Starting phenix.real_space_refine on Wed Jun 25 13:25:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1g_38835/06_2025/8y1g_38835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1g_38835/06_2025/8y1g_38835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y1g_38835/06_2025/8y1g_38835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1g_38835/06_2025/8y1g_38835.map" model { file = "/net/cci-nas-00/data/ceres_data/8y1g_38835/06_2025/8y1g_38835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1g_38835/06_2025/8y1g_38835.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.086 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 52 residue(s): 1.72s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29541 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "B" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "C" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 17.71, per 1000 atoms: 0.60 Number of scatterers: 29541 At special positions: 0 Unit cell: (166.311, 153.267, 205.443, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 171 16.00 O 5907 8.00 N 4734 7.00 C 18729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.02 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.02 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.02 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.04 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.04 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.02 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " MAN N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG I 2 " - " MAN I 3 " " NAG N 2 " - " MAN N 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN I 3 " - " MAN I 4 " " MAN N 3 " - " MAN N 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A2001 " - " ASN A 19 " " NAG A2002 " - " ASN A 29 " " NAG A2003 " - " ASN A 58 " " NAG A2004 " - " ASN A 114 " " NAG A2005 " - " ASN A 171 " " NAG A2006 " - " ASN A 192 " " NAG A2007 " - " ASN A 251 " " NAG A2008 " - " ASN A 433 " " NAG A2009 " - " ASN A 454 " " NAG A2010 " - " ASN A 684 " " NAG A2011 " - " ASN A 703 " " NAG A2012 " - " ASN A 725 " " NAG A2013 " - " ASN A 771 " " NAG A2014 " - " ASN A 776 " " NAG A2015 " - " ASN A 793 " " NAG A2016 " - " ASN A 924 " " NAG A2017 " - " ASN A1211 " " NAG B2001 " - " ASN B 19 " " NAG B2002 " - " ASN B 29 " " NAG B2003 " - " ASN B 58 " " NAG B2004 " - " ASN B 114 " " NAG B2005 " - " ASN B 171 " " NAG B2006 " - " ASN B 192 " " NAG B2007 " - " ASN B 251 " " NAG B2008 " - " ASN B 433 " " NAG B2009 " - " ASN B 454 " " NAG B2010 " - " ASN B 684 " " NAG B2011 " - " ASN B 703 " " NAG B2012 " - " ASN B 725 " " NAG B2013 " - " ASN B 771 " " NAG B2014 " - " ASN B 776 " " NAG B2015 " - " ASN B 793 " " NAG B2016 " - " ASN B 924 " " NAG B2017 " - " ASN B1211 " " NAG C2001 " - " ASN C 19 " " NAG C2002 " - " ASN C 29 " " NAG C2003 " - " ASN C 58 " " NAG C2004 " - " ASN C 114 " " NAG C2005 " - " ASN C 171 " " NAG C2006 " - " ASN C 192 " " NAG C2007 " - " ASN C 251 " " NAG C2008 " - " ASN C 433 " " NAG C2009 " - " ASN C 454 " " NAG C2010 " - " ASN C 684 " " NAG C2011 " - " ASN C 703 " " NAG C2012 " - " ASN C 725 " " NAG C2013 " - " ASN C 771 " " NAG C2014 " - " ASN C 776 " " NAG C2015 " - " ASN C 793 " " NAG C2016 " - " ASN C 924 " " NAG C2017 " - " ASN C1211 " " NAG D 1 " - " ASN A 132 " " NAG E 1 " - " ASN A 188 " " NAG F 1 " - " ASN A 335 " " NAG G 1 " - " ASN A 355 " " NAG H 1 " - " ASN A 664 " " NAG I 1 " - " ASN B 132 " " NAG J 1 " - " ASN B 188 " " NAG K 1 " - " ASN B 335 " " NAG L 1 " - " ASN B 355 " " NAG M 1 " - " ASN B 664 " " NAG N 1 " - " ASN C 132 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 335 " " NAG Q 1 " - " ASN C 355 " " NAG R 1 " - " ASN C 664 " Time building additional restraints: 7.75 Conformation dependent library (CDL) restraints added in 3.8 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: 75 helices and 68 sheets defined 23.1% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 41 through 45 removed outlier: 4.510A pdb=" N LEU A 44 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 45 " --> pdb=" O VAL A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 45' Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.548A pdb=" N TYR A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 3.689A 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 328 through 334 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.758A pdb=" N GLY A 380 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 381 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 4.985A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.600A pdb=" N ASN A 483 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 484 " --> pdb=" O VAL A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 863 Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.865A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 951 through 966 removed outlier: 3.960A pdb=" N ALA A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 4.064A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.776A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.794A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.686A pdb=" N TYR B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.581A pdb=" N ILE B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.333A pdb=" N GLY B 380 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.141A pdb=" N ARG B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASP B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.530A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 556 removed outlier: 3.830A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) 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 862 removed outlier: 3.517A pdb=" N MET B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 909 Processing helix chain 'B' and resid 914 through 924 removed outlier: 4.124A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.544A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 971 through 975 removed outlier: 3.817A pdb=" N ALA B 974 " --> pdb=" O TRP B 971 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 975 " --> pdb=" O SER B 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 971 through 975' Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.762A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 4.376A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1048 No H-bonds generated for 'chain 'B' and resid 1046 through 1048' Processing helix chain 'B' and resid 1057 through 1062 Processing helix chain 'B' and resid 1069 through 1113 removed outlier: 3.927A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.893A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.549A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.683A pdb=" N LEU C 401 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.958A 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 478 through 482 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 813 through 819 Processing helix chain 'C' and resid 822 through 830 Processing helix chain 'C' and resid 835 through 863 removed outlier: 3.713A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET C 862 " --> pdb=" O ALA C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.608A pdb=" N LEU C 888 " --> pdb=" O LYS C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 888' Processing helix chain 'C' and resid 901 through 910 removed outlier: 3.900A pdb=" N LYS C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.714A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 940 Processing helix chain 'C' and resid 952 through 965 Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 995 through 1000 Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.590A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1048 No H-bonds generated for 'chain 'C' and resid 1046 through 1048' Processing helix chain 'C' and resid 1057 through 1065 removed outlier: 3.731A pdb=" N ILE C1061 " --> pdb=" O SER C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1113 removed outlier: 3.868A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1167 No H-bonds generated for 'chain 'C' and resid 1165 through 1167' Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.060A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 629 " --> pdb=" O TYR C 622 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA C 315 " --> pdb=" O ASN C 621 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ASP C 623 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 317 " --> pdb=" O ASP C 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.792A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 67 Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.805A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 