00477 ( 66) link_NAG-ASN : angle 2.68935 ( 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 433 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 226 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.1873 (OUTLIER) cc_final: 0.1446 (tp) REVERT: B 118 TYR cc_start: 0.7586 (m-10) cc_final: 0.7369 (m-10) REVERT: B 153 TYR cc_start: 0.2629 (t80) cc_final: 0.1544 (t80) REVERT: B 213 TYR cc_start: 0.2681 (p90) cc_final: 0.2332 (p90) REVERT: B 266 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.5543 (t80) REVERT: B 1120 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6589 (mtt180) REVERT: B 1129 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5386 (t-90) REVERT: B 1173 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.6661 (ptmm) REVERT: B 1197 ILE cc_start: 0.6971 (mt) cc_final: 0.6580 (mm) REVERT: C 52 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6887 (mt) REVERT: C 112 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.6950 (m-10) REVERT: C 202 PHE cc_start: 0.5484 (m-10) cc_final: 0.4922 (m-10) REVERT: C 232 LEU cc_start: 0.7727 (mp) cc_final: 0.7260 (mp) REVERT: C 238 MET cc_start: 0.0527 (mtp) cc_final: 0.0137 (mtp) REVERT: C 240 LEU cc_start: 0.7283 (tp) cc_final: 0.6986 (mt) REVERT: C 248 ASN cc_start: 0.5362 (OUTLIER) cc_final: 0.4506 (m110) REVERT: C 309 PHE cc_start: 0.4378 (OUTLIER) cc_final: 0.3640 (p90) REVERT: C 500 LYS cc_start: 0.5048 (OUTLIER) cc_final: 0.4006 (ttpt) REVERT: C 511 TYR cc_start: 0.3859 (OUTLIER) cc_final: 0.3198 (m-80) REVERT: C 577 PHE cc_start: 0.7272 (p90) cc_final: 0.6627 (p90) REVERT: C 748 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6141 (tp) REVERT: C 828 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7984 (mm) REVERT: C 931 ILE cc_start: 0.5248 (OUTLIER) cc_final: 0.5014 (mt) REVERT: C 1002 LYS cc_start: 0.7056 (tptt) cc_final: 0.6668 (ptmm) REVERT: C 1159 SER cc_start: 0.1128 (OUTLIER) cc_final: 0.0658 (p) REVERT: A 18 PHE cc_start: 0.2801 (OUTLIER) cc_final: 0.1664 (t80) REVERT: A 34 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6042 (mmm160) REVERT: A 69 LYS cc_start: 0.7213 (tttm) cc_final: 0.6955 (mtpp) REVERT: A 213 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7404 (t80) REVERT: A 309 PHE cc_start: 0.5439 (OUTLIER) cc_final: 0.4389 (p90) REVERT: A 528 TYR cc_start: 0.0264 (OUTLIER) cc_final: -0.0055 (t80) REVERT: A 644 TRP cc_start: 0.7196 (OUTLIER) cc_final: 0.6899 (p-90) REVERT: A 737 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7685 (mmt-90) REVERT: A 835 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6920 (t80) REVERT: A 848 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: A 888 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.5861 (pp) outliers start: 207 outliers final: 137 residues processed: 402 average time/residue: 0.1680 time to fit residues: 113.4059 Evaluate side-chains 369 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 207 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 794 PHE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 644 TRP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 96 optimal weight: 0.8980 chunk 310 optimal weight: 0.7980 chunk 302 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 HIS B 881 ASN B 984 GLN C 140 GLN C 847 ASN C1136 ASN A 295 GLN A 465 HIS A 605 ASN A 876 HIS ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.195141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.159831 restraints weight = 72560.575| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 3.95 r_work: 0.4094 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 30389 Z= 0.152 Angle : 0.643 13.737 41578 Z= 0.323 Chirality : 0.046 0.349 4908 Planarity : 0.005 0.073 5172 Dihedral : 9.595 112.262 6010 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 6.72 % Allowed : 20.43 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.13), residues: 3618 helix: 0.47 (0.19), residues: 759 sheet: -1.80 (0.18), residues: 721 loop : -2.56 (0.12), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.025 0.002 TYR A 958 PHE 0.024 0.001 PHE B 121 TRP 0.016 0.001 TRP B 174 HIS 0.015 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00342 (30225) covalent geometry : angle 0.60945 (41157) SS BOND : bond 0.00339 ( 71) SS BOND : angle 1.39032 ( 142) hydrogen bonds : bond 0.03799 ( 859) hydrogen bonds : angle 5.90453 ( 2367) link_ALPHA1-3 : bond 0.00982 ( 6) link_ALPHA1-3 : angle 1.91574 ( 18) link_ALPHA1-4 : bond 0.01544 ( 3) link_ALPHA1-4 : angle 3.33364 ( 9) link_ALPHA1-6 : bond 0.00690 ( 3) link_ALPHA1-6 : angle 1.92637 ( 9) link_BETA1-4 : bond 0.00475 ( 15) link_BETA1-4 : angle 1.29889 ( 45) link_NAG-ASN : bond 0.00466 ( 66) link_NAG-ASN : angle 2.60297 ( 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 423 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 205 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 TYR cc_start: 0.3239 (OUTLIER) cc_final: 0.1860 (t80) REVERT: B 118 TYR cc_start: 0.7567 (m-10) cc_final: 0.7305 (m-10) REVERT: B 153 TYR cc_start: 0.2813 (t80) cc_final: 0.2452 (t80) REVERT: B 177 ASP cc_start: 0.3145 (OUTLIER) cc_final: 0.2083 (m-30) REVERT: B 213 TYR cc_start: 0.2911 (p90) cc_final: 0.2520 (p90) REVERT: B 266 TYR cc_start: 0.6848 (OUTLIER) cc_final: 0.5681 (t80) REVERT: B 321 ILE cc_start: 0.7133 (mt) cc_final: 0.6744 (mt) REVERT: B 630 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: B 986 ARG cc_start: 0.5394 (OUTLIER) cc_final: 0.5013 (mmp80) REVERT: B 1116 SER cc_start: 0.6004 (OUTLIER) cc_final: 0.5759 (m) REVERT: B 1120 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7051 (mtt180) REVERT: B 1129 HIS cc_start: 0.6509 (OUTLIER) cc_final: 0.5409 (t-90) REVERT: B 1193 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: B 1197 ILE cc_start: 0.6976 (mt) cc_final: 0.6605 (mm) REVERT: B 1212 PHE cc_start: 0.4304 (OUTLIER) cc_final: 0.2901 (m-80) REVERT: C 52 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6960 (mt) REVERT: C 112 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7008 (m-10) REVERT: C 202 PHE cc_start: 0.5411 (m-10) cc_final: 0.4974 (m-10) REVERT: C 238 MET cc_start: 0.0866 (mtp) cc_final: 0.0417 (mtp) REVERT: C 240 LEU cc_start: 0.7262 (tp) cc_final: 0.7004 (mt) REVERT: C 309 PHE cc_start: 0.4685 (OUTLIER) cc_final: 0.3859 (p90) REVERT: C 500 LYS cc_start: 0.4936 (OUTLIER) cc_final: 0.3832 (ttpt) REVERT: C 511 TYR cc_start: 0.4022 (OUTLIER) cc_final: 0.3270 (m-80) REVERT: C 577 PHE cc_start: 0.7449 (p90) cc_final: 0.6828 (p90) REVERT: C 632 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.6467 (pt) REVERT: C 748 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6160 (tp) REVERT: C 828 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7866 (mm) REVERT: C 1002 LYS cc_start: 0.7307 (tptt) cc_final: 0.6765 (ptmm) REVERT: A 18 PHE cc_start: 0.3158 (OUTLIER) cc_final: 0.2047 (t80) REVERT: A 34 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.5946 (mmm160) REVERT: A 69 LYS cc_start: 0.7162 (tttm) cc_final: 0.6938 (mtpp) REVERT: A 268 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7803 (pp) REVERT: A 309 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.4232 (p90) REVERT: A 528 TYR cc_start: 0.0194 (OUTLIER) cc_final: -0.0100 (t80) REVERT: A 644 TRP cc_start: 0.7196 (OUTLIER) cc_final: 0.6974 (p-90) REVERT: A 737 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7751 (mmt-90) REVERT: A 835 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6906 (t80) REVERT: A 888 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6090 (pp) outliers start: 218 outliers final: 154 residues processed: 393 average time/residue: 0.1762 time to fit residues: 116.8631 Evaluate side-chains 371 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 190 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 794 PHE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 644 TRP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 353 optimal weight: 0.7980 chunk 255 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN C 874 ASN C1136 ASN A 234 HIS A 265 GLN A 465 HIS A 683 GLN A1079 ASN ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.207264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.183911 restraints weight = 78855.479| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 2.33 r_work: 0.4173 