Starting phenix.real_space_refine on Wed Jun 25 14:27:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1f_38834/06_2025/8y1f_38834.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1f_38834/06_2025/8y1f_38834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y1f_38834/06_2025/8y1f_38834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1f_38834/06_2025/8y1f_38834.map" model { file = "/net/cci-nas-00/data/ceres_data/8y1f_38834/06_2025/8y1f_38834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1f_38834/06_2025/8y1f_38834.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.118 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 91 residue(s): 1.68s 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: 18.73, per 1000 atoms: 0.63 Number of scatterers: 29541 At special positions: 0 Unit cell: (151.093, 160.876, 167.398, 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=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 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: 7.72 Conformation dependent library (CDL) restraints added in 3.4 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: 81 helices and 71 sheets defined 24.1% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.594A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.594A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.670A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.512A pdb=" N LEU A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.857A pdb=" N ILE A 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.974A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.949A 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 442 through 448 removed outlier: 3.539A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.691A pdb=" N SER A 484 " --> pdb=" O VAL A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.563A pdb=" N CYS A 556 " --> pdb=" O GLU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 862 removed outlier: 3.865A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.767A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.605A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 941 " --> pdb=" O VAL A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.539A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.792A 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: 3.929A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.614A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.972A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.696A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.797A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.622A pdb=" N LEU B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 4.207A pdb=" N PHE B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.044A pdb=" N ARG B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 400 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.611A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.751A pdb=" N ASN B 483 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.912A pdb=" N GLU B 831 " --> pdb=" O ASP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 862 removed outlier: 3.959A pdb=" N ASN B 838 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 909 Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.987A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.653A 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: 4.036A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.819A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1062 Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 4.131A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.641A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.568A pdb=" N GLU C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 removed outlier: 4.027A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.559A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 394 through 402 removed outlier: 3.994A pdb=" N ARG C 398 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 442 through 447 Processing helix chain 'C' and resid 481 through 485 removed outlier: 3.947A pdb=" N SER C 484 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.752A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 813 through 819 Processing helix chain 'C' and resid 822 through 830 Processing helix chain 'C' and resid 831 through 833 No H-bonds generated for 'chain 'C' and resid 831 through 833' Processing helix chain 'C' and resid 834 through 862 removed outlier: 3.847A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 914 through 923 removed outlier: 3.888A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.531A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.615A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 4.134A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.673A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1057 through 1062 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.918A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 8.247A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.097A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 648 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 315 " --> pdb=" O CYS C 619 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 67 removed outlier: 7.986A pdb=" N GLN A 265 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP A 281 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.796A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N TYR A 158 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS A 175 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.534A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 146 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN A 188 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE A 148 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 186 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 150 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 109 through 112 Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA9, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.195A pdb=" N ALA A 315 " --> pdb=" O CYS A 619 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.673A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.783A pdb=" N SER A 422 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N CYS A 370 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN A 424 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE A 368 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A 426 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 428 " --> pdb=" O HIS A 364 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS A 364 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 345 through 349 Processing sheet with id=AB5, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB6, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB7, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.367A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AB9, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AC1, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.573A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 742 " --> pdb=" O MET A 738 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.219A pdb=" N SER A 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 786 through 789 removed outlier: 7.300A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 793 through 804 removed outlier: 6.812A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A1140 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.378A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC7, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AC8, first strand: chain 'A' and resid 1202 through 1205 Processing sheet with id=AC9, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.655A pdb=" N ASP B 38 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 59 through 67 removed outlier: 8.042A pdb=" N GLN B 265 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP B 281 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.949A pdb=" N THR B 241 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N TYR B 158 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS B 175 " --> pdb=" O TYR B 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.504A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD6, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD7, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AD8, first strand: chain 'B' and resid 315 through 319 removed outlier: 4.220A pdb=" N ALA B 315 " --> pdb=" O CYS B 619 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.713A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.549A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.576A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AE4, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.442A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AE6, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE7, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.417A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.005A pdb=" N SER B 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.866A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B1140 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR