Starting phenix.real_space_refine on Sat Feb 7 16:20:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1d_38832/02_2026/8y1d_38832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1d_38832/02_2026/8y1d_38832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y1d_38832/02_2026/8y1d_38832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1d_38832/02_2026/8y1d_38832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y1d_38832/02_2026/8y1d_38832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1d_38832/02_2026/8y1d_38832.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.111 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 217 5.16 5 C 22133 2.51 5 N 5668 2.21 5 O 6903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34921 Number of models: 1 Model: "" Number of chains: 23 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': 2, 'PTRANS': 50, 'TRANS': 1155} Chain: "C" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "D" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2690 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 328} Chain: "E" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2690 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 328} Chain: "F" 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: "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: 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: "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: 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: "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: 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: "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: 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: "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: "S" 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: "T" 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: 7.95, per 1000 atoms: 0.23 Number of scatterers: 34921 At special positions: 0 Unit cell: (159.789, 168.485, 243.488, 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 217 16.00 O 6903 8.00 N 5668 7.00 C 22133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=84, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.04 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.04 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.04 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.02 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.02 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.02 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.04 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.02 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.04 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.04 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.04 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.04 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.04 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.04 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.04 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 241 " distance=2.04 Simple disulfide: pdb=" SG CYS D 244 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 297 " distance=2.02 Simple disulfide: pdb=" SG CYS D 410 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 437 " - pdb=" SG CYS D 465 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 241 " distance=2.04 Simple disulfide: pdb=" SG CYS E 244 " - pdb=" SG CYS E 365 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 297 " distance=2.02 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 437 " - pdb=" SG CYS E 465 " 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 F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " " MAN K 3 " - " MAN K 6 " " MAN K 4 " - " MAN K 5 " " MAN P 3 " - " MAN P 6 " " MAN P 4 " - " MAN P 5 " ALPHA1-4 " NAG F 2 " - " MAN F 3 " " NAG K 2 " - " MAN K 3 " " NAG P 2 " - " MAN P 3 " ALPHA1-6 " MAN F 3 " - " MAN F 4 " " MAN K 3 " - " MAN K 4 " " MAN P 3 " - " MAN P 4 " BETA1-4 " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 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 F 1 " - " ASN A 132 " " NAG G 1 " - " ASN A 188 " " NAG H 1 " - " ASN A 335 " " NAG I 1 " - " ASN A 355 " " NAG J 1 " - " ASN A 664 " " NAG K 1 " - " ASN B 132 " " NAG L 1 " - " ASN B 188 " " NAG M 1 " - " ASN B 335 " " NAG N 1 " - " ASN B 355 " " NAG O 1 " - " ASN B 664 " " NAG P 1 " - " ASN C 132 " " NAG Q 1 " - " ASN C 188 " " NAG R 1 " - " ASN C 335 " " NAG S 1 " - " ASN C 355 " " NAG T 1 " - " ASN C 664 " Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8088 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 79 sheets defined 21.6% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.888A 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 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 376 through 381 removed outlier: 4.168A pdb=" N GLY A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 381' Processing helix chain 'A' and resid 394 through 402 removed outlier: 5.079A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.033A 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 447 removed outlier: 3.927A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.026A pdb=" N ASN A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.089A pdb=" N THR A 527 " --> pdb=" O PRO A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 863 Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 Processing helix chain 'A' and resid 1000 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.828A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.793A 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: 3.610A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 4.393A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.086A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.587A pdb=" N GLU B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 376 through 381 removed outlier: 4.171A pdb=" N GLY B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 381' Processing helix chain 'B' and resid 394 through 402 removed outlier: 5.080A pdb=" N ASP B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 442 through 447 removed outlier: 3.928A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 4.025A pdb=" N ASN B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.090A pdb=" N THR B 527 " --> pdb=" O PRO B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 830 Processing helix chain 'B' and resid 835 through 863 removed outlier: 3.643A 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 924 removed outlier: 4.038A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.574A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 Processing helix chain 'B' and resid 1000 through 1018 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.808A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.718A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1063 removed outlier: 3.601A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1113 removed outlier: 4.082A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.622A pdb=" N TYR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.758A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.531A 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 395 through 402 removed outlier: 4.009A pdb=" N ARG C 398 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.577A pdb=" N SER C 484 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.655A 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 696 through 704 Processing helix chain 'C' and resid 813 through 819 Processing helix chain 'C' and resid 822 through 830 Processing helix chain 'C' and resid 831 through 833 No H-bonds generated for 'chain 'C' and resid 831 through 833' Processing helix chain 'C' and resid 834 through 863 removed outlier: 3.551A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.533A pdb=" N LEU C 888 " --> pdb=" O LYS C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 888' Processing helix chain 'C' and resid 901 through 910 removed outlier: 3.904A pdb=" N LYS C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 923 removed outlier: 3.774A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 926 No H-bonds generated for 'chain 'C' and resid 924 through 926' Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.528A 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: 3.628A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.845A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.676A 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 1058 through 1063 Processing helix chain 'C' and resid 1069 through 1113 removed outlier: 3.944A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.682A pdb=" N HIS D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 411 removed outlier: 3.742A pdb=" N CYS D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 483 through 487 Processing helix