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30389 Z= 0.177 Angle : 0.670 14.084 41578 Z= 0.338 Chirality : 0.047 0.358 4908 Planarity : 0.005 0.072 5172 Dihedral : 9.485 112.768 6000 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 6.84 % Allowed : 20.58 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.13), residues: 3618 helix: 0.36 (0.19), residues: 760 sheet: -1.81 (0.18), residues: 714 loop : -2.52 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.030 0.002 TYR C 118 PHE 0.018 0.002 PHE C 764 TRP 0.014 0.001 TRP B 174 HIS 0.007 0.001 HIS B1129 Details of bonding type rmsd covalent geometry : bond 0.00400 (30225) covalent geometry : angle 0.63594 (41157) SS BOND : bond 0.00338 ( 71) SS BOND : angle 1.48863 ( 142) hydrogen bonds : bond 0.03979 ( 859) hydrogen bonds : angle 5.98351 ( 2367) link_ALPHA1-3 : bond 0.00993 ( 6) link_ALPHA1-3 : angle 1.89748 ( 18) link_ALPHA1-4 : bond 0.01545 ( 3) link_ALPHA1-4 : angle 3.32892 ( 9) link_ALPHA1-6 : bond 0.00684 ( 3) link_ALPHA1-6 : angle 1.91668 ( 9) link_BETA1-4 : bond 0.00489 ( 15) link_BETA1-4 : angle 1.31607 ( 45) link_NAG-ASN : bond 0.00487 ( 66) link_NAG-ASN : angle 2.70066 ( 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 420 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 198 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 TYR cc_start: 0.3279 (OUTLIER) cc_final: 0.1994 (t80) REVERT: B 153 TYR cc_start: 0.2526 (t80) cc_final: 0.1943 (t80) REVERT: B 177 ASP cc_start: 0.2656 (OUTLIER) cc_final: 0.1812 (m-30) REVERT: B 266 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.5797 (t80) REVERT: B 321 ILE cc_start: 0.7136 (mt) cc_final: 0.6803 (mt) REVERT: B 630 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: B 986 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.5158 (mmp80) REVERT: B 1120 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7241 (mtt180) REVERT: B 1129 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.5416 (t-90) REVERT: B 1131 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6644 (pt) REVERT: B 1193 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: B 1197 ILE cc_start: 0.6778 (mt) cc_final: 0.6575 (mm) REVERT: B 1212 PHE cc_start: 0.4347 (OUTLIER) cc_final: 0.2956 (m-80) REVERT: C 112 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6666 (m-10) REVERT: C 202 PHE cc_start: 0.5200 (m-10) cc_final: 0.4853 (m-10) REVERT: C 238 MET cc_start: 0.1256 (mtp) cc_final: 0.0851 (mtp) REVERT: C 240 LEU cc_start: 0.7221 (tp) cc_final: 0.6939 (mt) REVERT: C 248 ASN cc_start: 0.5366 (OUTLIER) cc_final: 0.4391 (m110) REVERT: C 309 PHE cc_start: 0.4690 (OUTLIER) cc_final: 0.3829 (p90) REVERT: C 500 LYS cc_start: 0.5391 (OUTLIER) cc_final: 0.4037 (ttpt) REVERT: C 511 TYR cc_start: 0.3166 (OUTLIER) cc_final: 0.2255 (m-80) REVERT: C 577 PHE cc_start: 0.6968 (p90) cc_final: 0.6431 (p90) REVERT: C 828 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7737 (mm) REVERT: C 1002 LYS cc_start: 0.7361 (tptt) cc_final: 0.6787 (ptmm) REVERT: A 18 PHE cc_start: 0.3082 (OUTLIER) cc_final: 0.1889 (t80) REVERT: A 34 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.5948 (mmm160) REVERT: A 69 LYS cc_start: 0.7188 (tttm) cc_final: 0.6975 (mtpp) REVERT: A 268 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7847 (pp) REVERT: A 309 PHE cc_start: 0.5412 (OUTLIER) cc_final: 0.4167 (p90) REVERT: A 528 TYR cc_start: 0.0406 (OUTLIER) cc_final: 0.0023 (t80) REVERT: A 644 TRP cc_start: 0.7238 (OUTLIER) cc_final: 0.6997 (p-90) REVERT: A 714 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: A 737 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7861 (mmt-90) REVERT: A 835 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6913 (t80) REVERT: A 888 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6298 (pp) REVERT: A 981 LEU cc_start: 0.4907 (OUTLIER) cc_final: 0.4132 (mm) outliers start: 222 outliers final: 163 residues processed: 391 average time/residue: 0.1648 time to fit residues: 109.8089 Evaluate side-chains 377 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 187 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain B residue 1182 ASP Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 