225 removed outlier: 6.877A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 113 Processing sheet with id=AA7, first strand: chain 'A' and resid 183 through 190 removed outlier: 3.817A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS A 151 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 307 removed outlier: 7.897A pdb=" N ARG A 676 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARG A 693 " --> pdb=" O ARG A 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 348 removed outlier: 3.710A pdb=" N TYR A 427 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS A 423 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN A 424 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE A 368 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR A 426 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS A 364 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.533A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB6, first strand: chain 'A' and resid 619 through 624 removed outlier: 3.537A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.795A pdb=" N LYS A 665 " --> pdb=" O ASP A 660 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 658 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 648 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 724 through 731 removed outlier: 4.698A pdb=" N THR A 766 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER A 728 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.304A pdb=" N SER A 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 786 through 789 removed outlier: 6.976A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 794 through 795 Processing sheet with id=AC3, first strand: chain 'A' and resid 798 through 804 removed outlier: 3.786A pdb=" N GLY A1140 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.478A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 866 through 868 removed outlier: 6.588A pdb=" N LEU A 867 " --> pdb=" O VAL C 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 3.671A pdb=" N LEU A1162 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 59 through 61 Processing sheet with id=AC8, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.228A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.614A pdb=" N PHE B 200 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.560A pdb=" N GLY B 81 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.582A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 140 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 147 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AD4, first strand: chain 'B' and resid 302 through 306 removed outlier: 3.601A pdb=" N TYR B 304 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 677 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 690 " --> pdb=" O LEU B 721 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 692 " --> pdb=" O CYS B 719 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 316 through 319 removed outlier: 6.275A pdb=" N VAL B 317 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 627 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 636 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 337 through 339 removed outlier: 7.329A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 345 through 350 removed outlier: 3.669A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 388 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN B 424 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE B 368 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR B 426 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 459 through 463 removed outlier: 3.544A pdb=" N SER B 576 " --> pdb=" O TYR B 462 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.416A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AE2, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.700A pdb=" N GLY B 657 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.338A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 773 through 775 removed outlier: 5.861A pdb=" N SER B 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 786 through 795 removed outlier: 6.825A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 798 through 804 removed outlier: 3.635A pdb=" N ILE B 803 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN B1136 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B1142 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B1134 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B1144 " --> pdb=" O SER B1132 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER B1132 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B1146 " --> pdb=" O ILE B1130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.564A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AE9, first strand: chain 'B' and resid 1162 through 1163 Processing sheet with id=AF1, first strand: chain 'B' and resid 1169 through 1172 Processing sheet with id=AF2, first strand: chain 'B' and resid 1175 through 1179 Processing sheet with id=AF3, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.820A pdb=" N ASP C 38 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 59 through 67 removed outlier: 3.565A pdb=" N THR C 59 " --> pdb=" O PHE C 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 262 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLN C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASP C 281 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.621A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.546A pdb=" N ILE C 124 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 136 " --> pdb=" O CYS C 151 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU C 146 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASN C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 109 through 112 removed outlier: 3.783A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 120 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 302 through 310 removed outlier: 4.732A pdb=" N VAL C 677 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY C 308 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY C 675 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG C 676 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG C 693 " --> pdb=" O ARG C 676 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.234A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.716A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 425 " --> pdb=" O SER C 590 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR C 426 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS C 364 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.716A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.599A pdb=" N PHE C 354 " --> pdb=" O CYS C 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG5, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.316A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 504 through 507 removed outlier: 3.624A pdb=" N TRP C 515 " --> pdb=" O ASP C 507 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.501A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 724 through 731 removed outlier: 10.724A pdb=" N TYR C 762 " --> pdb=" O ASN C 725 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N THR C 727 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N PHE C 764 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR C 729 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 786 through 791 removed outlier: 3.600A pdb=" N ILE C 788 " --> pdb=" O VAL C1156 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 794 through 804 removed outlier: 3.643A pdb=" N ALA C1137 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.209A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH4, first strand: chain 'C' and resid 1202 through 1205 Processing sheet with id=AH5, first strand: chain 'C' and resid 1175 through 1176 944 hydrogen bonds defined for protein. 2610 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: 13.92 Time building geometry restraints manager: 8.