chain 'D' and resid 488 through 492 removed outlier: 4.135A pdb=" N ASP D 491 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY D 492 " --> pdb=" O ARG D 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 488 through 492' Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 304 through 308 removed outlier: 3.683A pdb=" N HIS E 307 " --> pdb=" O ASN E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 removed outlier: 3.745A pdb=" N CYS E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 483 through 487 Processing helix chain 'E' and resid 488 through 492 removed outlier: 4.135A pdb=" N ASP E 491 " --> pdb=" O MET E 488 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY E 492 " --> pdb=" O ARG E 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 488 through 492' 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: 3.833A pdb=" N ASP A 38 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.057A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 648 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 67 removed outlier: 3.922A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.953A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.585A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (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 307 removed outlier: 7.671A pdb=" N ARG A 676 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG A 693 " --> pdb=" O ARG A 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 347 through 349 removed outlier: 6.680A pdb=" N TYR A 426 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AB2, first strand: chain 'A' and resid 382 through 383 removed outlier: 3.640A pdb=" N THR A 602 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.619A pdb=" N ASP A 578 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 576 " --> pdb=" O TYR A 462 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AB5, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AB6, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB7, first strand: chain 'A' and resid 581 through 582 Processing sheet with id=AB8, first strand: chain 'A' and resid 619 through 624 removed outlier: 3.973A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.623A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 736 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.388A pdb=" N SER A 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.853A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLY A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN A1136 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A1142 " --> pdb=" O VAL A1134 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1134 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A1144 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER A1132 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE A1146 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.406A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC5, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AC6, first strand: chain 'A' and resid 1202 through 1205 Processing sheet with id=AC7, first strand: chain 'A' and resid 1175 through 1180 Processing sheet with id=AC8, first strand: chain 'B' and resid 59 through 64 removed outlier: 7.803A pdb=" N GLN B 265 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP B 281 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AD1, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.604A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 146 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN B 188 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 148 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS B 186 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 150 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 221 through 227 removed outlier: 6.778A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD4, first strand: chain 'B' and resid 302 through 307 removed outlier: 7.603A pdb=" N ARG B 676 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG B 693 " --> pdb=" O ARG B 676 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 318 through 319 removed outlier: 5.478A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 347 through 349 removed outlier: 6.680A pdb=" N TYR B 426 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 347 through 349 Processing sheet with id=AD8, first strand: chain 'B' and resid 353 through 354 removed outlier: 3.639A pdb=" N THR B 602 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 459 through 463 removed outlier: 3.619A pdb=" N ASP B 578 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 576 " --> pdb=" O TYR B 462 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AE2, first strand: chain 'B' and resid 504 through 505 Processing sheet with id=AE3, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE4, first strand: chain 'B' and resid 581 through 582 Processing sheet with id=AE5, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.527A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 773 through 775 Processing sheet with id=AE7, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.849A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR B1148 " --> pdb=" O HIS B1129 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N HIS B1129 " --> pdb=" O TYR B1148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.849A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.328A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AF2, first strand: chain 'B' and resid 1202 through 1205 Processing sheet with id=AF3, first strand: chain 'C' and resid 59 through 67 removed outlier: 4.033A pdb=" N ASN C 278 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.642A pdb=" N PHE C 209 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER C 225 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 211 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AF6, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.692A pdb=" N TYR C 235 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 109 through 112 Processing sheet with id=AF8, first strand: chain 'C' and resid 302 through 306 Processing sheet with id=AF9, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.521A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.607A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.569A pdb=" N PHE C 354 " --> pdb=" O CYS C 603 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG4, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.646A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 473 through 477 removed outlier: 3.867A pdb=" N ARG C 502 " --> pdb=" O CYS C 474 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N CYS C 476 " --> pdb=" O ARG C 502 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 504 through 507 Processing sheet with id=AG7, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AG8, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.563A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.853A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.853A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.320A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH4, first strand: chain 'C' and resid 1202 through 1205 Processing sheet with id=AH5, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.519A pdb=" N SER D 167 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 196 through 200 removed outlier: 3.610A pdb=" N SER D 196 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN D 198 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 200 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AH8, first strand: chain 'D' and resid 279 through 281 Processing sheet with id=AH9, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AI1, first strand: chain 'D' and resid 401 through 403 removed outlier: 3.534A pdb=" N GLY D 457 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR D 447 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU D 455 " --> pdb=" O THR D 447 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 149 through 150 removed outlier: 3.520A pdb=" N SER E 167 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 196 through 200 removed outlier: 3.611A pdb=" N SER E 196 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 198 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 200 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 209 through 212 Processing sheet with id=AI5, first strand: chain 'E' and resid 279 through 281 Processing sheet with id=AI6, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AI7, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.534A pdb=" N GLY E 457 " --> pdb=" O LEU E 445 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR E 447 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU E 455 " --> pdb=" O THR E 447 " (cutoff:3.500A) 1121 hydrogen bonds defined for protein. 