794 PHE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1036 ASN Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1136 ASN Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 644 TRP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A 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: 1.9990 chunk 310 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 253 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 328 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 82 optimal weight: 0.0040 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 HIS B 881 ASN B1038 GLN C 799 HIS C 847 ASN A 465 HIS ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.208776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.186085 restraints weight = 79046.279| |-----------------------------------------------------------------------------| r_work (start): 0.4488 rms_B_bonded: 2.26 r_work: 0.4231 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30389 Z= 0.118 Angle : 0.620 19.317 41578 Z= 0.311 Chirality : 0.045 0.334 4908 Planarity : 0.004 0.072 5172 Dihedral : 9.070 112.091 5990 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.22 % Allowed : 21.35 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.13), residues: 3618 helix: 0.60 (0.19), residues: 765 sheet: -1.68 (0.19), residues: 717 loop : -2.44 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.023 0.001 TYR C 528 PHE 0.027 0.001 PHE B 121 TRP 0.015 0.001 TRP C 971 HIS 0.012 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00261 (30225) covalent geometry : angle 0.58789 (41157) SS BOND : bond 0.00420 ( 71) SS BOND : angle 1.29050 ( 142) hydrogen bonds : bond 0.03550 ( 859) hydrogen bonds : angle 5.69592 ( 2367) link_ALPHA1-3 : bond 0.01084 ( 6) link_ALPHA1-3 : angle 1.83635 ( 18) link_ALPHA1-4 : bond 0.01367 ( 3) link_ALPHA1-4 : angle 3.11866 ( 9) link_ALPHA1-6 : bond 0.00666 ( 3) link_ALPHA1-6 : angle 1.88045 ( 9) link_BETA1-4 : bond 0.00512 ( 15) link_BETA1-4 : angle 1.26169 ( 45) link_NAG-ASN : bond 0.00464 ( 66) link_NAG-ASN : angle 2.52009 ( 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 416 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 214 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 TYR cc_start: 0.3111 (OUTLIER) cc_final: 0.2024 (t80) REVERT: B 118 TYR cc_start: 0.7184 (m-10) cc_final: 0.6916 (m-10) REVERT: B 153 TYR cc_start: 0.2569 (t80) cc_final: 0.1939 (t80) REVERT: B 177 ASP cc_start: 0.2815 (OUTLIER) cc_final: 0.1972 (m-30) REVERT: B 218 MET cc_start: 0.5025 (mmt) cc_final: 0.4788 (mmp) REVERT: B 266 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.5706 (t80) REVERT: B 321 ILE cc_start: 0.7183 (mt) cc_final: 0.6836 (mt) REVERT: B 630 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: B 986 ARG cc_start: 0.5465 (OUTLIER) cc_final: 0.5249 (tpp-160) REVERT: B 1120 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6920 (mtt180) REVERT: B 1193 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.6445 (m-80) REVERT: B 1212 PHE cc_start: 0.4229 (OUTLIER) cc_final: 0.2867 (m-80) REVERT: C 52 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6935 (mt) REVERT: C 112 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6490 (m-10) REVERT: C 202 PHE cc_start: 0.5237 (m-10) cc_final: 0.4895 (m-10) REVERT: C 238 MET cc_start: 0.1043 (mtp) cc_final: 0.0630 (mtp) REVERT: C 240 LEU cc_start: 0.7169 (tp) cc_final: 0.6958 (mt) REVERT: C 248 ASN cc_start: 0.4798 (OUTLIER) cc_final: 0.4505 (m110) REVERT: C 309 PHE cc_start: 0.4773 (OUTLIER) cc_final: 0.3900 (p90) REVERT: C 500 LYS cc_start: 0.5337 (OUTLIER) cc_final: 0.4052 (ttpt) REVERT: C 511 TYR cc_start: 0.3502 (OUTLIER) cc_final: 0.2706 (m-80) REVERT: C 577 PHE cc_start: 0.6716 (p90) cc_final: 0.6222 (p90) REVERT: C 632 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.6569 (pt) REVERT: C 748 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6031 (tp) REVERT: C 828 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7771 (mm) REVERT: C 931 ILE cc_start: 0.5331 (OUTLIER) cc_final: 0.5094 (mt) REVERT: C 1002 LYS cc_start: 0.7350 (tptt) cc_final: 0.6771 (ptmm) REVERT: A 18 PHE cc_start: 0.2983 (OUTLIER) cc_final: 0.1781 (t80) REVERT: A 34 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6049 (mmm160) REVERT: A 309 PHE cc_start: 0.5360 (OUTLIER) cc_final: 0.4147 (p90) REVERT: A 528 TYR cc_start: 0.0473 (OUTLIER) cc_final: 0.0133 (t80) REVERT: A 737 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7733 (mmt-90) REVERT: A 835 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.6847 (t80) REVERT: A 888 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6265 (pp) outliers start: 202 outliers final: 148 residues processed: 391 average time/residue: 0.1730 time to fit residues: 114.7537 Evaluate side-chains 359 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 186 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 794 PHE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1210 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 222 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 314 optimal weight: 0.0070 chunk 203 optimal weight: 1.9990 chunk 356 optimal weight: 0.5980 chunk 295 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 chunk 230 optimal weight: 0.0050 overall best weight: 0.4812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS C 248 ASN A 295 GLN A 872 ASN ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.209648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.180771 restraints weight = 79662.485| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 3.67 r_work: 0.4199 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 30389 Z= 0.106 Angle : 0.601 16.963 41578 Z= 0.300 Chirality : 0.044 0.333 4908 Planarity : 0.004 0.071 5172 Dihedral : 8.640 111.414 5980 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.67 % Allowed : 22.24 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.13), residues: 3618 helix: 0.83 (0.19), residues: 770 sheet: -1.58 (0.19), residues: 720 loop : -2.36 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.022 0.001 TYR A 712 PHE 0.015 0.001 PHE B1008 TRP 0.016 0.001 TRP C 971 HIS 0.006 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00237 (30225) covalent geometry : angle 0.57226 (41157) SS BOND : bond 0.00219 ( 71) SS BOND : angle 1.05861 ( 142) hydrogen bonds : bond 0.03356 ( 859) hydrogen bonds : angle 5.42411 ( 2367) link_ALPHA1-3 : bond 0.00918 ( 6) link_ALPHA1-3 : angle 1.72823 ( 18) link_ALPHA1-4 : bond 0.01524 ( 3) link_ALPHA1-4 : angle 3.10864 ( 9) link_ALPHA1-6 : bond 0.00633 ( 3) link_ALPHA1-6 : angle 1.88386 ( 9) link_BETA1-4 : bond 0.00464 ( 15) link_BETA1-4 : angle 1.21067 ( 45) link_NAG-ASN : bond 0.00449 ( 66) link_NAG-ASN : angle 2.41664 ( 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 390 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 206 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 TYR cc_start: 0.3015 (OUTLIER) cc_final: 0.2048 (t80) REVERT: B 118 TYR cc_start: 0.7499 (m-10) cc_final: 0.7234 (m-10) REVERT: B 153 TYR cc_start: 0.2539 (t80) cc_final: 0.1628 (t80) REVERT: B 177 ASP cc_start: 0.2720 (OUTLIER) cc_final: 0.1912 (m-30) REVERT: B 266 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.5599 (t80) REVERT: B 321 ILE cc_start: 0.7207 (mt) cc_final: 0.6875 (mt) REVERT: B 630 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: B 1120 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6443 (mtt180) REVERT: B 1193 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: B 1212 PHE cc_start: 0.4091 (OUTLIER) cc_final: 0.2827 (m-80) REVERT: C 112 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7015 (m-10) REVERT: C 197 TRP cc_start: 0.6240 (OUTLIER) cc_final: 0.5519 (m-10) REVERT: C 202 PHE cc_start: 0.5260 (m-10) cc_final: 0.4738 (m-10) REVERT: C 309 PHE cc_start: 0.4780 (OUTLIER) cc_final: 0.3867 (p90) REVERT: C 500 LYS cc_start: 0.4894 (OUTLIER) cc_final: 0.3729 (ttpt) REVERT: C 511 TYR cc_start: 0.3771 (OUTLIER) cc_final: 0.3123 (m-80) REVERT: C 577 PHE cc_start: 0.7328 (p90) cc_final: 0.6729 (p90) REVERT: C 632 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.6465 (pt) REVERT: C 748 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6078 (tp) REVERT: C 828 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7664 (mm) REVERT: C 