B1148 " --> pdb=" O HIS B1129 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS B1129 " --> pdb=" O TYR B1148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.211A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AF3, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.552A pdb=" N GLY B1169 " --> pdb=" O MET B1205 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1175 through 1179 Processing sheet with id=AF5, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF6, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.595A pdb=" N ASP C 38 " --> pdb=" O PHE C 74 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 59 through 67 removed outlier: 8.062A pdb=" N GLN C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP C 281 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.925A pdb=" N THR C 241 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N TYR C 158 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS C 175 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.882A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 221 through 227 removed outlier: 5.252A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 109 through 113 Processing sheet with id=AG3, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AG4, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AG5, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.852A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'C' and resid 345 through 349 Processing sheet with id=AG7, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.568A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG9, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.480A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 504 through 507 Processing sheet with id=AH2, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AH3, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.541A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.964A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.964A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.313A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH8, first strand: chain 'C' and resid 1202 through 1205 1074 hydrogen bonds defined for protein. 2955 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: 16.24 Time building geometry restraints manager: 9.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9230 1.34 - 1.47: 7872 1.47 - 1.59: 12925 1.59 - 1.71: 0 1.71 - 1.83: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" C5 MAN I 3 " pdb=" O5 MAN I 3 " ideal model delta sigma weight residual 1.418 1.497 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CA ASP B 250 " pdb=" C ASP B 250 " ideal model delta sigma weight residual 1.523 1.571 -0.048 1.34e-02 5.57e+03 1.29e+01 bond pdb=" CA ASP A 250 " pdb=" C ASP A 250 " ideal model delta sigma weight residual 1.523 1.569 -0.046 1.34e-02 5.57e+03 1.18e+01 bond pdb=" C5 MAN D 3 " pdb=" O5 MAN D 3 " ideal model delta sigma weight residual 1.418 1.484 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C5 MAN N 3 " pdb=" O5 MAN N 3 " ideal model delta sigma weight residual 1.418 1.478 -0.060 2.00e-02 2.50e+03 8.91e+00 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 39398 1.65 - 3.30: 1510 3.30 - 4.95: 184 4.95 - 6.60: 49 6.60 - 8.25: 16 Bond angle restraints: 41157 Sorted by residual: angle pdb=" N ILE A 15 " pdb=" CA ILE A 15 " pdb=" C ILE A 15 " ideal model delta sigma weight residual 111.48 106.18 5.30 9.40e-01 1.13e+00 3.18e+01 angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 117.29 -6.59 1.22e+00 6.72e-01 2.91e+01 angle pdb=" C CYS A 819 " pdb=" N SER A 820 " pdb=" CA SER A 820 " ideal model delta sigma weight residual 121.19 129.44 -8.25 1.59e+00 3.96e-01 2.69e+01 angle pdb=" CA ASP A 250 " pdb=" C ASP A 250 " pdb=" O ASP A 250 " ideal model delta sigma weight residual 120.51 113.21 7.30 1.43e+00 4.89e-01 2.60e+01 angle pdb=" C CYS C 819 " pdb=" N SER C 820 " pdb=" CA SER C 820 " ideal model delta sigma weight residual 121.19 129.07 -7.88 1.59e+00 3.96e-01 2.46e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 18001 21.84 - 43.69: 922 43.69 - 65.53: 247 65.53 - 87.38: 45 87.38 - 109.22: 12 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 180.00 144.21 35.79 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA PRO B 969 " pdb=" C PRO B 969 " pdb=" N PRO B 970 " pdb=" CA PRO B 970 " ideal model delta harmonic sigma weight residual 180.00 145.82 34.18 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA PRO A 969 " pdb=" C PRO A 969 " pdb=" N PRO A 970 " pdb=" CA PRO A 970 " ideal model delta harmonic sigma weight residual 180.00 145.97 34.03 0 5.00e+00 4.00e-02 4.63e+01 ... (remaining 19224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4595 0.100 - 0.200: 299 0.200 - 0.300: 11 0.300 - 0.401: 1 0.401 - 0.501: 2 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG B2003 " pdb=" ND2 ASN B 58 " pdb=" C2 NAG B2003 " pdb=" O5 NAG B2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" C1 NAG A2003 " pdb=" ND2 ASN A 58 " pdb=" C2 NAG A2003 " pdb=" O5 NAG A2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.62e+00 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 -2.00 -0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 92 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 93 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 92 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 93 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 92 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 93 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.060 5.00e-02 4.00e+02 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7464 2.80 - 3.32: 23101 3.32 - 3.85: 47938 3.85 - 4.37: 55724 4.37 - 4.90: 98704 Nonbonded interactions: 232931 Sorted by model distance: nonbonded pdb=" OD1 ASP B 523 " pdb=" OG SER B 526 " model vdw 2.272 3.040 nonbonded pdb=" OG SER C 340 " pdb=" OD1 ASN C 343 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP C 523 " pdb=" OG SER C 526 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" O PHE B 473 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 625 " pdb=" OD1 ASP A 660 " model vdw 2.297 3.040 ... (remaining 232926 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: 3.330 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: 0.040 Extract box with map and model: 1.200 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 73.600 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 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 : 0.005 0.079 30390 Z= 0.260 Angle : 0.791 16.563 41580 Z= 0.425 Chirality : 0.052 0.501 4908 Planarity : 0.007 0.113 5172 Dihedral : 14.273 109.220 12183 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 6.87 % Allowed : 6.41 % Favored : 86.72 % 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: -2.79 (0.12), residues: 3618 helix: -1.82 (0.15), residues: 777 sheet: -1.02 (0.16), residues: 861 loop : -2.29 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 444 HIS 0.006 0.001 HIS C 201 PHE 0.023 0.002 PHE C 968 TYR 0.017 0.002 TYR C1148 ARG 0.004 0.001 ARG A 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 66) link_NAG-ASN : angle 3.03054 ( 198) link_ALPHA1-4 : bond 0.00852 ( 3) link_ALPHA1-4 : angle 3.74071 ( 9) link_ALPHA1-6 : bond 0.00245 ( 3) link_ALPHA1-6 : angle 1.70341 ( 9) link_BETA1-4 : bond 0.00597 ( 15) link_BETA1-4 : angle 1.95068 ( 45) link_ALPHA1-3 : bond 0.00475 ( 6) link_ALPHA1-3 : angle 1.87099 ( 18) hydrogen bonds : bond 0.21291 ( 1036) hydrogen bonds : angle 7.42979 ( 2955) SS BOND : bond 0.00229 ( 72) SS BOND : angle 0.84382 ( 144) covalent geometry : bond 0.00545 (30225) covalent geometry : angle 0.75860 (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 595 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 372 time to evaluate : 3.300 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 43 SER cc_start: 0.8866 (t) cc_final: 0.8578 (p) REVERT: A 83 LYS cc_start: 0.8164 (tttm) cc_final: 0.7957 (tttm) REVERT: A 84 TYR cc_start: 0.7870 (m-80) cc_final: 0.7580 (m-80) REVERT: A 113 VAL cc_start: 0.8315 (t) cc_final: 0.7892 (t) REVERT: A 187 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: A 206 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7261 (mtp85) REVERT: A 400 ASP cc_start: 0.8230 (m-30) cc_final: 0.7864 (m-30) REVERT: A 517 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6223 (ttp-170) REVERT: A 636 VAL cc_start: 0.8593 (p) cc_final: 0.8371 (m) REVERT: A 789 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8534 (mm-40) REVERT: A 828 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 835 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7442 (t80) REVERT: A 912 LYS cc_start: 0.8435 (tttt) cc_final: 0.8231 (ttmt) REVERT: A 1066 ASP cc_start: 0.6474 (OUTLIER) cc_final: 0.6273 (m-30) REVERT: A 1105 ARG cc_start: 0.7232 (ttt90) cc_final: 0.7018 (tpp80) REVERT: A 1131 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7892 (pp) REVERT: A 1219 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.5269 (p90) REVERT: B 84 TYR cc_start: 0.7940 (m-80) cc_final: 0.7702 (m-80) REVERT: B 116 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8130 (p) REVERT: B 155 MET cc_start: 0.9175 (mmm) cc_final: 0.8628 (mmm) REVERT: B 241 