2991 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: 9.77 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10066 1.33 - 1.46: 9092 1.46 - 1.58: 16329 1.58 - 1.71: 0 1.71 - 1.83: 262 Bond restraints: 35749 Sorted by residual: bond pdb=" N PRO A 325 " pdb=" CD PRO A 325 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.10e+01 bond pdb=" C LEU A 324 " pdb=" N PRO A 325 " ideal model delta sigma weight residual 1.331 1.387 -0.055 1.28e-02 6.10e+03 1.88e+01 bond pdb=" N PRO B 325 " pdb=" CD PRO B 325 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" C5 MAN P 3 " pdb=" O5 MAN P 3 " ideal model delta sigma weight residual 1.418 1.482 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C5 MAN K 3 " pdb=" O5 MAN K 3 " ideal model delta sigma weight residual 1.418 1.482 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 35744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 47409 2.77 - 5.53: 1122 5.53 - 8.30: 116 8.30 - 11.06: 21 11.06 - 13.83: 3 Bond angle restraints: 48671 Sorted by residual: angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 119.52 -8.82 1.22e+00 6.72e-01 5.23e+01 angle pdb=" C SER B 604 " pdb=" CA SER B 604 " pdb=" CB SER B 604 " ideal model delta sigma weight residual 109.80 121.07 -11.27 1.64e+00 3.72e-01 4.73e+01 angle pdb=" N PRO C 969 " pdb=" CA PRO C 969 " pdb=" C PRO C 969 " ideal model delta sigma weight residual 110.70 119.06 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N LYS D 340 " pdb=" CA LYS D 340 " pdb=" C LYS D 340 " ideal model delta sigma weight residual 111.36 117.73 -6.37 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N LYS E 340 " pdb=" CA LYS E 340 " pdb=" C LYS E 340 " ideal model delta sigma weight residual 111.36 117.68 -6.32 1.09e+00 8.42e-01 3.36e+01 ... (remaining 48666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 20526 22.98 - 45.96: 1487 45.96 - 68.94: 418 68.94 - 91.92: 56 91.92 - 114.90: 6 Dihedral angle restraints: 22493 sinusoidal: 9877 harmonic: 12616 Sorted by residual: dihedral pdb=" CA GLN E 327 " pdb=" C GLN E 327 " pdb=" N VAL E 328 " pdb=" CA VAL E 328 " ideal model delta harmonic sigma weight residual -180.00 -139.70 -40.30 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA GLN D 327 " pdb=" C GLN D 327 " pdb=" N VAL D 328 " pdb=" CA VAL D 328 " ideal model delta harmonic sigma weight residual -180.00 -139.80 -40.20 0 5.00e+00 4.00e-02 6.47e+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 180.00 142.58 37.42 0 5.00e+00 4.00e-02 5.60e+01 ... (remaining 22490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 5613 0.156 - 0.311: 79 0.311 - 0.467: 6 0.467 - 0.622: 3 0.622 - 0.778: 3 Chirality restraints: 5704 Sorted by residual: chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 19 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C1 NAG C2003 " pdb=" ND2 ASN C 58 " pdb=" C2 NAG C2003 " pdb=" O5 NAG C2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 132 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.74e+00 ... (remaining 5701 not shown) Planarity restraints: 6206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 171 " 0.206 2.00e-02 2.50e+03 2.28e-01 6.51e+02 pdb=" CG ASN B 171 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN B 171 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN B 171 " -0.361 2.00e-02 2.50e+03 pdb=" C1 NAG B2005 " 0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 188 " -0.180 2.00e-02 2.50e+03 2.27e-01 6.46e+02 pdb=" CG ASN C 188 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN C 188 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN C 188 " 0.395 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.253 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 132 " -0.038 2.00e-02 2.50e+03 4.40e-02 2.42e+01 pdb=" CG ASN C 132 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 132 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN C 132 " 0.074 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " -0.051 2.00e-02 2.50e+03 ... (remaining 6203 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7329 2.77 - 3.30: 29185 3.30 - 3.84: 57563 3.84 - 4.37: 66019 4.37 - 4.90: 115743 Nonbonded interactions: 275839 Sorted by model distance: nonbonded pdb=" O SER A 604 " pdb=" OG SER A 604 " model vdw 2.238 3.040 nonbonded pdb=" O SER C 740 " pdb=" OG SER C 740 " model vdw 2.245 3.040 nonbonded pdb=" CZ PHE B 354 " pdb=" OG SER B 604 " model vdw 2.264 3.340 nonbonded pdb=" O SER D 448 " pdb=" OG SER D 448 " model vdw 2.267 3.040 nonbonded pdb=" O SER E 448 " pdb=" OG SER E 448 " model vdw 2.267 3.040 ... (remaining 275834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.960 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5097 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 : 0.011 0.215 35926 Z= 0.467 Angle : 1.138 50.802 49118 Z= 0.592 Chirality : 0.066 0.778 5704 Planarity : 0.008 0.111 6140 Dihedral : 17.059 114.899 14153 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.01 % Favored : 89.94 % Rotamer: Outliers : 13.49 % Allowed : 11.80 % Favored : 74.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 2.66 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.11), residues: 4304 helix: -1.91 (0.15), residues: 772 sheet: -1.54 (0.16), residues: 934 loop : -3.15 (0.10), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 693 TYR 0.031 0.003 TYR B 203 PHE 0.032 0.004 PHE A 391 TRP 0.032 0.003 TRP A 515 HIS 0.012 0.002 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.01052 (35749) covalent geometry : angle 1.04222 (48671) SS BOND : bond 0.00563 ( 84) SS BOND : angle 1.47616 ( 168) hydrogen bonds : bond 0.18168 ( 1083) hydrogen bonds : angle 7.52294 ( 2991) link_ALPHA1-3 : bond 0.00312 ( 6) link_ALPHA1-3 : angle 1.72875 ( 18) link_ALPHA1-4 : bond 0.00844 ( 3) link_ALPHA1-4 : angle 3.77508 ( 9) link_ALPHA1-6 : bond 0.00221 ( 3) link_ALPHA1-6 : angle 1.73333 ( 9) link_BETA1-4 : bond 0.01477 ( 15) link_BETA1-4 : angle 3.00369 ( 45) link_NAG-ASN : bond 0.04812 ( 66) link_NAG-ASN : angle 7.02301 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 517 poor density : 276 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7411 (mmm) cc_final: 0.6629 (mmm) REVERT: A 187 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7457 (mtpm) REVERT: A 190 THR cc_start: 0.8296 (p) cc_final: 0.8079 (t) REVERT: A 206 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7127 (mtp180) REVERT: A 213 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.7262 (p90) REVERT: A 218 MET cc_start: 0.8236 (mtm) cc_final: 0.7964 (mtp) REVERT: A 262 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7751 (t) REVERT: A 318 TYR cc_start: 0.7266 (t80) cc_final: 0.6792 (t80) REVERT: A 371 ASN cc_start: 0.4212 (OUTLIER) cc_final: 0.3889 (p0) REVERT: A 431 LEU cc_start: 0.1207 (OUTLIER) cc_final: 0.0385 (mm) REVERT: A 437 ASN cc_start: 0.1869 (OUTLIER) cc_final: -0.0215 (p0) REVERT: A 706 PHE cc_start: 0.5103 (OUTLIER) cc_final: 0.4444 (t80) REVERT: A 714 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: A 726 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7889 (mt) REVERT: A 789 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7546 (mm110) REVERT: A 827 ASP cc_start: 0.7918 (m-30) cc_final: 0.7716 (m-30) REVERT: A 831 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7461 (mp0) REVERT: A 952 GLU cc_start: 0.7257 (tp30) cc_final: 0.7004 (mm-30) REVERT: A 1003 LEU cc_start: 0.8411 (mt) cc_final: 0.7906 (tt) REVERT: A 1059 GLN cc_start: 0.8614 (tp40) cc_final: 0.8272 (tp40) REVERT: A 1086 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7989 (m-40) REVERT: A 1095 ASP cc_start: 0.7030 (m-30) cc_final: 0.6391 (t0) REVERT: A 1105 ARG cc_start: 0.7050 (tpt170) cc_final: 0.6541 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6712 (tt0) cc_final: 0.6431 (tt0) REVERT: B 182 LEU cc_start: 0.5284 (OUTLIER) cc_final: 0.4702 (tp) REVERT: B 256 TYR cc_start: 0.8142 (t80) cc_final: 0.7783 (t80) REVERT: B 412 SER cc_start: 0.4828 (OUTLIER) cc_final: 0.4222 (m) REVERT: B 484 SER cc_start: 0.0088 (OUTLIER) cc_final: -0.0322 (t) REVERT: B 835 PHE cc_start: 0.8075 (t80) cc_final: 0.6732 (t80) REVERT: B 862 MET cc_start: 0.7995 (mmm) cc_final: 0.7686 (mmp) REVERT: B 902 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8215 (tt) REVERT: B 906 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8069 (mp) REVERT: B 1010 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7592 (tttp) REVERT: B 1012 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7870 (mt) REVERT: B 1030 GLN cc_start: 0.7389 (mt0) cc_final: 0.7047 (tp40) REVERT: B 1210 VAL cc_start: 0.9116 (m) cc_final: 0.8885 (p) REVERT: C 204 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6929 (pt0) REVERT: C 289 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7086 (mt-10) REVERT: C 375 LYS cc_start: 0.8146 (tptm) cc_final: 0.7828 (tptm) REVERT: C 384 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8163 (t0) REVERT: C 