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9155 1.34 - 1.46: 7977 1.46 - 1.59: 12895 1.59 - 1.71: 0 1.71 - 1.84: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" C5 MAN D 3 " pdb=" O5 MAN D 3 " ideal model delta sigma weight residual 1.418 1.507 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C1 MAN D 3 " pdb=" O5 MAN D 3 " ideal model delta sigma weight residual 1.399 1.468 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C VAL B 945 " pdb=" N LEU B 946 " ideal model delta sigma weight residual 1.329 1.266 0.063 1.86e-02 2.89e+03 1.14e+01 bond pdb=" C1 MAN N 6 " pdb=" O5 MAN N 6 " ideal model delta sigma weight residual 1.399 1.463 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C5 MAN I 3 " pdb=" O5 MAN I 3 " ideal model delta sigma weight residual 1.418 1.481 -0.063 2.00e-02 2.50e+03 9.97e+00 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 38868 1.96 - 3.92: 2028 3.92 - 5.89: 200 5.89 - 7.85: 49 7.85 - 9.81: 12 Bond angle restraints: 41157 Sorted by residual: angle pdb=" C HIS A 545 " pdb=" N CYS A 546 " pdb=" CA CYS A 546 " ideal model delta sigma weight residual 121.20 130.85 -9.65 1.40e+00 5.10e-01 4.76e+01 angle pdb=" N PRO B 969 " pdb=" CA PRO B 969 " pdb=" C PRO B 969 " ideal model delta sigma weight residual 110.70 118.30 -7.60 1.22e+00 6.72e-01 3.88e+01 angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" N PRO A1067 " pdb=" CA PRO A1067 " pdb=" C PRO A1067 " ideal model delta sigma weight residual 110.70 117.23 -6.53 1.22e+00 6.72e-01 2.86e+01 angle pdb=" N GLY C1127 " pdb=" CA GLY C1127 " pdb=" C GLY C1127 " ideal model delta sigma weight residual 112.68 106.46 6.22 1.26e+00 6.30e-01 2.44e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 17741 24.39 - 48.79: 1216 48.79 - 73.18: 229 73.18 - 97.58: 34 97.58 - 121.97: 7 Dihedral angle restraints: 19227 sinusoidal: 8589 harmonic: 10638 Sorted by residual: dihedral pdb=" CA PRO C 969 " pdb=" C PRO C 969 " pdb=" N PRO C 970 " pdb=" CA PRO C 970 " ideal model delta harmonic sigma weight residual 180.00 122.60 57.40 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA PRO C 92 " pdb=" C PRO C 92 " pdb=" N PRO C 93 " pdb=" CA PRO C 93 " ideal model delta harmonic sigma weight residual 180.00 127.81 52.19 0 5.00e+00 4.00e-02 1.09e+02 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 -139.48 -40.52 0 5.00e+00 4.00e-02 6.57e+01 ... (remaining 19224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 4811 0.141 - 0.283: 84 0.283 - 0.424: 9 0.424 - 0.565: 2 0.565 - 0.706: 2 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG A2003 " pdb=" ND2 ASN A 58 " pdb=" C2 NAG A2003 " pdb=" O5 NAG A2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C1 NAG C2003 " pdb=" ND2 ASN C 58 " pdb=" C2 NAG C2003 " pdb=" O5 NAG C2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.52e+00 chirality pdb=" C1 NAG C2006 " pdb=" ND2 ASN C 192 " pdb=" C2 NAG C2006 " pdb=" O5 NAG C2006 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 969 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 970 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 970 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 970 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 969 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO C 970 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO C 970 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 970 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 969 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO B 970 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO B 970 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 970 " 0.061 5.00e-02 4.00e+02 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5067 2.76 - 3.29: 25052 3.29 - 3.83: 48502 3.83 - 4.36: 55928 4.36 - 4.90: 98667 Nonbonded interactions: 233216 Sorted by model distance: nonbonded pdb=" O LEU B 935 " pdb=" OG SER B 939 " model vdw 2.222 3.040 nonbonded pdb=" O LEU C 431 " pdb=" OH TYR C 458 " model vdw 2.236 3.040 nonbonded pdb=" O PRO C 496 " pdb=" OG1 THR C 499 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 651 " pdb=" OG1 THR C 59 " model vdw 2.250 3.040 nonbonded pdb=" O VAL A 775 " pdb=" OG SER B 869 " model vdw 2.269 3.040 ... (remaining 233211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 62.070 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: 1.070 Check model and map are aligned: 0.210 Set scattering table: 0.230 Process input model: 68.950 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.200 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 30390 Z= 0.431 Angle : 1.018 18.245 41580 Z= 0.551 Chirality : 0.061 0.706 4908 Planarity : 0.008 0.115 5172 Dihedral : 16.465 121.972 12183 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.99 % Favored : 91.98 % Rotamer: Outliers : 12.14 % Allowed : 11.83 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.11), residues: 3618 helix: -2.43 (0.13), residues: 792 sheet: -2.32 (0.16), residues: 832 loop : -3.01 (0.11), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 174 HIS 0.013 0.002 HIS B1129 PHE 0.029 0.003 PHE C 74 TYR 0.037 0.003 TYR A 49 ARG 0.006 0.001 ARG B 502 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 66) link_NAG-ASN : angle 3.91656 ( 198) link_ALPHA1-4 : bond 0.01694 ( 3) link_ALPHA1-4 : angle 4.30164 ( 9) link_ALPHA1-6 : bond 0.00204 ( 3) link_ALPHA1-6 : angle 2.11034 ( 9) link_BETA1-4 : bond 0.00711 ( 15) link_BETA1-4 : angle 2.41769 ( 45) link_ALPHA1-3 : bond 0.00803 ( 6) link_ALPHA1-3 : angle 1.80750 ( 18) hydrogen bonds : bond 0.22296 ( 927) hydrogen bonds : angle 8.37948 ( 2610) SS BOND : bond 0.00526 ( 72) SS BOND : angle 1.16751 ( 144) covalent geometry : bond 0.00970 (30225) covalent geometry : angle 0.97704 (41157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 394 poor density : 265 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.5169 (OUTLIER) cc_final: 0.4944 (m110) REVERT: A 79 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5929 (mt) REVERT: A 162 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8191 (m) REVERT: A 187 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7628 (ttmt) REVERT: A 364 HIS cc_start: 0.4747 (OUTLIER) cc_final: 0.4473 (m-70) REVERT: A 431 LEU cc_start: 0.1505 (OUTLIER) cc_final: 0.1276 (tp) REVERT: A 587 ASN cc_start: 0.2003 (OUTLIER) cc_final: 0.1665 (m-40) REVERT: A 863 GLN cc_start: 0.8187 (tt0) cc_final: 0.7793 (tt0) REVERT: A 988 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8609 (t0) REVERT: A 1069 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: A 1149 LYS cc_start: 0.8305 (tttt) cc_final: 0.8054 (tptp) REVERT: B 22 ASN cc_start: 0.4695 (OUTLIER) cc_final: 0.4302 (t0) REVERT: B 30 LYS cc_start: 0.4797 (OUTLIER) cc_final: 0.4309 (tppt) REVERT: B 102 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6802 (tp) REVERT: B 184 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5180 (tt) REVERT: B 243 LYS cc_start: 0.5411 (OUTLIER) cc_final: 0.5118 (tttt) REVERT: B 378 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7811 (mm) REVERT: B 435 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8046 (p) REVERT: B 515 TRP cc_start: 0.4493 (p-90) cc_final: 0.4176 (p-90) REVERT: B 690 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8319 (mt) REVERT: B 891 LEU cc_start: 0.7545 (tp) cc_final: 0.7295 (tt) REVERT: B 1012 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8082 (tt) REVERT: B 1068 PRO cc_start: 0.8405 (Cg_exo) cc_final: 0.8128 (Cg_endo) REVERT: C 273 HIS cc_start: 0.6335 (m-70) cc_final: 0.5588 (m90) REVERT: C 399 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7078 (p0) REVERT: C 406 SER cc_start: 0.8056 (OUTLIER) cc_final: 0.7599 (t) REVERT: C 418 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8419 (mt) REVERT: C 651 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.8002 (m) REVERT: C 676 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7305 (ptp-170) REVERT: C 787 GLU cc_start: 0.6691 (tt0) cc_final: 0.6325 (tt0) REVERT: C 806 SER cc_start: 0.8898 (p) cc_final: 0.8590 (m) REVERT: C 994 MET cc_start: 0.7962 (tpp) cc_final: 0.7750 (mtp) REVERT: C 1120 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.6357 (mtt180) REVERT: C 1131 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8568 (pp) REVERT: C 1185 MET cc_start: 0.8440 (mmp) cc_final: 0.8041 (mmm) outliers start: 394 outliers final: 178 residues processed: 628 average time/residue: 0.9740 time to fit residues: 780.4890 Evaluate side-chains 352 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 149 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 988 ASN Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1069 GLU 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 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 995 ASP Chi-restraints excluded: chain B residue 1000 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1023 ASN Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1090 SER Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 897 SER Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 282 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 326 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 175 HIS A 204 GLN A 291 GLN A 351 ASN A 353 ASN A 384 ASN A 402 GLN A 440 ASN A 552 ASN A 595 ASN A 611 ASN A 630 GLN A 838 ASN A 859 ASN A 876 HIS A1001 GLN A1023 ASN A1049 ASN A1180 GLN B 26 ASN B 140 GLN B 152 GLN B 204 GLN B 248 