THR cc_start: 0.8506 (m) cc_final: 0.8088 (p) REVERT: B 248 ASN cc_start: 0.7647 (p0) cc_final: 0.7404 (p0) REVERT: B 305 ASP cc_start: 0.7887 (m-30) cc_final: 0.7674 (m-30) REVERT: B 345 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7593 (mm-30) REVERT: B 500 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7906 (ptmm) REVERT: B 503 HIS cc_start: 0.7537 (t70) cc_final: 0.7122 (t70) REVERT: B 511 TYR cc_start: 0.4097 (OUTLIER) cc_final: 0.3702 (m-80) REVERT: B 598 ASN cc_start: 0.8114 (m-40) cc_final: 0.7889 (m-40) REVERT: B 630 GLN cc_start: 0.8271 (mt0) cc_final: 0.7985 (mt0) REVERT: B 655 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8865 (mt) REVERT: B 714 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: B 788 ILE cc_start: 0.8798 (tt) cc_final: 0.8470 (mt) REVERT: B 800 GLU cc_start: 0.8199 (pm20) cc_final: 0.7923 (pt0) REVERT: B 862 MET cc_start: 0.8310 (mmm) cc_final: 0.8050 (mmm) REVERT: B 912 LYS cc_start: 0.8431 (tttt) cc_final: 0.8185 (ttmt) REVERT: B 1001 GLN cc_start: 0.6907 (tt0) cc_final: 0.6454 (tm-30) REVERT: B 1060 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7276 (mm-30) REVERT: B 1091 GLN cc_start: 0.6953 (tt0) cc_final: 0.6593 (tm-30) REVERT: B 1105 ARG cc_start: 0.6917 (ttt90) cc_final: 0.6655 (tpp80) REVERT: B 1149 LYS cc_start: 0.8656 (tttt) cc_final: 0.8362 (tttp) REVERT: B 1167 ASP cc_start: 0.7504 (m-30) cc_final: 0.7020 (t70) REVERT: C 24 PHE cc_start: 0.7852 (m-80) cc_final: 0.7591 (m-80) REVERT: C 38 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: C 112 TYR cc_start: 0.7759 (m-80) cc_final: 0.7328 (m-80) REVERT: C 155 MET cc_start: 0.8789 (mmm) cc_final: 0.8351 (mmm) REVERT: C 187 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7408 (ttmm) REVERT: C 213 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7292 (p90) REVERT: C 356 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8492 (mp) REVERT: C 374 ASP cc_start: 0.7206 (m-30) cc_final: 0.6166 (m-30) REVERT: C 402 GLN cc_start: 0.7661 (mm110) cc_final: 0.7333 (mm-40) REVERT: C 464 ASP cc_start: 0.7754 (m-30) cc_final: 0.7530 (m-30) REVERT: C 500 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7205 (mmtm) REVERT: C 655 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8818 (mt) REVERT: C 788 ILE cc_start: 0.8580 (tt) cc_final: 0.8204 (pt) REVERT: C 827 ASP cc_start: 0.7874 (m-30) cc_final: 0.7438 (m-30) REVERT: C 851 ASP cc_start: 0.7299 (m-30) cc_final: 0.7073 (m-30) REVERT: C 1091 GLN cc_start: 0.6951 (tt0) cc_final: 0.6578 (mt0) REVERT: C 1115 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8502 (mmmm) REVERT: C 1135 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8243 (mm110) REVERT: C 1219 TYR cc_start: 0.5555 (OUTLIER) cc_final: 0.5189 (m-80) outliers start: 223 outliers final: 72 residues processed: 554 average time/residue: 0.9851 time to fit residues: 681.2083 Evaluate side-chains 320 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 227 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP 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 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1155 THR Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 930 GLU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1115 LYS Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1135 GLN Chi-restraints excluded: chain C residue 1156 VAL 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: 4.9990 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 0.3980 chunk 93 optimal weight: 0.0060 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 204 GLN A 384 ASN A 630 GLN A 876 HIS A 984 GLN A1136 ASN A1180 GLN B 204 GLN B 353 ASN B 561 ASN B 587 ASN B 630 GLN B 821 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B1001 GLN B1079 ASN B1091 GLN C 204 GLN C 531 ASN C 552 ASN C 630 GLN C 799 HIS C 863 GLN C 894 GLN C 954 GLN C 984 GLN C1001 GLN C1079 ASN C1091 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.089914 restraints weight = 41721.210| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.72 r_work: 0.2870 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30390 Z= 0.129 Angle : 0.643 20.606 41580 Z= 0.324 Chirality : 0.047 0.673 4908 Planarity : 0.006 0.095 5172 Dihedral : 10.299 104.272 5996 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.68 % Allowed : 10.29 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 3618 helix: 0.21 (0.19), residues: 771 sheet: -0.71 (0.17), residues: 822 loop : -1.96 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.005 0.001 HIS C 201 PHE 0.021 0.001 PHE A 968 TYR 0.017 0.001 TYR C1148 ARG 0.003 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00818 ( 66) link_NAG-ASN : angle 3.72042 ( 198) link_ALPHA1-4 : bond 0.01325 ( 3) link_ALPHA1-4 : angle 3.70429 ( 9) link_ALPHA1-6 : bond 0.00518 ( 3) link_ALPHA1-6 : angle 1.40449 ( 9) link_BETA1-4 : bond 0.00367 ( 15) link_BETA1-4 : angle 1.31669 ( 45) link_ALPHA1-3 : bond 0.00422 ( 6) link_ALPHA1-3 : angle 2.04162 ( 18) hydrogen bonds : bond 0.05286 ( 1036) hydrogen bonds : angle 5.40751 ( 2955) SS BOND : bond 0.00286 ( 72) SS BOND : angle 1.50168 ( 144) covalent geometry : bond 0.00285 (30225) covalent geometry : angle 0.58022 (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 372 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 220 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.8503 (tttm) cc_final: 0.8073 (tttm) REVERT: A 187 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8419 (ttmm) REVERT: A 400 ASP cc_start: 0.8634 (m-30) cc_final: 0.8268 (m-30) REVERT: A 800 GLU cc_start: 0.8547 (pm20) cc_final: 0.8331 (pm20) REVERT: A 828 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8929 (tp) REVERT: A 835 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7132 (t80) REVERT: A 878 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7533 (t70) REVERT: A 900 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7946 (ptt180) REVERT: A 912 LYS cc_start: 0.8549 (tttt) cc_final: 0.8273 (ttmt) REVERT: A 1001 GLN cc_start: 0.7333 (tm-30) cc_final: 0.7010 (tm-30) REVERT: A 1066 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: A 1219 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5725 (p90) REVERT: B 84 TYR cc_start: 0.8400 (m-80) cc_final: 0.7976 (m-10) REVERT: B 194 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8881 (m) REVERT: B 241 THR cc_start: 0.8631 (m) cc_final: 0.8340 (p) REVERT: B 345 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8650 (mm-30) REVERT: B 433 ASN cc_start: 0.6402 (m-40) cc_final: 0.5449 (p0) REVERT: B 500 LYS cc_start: 0.8307 (mtmt) cc_final: 0.8008 (ptmm) REVERT: B 503 HIS cc_start: 0.7411 (t70) cc_final: 0.6858 (t70) REVERT: B 598 ASN cc_start: 0.8326 (m-40) cc_final: 0.8126 (m-40) REVERT: B 630 GLN cc_start: 0.8625 (mt0) cc_final: 0.8408 (mt0) REVERT: B 714 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8656 (m-30) REVERT: B 788 ILE cc_start: 0.9121 (tt) cc_final: 0.8852 (mt) REVERT: B 800 GLU cc_start: 0.9049 (pm20) cc_final: 0.8700 (pt0) REVERT: B 902 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7459 (mt) REVERT: B 903 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8398 (mp) REVERT: B 912 LYS cc_start: 0.8838 (tttt) cc_final: 0.8478 (ttmt) REVERT: B 1001 GLN cc_start: 0.7483 (tt0) cc_final: 0.6600 (tm-30) REVERT: B 1060 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8098 (tp30) REVERT: B 1091 GLN cc_start: 0.8321 (tt0) cc_final: 0.7856 (tm-30) REVERT: B 1105 ARG cc_start: 0.8547 (ttt90) cc_final: 0.8331 (tpp80) REVERT: B 1112 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8614 (mt-10) REVERT: B 1167 ASP cc_start: 0.8098 (m-30) cc_final: 0.7257 (t70) REVERT: C 112 TYR cc_start: 0.7628 (m-80) cc_final: 0.7201 (m-80) REVERT: C 155 MET cc_start: 0.9062 (mmm) cc_final: 0.8676 (mmm) REVERT: C 213 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8538 (p90) REVERT: C 374 ASP cc_start: 0.7976 (m-30) cc_final: 0.7209 (m-30) REVERT: C 402 GLN cc_start: 0.8260 (mm110) cc_final: 0.8025 (mm-40) REVERT: C 500 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7260 (mmtt) REVERT: C 655 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9125 (mt) REVERT: C 748 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7123 (pp) REVERT: C 827 ASP cc_start: 0.8355 (m-30) cc_final: 0.8007 (m-30) REVERT: C 977 VAL cc_start: 0.9210 (m) cc_final: 0.8988 (p) REVERT: C 994 MET cc_start: 0.8798 (tpp) cc_final: 0.8577 (tpt) REVERT: C 1003 LEU cc_start: 0.8322 (mm) cc_final: 0.7909 (tt) REVERT: C 1091 GLN cc_start: 0.8243 (tt0) cc_final: 0.7723 (mt0) REVERT: C 1219 TYR cc_start: 0.5805 (OUTLIER) cc_final: 0.5509 (m-80) outliers start: 152 outliers final: 84 residues processed: 344 average time/residue: 1.0560 time to fit residues: 457.6527 Evaluate side-chains 293 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 193 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 930 GLU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1206 ASN 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: 3.9990 chunk 207 optimal weight: 0.8980 chunk 323 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 263 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 356 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 894 GLN C1001 GLN