494 ILE cc_start: 0.6114 (mt) cc_final: 0.5871 (mt) REVERT: C 598 ASN cc_start: 0.7953 (m110) cc_final: 0.7732 (m110) REVERT: C 599 SER cc_start: 0.7653 (t) cc_final: 0.7228 (p) REVERT: C 640 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.5902 (p90) REVERT: C 655 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8806 (mt) REVERT: C 676 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7578 (ptm160) REVERT: C 863 GLN cc_start: 0.6947 (tp40) cc_final: 0.6734 (tp40) REVERT: C 885 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7821 (tptt) REVERT: C 986 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6415 (mmt180) REVERT: C 1001 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7182 (tm130) REVERT: C 1115 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8375 (mttt) REVERT: C 1185 MET cc_start: 0.7843 (mtp) cc_final: 0.7622 (mmm) REVERT: D 173 GLN cc_start: 0.0733 (OUTLIER) cc_final: 0.0336 (tp-100) REVERT: D 195 TYR cc_start: 0.2404 (OUTLIER) cc_final: 0.1903 (t80) REVERT: D 314 ILE cc_start: 0.1246 (OUTLIER) cc_final: 0.0985 (mp) REVERT: D 426 CYS cc_start: -0.0432 (OUTLIER) cc_final: -0.0948 (p) REVERT: D 465 CYS cc_start: 0.0202 (OUTLIER) cc_final: -0.0255 (p) REVERT: E 234 LYS cc_start: 0.0252 (OUTLIER) cc_final: 0.0032 (pttt) REVERT: E 273 LEU cc_start: 0.1885 (OUTLIER) cc_final: 0.1578 (tt) REVERT: E 286 ILE cc_start: -0.0046 (OUTLIER) cc_final: -0.0295 (pt) REVERT: E 371 MET cc_start: -0.0730 (OUTLIER) cc_final: -0.1336 (tmm) REVERT: E 430 LEU cc_start: 0.3937 (OUTLIER) cc_final: 0.2560 (pt) REVERT: E 440 ASP cc_start: -0.1274 (OUTLIER) cc_final: -0.1813 (t70) REVERT: E 465 CYS cc_start: 0.1135 (OUTLIER) cc_final: 0.0740 (t) outliers start: 517 outliers final: 182 residues processed: 748 average time/residue: 0.4821 time to fit residues: 463.1363 Evaluate side-chains 422 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 201 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG 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 262 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1183 SER Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 SER 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 124 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 640 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 898 SER Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 969 PRO Chi-restraints excluded: chain C residue 986 ARG Chi-restraints excluded: chain C residue 1001 GLN Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1115 LYS Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 429 PHE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 465 CYS Chi-restraints excluded: chain E residue 477 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.0050 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.1980 chunk 424 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 410 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN A 559 GLN A 561 ASN A 611 ASN A 630 GLN A 654 ASN A 863 GLN A 872 ASN A 876 HIS A 998 ASN A1001 GLN A1079 ASN A1136 ASN A1180 GLN B 22 ASN B 108 ASN B 323 ASN B 410 GLN B 413 ASN B 559 GLN B 621 ASN B 840 ASN B 876 HIS B1122 ASN C 152 GLN C 465 HIS C 630 GLN C 799 HIS C 876 HIS C 881 ASN C 998 ASN C1001 GLN C1122 ASN C1136 ASN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.219919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149488 restraints weight = 52270.838| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.18 r_work: 0.3355 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 35926 Z= 0.130 Angle : 0.701 13.993 49118 Z= 0.355 Chirality : 0.048 0.450 5704 Planarity : 0.006 0.095 6140 Dihedral : 11.987 104.143 6980 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.78 % Allowed : 16.36 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.12), residues: 4304 helix: 0.01 (0.18), residues: 793 sheet: -1.17 (0.16), residues: 950 loop : -2.64 (0.11), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 396 TYR 0.019 0.001 TYR E 474 PHE 0.025 0.001 PHE C 473 TRP 0.017 0.001 TRP B 515 HIS 0.005 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00278 (35749) covalent geometry : angle 0.66144 (48671) SS BOND : bond 0.00196 ( 84) SS BOND : angle 0.94495 ( 168) hydrogen bonds : bond 0.05079 ( 1083) hydrogen bonds : angle 5.66008 ( 2991) link_ALPHA1-3 : bond 0.00583 ( 6) link_ALPHA1-3 : angle 1.88200 ( 18) link_ALPHA1-4 : bond 0.01589 ( 3) link_ALPHA1-4 : angle 3.88600 ( 9) link_ALPHA1-6 : bond 0.00754 ( 3) link_ALPHA1-6 : angle 1.31553 ( 9) link_BETA1-4 : bond 0.00458 ( 15) link_BETA1-4 : angle 1.82078 ( 45) link_NAG-ASN : bond 0.00624 ( 66) link_NAG-ASN : angle 3.42198 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 214 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7643 (mmm) cc_final: 0.6919 (mmm) REVERT: A 342 LEU cc_start: 0.5355 (OUTLIER) cc_final: 0.5129 (mm) REVERT: A 371 ASN cc_start: 0.3009 (OUTLIER) cc_final: 0.2774 (p0) REVERT: A 431 LEU cc_start: 0.1552 (OUTLIER) cc_final: 0.0936 (mm) REVERT: A 437 ASN cc_start: 0.2449 (OUTLIER) cc_final: 0.0613 (OUTLIER) REVERT: A 676 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8517 (mtt180) REVERT: A 706 PHE cc_start: 0.5437 (OUTLIER) cc_final: 0.4861 (t80) REVERT: A 788 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8691 (mt) REVERT: A 789 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8227 (mm110) REVERT: A 831 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8122 (mp0) REVERT: A 903 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8374 (mp) REVERT: A 1003 LEU cc_start: 0.9019 (mt) cc_final: 0.8779 (tt) REVERT: A 1060 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8179 (tm-30) REVERT: A 1105 ARG cc_start: 0.8822 (tpt170) cc_final: 0.8607 (tpp-160) REVERT: B 182 LEU cc_start: 0.4668 (OUTLIER) cc_final: 0.4448 (tp) REVERT: B 256 TYR cc_start: 0.7800 (t80) cc_final: 0.7566 (t80) REVERT: B 509 THR cc_start: 0.0177 (OUTLIER) cc_final: -0.0045 (t) REVERT: B 800 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8478 (pp20) REVERT: B 835 PHE cc_start: 0.8155 (t80) cc_final: 0.7062 (t80) REVERT: B 906 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8767 (mt) REVERT: B 950 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9086 (mt) REVERT: B 1010 LYS cc_start: 0.9197 (ttmm) cc_final: 0.8993 (tttp) REVERT: B 1012 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8999 (mt) REVERT: B 1210 VAL cc_start: 0.9207 (m) cc_final: 0.8953 (p) REVERT: C 140 GLN cc_start: 0.8000 (tt0) cc_final: 0.7345 (mt0) REVERT: C 204 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: C 289 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8389 (mt-10) REVERT: C 361 ARG cc_start: 0.8072 (ptp-110) cc_final: 0.7704 (mtm110) REVERT: C 676 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7756 (ptm160) REVERT: C 879 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8632 (m) REVERT: C 1002 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8075 (mmmm) REVERT: C 1096 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8859 (tp) REVERT: D 188 MET cc_start: 0.1376 (tpp) cc_final: -0.0389 (ptt) REVERT: D 371 MET cc_start: 0.0404 (tmm) cc_final: 0.0147 (tpp) REVERT: D 426 CYS cc_start: 0.1179 (OUTLIER) cc_final: -0.0289 (p) REVERT: D 465 CYS cc_start: 0.0217 (OUTLIER) cc_final: -0.0676 (p) REVERT: D 478 MET cc_start: 0.1013 (ttm) cc_final: 0.0104 (mtp) REVERT: E 371 MET cc_start: -0.0509 (OUTLIER) cc_final: -0.0897 (tmm) outliers start: 260 outliers final: 128 residues processed: 447 average time/residue: 0.5228 time to fit residues: 297.8834 Evaluate side-chains 336 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 186 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR 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 B residue 34 ARG Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1118 SER 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 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 429 PHE Chi-restraints excluded: chain E residue 465 CYS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 159 optimal weight: 30.0000 chunk 382 optimal weight: 0.6980 chunk 386 optimal weight: 10.0000 chunk 368 optimal weight: 40.0000 chunk 254 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 404 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 286 optimal weight: 0.0870 overall best weight: 4.