ASN B 410 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 531 ASN B 598 ASN B 605 ASN B 630 GLN ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 ASN B1001 GLN B1038 GLN B1136 ASN C 204 GLN C 248 ASN C 395 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN C 598 ASN C 630 GLN C 646 ASN C 876 HIS C1091 GLN ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.156154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.108606 restraints weight = 51596.759| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.41 r_work: 0.3328 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30390 Z= 0.138 Angle : 0.679 17.272 41580 Z= 0.341 Chirality : 0.050 1.085 4908 Planarity : 0.006 0.100 5172 Dihedral : 11.813 113.237 6158 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.24 % Allowed : 16.51 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.21 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.13), residues: 3618 helix: -0.29 (0.18), residues: 792 sheet: -1.63 (0.17), residues: 816 loop : -2.51 (0.12), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 971 HIS 0.009 0.001 HIS C 201 PHE 0.021 0.001 PHE A 968 TYR 0.019 0.001 TYR B 427 ARG 0.006 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 66) link_NAG-ASN : angle 3.54959 ( 198) link_ALPHA1-4 : bond 0.01748 ( 3) link_ALPHA1-4 : angle 3.73338 ( 9) link_ALPHA1-6 : bond 0.00750 ( 3) link_ALPHA1-6 : angle 1.95148 ( 9) link_BETA1-4 : bond 0.00406 ( 15) link_BETA1-4 : angle 1.22416 ( 45) link_ALPHA1-3 : bond 0.00665 ( 6) link_ALPHA1-3 : angle 1.89281 ( 18) hydrogen bonds : bond 0.05004 ( 927) hydrogen bonds : angle 5.70960 ( 2610) SS BOND : bond 0.00626 ( 72) SS BOND : angle 1.27982 ( 144) covalent geometry : bond 0.00295 (30225) covalent geometry : angle 0.62629 (41157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 194 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.6411 (OUTLIER) cc_final: 0.6053 (m110) REVERT: A 75 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6755 (mtp85) REVERT: A 79 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5773 (tt) REVERT: A 162 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7894 (m) REVERT: A 187 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7517 (mmmt) REVERT: A 418 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5622 (mm) REVERT: A 431 LEU cc_start: 0.1554 (OUTLIER) cc_final: 0.1312 (mt) REVERT: A 737 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8727 (mtm180) REVERT: A 863 GLN cc_start: 0.8166 (tt0) cc_final: 0.7958 (tt0) REVERT: A 988 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8872 (t0) REVERT: A 1069 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: B 30 LYS cc_start: 0.4897 (OUTLIER) cc_final: 0.4243 (tppt) REVERT: B 34 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5413 (ptm160) REVERT: B 184 LEU cc_start: 0.4360 (OUTLIER) cc_final: 0.4098 (tt) REVERT: B 375 LYS cc_start: 0.7547 (ptmt) cc_final: 0.7027 (pptt) REVERT: B 396 ARG cc_start: 0.8186 (ptt-90) cc_final: 0.7938 (ptt90) REVERT: B 560 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7158 (pp) REVERT: B 782 VAL cc_start: 0.8563 (t) cc_final: 0.8362 (m) REVERT: B 883 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7529 (t0) REVERT: B 891 LEU cc_start: 0.7884 (tp) cc_final: 0.7548 (tp) REVERT: B 1012 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8127 (tt) REVERT: B 1185 MET cc_start: 0.6943 (mmm) cc_final: 0.6640 (mmm) REVERT: C 193 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8489 (p) REVERT: C 273 HIS cc_start: 0.6613 (m-70) cc_final: 0.6180 (m90) REVERT: C 399 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6974 (p0) REVERT: C 458 TYR cc_start: 0.7992 (m-10) cc_final: 0.7667 (m-80) REVERT: C 472 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.6986 (t70) REVERT: C 473 PHE cc_start: 0.8150 (t80) cc_final: 0.7944 (t80) REVERT: C 555 LYS cc_start: 0.7762 (mttt) cc_final: 0.7494 (mptt) REVERT: C 668 THR cc_start: 0.8619 (p) cc_final: 0.8383 (t) REVERT: C 787 GLU cc_start: 0.6931 (tt0) cc_final: 0.6584 (tt0) REVERT: C 1124 CYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7356 (m) REVERT: C 1185 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7779 (mmm) REVERT: C 1219 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.6256 (p90) outliers start: 235 outliers final: 112 residues processed: 407 average time/residue: 0.9031 time to fit residues: 473.7236 Evaluate side-chains 288 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 154 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 988 ASN Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1000 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 897 SER Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1185 MET Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 251 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 120 optimal weight: 20.0000 chunk 269 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 chunk 263 optimal weight: 7.9990 chunk 91 optimal weight: 0.0050 chunk 356 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS A 465 HIS A 561 ASN A1206 ASN B 26 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN B 863 GLN B 872 ASN B 894 GLN B1023 ASN C 545 HIS C 863 GLN C 984 GLN ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.156336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108662 restraints weight = 51407.011| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.93 r_work: 0.3368 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30390 Z= 0.127 Angle : 0.653 19.787 41580 Z= 0.321 Chirality : 0.052 1.348 4908 Planarity : 0.006 0.105 5172 Dihedral : 10.745 109.191 5998 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.76 % Allowed : 18.55 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3618 helix: 0.50 (0.19), residues: 791 sheet: -1.29 (0.17), residues: 820 loop : -2.24 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 515 HIS 0.007 0.001 HIS C 201 PHE 0.022 0.001 PHE A 968 TYR 0.029 0.001 TYR C 427 ARG 0.004 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 66) link_NAG-ASN : angle 3.79923 ( 198) link_ALPHA1-4 : bond 0.01961 ( 3) link_ALPHA1-4 : angle 3.48329 ( 9) link_ALPHA1-6 : bond 0.00920 ( 3) link_ALPHA1-6 : angle 1.94788 ( 9) link_BETA1-4 : bond 0.00426 ( 15) link_BETA1-4 : angle 1.26867 ( 45) link_ALPHA1-3 : bond 0.00919 ( 6) link_ALPHA1-3 : angle 1.91527 ( 18) hydrogen bonds : bond 0.04540 ( 927) hydrogen bonds : angle 5.26055 ( 2610) SS BOND : bond 0.00246 ( 72) SS BOND : angle 1.29065 ( 144) covalent geometry : bond 0.00278 (30225) covalent geometry : angle 0.59103 (41157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 171 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8228 (mp) REVERT: A 79 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5846 (tt) REVERT: A 112 TYR cc_start: 0.7817 (m-80) cc_final: 0.6512 (m-80) REVERT: A 187 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7659 (mmmt) REVERT: A 662 LEU cc_start: 0.8199 (mm) cc_final: 0.7721 (tp) REVERT: A 863 GLN cc_start: 0.8323 (tt0) cc_final: 0.8119 (tt0) REVERT: A 988 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8903 (t0) REVERT: A 1069 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: B 30 LYS cc_start: 0.5236 (OUTLIER) cc_final: 0.4509 (tppt) REVERT: B 184 LEU cc_start: 0.4199 (OUTLIER) cc_final: 0.3927 (tt) REVERT: B 346 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6574 (ptm160) REVERT: B 375 LYS cc_start: 0.7698 (ptmt) cc_final: 0.7126 (pptt) REVERT: B 396 ARG cc_start: 0.8184 (ptt-90) cc_final: 0.7086 (ptt90) REVERT: B 690 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8630 (mt) REVERT: B 782 VAL cc_start: 0.8579 (t) cc_final: 0.8364 (m) REVERT: B 891 LEU cc_start: 0.7273 (tp) cc_final: 0.6890 (tp) REVERT: B 1012 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8250 (tt) REVERT: B 1117 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6455 (mm110) REVERT: B 1185 MET cc_start: 0.6962 (mmm) cc_final: 0.6724 (mmm) REVERT: C 273 HIS cc_start: 0.6724 (m-70) cc_final: 0.6270 (m90) REVERT: C 326 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7408 (t0) REVERT: C 367 SER cc_start: 0.7581 (OUTLIER) cc_final: 0.7142 (p) REVERT: C 399 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7034 (p0) REVERT: C 458 TYR cc_start: 0.8105 (m-80) cc_final: 0.7808 (m-80) REVERT: C 472 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7063 (t70) REVERT: C 473 PHE cc_start: 0.8047 (t80) cc_final: 0.7754 (t80) REVERT: C 1124 CYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7629 (m) REVERT: C 1219 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6344 (p90) outliers start: 187 outliers final: 114 residues processed: 336 average time/residue: 1.0353 time to fit residues: 