C1135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.088880 restraints weight = 41737.611| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.54 r_work: 0.2845 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30390 Z= 0.163 Angle : 0.648 16.875 41580 Z= 0.326 Chirality : 0.047 0.770 4908 Planarity : 0.006 0.097 5172 Dihedral : 9.615 100.750 5940 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.44 % Allowed : 10.94 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3618 helix: 0.93 (0.20), residues: 771 sheet: -0.55 (0.17), residues: 816 loop : -1.78 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 444 HIS 0.007 0.001 HIS B 799 PHE 0.018 0.001 PHE B 968 TYR 0.017 0.001 TYR C1148 ARG 0.004 0.000 ARG B 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 66) link_NAG-ASN : angle 3.31155 ( 198) link_ALPHA1-4 : bond 0.01322 ( 3) link_ALPHA1-4 : angle 3.67192 ( 9) link_ALPHA1-6 : bond 0.00550 ( 3) link_ALPHA1-6 : angle 1.60171 ( 9) link_BETA1-4 : bond 0.00236 ( 15) link_BETA1-4 : angle 1.39576 ( 45) link_ALPHA1-3 : bond 0.00438 ( 6) link_ALPHA1-3 : angle 2.04220 ( 18) hydrogen bonds : bond 0.05239 ( 1036) hydrogen bonds : angle 5.13726 ( 2955) SS BOND : bond 0.00251 ( 72) SS BOND : angle 1.47639 ( 144) covalent geometry : bond 0.00389 (30225) covalent geometry : angle 0.59664 (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 353 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 209 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.8570 (tttm) cc_final: 0.8111 (tttm) REVERT: A 187 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8410 (ttmm) REVERT: A 400 ASP cc_start: 0.8604 (m-30) cc_final: 0.8199 (m-30) REVERT: A 828 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8924 (tp) REVERT: A 835 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7140 (t80) REVERT: A 900 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8005 (ptt180) REVERT: A 912 LYS cc_start: 0.8548 (tttt) cc_final: 0.8286 (ttmt) REVERT: A 1066 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: A 1091 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: A 1219 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.5719 (p90) REVERT: B 84 TYR cc_start: 0.8422 (m-80) cc_final: 0.8007 (m-10) REVERT: B 241 THR cc_start: 0.8794 (m) cc_final: 0.8411 (p) REVERT: B 345 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8661 (mm-30) REVERT: B 500 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7878 (ptmm) REVERT: B 503 HIS cc_start: 0.7600 (t70) cc_final: 0.7086 (t70) REVERT: B 598 ASN cc_start: 0.8319 (m-40) cc_final: 0.8114 (m-40) REVERT: B 630 GLN cc_start: 0.8692 (mt0) cc_final: 0.8477 (mt0) REVERT: B 714 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8674 (m-30) REVERT: B 788 ILE cc_start: 0.9100 (tt) cc_final: 0.8883 (mt) REVERT: B 800 GLU cc_start: 0.9045 (pm20) cc_final: 0.8716 (pt0) REVERT: B 902 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7631 (mt) REVERT: B 903 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8451 (mp) REVERT: B 912 LYS cc_start: 0.8765 (tttt) cc_final: 0.8439 (ttmt) REVERT: B 1001 GLN cc_start: 0.7515 (tt0) cc_final: 0.6721 (tm-30) REVERT: B 1060 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8086 (tp30) REVERT: B 1091 GLN cc_start: 0.8318 (tt0) cc_final: 0.8079 (tt0) REVERT: B 1105 ARG cc_start: 0.8596 (ttt90) cc_final: 0.8361 (tpp80) REVERT: B 1112 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8647 (mt-10) REVERT: B 1167 ASP cc_start: 0.8047 (m-30) cc_final: 0.6896 (t70) REVERT: C 38 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8545 (m-30) REVERT: C 155 MET cc_start: 0.9105 (mmm) cc_final: 0.8705 (mmm) REVERT: C 213 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8581 (p90) REVERT: C 374 ASP cc_start: 0.8004 (m-30) cc_final: 0.7337 (m-30) REVERT: C 402 GLN cc_start: 0.8299 (mm110) cc_final: 0.8012 (mm-40) REVERT: C 500 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7282 (mmtm) REVERT: C 655 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9082 (mt) REVERT: C 748 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7020 (mt) REVERT: C 827 ASP cc_start: 0.8359 (m-30) cc_final: 0.7988 (m-30) REVERT: C 934 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8285 (mm) REVERT: C 1003 LEU cc_start: 0.8306 (mm) cc_final: 0.7934 (tt) REVERT: C 1091 GLN cc_start: 0.8271 (tt0) cc_final: 0.7746 (mt0) REVERT: C 1219 TYR cc_start: 0.5642 (OUTLIER) cc_final: 0.5254 (m-80) outliers start: 144 outliers final: 99 residues processed: 323 average time/residue: 0.9492 time to fit residues: 390.3270 Evaluate side-chains 311 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 195 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 38 ASP 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 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 967 MET Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 272 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 326 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN A 872 ASN C 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.088134 restraints weight = 41924.882| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.54 r_work: 0.2839 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30390 Z= 0.180 Angle : 0.649 15.538 41580 Z= 0.326 Chirality : 0.048 0.827 4908 Planarity : 0.005 0.097 5172 Dihedral : 8.949 95.288 5931 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.05 % Allowed : 11.03 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 3618 helix: 1.18 (0.20), residues: 774 sheet: -0.50 (0.17), residues: 840 loop : -1.69 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 515 HIS 0.010 0.001 HIS B 799 PHE 0.018 0.002 PHE C 968 TYR 0.018 0.002 TYR C1148 ARG 0.004 0.000 ARG B 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 66) link_NAG-ASN : angle 3.17650 ( 198) link_ALPHA1-4 : bond 0.01425 ( 3) link_ALPHA1-4 : angle 3.67266 ( 9) link_ALPHA1-6 : bond 0.00521 ( 3) link_ALPHA1-6 : angle 1.64630 ( 9) link_BETA1-4 : bond 0.00231 ( 15) link_BETA1-4 : angle 1.47993 ( 45) link_ALPHA1-3 : bond 0.00456 ( 6) link_ALPHA1-3 : angle 2.13394 ( 18) hydrogen bonds : bond 0.05314 ( 1036) hydrogen bonds : angle 5.02733 ( 2955) SS BOND : bond 0.00329 ( 72) SS BOND : angle 1.29281 ( 144) covalent geometry : bond 0.00434 (30225) covalent geometry : angle 0.60287 (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 368 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 204 time to evaluate : 3.311 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 83 LYS cc_start: 0.8585 (tttm) cc_final: 0.8057 (tttm) REVERT: A 187 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8399 (ttmm) REVERT: A 206 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8427 (mtp85) REVERT: A 400 ASP cc_start: 0.8545 (m-30) cc_final: 0.8175 (m-30) REVERT: A 573 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8190 (mt) REVERT: A 828 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8950 (tp) REVERT: A 835 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7191 (t80) REVERT: A 878 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7456 (p0) REVERT: A 900 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8005 (ptt180) REVERT: A 912 LYS cc_start: 0.8555 (tttt) cc_final: 0.8312 (ttmt) REVERT: A 1066 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6890 (m-30) REVERT: A 1091 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: A 1219 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5774 (p90) REVERT: B 84 TYR cc_start: 0.8419 (m-80) cc_final: 0.7985 (m-10) REVERT: B 116 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7322 (p) REVERT: B 213 TYR cc_start: 0.9315 (OUTLIER) cc_final: 0.8577 (p90) REVERT: B 241 THR cc_start: 0.8760 (m) cc_final: 0.8414 (p) REVERT: B 345 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8684 (mm-30) REVERT: B 500 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7873 (ptmm) REVERT: B 503 HIS cc_start: 0.7802 (t70) cc_final: 0.7269 (t70) REVERT: B 598 ASN cc_start: 0.8287 (m-40) cc_final: 0.8082 (m-40) REVERT: B 630 GLN cc_start: 0.8716 (mt0) cc_final: 0.8472 (mt0) REVERT: B 714 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8650 (m-30) REVERT: B 800 GLU cc_start: 0.9093 (pm20) cc_final: 0.8731 (pt0) REVERT: B 902 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7756 (mt) REVERT: B 903 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8485 (mp) REVERT: B 912 LYS cc_start: 0.8785 (tttt) cc_final: 0.8463 (ttmt) REVERT: B 1001 GLN cc_start: 0.7530 (tt0) cc_final: 0.6800 (tm-30) REVERT: B 1060 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8102 (tp30) REVERT: B 1091 GLN cc_start: 0.8356 (tt0) cc_final: 0.8138 (tt0) REVERT: B 1105 ARG cc_start: 0.8586 (ttt90) cc_final: 0.8371 (tpp80) REVERT: B 1112 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8709 (mt-10) REVERT: B 1167 ASP cc_start: 0.8041 (m-30) cc_final: 0.6906 (t70) REVERT: C 29 ASN cc_start: 0.6488 (OUTLIER) cc_final: 0.6198 (m110) REVERT: C 38 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8515 (m-30) REVERT: C 112 TYR cc_start: 0.7750 (m-80) cc_final: 0.7356 (m-80) REVERT: C 155 MET cc_start: 0.9136 (mmm) cc_final: 0.8720 (mmm) REVERT: C 213 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.8578 (p90) REVERT: C 374 ASP cc_start: 0.8013 (m-30) cc_final: 0.7397 (m-30) REVERT: C 402 GLN cc_start: 0.8343 (mm110) cc_final: 0.8069 (mm-40) REVERT: C 500 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7274 (mmtm) REVERT: C 655 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9005 (mt) REVERT: C 748 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7017 (mt) REVERT: C 827 ASP cc_start: 0.8412 (m-30) cc_final: 0.8050 (m-30) REVERT: C 934 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8307 (mm) REVERT: C 1003 LEU cc_start: 0.8385 (mm) cc_final: 0.8003 (tt) REVERT: C 1028 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8686 (tttt) REVERT: C 1091 GLN cc_start: 0.8270 (tt0) cc_final: 0.7784 (mt0) REVERT: C 1131 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8688 (pp) REVERT: C 1219 TYR cc_start: 0.5561 (OUTLIER) cc_final: 0.5107 (m-80) outliers start: 164 outliers final: 107 residues processed: 337 average time/residue: 1.2192 time to fit residues: 513.7156 Evaluate side-chains 324 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 192 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 930 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1156 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: 8.9990 chunk 333 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 338 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 118 optimal weight: 0.0050 chunk 266 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 821 ASN C 483 ASN C 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.089370 restraints weight = 41667.618| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.59 r_work: 0.2862 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1825 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= 0.138 Angle : 0.620 19.279 41580 Z= 0.307 Chirality : 0.053 2.003 4908 Planarity : 0.005 0.093 5172 Dihedral : 8.408 93.803 5931 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.56 % Allowed : 12.11 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.92 (0.13), residues: 3618 helix: 1.38 (0.20), residues: 777 sheet: -0.33 (0.17), residues: 810 loop : -1.59 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 444 HIS 0.008 0.001 HIS B 799 PHE 0.016 0.001 PHE B 968 TYR 0.015 0.001 TYR B 203 ARG 0.002 0.000 ARG B 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 66) link_NAG-ASN : angle 3.38104 ( 198) link_ALPHA1-4 : bond 0.01522 ( 3) link_ALPHA1-4 : angle 3.57201 ( 9) link_ALPHA1-6 : bond 0.00531 ( 3) link_ALPHA1-6 : angle 1.73538 ( 9) link_BETA1-4 : bond 0.00248 ( 15) link_BETA1-4 : angle 1.40365 ( 45) link_ALPHA1-3 : bond 0.00488 ( 6) link_ALPHA1-3 : angle 2.15007 ( 18) hydrogen bonds : bond 0.04694 ( 1036) hydrogen bonds : angle 4.84248 ( 2955) SS BOND : bond 0.00272 ( 72) SS BOND : angle 1.14417 ( 144) covalent geometry : bond 0.00323 (30225) covalent geometry : angle 0.56697 (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 358 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 210 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.8586 (tttm) cc_final: 0.8081 (tttm) REVERT: A 187 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8437 (ttmm) REVERT: A 206 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8377 (mtp85) REVERT: A 400 ASP cc_start: 0.8485 (m-30) cc_final: 0.8132 (m-30) REVERT: A 573 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8183 (mt) REVERT: A 835 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7180 (t80) REVERT: A 891 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8409 (tt) REVERT: A 900 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8042 (ptt180) REVERT: A 912 LYS cc_start: 0.8554 (tttt) cc_final: 0.8305 (ttmt) REVERT: A 1066 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6969 (m-30) REVERT: A 1091 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: A 1219 TYR cc_start: 0.6331 (OUTLIER) cc_final: 0.5779 (p90) REVERT: B 84 TYR cc_start: 0.8440 (m-80) cc_final: 0.7978 (m-10) REVERT: B 241 THR cc_start: 0.8739 (m) cc_final: 0.8402 (p) REVERT: B 345 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8603 (mm-30) REVERT: B 500 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7919 (ptmm) REVERT: B 503 HIS cc_start: 0.7878 (t70) cc_final: 0.7440 (t70) REVERT: B 598 ASN cc_start: 0.8332 (m-40) cc_final: 0.8107 (m-40) REVERT: B 630 GLN cc_start: 0.8675 (mt0) cc_final: 0.8435 (mt0) REVERT: B 714 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8663 (m-30) REVERT: B 800 GLU cc_start: 0.9106 (pm20) cc_final: 0.8737 (pt0) REVERT: B 902 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7839 (mt) REVERT: B 903 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 912 LYS cc_start: 0.8821 (tttt) cc_final: 0.8481 (ttmt) REVERT: B 930 GLU cc_start: 0.4376 (OUTLIER) cc_final: 0.4170 (pm20) REVERT: B 1001 GLN cc_start: 0.7492 (tt0) cc_final: 0.6770 (tm-30) REVERT: B 1060 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8105 (tp30) REVERT: B 1091 GLN cc_start: 0.8343 (tt0) cc_final: 0.8109 (tt0) REVERT: B 1096 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9045 (tp) REVERT: B 1105 ARG cc_start: 0.8570 (ttt90) cc_final: 0.8359 (tpp80) REVERT: B 1112 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8636 (mt-10) REVERT: B 1167 ASP cc_start: 0.8047 (m-30) cc_final: 0.6950 (t70) REVERT: C 29 ASN cc_start: 0.6483 (OUTLIER) cc_final: 0.6193 (m110) REVERT: C 155 MET cc_start: 0.9162 (mmm) cc_final: 0.8744 (mmm) REVERT: C 213 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8599 (p90) REVERT: C 374 ASP cc_start: 0.7997 (m-30) cc_final: 0.7407 (m-30) REVERT: C 402 GLN cc_start: 0.8342 (mm110) cc_final: 0.8076 (mm-40) REVERT: C 500 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7309 (mmtm) REVERT: C 655 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9038 (mt) REVERT: C 748 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6957 (mt) REVERT: C 827 ASP cc_start: 0.8402 (m-30) cc_final: 0.8039 (m-30) REVERT: C 934 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8248 (mm) REVERT: C 1003 LEU cc_start: 0.8386 (mm) cc_final: 0.8001 (tt) REVERT: C 1028 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8687 (tttt) REVERT: C 1091 GLN cc_start: 0.8252 (tt0) cc_final: 0.7805 (mt0) REVERT: C 1185 MET cc_start: 0.8885 (mtt) cc_final: 0.8630 (mmm) REVERT: C 1219 TYR cc_start: 0.5481 (OUTLIER) cc_final: 0.5176 (m-80) outliers start: 148 outliers final: 95 residues processed: 330 average time/residue: 1.0167 time to fit residues: 421.2171 Evaluate side-chains 314 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 197 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 930 GLU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 29 ASN 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 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 287 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 343 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 199 optimal weight: 0.0770 chunk 107 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 483 ASN C 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.087685 restraints weight = 41492.268| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.54 r_work: 0.2834 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1900 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= 0.203 Angle : 0.672 20.106 41580 Z= 0.335 Chirality : 0.054 1.880 4908 Planarity : 0.005 0.099 5172 Dihedral : 8.260 94.639 5925 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.11 % Allowed : 11.86 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 3618 helix: 1.28 (0.20), residues: 774 sheet: -0.35 (0.17), residues: 867 loop : -1.58 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 344 HIS 0.007 0.001 HIS C 201 PHE 0.017 0.002 PHE C 968 TYR 0.019 0.002 TYR C1148 ARG 0.005 0.000 ARG B 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 66) link_NAG-ASN : angle 3.37847 ( 198) link_ALPHA1-4 : bond 0.01658 ( 3) link_ALPHA1-4 : angle 3.62087 ( 9) link_ALPHA1-6 : bond 0.00471 ( 3) link_ALPHA1-6 : angle 1.83472 ( 9) link_BETA1-4 : bond 0.00226 ( 15) link_BETA1-4 : angle 1.56248 ( 45) link_ALPHA1-3 : bond 0.00444 ( 6) link_ALPHA1-3 : angle 2.27371 ( 18) hydrogen bonds : bond 0.05430 ( 1036) hydrogen bonds : angle 4.96163 ( 2955) SS BOND : bond 0.00320 ( 72) SS BOND : angle 1.23657 ( 144) covalent geometry : bond 0.00495 (30225) covalent geometry : angle 0.62279 (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 361 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 195 time to evaluate : 3.596 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 83 LYS cc_start: 0.8582 (tttm) cc_final: 0.8073 (tttm) REVERT: A 187 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8429 (ttmm) REVERT: A 206 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8419 (mtp85) REVERT: A 255 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8595 (mm-30) REVERT: A 263 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8861 (ttt180) REVERT: A 400 ASP cc_start: 0.8548 (m-30) cc_final: 0.8209 (m-30) REVERT: A 456 SER cc_start: 0.8445 (t) cc_final: 0.8238 (t) REVERT: A 573 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 835 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7257 (t80) REVERT: A 891 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 900 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8259 (ptt180) REVERT: A 912 LYS cc_start: 0.8545 (tttt) cc_final: 0.8337 (ttmt) REVERT: A 1066 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: A 1071 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7821 (mm110) REVERT: A 1091 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: A 1219 TYR cc_start: 0.6346 (OUTLIER) cc_final: 0.5799 (p90) REVERT: B 84 TYR cc_start: 0.8397 (m-80) cc_final: 0.7930 (m-10) REVERT: B 116 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7482 (p) REVERT: B 194 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.9045 (m) REVERT: B 213 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.8625 (p90) REVERT: B 241 THR cc_start: 0.8774 (m) cc_final: 0.8447 (p) REVERT: B 345 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8713 (mm-30) REVERT: B 402 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7712 (tp40) REVERT: B 500 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7902 (ptmm) REVERT: B 503 HIS cc_start: 0.8029 (t70) cc_final: 0.7582 (t70) REVERT: B 529 SER cc_start: 0.8402 (t) cc_final: 0.8161 (p) REVERT: B 537 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8364 (tttt) REVERT: B 598 ASN cc_start: 0.8347 (m-40) cc_final: 0.8077 (m110) REVERT: B 630 GLN cc_start: 0.8728 (mt0) cc_final: 0.8483 (mt0) REVERT: B 714 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8641 (m-30) REVERT: B 800 GLU cc_start: 0.9118 (pm20) cc_final: 0.8746 (pt0) REVERT: B 903 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 912 LYS cc_start: 0.8826 (tttt) cc_final: 0.8482 (ttmt) REVERT: B 930 GLU cc_start: 0.4472 (OUTLIER) cc_final: 0.4206 (pm20) REVERT: B 1001 GLN cc_start: 0.7507 (tt0) cc_final: 0.6773 (tm-30) REVERT: B 1060 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8149 (tp30) REVERT: B 1091 GLN cc_start: 0.8424 (tt0) cc_final: 0.8212 (tt0) REVERT: B 1096 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9086 (tp) REVERT: B 1105 ARG cc_start: 0.8593 (ttt90) cc_final: 0.8361 (tpp80) REVERT: B 1112 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8739 (mt-10) REVERT: C 29 ASN cc_start: 0.6346 (OUTLIER) cc_final: 0.6056 (m110) REVERT: C 38 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: C 112 TYR cc_start: 0.7828 (m-80) cc_final: 0.7432 (m-80) REVERT: C 155 MET cc_start: 0.9171 (mmm) cc_final: 0.8733 (mmm) REVERT: C 213 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8455 (p90) REVERT: C 374 ASP cc_start: 0.7978 (m-30) cc_final: 0.7263 (m-30) REVERT: C 402 GLN cc_start: 0.8233 (mm110) cc_final: 0.7996 (mm-40) REVERT: C 500 LYS cc_start: 0.8147 (mtmt) cc_final: 0.7405 (mmtm) REVERT: C 655 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9038 (mt) REVERT: C 748 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6998 (mt) REVERT: C 827 ASP cc_start: 0.8434 (m-30) cc_final: 0.8079 (m-30) REVERT: C 934 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8362 (mm) REVERT: C 1003 LEU cc_start: 0.8449 (mm) cc_final: 0.8064 (tt) REVERT: C 1028 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8735 (tttt) REVERT: C 1091 GLN cc_start: 0.8325 (tt0) cc_final: 0.7886 (mt0) REVERT: C 1096 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8885 (tp) REVERT: C 1185 MET cc_start: 0.8921 (mtt) cc_final: 0.8707 (mmm) REVERT: C 1219 TYR cc_start: 0.5351 (OUTLIER) cc_final: 0.4974 (m-80) outliers start: 166 outliers final: 101 residues processed: 334 average time/residue: 0.9902 time to fit residues: 415.6134 Evaluate side-chains 321 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 189 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 930 GLU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 351 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN C 531 ASN C1001 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.089107 restraints weight = 41635.556| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.53 r_work: 0.2856 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1980 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= 0.137 Angle : 0.621 21.700 41580 Z= 0.309 Chirality : 0.051 1.655 4908 Planarity : 0.005 0.092 5172 Dihedral : 7.760 94.003 5923 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.25 % Allowed : 12.82 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.82 (0.14), residues: 3618 helix: 1.50 (0.20), residues: 774 sheet: -0.34 (0.17), residues: 834 loop : -1.51 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 444 HIS 0.007 0.001 HIS B 799 PHE 0.015 0.001 PHE B 968 TYR 0.016 0.001 TYR B 203 ARG 0.002 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 66) link_NAG-ASN : angle 3.29880 ( 198) link_ALPHA1-4 : bond 0.01769 ( 3) link_ALPHA1-4 : angle 3.53359 ( 9) link_ALPHA1-6 : bond 0.00399 ( 3) link_ALPHA1-6 : angle 1.99023 ( 9) link_BETA1-4 : bond 0.00241 ( 15) link_BETA1-4 : angle 1.43555 ( 45) link_ALPHA1-3 : bond 0.00519 ( 6) link_ALPHA1-3 : angle 2.30844 ( 18) hydrogen bonds : bond 0.04635 ( 1036) hydrogen bonds : angle 4.81158 ( 2955) SS BOND : bond 0.00368 ( 72) SS BOND : angle 1.04864 ( 144) covalent geometry : bond 0.00322 (30225) covalent geometry : angle 0.57077 (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 330 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 192 time to evaluate : 3.591 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 83 LYS cc_start: 0.8580 (tttm) cc_final: 0.8073 (tttm) REVERT: A 187 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8385 (ttmm) REVERT: A 206 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8418 (mtp85) REVERT: A 255 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8589 (mm-30) REVERT: A 400 ASP cc_start: 0.8478 (m-30) cc_final: 0.8115 (m-30) REVERT: A 573 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8167 (mt) REVERT: A 835 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7128 (t80) REVERT: A 891 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8382 (tt) REVERT: A 900 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8046 (ptt180) REVERT: A 912 LYS cc_start: 0.8526 (tttt) cc_final: 0.8289 (ttmt) REVERT: A 1066 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: A 1071 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7624 (mm110) REVERT: A 1091 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: A 1219 TYR cc_start: 0.6351 (OUTLIER) cc_final: 0.5835 (p90) REVERT: B 84 TYR cc_start: 0.8416 (m-80) cc_final: 0.7939 (m-10) REVERT: B 116 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7432 (p) REVERT: B 213 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8567 (p90) REVERT: B 241 THR cc_start: 0.8746 (m) cc_final: 0.8407 (p) REVERT: B 345 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8607 (mm-30) REVERT: B 500 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7828 (ptmm) REVERT: B 503 HIS cc_start: 0.7977 (t70) cc_final: 0.7513 (t70) REVERT: B 537 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8344 (tttt) REVERT: B 598 ASN cc_start: 0.8308 (m-40) cc_final: 0.8030 (m110) REVERT: B 630 GLN cc_start: 0.8662 (mt0) cc_final: 0.8417 (mt0) REVERT: B 714 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8622 (m-30) REVERT: B 782 VAL cc_start: 0.8587 (t) cc_final: 0.8245 (m) REVERT: B 800 GLU cc_start: 0.9110 (pm20) cc_final: 0.8726 (pt0) REVERT: B 903 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8518 (mt) REVERT: B 912 LYS cc_start: 0.8777 (tttt) cc_final: 0.8412 (ttmt) REVERT: B 930 GLU cc_start: 0.4418 (OUTLIER) cc_final: 0.4167 (pm20) REVERT: B 1001 GLN cc_start: 0.7411 (tt0) cc_final: 0.6740 (tm-30) REVERT: B 1060 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8097 (tp30) REVERT: B 1091 GLN cc_start: 0.8336 (tt0) cc_final: 0.8104 (tt0) REVERT: B 1096 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9089 (tp) REVERT: B 1105 ARG cc_start: 0.8539 (ttt90) cc_final: 0.8317 (tpp80) REVERT: B 1112 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: C 14 VAL cc_start: 0.6929 (OUTLIER) cc_final: 0.6434 (p) REVERT: C 29 ASN cc_start: 0.6478 (OUTLIER) cc_final: 0.6180 (m110) REVERT: C 155 MET cc_start: 0.9160 (mmm) cc_final: 0.8625 (mmm) REVERT: C 213 TYR cc_start: 0.9160 (OUTLIER) cc_final: 0.8567 (p90) REVERT: C 374 ASP cc_start: 0.7934 (m-30) cc_final: 0.7238 (m-30) REVERT: C 402 GLN cc_start: 0.8178 (mm110) cc_final: 0.7939 (mm-40) REVERT: C 500 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7257 (mmtm) REVERT: C 655 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9029 (mt) REVERT: C 735 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8259 (p0) REVERT: C 748 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7001 (mt) REVERT: C 827 ASP cc_start: 0.8383 (m-30) cc_final: 0.7979 (m-30) REVERT: C 1003 LEU cc_start: 0.8387 (mm) cc_final: 0.7973 (tt) REVERT: C 1028 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8692 (tttt) REVERT: C 1079 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8850 (m110) REVERT: C 1091 GLN cc_start: 0.8245 (tt0) cc_final: 0.7789 (mt0) REVERT: C 1096 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8826 (tp) REVERT: C 1185 MET cc_start: 0.8885 (mtt) cc_final: 0.8661 (mmm) outliers start: 138 outliers final: 93 residues processed: 306 average time/residue: 1.0426 time to fit residues: 398.8426 Evaluate side-chains 313 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 192 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 