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 351 ASN A 437 ASN A 445 ASN B 410 GLN B 445 ASN B 984 GLN C 248 ASN C 465 HIS C 598 ASN C1023 ASN C1136 ASN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN ** E 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.212513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144403 restraints weight = 51612.684| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.97 r_work: 0.3225 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 35926 Z= 0.355 Angle : 0.866 16.208 49118 Z= 0.435 Chirality : 0.055 0.564 5704 Planarity : 0.006 0.123 6140 Dihedral : 11.243 97.248 6794 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.06 % Favored : 90.87 % Rotamer: Outliers : 7.49 % Allowed : 17.09 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.12), residues: 4304 helix: -0.14 (0.18), residues: 800 sheet: -1.13 (0.16), residues: 945 loop : -2.60 (0.11), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 693 TYR 0.030 0.003 TYR B 622 PHE 0.031 0.003 PHE C 968 TRP 0.023 0.002 TRP C 515 HIS 0.011 0.002 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00858 (35749) covalent geometry : angle 0.82643 (48671) SS BOND : bond 0.00614 ( 84) SS BOND : angle 1.34856 ( 168) hydrogen bonds : bond 0.07620 ( 1083) hydrogen bonds : angle 5.79696 ( 2991) link_ALPHA1-3 : bond 0.00404 ( 6) link_ALPHA1-3 : angle 2.04062 ( 18) link_ALPHA1-4 : bond 0.01400 ( 3) link_ALPHA1-4 : angle 3.70189 ( 9) link_ALPHA1-6 : bond 0.00635 ( 3) link_ALPHA1-6 : angle 1.38603 ( 9) link_BETA1-4 : bond 0.00556 ( 15) link_BETA1-4 : angle 1.69632 ( 45) link_NAG-ASN : bond 0.00659 ( 66) link_NAG-ASN : angle 3.84460 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 189 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7483 (mmm) cc_final: 0.6844 (mmm) REVERT: A 187 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8223 (mtpm) REVERT: A 213 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8497 (p90) REVERT: A 431 LEU cc_start: 0.0845 (OUTLIER) cc_final: 0.0622 (pp) REVERT: A 516 CYS cc_start: 0.0205 (OUTLIER) cc_final: -0.0820 (m) REVERT: A 676 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8563 (mtt180) REVERT: A 706 PHE cc_start: 0.5464 (OUTLIER) cc_final: 0.4856 (t80) REVERT: A 737 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.8363 (mtt180) REVERT: A 789 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8428 (mm110) REVERT: A 828 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8928 (tp) REVERT: A 903 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 952 GLU cc_start: 0.7975 (tp30) cc_final: 0.7751 (mm-30) REVERT: A 1001 GLN cc_start: 0.7951 (tt0) cc_final: 0.7600 (mt0) REVERT: A 1069 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: B 28 TYR cc_start: 0.4187 (OUTLIER) cc_final: 0.3655 (p90) REVERT: B 182 LEU cc_start: 0.4756 (OUTLIER) cc_final: 0.4476 (tp) REVERT: B 835 PHE cc_start: 0.8196 (t80) cc_final: 0.7209 (t80) REVERT: B 849 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9135 (mp) REVERT: B 1012 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8972 (mt) REVERT: B 1115 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8159 (mptm) REVERT: B 1210 VAL cc_start: 0.9212 (m) cc_final: 0.8984 (p) REVERT: C 140 GLN cc_start: 0.7997 (tt0) cc_final: 0.7350 (mt0) REVERT: C 289 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8293 (mt-10) REVERT: C 361 ARG cc_start: 0.8113 (ptp-110) cc_final: 0.7735 (mtm110) REVERT: C 384 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8670 (t0) REVERT: C 640 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.6533 (p90) REVERT: C 676 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7372 (ptm160) REVERT: C 879 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8647 (m) REVERT: C 885 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8362 (tptt) REVERT: C 1001 GLN cc_start: 0.8073 (tt0) cc_final: 0.7861 (tm-30) REVERT: C 1115 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8709 (mmmt) REVERT: D 426 CYS cc_start: 0.1358 (OUTLIER) cc_final: 0.0247 (p) REVERT: D 433 ASN cc_start: 0.0485 (OUTLIER) cc_final: -0.0174 (t0) REVERT: D 465 CYS cc_start: 0.0347 (OUTLIER) cc_final: -0.0589 (p) REVERT: E 177 ASN cc_start: 0.2806 (OUTLIER) cc_final: 0.2583 (p0) REVERT: E 185 CYS cc_start: 0.2719 (m) cc_final: 0.2297 (t) REVERT: E 327 GLN cc_start: 0.0511 (OUTLIER) cc_final: 0.0113 (pt0) outliers start: 287 outliers final: 164 residues processed: 453 average time/residue: 0.5156 time to fit residues: 297.1359 Evaluate side-chains 370 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 179 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 640 TYR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1072 VAL 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 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 465 CYS Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 350 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 301 optimal weight: 1.9990 chunk 348 optimal weight: 0.5980 chunk 367 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 264 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 GLN C 465 HIS C 552 ASN C 598 ASN C1023 ASN C1136 ASN D 253 GLN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 HIS ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.215993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149313 restraints weight = 51874.824| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.97 r_work: 0.3316 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35926 Z= 0.120 Angle : 0.638 13.772 49118 Z= 0.323 Chirality : 0.046 0.440 5704 Planarity : 0.005 0.110 6140 Dihedral : 9.921 96.677 6767 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.72 % Allowed : 18.89 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.12), residues: 4304 helix: 0.68 (0.19), residues: 800 sheet: -0.93 (0.16), residues: 949 loop : -2.37 (0.11), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 34 TYR 0.020 0.001 TYR A 203 PHE 0.023 0.001 PHE C 968 TRP 0.013 0.001 TRP A 971 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00264 (35749) covalent geometry : angle 0.60330 (48671) SS BOND : bond 0.00308 ( 84) SS BOND : angle 0.88469 ( 168) hydrogen bonds : bond 0.04654 ( 1083) hydrogen bonds : angle 5.24105 ( 2991) link_ALPHA1-3 : bond 0.00518 ( 6) link_ALPHA1-3 : angle 1.84037 ( 18) link_ALPHA1-4 : bond 0.01554 ( 3) link_ALPHA1-4 : angle 3.70266 ( 9) link_ALPHA1-6 : bond 0.00586 ( 3) link_ALPHA1-6 : angle 1.47921 ( 9) link_BETA1-4 : bond 0.00456 ( 15) link_BETA1-4 : angle 1.30207 ( 45) link_NAG-ASN : bond 0.00570 ( 66) link_NAG-ASN : angle 3.06137 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 194 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8490 (t70) cc_final: 0.8141 (t70) REVERT: A 155 MET cc_start: 0.7685 (mmm) cc_final: 0.7015 (mmm) REVERT: A 180 GLU cc_start: 0.6689 (tm-30) cc_final: 0.6367 (tm-30) REVERT: A 320 ARG cc_start: 0.7803 (mmp80) cc_final: 0.7486 (mmp-170) REVERT: A 342 LEU cc_start: 0.4973 (OUTLIER) cc_final: 0.4765 (mm) REVERT: A 431 LEU cc_start: 0.1426 (OUTLIER) cc_final: 0.1083 (mm) REVERT: A 516 CYS cc_start: 0.1160 (OUTLIER) cc_final: 0.0301 (m) REVERT: A 676 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8797 (mtm180) REVERT: A 706 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.4911 (t80) REVERT: A 726 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8770 (mt) REVERT: A 789 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8373 (mm110) REVERT: A 903 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 952 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: A 1059 GLN cc_start: 0.9019 (tp40) cc_final: 0.8702 (tp40) REVERT: A 1069 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: B 28 TYR cc_start: 0.4005 (OUTLIER) cc_final: 0.3759 (p90) REVERT: B 182 LEU cc_start: 0.4553 (OUTLIER) cc_final: 0.4336 (tp) REVERT: B 256 TYR cc_start: 0.7876 (t80) cc_final: 0.7651 (t80) REVERT: B 284 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.8173 (m) REVERT: B 609 TYR cc_start: 0.4811 (OUTLIER) cc_final: 0.4111 (t80) REVERT: B 748 LEU cc_start: 0.7130 (tm) cc_final: 0.6740 (pt) REVERT: B 800 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8463 (pp20) REVERT: B 835 PHE cc_start: 0.8297 (t80) cc_final: 0.7273 (t80) REVERT: B 1012 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9047 (mt) REVERT: B 1210 VAL cc_start: 0.9177 (m) cc_final: 0.8926 (p) REVERT: C 140 GLN cc_start: 0.8002 (tt0) cc_final: 0.7405 (mt0) REVERT: C 289 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8472 (mt-10) REVERT: C 361 ARG cc_start: 0.8053 (ptp-110) cc_final: 0.7702 (mtm110) REVERT: C 676 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7752 (ptm160) REVERT: C 891 LEU cc_start: 0.8736 (tt) cc_final: 0.8393 (tp) REVERT: D 188 MET cc_start: 0.0569 (OUTLIER) cc_final: 0.0197 (tpp) REVERT: D 426 CYS cc_start: 0.1388 (OUTLIER) cc_final: 0.0320 (p) REVERT: D 433 ASN cc_start: 0.0541 (OUTLIER) cc_final: 0.0005 (t0) REVERT: D 456 ILE cc_start: 0.2026 (OUTLIER) cc_final: 0.1591 (tp) REVERT: D 465 CYS cc_start: 0.0507 (OUTLIER) cc_final: -0.0559 (p) REVERT: D 478 MET cc_start: 0.0629 (OUTLIER) cc_final: 0.0252 (mtp) outliers start: 219 outliers final: 114 residues processed: 387 average time/residue: 0.5634 time to fit residues: 278.4102 Evaluate side-chains 316 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 178 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 243 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 