1002 LYS cc_start: 0.7223 (tptt) cc_final: 0.6759 (ptmm) REVERT: A 18 PHE cc_start: 0.3007 (OUTLIER) cc_final: 0.1961 (t80) REVERT: A 34 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6360 (mmm160) REVERT: A 213 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7410 (t80) REVERT: A 309 PHE cc_start: 0.5200 (OUTLIER) cc_final: 0.4012 (p90) REVERT: A 528 TYR cc_start: 0.0434 (OUTLIER) cc_final: 0.0069 (t80) REVERT: A 714 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: A 737 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.5801 (mmt-90) REVERT: A 738 MET cc_start: 0.7144 (mmp) cc_final: 0.6884 (mmt) REVERT: A 835 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6800 (t80) REVERT: A 888 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6030 (pp) outliers start: 184 outliers final: 131 residues processed: 361 average time/residue: 0.1714 time to fit residues: 105.7586 Evaluate side-chains 349 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 194 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 241 optimal weight: 10.0000 chunk 345 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 200 optimal weight: 0.0040 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 76 optimal weight: 0.0670 chunk 287 optimal weight: 2.9990 chunk 211 optimal weight: 0.0000 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 998 ASN A 295 GLN A 465 HIS A 872 ASN ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.209707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.180158 restraints weight = 79352.935| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 3.63 r_work: 0.4193 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30389 Z= 0.109 Angle : 0.611 16.107 41578 Z= 0.303 Chirality : 0.045 0.330 4908 Planarity : 0.004 0.070 5172 Dihedral : 8.319 110.957 5957 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.27 % Allowed : 22.83 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3618 helix: 0.90 (0.19), residues: 768 sheet: -1.48 (0.19), residues: 705 loop : -2.28 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 264 TYR 0.023 0.001 TYR A 236 PHE 0.024 0.001 PHE C1177 TRP 0.018 0.001 TRP C 971 HIS 0.004 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00243 (30225) covalent geometry : angle 0.57937 (41157) SS BOND : bond 0.00226 ( 71) SS BOND : angle 1.18034 ( 142) hydrogen bonds : bond 0.03298 ( 859) hydrogen bonds : angle 5.34513 ( 2367) link_ALPHA1-3 : bond 0.00877 ( 6) link_ALPHA1-3 : angle 1.72201 ( 18) link_ALPHA1-4 : bond 0.01485 ( 3) link_ALPHA1-4 : angle 3.11002 ( 9) link_ALPHA1-6 : bond 0.00614 ( 3) link_ALPHA1-6 : angle 1.89576 ( 9) link_BETA1-4 : bond 0.00480 ( 15) link_BETA1-4 : angle 1.20829 ( 45) link_NAG-ASN : bond 0.00446 ( 66) link_NAG-ASN : angle 2.51518 ( 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 373 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 202 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: symmetry clash REVERT: B 50 TYR cc_start: 0.3056 (OUTLIER) cc_final: 0.2189 (t80) REVERT: B 153 TYR cc_start: 0.2442 (t80) cc_final: 0.1532 (t80) REVERT: B 177 ASP cc_start: 0.2687 (OUTLIER) cc_final: 0.1920 (m-30) REVERT: B 266 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.5518 (t80) REVERT: B 321 ILE cc_start: 0.7207 (mt) cc_final: 0.6878 (mt) REVERT: B 630 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: B 1116 SER cc_start: 0.6075 (OUTLIER) cc_final: 0.5713 (m) REVERT: B 1193 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: B 1212 PHE cc_start: 0.4105 (OUTLIER) cc_final: 0.3715 (m-10) REVERT: C 52 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6987 (mt) REVERT: C 112 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7037 (m-10) REVERT: C 155 MET cc_start: 0.3413 (tpp) cc_final: 0.3008 (tpp) REVERT: C 197 TRP cc_start: 0.6269 (OUTLIER) cc_final: 0.5550 (m-10) REVERT: C 202 PHE cc_start: 0.5321 (m-10) cc_final: 0.4826 (m-10) REVERT: C 309 PHE cc_start: 0.4647 (OUTLIER) cc_final: 0.3759 (p90) REVERT: C 500 LYS cc_start: 0.4878 (OUTLIER) cc_final: 0.3720 (ttpt) REVERT: C 511 TYR cc_start: 0.3534 (OUTLIER) cc_final: 0.2878 (m-80) REVERT: C 577 PHE cc_start: 0.7316 (p90) cc_final: 