930 GLU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1079 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 205 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 HIS C 531 ASN C1001 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.087471 restraints weight = 41916.402| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.70 r_work: 0.2838 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30390 Z= 0.188 Angle : 0.653 22.513 41580 Z= 0.327 Chirality : 0.051 1.570 4908 Planarity : 0.005 0.095 5172 Dihedral : 7.751 93.842 5917 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.37 % Allowed : 12.69 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.87 (0.13), residues: 3618 helix: 1.41 (0.20), residues: 774 sheet: -0.39 (0.17), residues: 843 loop : -1.52 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 644 HIS 0.007 0.001 HIS C 201 PHE 0.017 0.002 PHE C 968 TYR 0.019 0.002 TYR C1148 ARG 0.004 0.000 ARG B 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 66) link_NAG-ASN : angle 3.31870 ( 198) link_ALPHA1-4 : bond 0.01754 ( 3) link_ALPHA1-4 : angle 3.53360 ( 9) link_ALPHA1-6 : bond 0.00406 ( 3) link_ALPHA1-6 : angle 2.02199 ( 9) link_BETA1-4 : bond 0.00223 ( 15) link_BETA1-4 : angle 1.56594 ( 45) link_ALPHA1-3 : bond 0.00478 ( 6) link_ALPHA1-3 : angle 2.42474 ( 18) hydrogen bonds : bond 0.05251 ( 1036) hydrogen bonds : angle 4.91072 ( 2955) SS BOND : bond 0.00313 ( 72) SS BOND : angle 1.14653 ( 144) covalent geometry : bond 0.00456 (30225) covalent geometry : angle 0.60413 (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 336 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 194 time to evaluate : 3.210 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 83 LYS cc_start: 0.8586 (tttm) cc_final: 0.7994 (tttm) REVERT: A 84 TYR cc_start: 0.8263 (m-80) cc_final: 0.7878 (m-80) REVERT: A 187 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8390 (ttmm) REVERT: A 206 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8409 (mtp85) REVERT: A 255 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8571 (mm-30) REVERT: A 263 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8854 (ttt180) REVERT: A 400 ASP cc_start: 0.8496 (m-30) cc_final: 0.8111 (m-30) REVERT: A 456 SER cc_start: 0.8518 (t) cc_final: 0.8298 (t) REVERT: A 573 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 835 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7158 (t80) REVERT: A 891 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8360 (tt) REVERT: A 900 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7962 (ptt180) REVERT: A 912 LYS cc_start: 0.8533 (tttt) cc_final: 0.8290 (ttmt) REVERT: A 952 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 1066 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: A 1071 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7725 (mm110) REVERT: A 1091 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: A 1219 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.5783 (p90) REVERT: B 64 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.9076 (m) REVERT: B 84 TYR cc_start: 0.8386 (m-80) cc_final: 0.7900 (m-10) REVERT: B 116 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7406 (p) REVERT: B 213 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.8599 (p90) REVERT: B 241 THR cc_start: 0.8776 (m) cc_final: 0.8437 (p) REVERT: B 345 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8673 (mm-30) REVERT: B 500 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7849 (ptmm) REVERT: B 503 HIS cc_start: 0.8018 (t70) cc_final: 0.7591 (t70) REVERT: B 537 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8345 (tttt) REVERT: B 598 ASN cc_start: 0.8289 (m-40) cc_final: 0.8056 (m-40) REVERT: B 630 GLN cc_start: 0.8695 (mt0) cc_final: 0.8459 (mt0) REVERT: B 714 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8599 (m-30) REVERT: B 782 VAL cc_start: 0.8561 (t) cc_final: 0.8226 (m) REVERT: B 800 GLU cc_start: 0.9113 (pm20) cc_final: 0.8738 (pt0) REVERT: B 903 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8543 (mt) REVERT: B 912 LYS cc_start: 0.8720 (tttt) cc_final: 0.8349 (ttmt) REVERT: B 930 GLU cc_start: 0.4422 (OUTLIER) cc_final: 0.4167 (pm20) REVERT: B 1001 GLN cc_start: 0.7486 (tt0) cc_final: 0.6759 (tm-30) REVERT: B 1060 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8108 (tp30) REVERT: B 1091 GLN cc_start: 0.8380 (tt0) cc_final: 0.8148 (tt0) REVERT: B 1096 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9065 (tp) REVERT: B 1105 ARG cc_start: 0.8576 (ttt90) cc_final: 0.8305 (tpp80) REVERT: B 1112 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8721 (mt-10) REVERT: C 29 ASN cc_start: 0.6337 (OUTLIER) cc_final: 0.6042 (m110) REVERT: C 155 MET cc_start: 0.9151 (mmm) cc_final: 0.8713 (mmm) REVERT: C 213 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8433 (p90) REVERT: C 374 ASP cc_start: 0.7936 (m-30) cc_final: 0.7141 (m-30) REVERT: C 402 GLN cc_start: 0.8218 (mm110) cc_final: 0.7987 (mm-40) REVERT: C 500 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7286 (mmtm) REVERT: C 655 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.8997 (mt) REVERT: C 748 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6980 (mt) REVERT: C 827 ASP cc_start: 0.8406 (m-30) cc_final: 0.8045 (m-30) REVERT: C 1003 LEU cc_start: 0.8421 (mm) cc_final: 0.7985 (tt) REVERT: C 1028 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8691 (tttt) REVERT: C 1079 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8840 (m110) REVERT: C 1091 GLN cc_start: 0.8268 (tt0) cc_final: 0.7820 (mt0) REVERT: C 1096 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8827 (tp) outliers start: 142 outliers final: 102 residues processed: 315 average time/residue: 1.0802 time to fit residues: 425.3642 Evaluate side-chains 320 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 189 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 930 GLU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1079 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 273 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 290 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.088805 restraints weight = 41698.302| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.53 r_work: 0.2856 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 0.092 30390 Z= 0.145 Angle : 0.625 23.267 41580 Z= 0.312 Chirality : 0.049 1.357 4908 Planarity : 0.005 0.088 5172 Dihedral : 7.518 93.714 5917 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.25 % Allowed : 13.03 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.78 (0.14), residues: 3618 helix: 1.54 (0.20), residues: 774 sheet: -0.36 (0.17), residues: 840 loop : -1.47 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 644 HIS 0.007 0.001 HIS A 799 PHE 0.015 0.001 PHE B 968 TYR 0.016 0.001 TYR B 203 ARG 0.003 0.000 ARG B 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 66) link_NAG-ASN : angle 3.25234 ( 198) link_ALPHA1-4 : bond 0.01747 ( 3) link_ALPHA1-4 : angle 3.37311 ( 9) link_ALPHA1-6 : bond 0.00370 ( 3) link_ALPHA1-6 : angle 2.05391 ( 9) link_BETA1-4 : bond 0.00237 ( 15) link_BETA1-4 : angle 1.49127 ( 45) link_ALPHA1-3 : bond 0.00537 ( 6) link_ALPHA1-3 : angle 2.45168 ( 18) hydrogen bonds : bond 0.04725 ( 1036) hydrogen bonds : angle 4.81355 ( 2955) SS BOND : bond 0.00367 ( 72) SS BOND : angle 1.15011 ( 144) covalent geometry : bond 0.00345 (30225) covalent geometry : angle 0.57502 (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 329 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 191 time to evaluate : 3.339 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 83 LYS cc_start: 0.8584 (tttm) cc_final: 0.8090 (tttm) REVERT: A 187 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8414 (ttmm) REVERT: A 206 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8452 (mtp85) REVERT: A 255 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: A 263 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8822 (ttt180) REVERT: A 351 ASN cc_start: 0.8837 (t0) cc_final: 0.8507 (t0) REVERT: A 400 ASP cc_start: 0.8491 (m-30) cc_final: 0.8138 (m-30) REVERT: A 456 SER cc_start: 0.8513 (t) cc_final: 0.8302 (t) REVERT: A 573 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8239 (mt) REVERT: A 835 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7154 (t80) REVERT: A 891 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 900 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8038 (ptt180) REVERT: A 912 LYS cc_start: 0.8534 (tttt) cc_final: 0.8310 (ttmt) REVERT: A 1066 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: A 1071 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7688 (mm110) REVERT: A 1091 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: A 1219 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.5792 (p90) REVERT: B 64 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9178 (m) REVERT: B 84 TYR cc_start: 0.8419 (m-80) cc_final: 0.7923 (m-10) REVERT: B 116 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7465 (p) REVERT: B 213 TYR cc_start: 0.9292 (OUTLIER) cc_final: 0.8555 (p90) REVERT: B 241 THR cc_start: 0.8767 (m) cc_final: 0.8451 (p) REVERT: B 345 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8656 (mm-30) REVERT: B 500 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7898 (ptmm) REVERT: B 503 HIS cc_start: 0.8023 (t70) cc_final: 0.7550 (t70) REVERT: B 537 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8354 (tttt) REVERT: B 598 ASN cc_start: 0.8376 (m-40) cc_final: 0.8138 (m-40) REVERT: B 630 GLN cc_start: 0.8692 (mt0) cc_final: 0.8449 (mt0) REVERT: B 714 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: B 782 VAL cc_start: 0.8572 (t) cc_final: 0.8260 (m) REVERT: B 800 GLU cc_start: 0.9111 (pm20) cc_final: 0.8730 (pt0) REVERT: B 903 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8565 (mt) REVERT: B 912 LYS cc_start: 0.8704 (tttt) cc_final: 0.8364 (ttmt) REVERT: B 930 GLU cc_start: 0.4413 (OUTLIER) cc_final: 0.4166 (pm20) REVERT: B 1001 GLN cc_start: 0.7455 (tt0) cc_final: 0.6752 (tm-30) REVERT: B 1060 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8128 (tp30) REVERT: B 1091 GLN cc_start: 0.8364 (tt0) cc_final: 0.8132 (tt0) REVERT: B 1096 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9096 (tp) REVERT: B 1105 ARG cc_start: 0.8575 (ttt90) cc_final: 0.8345 (tpp80) REVERT: B 1112 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8648 (mt-10) REVERT: C 29 ASN cc_start: 0.6467 (OUTLIER) cc_final: 0.6169 (m110) REVERT: C 155 MET cc_start: 0.9172 (mmm) cc_final: 0.8633 (mmm) REVERT: C 213 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8580 (p90) REVERT: C 374 ASP cc_start: 0.7936 (m-30) cc_final: 0.7168 (m-30) REVERT: C 402 GLN cc_start: 0.8188 (mm110) cc_final: 0.7955 (mm-40) REVERT: C 500 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7271 (mmtm) REVERT: C 531 ASN cc_start: 0.8896 (m-40) cc_final: 0.8694 (m-40) REVERT: C 655 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9043 (mt) REVERT: C 748 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6954 (mt) REVERT: C 827 ASP cc_start: 0.8416 (m-30) cc_final: 0.8054 (m-30) REVERT: C 1028 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8715 (tttt) REVERT: C 1079 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8837 (m110) REVERT: C 1091 GLN cc_start: 0.8250 (tt0) cc_final: 0.7816 (mt0) REVERT: C 1096 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8822 (tp) outliers start: 138 outliers final: 101 residues processed: 305 average time/residue: 0.9640 time to fit residues: 368.8160 Evaluate side-chains 317 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 188 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 930 GLU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1079 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 237 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 312 optimal weight: 0.5980 chunk 236 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.089962 restraints weight = 41881.033| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.55 r_work: 0.2868 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30390 Z= 0.124 Angle : 0.594 25.164 41580 Z= 0.297 Chirality : 0.047 1.023 4908 Planarity : 0.005 0.082 5172 Dihedral : 7.112 92.746 5917 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.91 % Allowed : 13.37 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.66 (0.14), residues: 3618 helix: 1.67 (0.20), residues: 777 sheet: -0.28 (0.17), residues: 900 loop : -1.44 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 444 HIS 0.007 0.001 HIS B 799 PHE 0.013 0.001 PHE B 968 TYR 0.015 0.001 TYR B 203 ARG 0.002 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 66) link_NAG-ASN : angle 3.18101 ( 198) link_ALPHA1-4 : bond 0.01779 ( 3) link_ALPHA1-4 : angle 3.32024 ( 9) link_ALPHA1-6 : bond 0.00362 ( 3) link_ALPHA1-6 : angle 2.03737 ( 9) link_BETA1-4 : bond 0.00250 ( 15) link_BETA1-4 : angle 1.41054 ( 45) link_ALPHA1-3 : bond 0.00569 ( 6) link_ALPHA1-3 : angle 2.43424 ( 18) hydrogen bonds : bond 0.04315 ( 1036) hydrogen bonds : angle 4.68812 ( 2955) SS BOND : bond 0.00296 ( 72) SS BOND : angle 1.04400 ( 144) covalent geometry : bond 0.00288 (30225) covalent geometry : angle 0.54438 (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 330 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 203 time to evaluate : 3.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.8580 (tttm) cc_final: 0.7968 (tttm) REVERT: A 84 TYR cc_start: 0.8253 (m-80) cc_final: 0.7861 (m-80) REVERT: A 187 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8359 (ttmm) REVERT: A 206 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8384 (mtp85) REVERT: A 351 ASN cc_start: 0.8820 (t0) cc_final: 0.8513 (t0) REVERT: A 400 ASP cc_start: 0.8453 (m-30) cc_final: 0.8063 (m-30) REVERT: A 835 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7094 (t80) REVERT: A 900 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8026 (ptt180) REVERT: A 912 LYS cc_start: 0.8485 (tttt) cc_final: 0.8243 (ttmt) REVERT: A 1066 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: A 1071 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7556 (mm110) REVERT: A 1091 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: A 1219 TYR cc_start: 0.6323 (OUTLIER) cc_final: 0.5807 (p90) REVERT: B 84 TYR cc_start: 0.8417 (m-80) cc_final: 0.7917 (m-10) REVERT: B 116 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7407 (p) REVERT: B 241 THR cc_start: 0.8748 (m) cc_final: 0.8417 (p) REVERT: B 289 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: B 345 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8574 (mm-30) REVERT: B 500 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7882 (ptmm) REVERT: B 503 HIS cc_start: 0.8050 (t70) cc_final: 0.7441 (t70) REVERT: B 537 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8316 (tttt) REVERT: B 598 ASN cc_start: 0.8344 (m-40) cc_final: 0.8094 (m-40) REVERT: B 630 GLN cc_start: 0.8617 (mt0) cc_final: 0.8388 (mt0) REVERT: B 714 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: B 782 VAL cc_start: 0.8557 (t) cc_final: 0.8248 (m) REVERT: B 800 GLU cc_start: 0.9102 (pm20) cc_final: 0.8712 (pt0) REVERT: B 903 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8528 (mt) REVERT: B 912 LYS cc_start: 0.8690 (tttt) cc_final: 0.8332 (ttmt) REVERT: B 1001 GLN cc_start: 0.7386 (tt0) cc_final: 0.6653 (tm-30) REVERT: B 1060 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8068 (tp30) REVERT: B 1091 GLN cc_start: 0.8324 (tt0) cc_final: 0.7909 (tm-30) REVERT: B 1105 ARG cc_start: 0.8521 (ttt90) cc_final: 0.8255 (tpp80) REVERT: B 1112 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8593 (mt-10) REVERT: C 155 MET cc_start: 0.9150 (mmm) cc_final: 0.8621 (mmm) REVERT: C 213 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8627 (p90) REVERT: C 374 ASP cc_start: 0.7885 (m-30) cc_final: 0.7175 (m-30) REVERT: C 402 GLN cc_start: 0.8185 (mm110) cc_final: 0.7955 (mm-40) REVERT: C 500 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7239 (mmtm) REVERT: C 501 TYR cc_start: 0.8774 (m-80) cc_final: 0.8414 (m-80) REVERT: C 655 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9001 (mt) REVERT: C 748 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6935 (mt) REVERT: C 827 ASP cc_start: 0.8375 (m-30) cc_final: 0.8015 (m-30) REVERT: C 1028 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8640 (tttt) REVERT: C 1091 GLN cc_start: 0.8196 (tt0) cc_final: 0.7747 (mt0) REVERT: C 1096 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8790 (tp) outliers start: 127 outliers final: 88 residues processed: 308 average time/residue: 0.9975 time to fit residues: 385.6223 Evaluate side-chains 299 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 192 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 316 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 308 optimal weight: 1.9990 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 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS B 821 ASN C 531 ASN C1001 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.090571 restraints weight = 41783.153| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.57 r_work: 0.2866 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30390 Z= 0.117 Angle : 0.603 24.635 41580 Z= 0.298 Chirality : 0.048 0.945 4908 Planarity : 0.005 0.075 5172 Dihedral : 6.906 92.277 5910 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.54 % Allowed : 13.83 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.60 (0.14), residues: 3618 helix: 1.72 (0.20), residues: 780 sheet: -0.26 (0.17), residues: 900 loop : -1.40 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 444 HIS 0.010 0.001 HIS B 799 PHE 0.013 0.001 PHE B 968 TYR 0.015 0.001 TYR B 203 ARG 0.002 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 66) link_NAG-ASN : angle 3.41767 ( 198) link_ALPHA1-4 : bond 0.01784 ( 3) link_ALPHA1-4 : angle 3.27718 ( 9) link_ALPHA1-6 : bond 0.00378 ( 3) link_ALPHA1-6 : angle 2.03975 ( 9) link_BETA1-4 : bond 0.00248 ( 15) link_BETA1-4 : angle 1.39438 ( 45) link_ALPHA1-3 : bond 0.00594 ( 6) link_ALPHA1-3 : angle 2.41291 ( 18) hydrogen bonds : bond 0.04218 ( 1036) hydrogen bonds : angle 4.63918 ( 2955) SS BOND : bond 0.00303 ( 72) SS BOND : angle 0.96472 ( 144) covalent geometry : bond 0.00269 (30225) covalent geometry : angle 0.54755 (41157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23849.10 seconds wall clock time: 414 minutes 15.33 seconds (24855.33 seconds total)