338 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 410 optimal weight: 40.0000 chunk 334 optimal weight: 0.9990 chunk 339 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 438 ASN B 160 HIS ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 598 ASN ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN E 227 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.217660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.149886 restraints weight = 51877.837| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 4.09 r_work: 0.3305 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35926 Z= 0.142 Angle : 0.631 14.072 49118 Z= 0.320 Chirality : 0.046 0.447 5704 Planarity : 0.005 0.111 6140 Dihedral : 9.332 94.916 6747 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.32 % Allowed : 19.44 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4304 helix: 0.89 (0.20), residues: 800 sheet: -0.85 (0.16), residues: 951 loop : -2.26 (0.11), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1064 TYR 0.020 0.001 TYR B 203 PHE 0.020 0.001 PHE C 473 TRP 0.013 0.001 TRP A 174 HIS 0.007 0.001 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00328 (35749) covalent geometry : angle 0.59912 (48671) SS BOND : bond 0.00265 ( 84) SS BOND : angle 0.70001 ( 168) hydrogen bonds : bond 0.04931 ( 1083) hydrogen bonds : angle 5.12755 ( 2991) link_ALPHA1-3 : bond 0.00492 ( 6) link_ALPHA1-3 : angle 1.77168 ( 18) link_ALPHA1-4 : bond 0.01629 ( 3) link_ALPHA1-4 : angle 3.63119 ( 9) link_ALPHA1-6 : bond 0.00582 ( 3) link_ALPHA1-6 : angle 1.38810 ( 9) link_BETA1-4 : bond 0.00483 ( 15) link_BETA1-4 : angle 1.37083 ( 45) link_NAG-ASN : bond 0.00506 ( 66) link_NAG-ASN : angle 2.97125 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 192 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8505 (t70) cc_final: 0.8160 (t70) REVERT: A 155 MET cc_start: 0.7699 (mmm) cc_final: 0.7061 (mmm) REVERT: A 180 GLU cc_start: 0.6567 (tm-30) cc_final: 0.6160 (tm-30) REVERT: A 320 ARG cc_start: 0.7805 (mmp80) cc_final: 0.7568 (mmp-170) REVERT: A 431 LEU cc_start: 0.1404 (OUTLIER) cc_final: 0.0949 (mm) REVERT: A 676 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8562 (mtt180) REVERT: A 706 PHE cc_start: 0.5456 (OUTLIER) cc_final: 0.4887 (t80) REVERT: A 737 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8428 (mtt180) REVERT: A 789 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8437 (mm-40) REVERT: A 891 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7945 (tp) REVERT: A 903 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 952 GLU cc_start: 0.7973 (tp30) cc_final: 0.7752 (mm-30) REVERT: A 1069 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: B 28 TYR cc_start: 0.4062 (OUTLIER) cc_final: 0.3836 (p90) REVERT: B 213 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7252 (t80) REVERT: B 256 TYR cc_start: 0.7926 (t80) cc_final: 0.7706 (t80) REVERT: B 609 TYR cc_start: 0.4612 (OUTLIER) cc_final: 0.3873 (t80) REVERT: B 748 LEU cc_start: 0.7090 (tm) cc_final: 0.6655 (pt) REVERT: B 800 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8526 (pp20) REVERT: B 835 PHE cc_start: 0.8318 (t80) cc_final: 0.7298 (t80) REVERT: B 1210 VAL cc_start: 0.9181 (m) cc_final: 0.8927 (p) REVERT: C 140 GLN cc_start: 0.8034 (tt0) cc_final: 0.7428 (mt0) REVERT: C 289 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8460 (mt-10) REVERT: C 361 ARG cc_start: 0.8027 (ptp-110) cc_final: 0.7733 (mtm110) REVERT: C 384 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8686 (t0) REVERT: C 676 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7674 (ptm160) REVERT: D 188 MET cc_start: 0.0607 (OUTLIER) cc_final: -0.0500 (tmt) REVERT: D 320 MET cc_start: 0.1624 (mtm) cc_final: -0.0096 (ppp) REVERT: D 426 CYS cc_start: 0.1427 (OUTLIER) cc_final: 0.0165 (p) REVERT: D 433 ASN cc_start: 0.0499 (OUTLIER) cc_final: -0.0034 (t0) REVERT: D 456 ILE cc_start: 0.1885 (OUTLIER) cc_final: 0.1566 (tp) REVERT: D 465 CYS cc_start: 0.0377 (OUTLIER) cc_final: -0.0824 (p) REVERT: D 478 MET cc_start: 0.0772 (OUTLIER) cc_final: 0.0404 (mtp) REVERT: E 327 GLN cc_start: 0.0998 (OUTLIER) cc_final: 0.0468 (pt0) outliers start: 204 outliers final: 124 residues processed: 374 average time/residue: 0.5433 time to fit residues: 256.8385 Evaluate side-chains 324 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 178 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER 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 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 425 optimal weight: 40.0000 chunk 396 optimal weight: 0.0970 chunk 320 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 239 optimal weight: 0.5980 chunk 246 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 391 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 255 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 overall best weight: 1.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 HIS B 395 ASN B 894 GLN C 465 HIS C 598 ASN ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.217607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.151430 restraints weight = 51846.268| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.87 r_work: 0.3297 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35926 Z= 0.146 Angle : 0.626 14.009 49118 Z= 0.317 Chirality : 0.046 0.439 5704 Planarity : 0.005 0.111 6140 Dihedral : 8.941 93.490 6729 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.32 % Allowed : 19.57 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.12), residues: 4304 helix: 0.94 (0.20), residues: 802 sheet: -0.76 (0.16), residues: 954 loop : -2.20 (0.11), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1064 TYR 0.019 0.001 TYR B 203 PHE 0.019 0.001 PHE C 968 TRP 0.012 0.001 TRP B 971 HIS 0.006 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00342 (35749) covalent geometry : angle 0.59423 (48671) SS BOND : bond 0.00320 ( 84) SS BOND : angle 0.74767 ( 168) hydrogen bonds : bond 0.04912 ( 1083) hydrogen bonds : angle 5.07304 ( 2991) link_ALPHA1-3 : bond 0.00500 ( 6) link_ALPHA1-3 : angle 1.76441 ( 18) link_ALPHA1-4 : bond 0.01529 ( 3) link_ALPHA1-4 : angle 3.52823 ( 9) link_ALPHA1-6 : bond 0.00556 ( 3) link_ALPHA1-6 : angle 1.39491 ( 9) link_BETA1-4 : bond 0.00460 ( 15) link_BETA1-4 : angle 1.33545 ( 45) link_NAG-ASN : bond 0.00507 ( 66) link_NAG-ASN : angle 2.92551 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 185 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8223 (t70) cc_final: 0.7914 (t70) REVERT: A 155 MET cc_start: 0.7669 (mmm) cc_final: 0.7011 (mmm) REVERT: A 180 GLU cc_start: 0.6511 (tm-30) cc_final: 0.6155 (tm-30) REVERT: A 187 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8142 (mtpm) REVERT: A 320 ARG cc_start: 0.7847 (mmp80) cc_final: 0.7617 (mmp-170) REVERT: A 431 LEU cc_start: 0.1507 (OUTLIER) cc_final: 0.0933 (mm) REVERT: A 676 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8411 (mtt180) REVERT: A 706 PHE cc_start: 0.5190 (OUTLIER) cc_final: 0.4587 (t80) REVERT: A 726 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8772 (mt) REVERT: A 737 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8344 (mtt180) REVERT: A 789 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8315 (mm110) REVERT: A 891 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7915 (tp) REVERT: A 903 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 952 GLU cc_start: 0.7734 (tp30) cc_final: 0.7504 (mm-30) REVERT: A 1069 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: B 213 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7008 (t80) REVERT: B 609 TYR cc_start: 0.4580 (OUTLIER) cc_final: 0.3847 (t80) REVERT: B 748 LEU cc_start: 0.7094 (tm) cc_final: 0.6682 (pt) REVERT: B 800 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8309 (pp20) REVERT: B 835 PHE cc_start: 0.8151 (t80) cc_final: 0.7163 (t80) REVERT: B 1210 VAL cc_start: 0.9166 (m) cc_final: 0.8959 (p) REVERT: C 140 GLN cc_start: 0.7949 (tt0) cc_final: 0.7274 (mt0) REVERT: C 289 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: C 361 ARG cc_start: 0.8010 (ptp-110) cc_final: 0.7754 (mtm110) REVERT: C 384 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8544 (t0) REVERT: C 539 VAL cc_start: 0.8586 (t) cc_final: 0.8200 (m) REVERT: C 676 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7517 (ptm160) REVERT: C 885 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8315 (tptt) REVERT: D 188 MET cc_start: 0.0828 (OUTLIER) cc_final: -0.0449 (tmt) REVERT: D 320 MET cc_start: 0.1622 (mtm) cc_final: -0.0115 (ppp) REVERT: D 426 CYS cc_start: 0.1203 (OUTLIER) cc_final: 0.0080 (p) REVERT: D 456 ILE cc_start: 0.2427 (OUTLIER) cc_final: 0.1943 (tp) REVERT: D 465 CYS cc_start: -0.0664 (OUTLIER) cc_final: -0.1980 (p) REVERT: D 478 MET cc_start: 0.0906 (OUTLIER) cc_final: 0.0439 (mtp) REVERT: E 327 GLN cc_start: 0.1064 (OUTLIER) cc_final: 0.0435 (pt0) outliers start: 204 outliers final: 