443.7876 Evaluate side-chains 277 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 146 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 988 ASN Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1117 GLN Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 897 SER Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 272 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 326 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 ASN A1079 ASN A1206 ASN B 201 HIS B 295 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS B 531 ASN ** B 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN C 583 ASN C 863 GLN ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.153127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105593 restraints weight = 51944.193| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.35 r_work: 0.3287 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30390 Z= 0.265 Angle : 0.724 14.128 41580 Z= 0.362 Chirality : 0.049 0.556 4908 Planarity : 0.006 0.106 5172 Dihedral : 10.305 109.479 5962 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 6.90 % Allowed : 18.39 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.13), residues: 3618 helix: 0.30 (0.19), residues: 788 sheet: -1.28 (0.17), residues: 846 loop : -2.28 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 174 HIS 0.010 0.001 HIS C 201 PHE 0.021 0.002 PHE A 968 TYR 0.024 0.002 TYR B 622 ARG 0.005 0.001 ARG B1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 66) link_NAG-ASN : angle 3.27086 ( 198) link_ALPHA1-4 : bond 0.01895 ( 3) link_ALPHA1-4 : angle 3.57128 ( 9) link_ALPHA1-6 : bond 0.00520 ( 3) link_ALPHA1-6 : angle 1.94065 ( 9) link_BETA1-4 : bond 0.00344 ( 15) link_BETA1-4 : angle 1.36673 ( 45) link_ALPHA1-3 : bond 0.00763 ( 6) link_ALPHA1-3 : angle 1.90992 ( 18) hydrogen bonds : bond 0.05694 ( 927) hydrogen bonds : angle 5.47394 ( 2610) SS BOND : bond 0.00422 ( 72) SS BOND : angle 1.53609 ( 144) covalent geometry : bond 0.00625 (30225) covalent geometry : angle 0.68014 (41157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 145 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.6161 (OUTLIER) cc_final: 0.5842 (m110) REVERT: A 75 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6804 (mtp85) REVERT: A 79 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6427 (mt) REVERT: A 162 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7923 (m) REVERT: A 187 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7631 (mmmt) REVERT: A 201 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8061 (m90) REVERT: A 662 LEU cc_start: 0.8139 (mm) cc_final: 0.7664 (tp) REVERT: A 696 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7270 (mtpt) REVERT: A 845 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: A 863 GLN cc_start: 0.8360 (tt0) cc_final: 0.8155 (tt0) REVERT: A 988 ASN cc_start: 0.9231 (OUTLIER) cc_final: 0.8790 (t0) REVERT: A 994 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7599 (tpt) REVERT: A 1069 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: B 30 LYS cc_start: 0.5189 (OUTLIER) cc_final: 0.4546 (tppt) REVERT: B 34 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5467 (ptm160) REVERT: B 184 LEU cc_start: 0.3971 (OUTLIER) cc_final: 0.3725 (tt) REVERT: B 236 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.6718 (t80) REVERT: B 243 LYS cc_start: 0.5386 (OUTLIER) cc_final: 0.5124 (tttt) REVERT: B 346 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6696 (ptm160) REVERT: B 375 LYS cc_start: 0.7568 (ptmt) cc_final: 0.7075 (pptt) REVERT: B 511 TYR cc_start: 0.2236 (OUTLIER) cc_final: 0.1964 (p90) REVERT: B 578 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: B 690 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8557 (mt) REVERT: B 883 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7568 (t0) REVERT: B 891 LEU cc_start: 0.7379 (tp) cc_final: 0.7038 (tp) REVERT: B 1012 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8211 (tt) REVERT: B 1117 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.6457 (mm110) REVERT: B 1185 MET cc_start: 0.6958 (mmm) cc_final: 0.6686 (mmm) REVERT: C 54 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8149 (mtp85) REVERT: C 205 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: C 273 HIS cc_start: 0.6692 (m-70) cc_final: 0.6231 (m90) REVERT: C 367 SER cc_start: 0.7494 (OUTLIER) cc_final: 0.7051 (p) REVERT: C 472 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.6995 (t70) REVERT: C 473 PHE cc_start: 0.8089 (t80) cc_final: 0.7817 (t80) REVERT: C 555 LYS cc_start: 0.7674 (mttt) cc_final: 0.7421 (mptt) REVERT: C 597 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7839 (mt) REVERT: C 644 TRP cc_start: 0.8113 (OUTLIER) cc_final: 0.7244 (p-90) REVERT: C 789 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: C 955 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8710 (mm) REVERT: C 1124 CYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7332 (m) REVERT: C 1185 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8387 (mmm) REVERT: C 1219 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.6516 (p90) outliers start: 224 outliers final: 137 residues processed: 346 average time/residue: 0.9111 time to fit residues: 406.1819 Evaluate side-chains 303 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 132 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 988 ASN Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1117 GLN Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 24 PHE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 644 TRP Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 897 SER Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1185 MET Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 120 optimal weight: 10.0000 chunk 333 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 266 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1206 ASN B 531 ASN B 838 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 583 ASN C 863 GLN ** C1136 ASN ** 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 = 0.4178 r_free = 0.4178 target = 0.155676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107942 restraints weight = 51377.858| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.96 r_work: 0.3366 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30390 Z= 0.126 Angle : 0.618 13.481 41580 Z= 0.308 Chirality : 0.046 0.481 4908 Planarity : 0.005 0.100 5172 Dihedral : 9.584 106.471 5959 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.48 % Allowed : 20.02 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3618 helix: 0.77 (0.20), residues: 793 sheet: -1.17 (0.17), residues: 843 loop : -2.09 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 515 HIS 0.020 0.001 HIS B 465 PHE 0.018 0.001 PHE A 968 TYR 0.015 0.001 TYR A 822 ARG 0.007 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 66) link_NAG-ASN : angle 2.84153 ( 198) link_ALPHA1-4 : bond 0.01593 ( 3) link_ALPHA1-4 : angle 3.39063 ( 9) link_ALPHA1-6 : bond 0.00592 ( 3) link_ALPHA1-6 : angle 1.90999 ( 9) link_BETA1-4 : bond 0.00428 ( 15) link_BETA1-4 : angle 1.12925 ( 45) link_ALPHA1-3 : bond 0.00737 ( 6) link_ALPHA1-3 : angle 1.87122 ( 18) hydrogen bonds : bond 0.04336 ( 927) hydrogen bonds : angle 5.06549 ( 2610) SS BOND : bond 0.00206 ( 72) SS BOND : angle 1.02164 ( 144) covalent geometry : bond 0.00282 (30225) covalent geometry : angle 0.58102 (41157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 152 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8213 (mp) REVERT: A 79 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6173 (tt) REVERT: A 112 TYR cc_start: 0.7918 (m-80) cc_final: 0.7050 (m-80) REVERT: A 187 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7723 (mmmt) REVERT: A 662 LEU cc_start: 0.8255 (mm) cc_final: 0.7755 (tp) REVERT: A 696 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7015 (mtpt) REVERT: A 737 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8162 (mtp180) REVERT: A 831 GLU cc_start: 0.8792 (pt0) cc_final: 0.8514 (pp20) REVERT: A 863 GLN cc_start: 0.8354 (tt0) cc_final: 0.8110 (tt0) REVERT: A 988 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8851 (t0) REVERT: A 994 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7713 (tpt) REVERT: A 1069 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: B 30 LYS cc_start: 0.5407 (OUTLIER) cc_final: 0.4709 (tppt) REVERT: B 34 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5626 (ptm160) REVERT: B 184 LEU cc_start: 0.4082 (OUTLIER) cc_final: 0.3809 (tt) REVERT: B 236 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6868 (t80) REVERT: B 346 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6853 (ptm160) REVERT: B 375 LYS cc_start: 0.7666 (ptmt) cc_final: 0.7141 (pptt) REVERT: B 690 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8584 (mt) REVERT: B 1012 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8208 (tt) REVERT: B 1117 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6320 (mm110) REVERT: B 1185 MET cc_start: 0.7005 (mmm) cc_final: 0.6646 (mmm) REVERT: C 54 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8238 (mtp85) REVERT: C 273 HIS cc_start: 0.6739 (m-70) cc_final: 0.6258 (m90) REVERT: C 277 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8962 (p) REVERT: C 319 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8129 (mmp80) REVERT: C 367 SER cc_start: 0.7570 (OUTLIER) cc_final: 0.7175 (p) REVERT: C 402 GLN cc_start: 0.7642 (mm110) cc_final: 0.7337 (mt0) REVERT: C 472 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7034 (t70) REVERT: C 473 PHE cc_start: 0.8075 (t80) cc_final: 0.7809 (t80) REVERT: C 555 LYS cc_start: 0.7672 (mttt) cc_final: 0.7372 (mptt) REVERT: C 789 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: C 1124 CYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7639 (m) REVERT: C 1185 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7955 (mmm) outliers start: 178 outliers final: 101 residues processed: 312 average time/residue: 0.9741 time to fit residues: 391.9541 Evaluate side-chains 260 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 135 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 988 ASN Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1117 GLN Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 897 SER Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1185 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 287 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 HIS B 531 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 ASN ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.154048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106880 restraints weight = 51326.864| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.32 r_work: 0.3309 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30390 Z= 0.198 Angle : 0.664 19.670 41580 Z= 0.331 Chirality : 0.047 0.397 4908 Planarity : 0.005 0.106 5172 Dihedral : 9.435 105.924 5947 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.28 % Allowed : 19.44 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3618 helix: 0.63 (0.19), residues: 795 sheet: -1.20 (0.18), residues: 839 loop : -2.07 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 174 HIS 0.008 0.001 HIS B1129 PHE 0.022 0.002 PHE B 453 TYR 0.032 0.002 TYR C 427 ARG 0.007 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 66) link_NAG-ASN : angle 3.33553 ( 198) link_ALPHA1-4 : bond 0.01620 ( 3) link_ALPHA1-4 : angle 3.47150 ( 9) link_ALPHA1-6 : bond 0.00482 ( 3) link_ALPHA1-6 : angle 1.95069 ( 9) link_BETA1-4 : bond 0.00372 ( 15) link_BETA1-4 : angle 1.26337 ( 45) link_ALPHA1-3 : bond 0.00747 ( 6) link_ALPHA1-3 : angle 1.88054 ( 18) hydrogen bonds : bond 0.04945 ( 927) hydrogen bonds : angle 5.17575 ( 2610) SS BOND : bond 0.00297 ( 72) SS BOND : angle 1.18733 ( 144) covalent geometry : bond 0.00466 (30225) covalent geometry : angle 0.61697 (41157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 137 time to evaluate : 5.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 75 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6795 (mtp85) REVERT: A 112 TYR cc_start: 0.7878 (m-80) cc_final: 0.6942 (m-80) REVERT: A 155 MET cc_start: 0.7248 (mmm) cc_final: 0.6984 (mmt) REVERT: A 162 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7801 (m) REVERT: A 187 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7671 (mmmt) REVERT: A 455 VAL cc_start: 0.1125 (OUTLIER) cc_final: 0.0848 (t) REVERT: A 662 LEU cc_start: 0.8253 (mm) cc_final: 0.7765 (tp) REVERT: A 696 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7222 (mtpt) REVERT: A 737 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7818 (mtp180) REVERT: A 831 GLU cc_start: 0.8620 (pt0) cc_final: 0.8406 (pp20) REVERT: A 863 GLN cc_start: 0.8283 (tt0) cc_final: 0.8069 (tt0) REVERT: A 988 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8793 (t0) REVERT: A 994 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7669 (tpt) REVERT: A 1069 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: B 30 LYS cc_start: 0.5377 (OUTLIER) cc_final: 0.4687 (tppt) REVERT: B 34 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5613 (ptm160) REVERT: B 184 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3731 (tt) REVERT: B 236 TYR cc_start: 0.6850 (t80) cc_final: 0.6639 (t80) REVERT: B 243 LYS cc_start: 0.5677 (OUTLIER) cc_final: 0.5334 (tttt) REVERT: B 346 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6642 (ptm160) REVERT: B 375 LYS cc_start: 0.7633 (ptmt) cc_final: 0.7149 (pptt) REVERT: B 393 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8073 (pp) REVERT: B 578 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: B 676 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6555 (ptp-170) REVERT: B 690 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8532 (mt) REVERT: B 883 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7561 (t0) REVERT: B 1012 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8187 (tt) REVERT: B 1117 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.6403 (mm110) REVERT: B 1185 MET cc_start: 0.6962 (mmm) cc_final: 0.6610 (mmm) REVERT: C 54 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8108 (mtp85) REVERT: C 205 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: C 273 HIS cc_start: 0.6638 (m-70) cc_final: 0.6160 (m90) REVERT: C 277 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8959 (p) REVERT: C 319 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8010 (mmp80) REVERT: C 367 SER cc_start: 0.7567 (OUTLIER) cc_final: 0.7144 (p) REVERT: C 402 GLN cc_start: 0.7530 (mm110) cc_final: 0.7321 (mt0) REVERT: C 472 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.6962 (t70) REVERT: C 473 PHE cc_start: 0.8084 (t80) cc_final: 0.7769 (t80) REVERT: C 555 LYS cc_start: 0.7659 (mttt) cc_final: 0.7406 (mptt) REVERT: C 955 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8662 (mm) REVERT: C 1124 CYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7344 (m) REVERT: C 1185 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7818 (mmm) outliers start: 204 outliers final: 122 residues processed: 320 average time/residue: 1.4190 time to fit residues: 600.3659 Evaluate side-chains 285 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 132 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 988 ASN Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 883 ASP Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1117 GLN Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1185 MET Chi-restraints excluded: chain C residue 1203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 351 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 293 optimal weight: 7.9990 chunk 23 optimal weight: 0.0270 chunk 153 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 243 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 HIS B 531 ASN B 789 GLN C 583 ASN C 863 GLN ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.156317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109001 restraints weight = 51275.089| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.93 r_work: 0.3380 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30390 Z= 0.108 Angle : 0.597 16.271 41580 Z= 0.296 Chirality : 0.045 0.375 4908 Planarity : 0.005 0.098 5172 Dihedral : 8.820 103.404 5942 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.56 % Allowed : 21.23 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3618 helix: 1.03 (0.20), residues: 793 sheet: -0.99 (0.18), residues: 825 loop : -1.90 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 515 HIS 0.013 0.001 HIS B 465 PHE 0.019 0.001 PHE B 467 TYR 0.027 0.001 TYR C 427 ARG 0.005 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 66) link_NAG-ASN : angle 2.95636 ( 198) link_ALPHA1-4 : bond 0.01392 ( 3) link_ALPHA1-4 : angle 3.38338 ( 9) link_ALPHA1-6 : bond 0.00786 ( 3) link_ALPHA1-6 : angle 1.94716 ( 9) link_BETA1-4 : bond 0.00421 ( 15) link_BETA1-4 : angle 1.11800 ( 45) link_ALPHA1-3 : bond 0.00763 ( 6) link_ALPHA1-3 : angle 1.92665 ( 18) hydrogen bonds : bond 0.03990 ( 927) hydrogen bonds : angle 4.86653 ( 2610) SS BOND : bond 0.00191 ( 72) SS BOND : angle 1.13638 ( 144) covalent geometry : bond 0.00237 (30225) covalent geometry : angle 0.55447 (41157) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 162 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8271 (mp) REVERT: A 79 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6691 (tt) REVERT: A 112 TYR cc_start: 0.7813 (m-80) cc_final: 0.7037 (m-80) REVERT: A 186 LYS cc_start: 0.8673 (ttmp) cc_final: 0.8401 (tptt) REVERT: A 187 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7668 (mmmt) REVERT: A 662 LEU cc_start: 0.8293 (mm) cc_final: 0.7784 (tp) REVERT: A 696 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6952 (mtpt) REVERT: A 737 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8150 (mtp180) REVERT: A 863 GLN cc_start: 0.8249 (tt0) cc_final: 0.8031 (tt0) REVERT: A 1069 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: B 30 LYS cc_start: 0.5406 (OUTLIER) cc_final: 0.4756 (tppt) REVERT: B 34 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.5765 (ppp80) REVERT: B 39 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6947 (t) REVERT: B 184 LEU cc_start: 0.4060 (OUTLIER) cc_final: 0.3774 (tt) REVERT: B 346 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6817 (ptm160) REVERT: B 375 LYS cc_start: 0.7628 (ptmt) cc_final: 0.7118 (pptt) REVERT: B 527 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8110 (m) REVERT: B 578 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: B 1012 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8176 (tt) REVERT: B 1185 MET cc_start: 0.6985 (mmm) cc_final: 0.6670 (mmm) REVERT: C 54 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8225 (mtp85) REVERT: C 273 HIS cc_start: 0.6653 (m-70) cc_final: 0.6185 (m90) REVERT: C 326 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7364 (t0) REVERT: C 367 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.7183 (p) REVERT: C 402 GLN cc_start: 0.7608 (mm110) cc_final: 0.7330 (mt0) REVERT: C 408 PHE cc_start: 0.7276 (m-10) cc_final: 0.6679 (m-10) REVERT: C 462 TYR cc_start: 0.7985 (p90) cc_final: 0.7657 (p90) REVERT: C 472 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7010 (t70) REVERT: C 473 PHE cc_start: 0.8080 (t80) cc_final: 0.7758 (t80) REVERT: C 955 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8677 (mm) REVERT: C 967 MET cc_start: 0.7842 (mtt) cc_final: 0.7479 (mtm) REVERT: C 1124 CYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7520 (m) REVERT: C 1185 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7966 (mmm) outliers start: 148 outliers final: 87 residues processed: 292 average time/residue: 0.9982 time to fit residues: 370.8590 Evaluate side-chains 243 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 135 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 986 ARG Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1185 MET Chi-restraints excluded: chain C residue 1208 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 465 HIS B 531 ASN B 561 ASN B 789 GLN B 799 HIS B 998 ASN C 863 GLN ** C1136 ASN ** 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 = 0.4190 r_free = 0.4190 target = 0.156602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109303 restraints weight = 51726.511| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.00 r_work: 0.3391 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30390 Z= 0.108 Angle : 0.582 12.505 41580 Z= 0.292 Chirality : 0.044 0.364 4908 Planarity : 0.005 0.105 5172 Dihedral : 8.380 103.682 5926 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.16 % Allowed : 22.00 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3618 helix: 1.17 (0.20), residues: 793 sheet: -0.81 (0.18), residues: 828 loop : -1.83 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 515 HIS 0.008 0.001 HIS B 465 PHE 0.018 0.001 PHE B 467 TYR 0.013 0.001 TYR B 673 ARG 0.005 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 66) link_NAG-ASN : angle 2.76296 ( 198) link_ALPHA1-4 : bond 0.01580 ( 3) link_ALPHA1-4 : angle 3.40044 ( 9) link_ALPHA1-6 : bond 0.00507 ( 3) link_ALPHA1-6 : angle 1.92191 ( 9) link_BETA1-4 : bond 0.00388 ( 15) link_BETA1-4 : angle 1.14106 ( 45) link_ALPHA1-3 : bond 0.00660 ( 6) link_ALPHA1-3 : angle 1.86635 ( 18) hydrogen bonds : bond 0.03854 ( 927) hydrogen bonds : angle 4.75661 ( 2610) SS BOND : bond 0.00179 ( 72) SS BOND : angle 1.03206 ( 144) covalent geometry : bond 0.00239 (30225) covalent geometry : angle 0.54331 (41157) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 146 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6665 (tt) REVERT: A 186 LYS cc_start: 0.8663 (ttmp) cc_final: 0.8390 (tptt) REVERT: A 662 LEU cc_start: 0.8314 (mm) cc_final: 0.7781 (tp) REVERT: A 696 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6959 (mtpt) REVERT: A 863 GLN cc_start: 0.8201 (tt0) cc_final: 0.7990 (tt0) REVERT: A 1069 GLU cc_start: 0.8414 (tp30) cc_final: 0.7740 (mp0) REVERT: B 30 LYS cc_start: 0.5411 (OUTLIER) cc_final: 0.4791 (tppt) REVERT: B 34 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5744 (ppp80) REVERT: B 39 VAL cc_start: 0.7171 (OUTLIER) cc_final: 0.6955 (t) REVERT: B 184 LEU cc_start: 0.4037 (OUTLIER) cc_final: 0.3757 (tt) REVERT: B 238 MET cc_start: 0.6510 (mmp) cc_final: 0.6142 (mpm) REVERT: B 346 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6739 (ptm160) REVERT: B 375 LYS cc_start: 0.7628 (ptmt) cc_final: 0.7162 (pptt) REVERT: B 527 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8113 (m) REVERT: B 578 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: B 1012 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8180 (tt) REVERT: B 1185 MET cc_start: 0.6959 (mmm) cc_final: 0.6653 (mmm) REVERT: C 111 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5689 (mm) REVERT: C 205 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: C 273 HIS cc_start: 0.6640 (m-70) cc_final: 0.6145 (m90) REVERT: C 367 SER cc_start: 0.7437 (OUTLIER) cc_final: 0.7197 (p) REVERT: C 402 GLN cc_start: 0.7588 (mm110) cc_final: 0.7315 (mt0) REVERT: C 408 PHE cc_start: 0.7372 (m-10) cc_final: 0.6817 (m-10) REVERT: C 462 TYR cc_start: 0.8046 (p90) cc_final: 0.7597 (p90) REVERT: C 472 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.6970 (t70) REVERT: C 473 PHE cc_start: 0.8088 (t80) cc_final: 0.7797 (t80) REVERT: C 555 LYS cc_start: 0.7496 (mttt) cc_final: 0.7231 (mptt) REVERT: C 955 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8644 (mm) REVERT: C 967 MET cc_start: 0.7788 (mtt) cc_final: 0.7382 (mtm) REVERT: C 1124 CYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7388 (m) REVERT: C 1182 ASP cc_start: 0.8082 (m-30) cc_final: 0.7797 (t0) REVERT: C 1185 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7938 (mmm) outliers start: 135 outliers final: 81 residues processed: 265 average time/residue: 0.8576 time to fit residues: 296.2346 Evaluate side-chains 233 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 135 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1185 MET Chi-restraints excluded: chain C residue 1208 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 273 optimal weight: 1.9990 chunk 355 optimal weight: 0.5980 chunk 307 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 242 optimal weight: 0.0020 chunk 224 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN B 789 GLN C 863 GLN C1001 GLN ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.155968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108504 restraints weight = 51487.459| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.00 r_work: 0.3375 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30390 Z= 0.133 Angle : 0.598 12.732 41580 Z= 0.300 Chirality : 0.045 0.356 4908 Planarity : 0.005 0.101 5172 Dihedral : 8.017 103.599 5903 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.00 % Allowed : 22.18 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3618 helix: 1.13 (0.20), residues: 793 sheet: -0.84 (0.18), residues: 833 loop : -1.79 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 515 HIS 0.007 0.001 HIS C 201 PHE 0.028 0.001 PHE C 453 TYR 0.015 0.001 TYR B 673 ARG 0.005 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 66) link_NAG-ASN : angle 2.66006 ( 198) link_ALPHA1-4 : bond 0.01688 ( 3) link_ALPHA1-4 : angle 3.43048 ( 9) link_ALPHA1-6 : bond 0.00481 ( 3) link_ALPHA1-6 : angle 1.92921 ( 9) link_BETA1-4 : bond 0.00384 ( 15) link_BETA1-4 : angle 1.16481 ( 45) link_ALPHA1-3 : bond 0.00703 ( 6) link_ALPHA1-3 : angle 1.85053 ( 18) hydrogen bonds : bond 0.04084 ( 927) hydrogen bonds : angle 4.77768 ( 2610) SS BOND : bond 0.00240 ( 72) SS BOND : angle 0.98318 ( 144) covalent geometry : bond 0.00307 (30225) covalent geometry : angle 0.56347 (41157) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 144 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6710 (tt) REVERT: A 112 TYR cc_start: 0.7735 (m-80) cc_final: 0.6864 (m-10) REVERT: A 187 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7746 (mmmt) REVERT: A 455 VAL cc_start: 0.0993 (OUTLIER) cc_final: 0.0721 (t) REVERT: A 662 LEU cc_start: 