0.6751 (p90) REVERT: C 632 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6473 (pt) REVERT: C 748 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6087 (tp) REVERT: C 828 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7727 (mm) REVERT: C 994 MET cc_start: 0.5537 (mmm) cc_final: 0.5132 (tpt) REVERT: C 1002 LYS cc_start: 0.7179 (tptt) cc_final: 0.6730 (ptmm) REVERT: A 18 PHE cc_start: 0.2974 (OUTLIER) cc_final: 0.1912 (t80) REVERT: A 34 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6440 (mmm160) REVERT: A 213 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7483 (t80) REVERT: A 268 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7639 (pp) REVERT: A 309 PHE cc_start: 0.5116 (OUTLIER) cc_final: 0.3997 (p90) REVERT: A 366 ASP cc_start: 0.2072 (OUTLIER) cc_final: 0.1647 (m-30) REVERT: A 528 TYR cc_start: 0.0439 (OUTLIER) cc_final: 0.0078 (t80) REVERT: A 714 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: A 737 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.5532 (mmt-90) REVERT: A 738 MET cc_start: 0.7172 (mmp) cc_final: 0.6892 (mmt) REVERT: A 888 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6002 (pp) REVERT: A 1205 MET cc_start: 0.4423 (ptm) cc_final: 0.3221 (tpp) outliers start: 171 outliers final: 131 residues processed: 344 average time/residue: 0.1588 time to fit residues: 94.0784 Evaluate side-chains 350 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 193 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 123 optimal weight: 5.9990 chunk 296 optimal weight: 30.0000 chunk 235 optimal weight: 0.9990 chunk 358 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 315 optimal weight: 0.9990 chunk 20 optimal weight: 0.0020 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 465 HIS ** A1117 GLN ** 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 = 0.4928 r_free = 0.4928 target = 0.209613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.179740 restraints weight = 79154.117| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 3.52 r_work: 0.4199 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30389 Z= 0.112 Angle : 0.615 15.861 41578 Z= 0.306 Chirality : 0.045 0.331 4908 Planarity : 0.004 0.070 5172 Dihedral : 8.154 110.711 5951 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.02 % Allowed : 23.17 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -2.00 (0.13), residues: 3618 helix: 0.95 (0.19), residues: 768 sheet: -1.46 (0.19), residues: 694 loop : -2.25 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.023 0.001 TYR C 667 PHE 0.019 0.001 PHE A 467 TRP 0.018 0.001 TRP C 971 HIS 0.012 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00252 (30225) covalent geometry : angle 0.58580 (41157) SS BOND : bond 0.00214 ( 71) SS BOND : angle 1.16215 ( 142) hydrogen bonds : bond 0.03304 ( 859) hydrogen bonds : angle 5.29226 ( 2367) link_ALPHA1-3 : bond 0.00854 ( 6) link_ALPHA1-3 : angle 1.71459 ( 18) link_ALPHA1-4 : bond 0.01507 ( 3) link_ALPHA1-4 : angle 3.11281 ( 9) link_ALPHA1-6 : bond 0.00606 ( 3) link_ALPHA1-6 : angle 1.88596 ( 9) link_BETA1-4 : bond 0.00471 ( 15) link_BETA1-4 : angle 1.20761 ( 45) link_NAG-ASN : bond 0.00461 ( 66) link_NAG-ASN : angle 2.45254 ( 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 359 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 196 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 TYR cc_start: 0.3068 (OUTLIER) cc_final: 0.2198 (t80) REVERT: B 118 TYR cc_start: 0.7463 (m-10) cc_final: 0.7259 (m-10) REVERT: B 153 TYR cc_start: 0.2447 (t80) cc_final: 0.2040 (t80) REVERT: B 177 ASP cc_start: 0.2464 (OUTLIER) cc_final: 0.1765 (m-30) REVERT: B 266 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.5526 (t80) REVERT: B 321 ILE cc_start: 0.7166 (mt) cc_final: 0.6822 (mt) REVERT: B 517 ARG cc_start: 0.1925 (OUTLIER) cc_final: 0.1571 (ptm160) REVERT: B 630 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: B 988 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7388 (t0) REVERT: B 1116 SER cc_start: 0.6112 (OUTLIER) cc_final: 0.5751 (m) REVERT: B 1193 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: B 1212 PHE cc_start: 0.4200 (OUTLIER) cc_final: 