0.8311 (mm) cc_final: 0.7783 (tp) REVERT: A 696 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7029 (mtpt) REVERT: A 863 GLN cc_start: 0.8248 (tt0) cc_final: 0.8034 (tt0) REVERT: A 1069 GLU cc_start: 0.8479 (tp30) cc_final: 0.7836 (mp0) REVERT: B 30 LYS cc_start: 0.5447 (OUTLIER) cc_final: 0.4847 (tppt) REVERT: B 34 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5753 (ptm160) REVERT: B 39 VAL cc_start: 0.7171 (OUTLIER) cc_final: 0.6942 (t) REVERT: B 184 LEU cc_start: 0.4056 (OUTLIER) cc_final: 0.3778 (tt) REVERT: B 243 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5452 (tttt) REVERT: B 346 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6757 (ptm160) REVERT: B 375 LYS cc_start: 0.7617 (ptmt) cc_final: 0.7122 (pptt) REVERT: B 527 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8137 (m) REVERT: B 578 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: B 676 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.6580 (ptp-170) REVERT: B 690 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8570 (mt) REVERT: B 1012 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8180 (tt) REVERT: C 54 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8249 (mtp85) REVERT: C 118 TYR cc_start: 0.7225 (m-80) cc_final: 0.7022 (m-80) REVERT: C 205 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: C 273 HIS cc_start: 0.6647 (m-70) cc_final: 0.6150 (m90) REVERT: C 319 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8164 (mmp80) REVERT: C 367 SER cc_start: 0.7444 (OUTLIER) cc_final: 0.7209 (p) REVERT: C 402 GLN cc_start: 0.7603 (mm110) cc_final: 0.7312 (mt0) REVERT: C 408 PHE cc_start: 0.7338 (m-10) cc_final: 0.6926 (m-10) REVERT: C 472 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.6984 (t70) REVERT: C 473 PHE cc_start: 0.8093 (t80) cc_final: 0.7803 (t80) REVERT: C 955 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8708 (mm) REVERT: C 967 MET cc_start: 0.7820 (mtt) cc_final: 0.7489 (mtm) REVERT: C 1124 CYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7438 (m) REVERT: C 1182 ASP cc_start: 0.8107 (m-30) cc_final: 0.7859 (t0) REVERT: C 1185 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7960 (mmm) outliers start: 130 outliers final: 84 residues processed: 260 average time/residue: 0.8948 time to fit residues: 303.5404 Evaluate side-chains 240 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 133 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1185 MET Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 237 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 312 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 269 optimal weight: 0.9980 chunk 29 optimal weight: 0.0470 chunk 148 optimal weight: 0.0040 chunk 206 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 overall best weight: 0.5690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 ASN B 789 GLN C 863 GLN ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.156947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109737 restraints weight = 51591.386| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.98 r_work: 0.3396 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30390 Z= 0.105 Angle : 0.587 12.769 41580 Z= 0.292 Chirality : 0.045 0.431 4908 Planarity : 0.005 0.103 5172 Dihedral : 8.405 125.130 5900 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.45 % Allowed : 22.77 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3618 helix: 1.27 (0.20), residues: 793 sheet: -0.78 (0.18), residues: 831 loop : -1.71 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 515 HIS 0.006 0.001 HIS C 201 PHE 0.018 0.001 PHE C 453 TYR 0.013 0.001 TYR B 213 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 66) link_NAG-ASN : angle 2.65356 ( 198) link_ALPHA1-4 : bond 0.01544 ( 3) link_ALPHA1-4 : angle 3.41042 ( 9) link_ALPHA1-6 : bond 0.00506 ( 3) link_ALPHA1-6 : angle 1.91219 ( 9) link_BETA1-4 : bond 0.00413 ( 15) link_BETA1-4 : angle 1.12802 ( 45) link_ALPHA1-3 : bond 0.00676 ( 6) link_ALPHA1-3 : angle 1.86755 ( 18) hydrogen bonds : bond 0.03736 ( 927) hydrogen bonds : angle 4.68497 ( 2610) SS BOND : bond 0.00181 ( 72) SS BOND : angle 0.86189 ( 144) covalent geometry : bond 0.00232 (30225) covalent geometry : angle 0.55214 (41157) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 151 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6656 (tt) REVERT: A 112 TYR cc_start: 0.7777 (m-80) cc_final: 0.7028 (m-80) REVERT: A 186 LYS cc_start: 0.8575 (ttmp) cc_final: 0.8349 (tptt) REVERT: A 187 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7731 (mmmt) REVERT: A 662 LEU cc_start: 0.8181 (mm) cc_final: 0.7704 (tp) REVERT: A 696 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6932 (mtpt) REVERT: A 863 GLN cc_start: 0.8154 (tt0) cc_final: 0.7943 (tt0) REVERT: A 1069 GLU cc_start: 0.8456 (tp30) cc_final: 0.7847 (mp0) REVERT: B 30 LYS cc_start: 0.5310 (OUTLIER) cc_final: 0.4676 (tppt) REVERT: B 34 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5739 (ppp80) REVERT: B 39 VAL cc_start: 0.7103 (OUTLIER) cc_final: 0.6888 (t) REVERT: B 182 LEU cc_start: 0.7684 (mp) cc_final: 0.7080 (tt) REVERT: B 184 LEU cc_start: 0.4031 (OUTLIER) cc_final: 0.3506 (tt) REVERT: B 238 MET cc_start: 0.6344 (mmp) cc_final: 0.6101 (mmp) REVERT: B 243 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5442 (tttt) REVERT: B 346 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6761 (ptm160) REVERT: B 375 LYS cc_start: 0.7605 (ptmt) cc_final: 0.7152 (pptt) REVERT: B 455 VAL cc_start: 0.8753 (m) cc_final: 0.8547 (t) REVERT: B 527 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8143 (m) REVERT: B 578 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: B 1012 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8202 (tt) REVERT: B 1185 MET cc_start: 0.6886 (mmm) cc_final: 0.6666 (mmm) REVERT: C 111 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5721 (mm) REVERT: C 205 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: C 273 HIS cc_start: 0.6642 (m-70) cc_final: 0.6152 (m90) REVERT: C 319 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8193 (mmp80) REVERT: C 367 SER cc_start: 0.7436 (OUTLIER) cc_final: 0.7220 (p) REVERT: C 402 GLN cc_start: 0.7613 (mm110) cc_final: 0.7329 (mt0) REVERT: C 408 PHE cc_start: 0.7341 (m-10) cc_final: 0.6916 (m-10) REVERT: C 472 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.6923 (t70) REVERT: C 473 PHE cc_start: 0.8082 (t80) cc_final: 0.7772 (t80) REVERT: C 555 LYS cc_start: 0.7515 (mttt) cc_final: 0.7241 (mptt) REVERT: C 955 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8672 (mm) REVERT: C 1124 CYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7357 (m) REVERT: C 1182 ASP cc_start: 0.8069 (m-30) cc_final: 0.7847 (t0) REVERT: C 1185 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7924 (mmm) outliers start: 112 outliers final: 75 residues processed: 249 average time/residue: 0.9242 time to fit residues: 298.7784 Evaluate side-chains 231 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 136 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1185 MET Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 110 optimal weight: 0.0020 chunk 156 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 ASN C 863 GLN C1001 GLN ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.156817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109709 restraints weight = 51445.494| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.94 r_work: 0.3393 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30390 Z= 0.115 Angle : 0.682 51.517 41580 Z= 0.362 Chirality : 0.045 0.353 4908 Planarity : 0.005 0.102 5172 Dihedral : 8.167 102.866 5896 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.23 % Allowed : 23.11 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3618 helix: 1.27 (0.20), residues: 793 sheet: -0.73 (0.18), residues: 838 loop : -1.71 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 515 HIS 0.006 0.001 HIS C 201 PHE 0.012 0.001 PHE C 968 TYR 0.030 0.001 TYR C 427 ARG 0.005 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 66) link_NAG-ASN : angle 2.55853 ( 198) link_ALPHA1-4 : bond 0.01609 ( 3) link_ALPHA1-4 : angle 3.39544 ( 9) link_ALPHA1-6 : bond 0.00496 ( 3) link_ALPHA1-6 : angle 1.92441 ( 9) link_BETA1-4 : bond 0.00405 ( 15) link_BETA1-4 : angle 1.13184 ( 45) link_ALPHA1-3 : bond 0.00696 ( 6) link_ALPHA1-3 : angle 1.84839 ( 18) hydrogen bonds : bond 0.03795 ( 927) hydrogen bonds : angle 4.68465 ( 2610) SS BOND : bond 0.00192 ( 72) SS BOND : angle 1.09581 ( 144) covalent geometry : bond 0.00260 (30225) covalent geometry : angle 0.65409 (41157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27815.47 seconds wall clock time: 482 minutes 45.99 seconds (28965.99 seconds total)