0.3773 (m-10) REVERT: C 52 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6938 (mt) REVERT: C 112 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6944 (m-10) REVERT: C 155 MET cc_start: 0.4129 (tpp) cc_final: 0.3726 (tpp) REVERT: C 197 TRP cc_start: 0.6335 (OUTLIER) cc_final: 0.5678 (m-10) REVERT: C 202 PHE cc_start: 0.5317 (m-10) cc_final: 0.4835 (m-10) REVERT: C 309 PHE cc_start: 0.4677 (OUTLIER) cc_final: 0.3825 (p90) REVERT: C 500 LYS cc_start: 0.4845 (OUTLIER) cc_final: 0.3685 (ttpt) REVERT: C 511 TYR cc_start: 0.3518 (OUTLIER) cc_final: 0.2775 (m-80) REVERT: C 577 PHE cc_start: 0.7332 (p90) cc_final: 0.6814 (p90) REVERT: C 632 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.6374 (pt) REVERT: C 748 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.5985 (tp) REVERT: C 828 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7738 (mm) REVERT: C 1002 LYS cc_start: 0.7196 (tptt) cc_final: 0.6736 (ptmm) REVERT: A 18 PHE cc_start: 0.2966 (OUTLIER) cc_final: 0.1916 (t80) REVERT: A 34 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6581 (mmm160) REVERT: A 213 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7476 (t80) REVERT: A 309 PHE cc_start: 0.5063 (OUTLIER) cc_final: 0.3975 (p90) REVERT: A 366 ASP cc_start: 0.2088 (OUTLIER) cc_final: 0.1724 (m-30) REVERT: A 528 TYR cc_start: 0.0435 (OUTLIER) cc_final: 0.0080 (t80) REVERT: A 714 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: A 738 MET cc_start: 0.7181 (mmp) cc_final: 0.6900 (mmt) REVERT: A 888 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6016 (pp) outliers start: 163 outliers final: 126 residues processed: 333 average time/residue: 0.1622 time to fit residues: 93.3603 Evaluate side-chains 340 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 188 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 988 ASN Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1113 CYS Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1129 HIS Chi-restraints excluded: chain B residue 1152 SER Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1193 TYR Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1133 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A 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: 7.9990 chunk 274 optimal weight: 9.9990 chunk 339 optimal weight: 0.6980 chunk 278 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 266 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 253 optimal weight: 8.9990 chunk 353 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 881 ASN C 847 ASN C1092 GLN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.206435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.182956 restraints weight = 78777.464| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 2.29 r_work: 0.4185 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4085 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 30389 Z= 0.208 Angle : 0.717 14.895 41578 Z= 0.359 Chirality : 0.048 0.373 4908 Planarity : 0.005 0.070 5172 Dihedral : 8.678 111.695 5942 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 5.08 % Allowed : 23.04 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.13), residues: 3618 helix: 0.35 (0.19), residues: 766 sheet: -1.58 (0.19), residues: 705 loop : -2.35 (0.12), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1120 TYR 0.032 0.002 TYR A 958 PHE 0.022 0.002 PHE C 764 TRP 0.013 0.002 TRP C 444 HIS 0.008 0.001 HIS B1129 Details of bonding type rmsd covalent geometry : bond 0.00476 (30225) covalent geometry : angle 0.68875 (41157) SS BOND : bond 0.00377 ( 71) SS BOND : angle 1.38009 ( 142) hydrogen bonds : bond 0.04145 ( 859) hydrogen bonds : angle 5.82282 ( 2367) link_ALPHA1-3 : bond 0.00883 ( 6) link_ALPHA1-3 : angle 1.82094 ( 18) link_ALPHA1-4 : bond 0.01464 ( 3) link_ALPHA1-4 : angle 3.26708 ( 9) link_ALPHA1-6 : bond 0.00696 ( 3) link_ALPHA1-6 : angle 1.92470 ( 9) link_BETA1-4 : bond 0.00517 ( 15) link_BETA1-4 : angle 1.36014 ( 45) link_NAG-ASN : bond 0.00488 ( 66) link_NAG-ASN : angle 2.59530 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10902.55 seconds wall clock time: 186 minutes 18.76 seconds (11178.76 seconds total)