129 residues processed: 366 average time/residue: 0.5412 time to fit residues: 250.7820 Evaluate side-chains 328 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 176 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 977 VAL 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 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 714 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 317 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 chunk 72 optimal weight: 0.0270 chunk 393 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 423 optimal weight: 50.0000 chunk 391 optimal weight: 20.0000 chunk 30 optimal weight: 0.4980 chunk 191 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 HIS B 395 ASN B 894 GLN C 204 GLN C 465 HIS C 598 ASN ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.218407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152168 restraints weight = 51914.327| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.15 r_work: 0.3311 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35926 Z= 0.116 Angle : 0.602 13.717 49118 Z= 0.305 Chirality : 0.046 0.419 5704 Planarity : 0.005 0.107 6140 Dihedral : 8.565 93.250 6721 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.78 % Allowed : 20.12 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.13), residues: 4304 helix: 1.13 (0.20), residues: 801 sheet: -0.73 (0.16), residues: 957 loop : -2.10 (0.11), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1064 TYR 0.018 0.001 TYR B1148 PHE 0.018 0.001 PHE C 968 TRP 0.011 0.001 TRP A 174 HIS 0.015 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00260 (35749) covalent geometry : angle 0.57158 (48671) SS BOND : bond 0.00241 ( 84) SS BOND : angle 0.70773 ( 168) hydrogen bonds : bond 0.04396 ( 1083) hydrogen bonds : angle 4.94912 ( 2991) link_ALPHA1-3 : bond 0.00498 ( 6) link_ALPHA1-3 : angle 1.75879 ( 18) link_ALPHA1-4 : bond 0.01584 ( 3) link_ALPHA1-4 : angle 3.37983 ( 9) link_ALPHA1-6 : bond 0.00529 ( 3) link_ALPHA1-6 : angle 1.42748 ( 9) link_BETA1-4 : bond 0.00454 ( 15) link_BETA1-4 : angle 1.35567 ( 45) link_NAG-ASN : bond 0.00481 ( 66) link_NAG-ASN : angle 2.81868 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 183 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8435 (t70) cc_final: 0.8079 (t70) REVERT: A 155 MET cc_start: 0.7731 (mmm) cc_final: 0.6999 (mmm) REVERT: A 180 GLU cc_start: 0.6564 (tm-30) cc_final: 0.6122 (tm-30) REVERT: A 187 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8264 (mtpm) REVERT: A 320 ARG cc_start: 0.8062 (mmp80) cc_final: 0.7701 (mmp-170) REVERT: A 431 LEU cc_start: 0.1621 (OUTLIER) cc_final: 0.0946 (mm) REVERT: A 676 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8724 (mtp180) REVERT: A 706 PHE cc_start: 0.5555 (OUTLIER) cc_final: 0.5017 (t80) REVERT: A 726 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8798 (mt) REVERT: A 737 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8414 (mtt180) REVERT: A 789 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8249 (mm110) REVERT: A 891 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8011 (tp) REVERT: A 903 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8549 (mp) REVERT: A 952 GLU cc_start: 0.7998 (tp30) cc_final: 0.7789 (mm-30) REVERT: A 1069 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: B 213 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7348 (t80) REVERT: B 800 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8536 (pp20) REVERT: B 835 PHE cc_start: 0.8315 (t80) cc_final: 0.7267 (t80) REVERT: B 1210 VAL cc_start: 0.9152 (m) cc_final: 0.8897 (p) REVERT: C 140 GLN cc_start: 0.8072 (tt0) cc_final: 0.7499 (mt0) REVERT: C 187 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7034 (mmmt) REVERT: C 204 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8076 (pp30) REVERT: C 289 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: C 361 ARG cc_start: 0.8016 (ptp-110) cc_final: 0.7737 (mtm110) REVERT: C 384 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8647 (t0) REVERT: C 539 VAL cc_start: 0.8660 (t) cc_final: 0.8249 (m) REVERT: C 676 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7712 (ptm160) REVERT: D 188 MET cc_start: 0.0542 (OUTLIER) cc_final: -0.0502 (tmt) REVERT: D 320 MET cc_start: 0.1724 (mtm) cc_final: -0.0084 (ppp) REVERT: D 426 CYS cc_start: 0.1461 (OUTLIER) cc_final: 0.0370 (p) REVERT: D 433 ASN cc_start: 0.0139 (OUTLIER) cc_final: -0.0096 (m110) REVERT: D 456 ILE cc_start: 0.2129 (OUTLIER) cc_final: 0.1769 (tp) REVERT: D 465 CYS cc_start: -0.0543 (OUTLIER) cc_final: -0.1991 (p) REVERT: D 478 MET cc_start: 0.0635 (OUTLIER) cc_final: 0.0404 (mtp) REVERT: E 210 MET cc_start: -0.0020 (mmm) cc_final: -0.0292 (ttm) REVERT: E 327 GLN cc_start: 0.0976 (OUTLIER) cc_final: 0.0527 (pt0) REVERT: E 488 MET cc_start: -0.0264 (OUTLIER) cc_final: -0.1168 (tpt) outliers start: 183 outliers final: 117 residues processed: 344 average time/residue: 0.5571 time to fit residues: 242.2360 Evaluate side-chains 320 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 178 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER 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 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 122 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 298 optimal weight: 0.0980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 HIS B 545 HIS ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN B 894 GLN C 465 HIS C 598 ASN ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.215524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148036 restraints weight = 51497.011| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 4.39 r_work: 0.3282 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35926 Z= 0.168 Angle : 0.638 14.212 49118 Z= 0.323 Chirality : 0.047 0.440 5704 Planarity : 0.005 0.112 6140 Dihedral : 8.617 92.148 6714 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.71 % Favored : 93.26 % Rotamer: Outliers : 4.91 % Allowed : 20.02 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.13), residues: 4304 helix: 1.01 (0.20), residues: 790 sheet: -0.71 (0.16), residues: 957 loop : -2.06 (0.11), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1064 TYR 0.021 0.002 TYR B 203 PHE 0.020 0.002 PHE C 968 TRP 0.013 0.001 TRP B 971 HIS 0.026 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00400 (35749) covalent geometry : angle 0.60793 (48671) SS BOND : bond 0.00296 ( 84) SS BOND : angle 0.76698 ( 168) hydrogen bonds : bond 0.05170 ( 1083) hydrogen bonds : angle 5.05007 ( 2991) link_ALPHA1-3 : bond 0.00461 ( 6) link_ALPHA1-3 : angle 1.72509 ( 18) link_ALPHA1-4 : bond 0.01452 ( 3) link_ALPHA1-4 : angle 3.37567 ( 9) link_ALPHA1-6 : bond 0.00530 ( 3) link_ALPHA1-6 : angle 1.37561 ( 9) link_BETA1-4 : bond 0.00448 ( 15) link_BETA1-4 : angle 1.35719 ( 45) link_NAG-ASN : bond 0.00475 ( 66) link_NAG-ASN : angle 2.87006 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 180 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8477 (t70) cc_final: 0.8134 (t70) REVERT: A 155 MET cc_start: 0.7750 (mmm) cc_final: 0.7023 (mmm) REVERT: A 180 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6226 (tm-30) REVERT: A 187 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8271 (mtpm) REVERT: A 320 ARG cc_start: 0.8034 (mmp80) cc_final: 0.7650 (mmp-170) REVERT: A 676 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8590 (mtt180) REVERT: A 706 PHE cc_start: 0.5407 (OUTLIER) cc_final: 0.4840 (t80) REVERT: A 726 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8871 (mt) REVERT: A 737 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8394 (mtt180) REVERT: A 789 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8377 (mm110) REVERT: A 891 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7912 (tp) REVERT: A 903 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8538 (mp) REVERT: A 952 GLU cc_start: 0.8043 (tp30) cc_final: 0.7835 (mm-30) REVERT: A 1069 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: B 123 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7223 (t) REVERT: B 140 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6690 (tp40) REVERT: B 213 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7299 (t80) REVERT: B 609 TYR cc_start: 0.4707 (OUTLIER) cc_final: 0.3965 (t80) REVERT: B 748 LEU cc_start: 0.7156 (tm) cc_final: 0.6793 (pt) REVERT: B 800 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8559 (pp20) REVERT: B 835 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7378 (t80) REVERT: B 1210 VAL cc_start: 0.9160 (m) cc_final: 0.8919 (p) REVERT: C 140 GLN cc_start: 0.8091 (tt0) cc_final: 0.7468 (mt0) REVERT: C 204 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8196 (pp30) REVERT: C 289 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8481 (mt-10) REVERT: C 384 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8707 (t0) REVERT: C 405 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7419 (p) REVERT: C 539 VAL cc_start: 0.8664 (t) cc_final: 0.8275 (m) REVERT: C 676 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.7671 (ptm160) REVERT: C 885 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8376 (tptt) REVERT: D 188 MET cc_start: 0.0764 (OUTLIER) cc_final: -0.0613 (tmt) REVERT: D 320 MET cc_start: 0.1702 (mtm) cc_final: -0.0143 (ppp) REVERT: D 371 MET cc_start: 0.0390 (OUTLIER) cc_final: -0.0468 (tpp) REVERT: D 424 MET cc_start: 0.2733 (OUTLIER) cc_final: 0.2406 (ptm) REVERT: D 426 CYS cc_start: 0.1178 (OUTLIER) cc_final: 0.0265 (p) REVERT: D 456 ILE cc_start: 0.2609 (OUTLIER) cc_final: 0.2346 (tp) REVERT: D 465 CYS cc_start: -0.0859 (OUTLIER) cc_final: -0.2254 (p) REVERT: D 478 MET cc_start: 0.0783 (OUTLIER) cc_final: 0.0425 (mtp) REVERT: E 327 GLN cc_start: 0.0831 (OUTLIER) cc_final: 0.0321 (pt0) REVERT: E 413 ARG cc_start: 0.1290 (OUTLIER) cc_final: 0.0994 (mmm-85) outliers start: 188 outliers final: 129 residues processed: 345 average time/residue: 0.5388 time to fit residues: 236.0349 Evaluate side-chains 331 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 172 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1063 SER 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 1203 VAL Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 714 ASP Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 413 ARG Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 478 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 245 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 398 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 425 optimal weight: 0.4980 chunk 279 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 HIS B 545 HIS ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN B 894 GLN C 465 HIS C 598 ASN ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.218570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152523 restraints weight = 51851.107| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.01 r_work: 0.3348 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35926 Z= 0.112 Angle : 0.583 13.568 49118 Z= 0.295 Chirality : 0.045 0.406 5704 Planarity : 0.005 0.104 6140 Dihedral : 8.137 91.583 6712 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.15 % Allowed : 20.96 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 4304 helix: 1.31 (0.20), residues: 789 sheet: -0.63 (0.16), residues: 964 loop : -1.97 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 361 TYR 0.019 0.001 TYR A 203 PHE 0.019 0.001 PHE C 968 TRP 0.014 0.001 TRP A 174 HIS 0.008 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00251 (35749) covalent geometry : angle 0.55464 (48671) SS BOND : bond 0.00284 ( 84) SS BOND : angle 0.64819 ( 168) hydrogen bonds : bond 0.04180 ( 1083) hydrogen bonds : angle 4.85099 ( 2991) link_ALPHA1-3 : bond 0.00521 ( 6) link_ALPHA1-3 : angle 1.70204 ( 18) link_ALPHA1-4 : bond 0.01548 ( 3) link_ALPHA1-4 : angle 3.46058 ( 9) link_ALPHA1-6 : bond 0.00543 ( 3) link_ALPHA1-6 : angle 1.44827 ( 9) link_BETA1-4 : bond 0.00440 ( 15) link_BETA1-4 : angle 1.23642 ( 45) link_NAG-ASN : bond 0.00494 ( 66) link_NAG-ASN : angle 2.66172 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 187 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8407 (t70) cc_final: 0.8056 (t70) REVERT: A 155 MET cc_start: 0.7789 (mmm) cc_final: 0.7114 (mmm) REVERT: A 180 GLU cc_start: 0.6625 (tm-30) cc_final: 0.6161 (tm-30) REVERT: A 187 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8234 (mtpm) REVERT: A 320 ARG cc_start: 0.7918 (mmp80) cc_final: 0.7682 (mmp-170) REVERT: A 706 PHE cc_start: 0.5487 (OUTLIER) cc_final: 0.4930 (t80) REVERT: A 726 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8782 (mt) REVERT: A 737 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8405 (mtt180) REVERT: A 789 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8183 (mm-40) REVERT: A 952 GLU cc_start: 0.7946 (tp30) cc_final: 0.7743 (mm-30) REVERT: A 1069 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: B 213 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7348 (t80) REVERT: B 748 LEU cc_start: 0.7169 (tm) cc_final: 0.6764 (pt) REVERT: B 800 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8498 (pp20) REVERT: B 835 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7292 (t80) REVERT: B 1210 VAL cc_start: 0.9130 (m) cc_final: 0.8901 (p) REVERT: C 140 GLN cc_start: 0.8048 (tt0) cc_final: 0.7426 (mt0) REVERT: C 539 VAL cc_start: 0.8643 (t) cc_final: 0.8201 (m) REVERT: C 601 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8584 (t) REVERT: D 188 MET cc_start: 0.0419 (OUTLIER) cc_final: -0.0691 (ptt) REVERT: D 320 MET cc_start: 0.1723 (mtm) cc_final: -0.0216 (ppp) REVERT: D 371 MET cc_start: 0.0211 (OUTLIER) cc_final: -0.0700 (tpp) REVERT: D 424 MET cc_start: 0.2744 (OUTLIER) cc_final: 0.2407 (ptm) REVERT: D 426 CYS cc_start: 0.1566 (OUTLIER) cc_final: 0.0719 (p) REVERT: D 456 ILE cc_start: 0.2047 (OUTLIER) cc_final: 0.1714 (tp) REVERT: D 478 MET cc_start: 0.0738 (ptm) cc_final: 0.0472 (mmm) REVERT: E 327 GLN cc_start: 0.0693 (OUTLIER) cc_final: 0.0044 (pm20) REVERT: E 488 MET cc_start: -0.0658 (OUTLIER) cc_final: -0.1544 (tpt) outliers start: 159 outliers final: 111 residues processed: 324 average time/residue: 0.5492 time to fit residues: 223.9999 Evaluate side-chains 305 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 177 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER 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 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 714 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 37 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 379 optimal weight: 0.0020 chunk 320 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 364 optimal weight: 30.0000 chunk 187 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN B 160 HIS B 545 HIS ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN B 863 GLN B 894 GLN C 465 HIS C 598 ASN C 863 GLN ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.218643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152992 restraints weight = 52251.646| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 4.03 r_work: 0.3340 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35926 Z= 0.117 Angle : 0.590 13.644 49118 Z= 0.299 Chirality : 0.045 0.424 5704 Planarity : 0.005 0.111 6140 Dihedral : 7.851 91.156 6696 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.52 % Allowed : 21.50 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 4304 helix: 1.34 (0.20), residues: 790 sheet: -0.59 (0.16), residues: 967 loop : -1.95 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C1064 TYR 0.027 0.001 TYR B 90 PHE 0.017 0.001 PHE C 473 TRP 0.017 0.001 TRP A 174 HIS 0.010 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00266 (35749) covalent geometry : angle 0.56180 (48671) SS BOND : bond 0.00222 ( 84) SS BOND : angle 0.68614 ( 168) hydrogen bonds : bond 0.04294 ( 1083) hydrogen bonds : angle 4.82659 ( 2991) link_ALPHA1-3 : bond 0.00544 ( 6) link_ALPHA1-3 : angle 1.66633 ( 18) link_ALPHA1-4 : bond 0.01620 ( 3) link_ALPHA1-4 : angle 3.46192 ( 9) link_ALPHA1-6 : bond 0.00528 ( 3) link_ALPHA1-6 : angle 1.44482 ( 9) link_BETA1-4 : bond 0.00446 ( 15) link_BETA1-4 : angle 1.24084 ( 45) link_NAG-ASN : bond 0.00489 ( 66) link_NAG-ASN : angle 2.64885 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 180 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8390 (t70) cc_final: 0.8045 (t70) REVERT: A 155 MET cc_start: 0.7740 (mmm) cc_final: 0.7065 (mmm) REVERT: A 180 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6156 (tm-30) REVERT: A 187 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8230 (mtpm) REVERT: A 545 HIS cc_start: 0.3475 (OUTLIER) cc_final: 0.3159 (m170) REVERT: A 706 PHE cc_start: 0.5267 (OUTLIER) cc_final: 0.4685 (t80) REVERT: A 726 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8792 (mt) REVERT: A 737 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8434 (mtt180) REVERT: A 1069 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: B 213 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7347 (t80) REVERT: B 748 LEU cc_start: 0.7135 (tm) cc_final: 0.6740 (pt) REVERT: B 800 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8509 (pp20) REVERT: B 835 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7300 (t80) REVERT: B 894 GLN cc_start: 0.6083 (OUTLIER) cc_final: 0.5741 (mp10) REVERT: B 1210 VAL cc_start: 0.9126 (m) cc_final: 0.8890 (p) REVERT: C 132 ASN cc_start: 0.6107 (OUTLIER) cc_final: 0.5779 (p0) REVERT: C 140 GLN cc_start: 0.8021 (tt0) cc_final: 0.7395 (mt0) REVERT: C 361 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7051 (mtm110) REVERT: C 539 VAL cc_start: 0.8634 (t) cc_final: 0.8189 (m) REVERT: C 601 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8561 (t) REVERT: D 188 MET cc_start: 0.0328 (OUTLIER) cc_final: -0.0041 (tpp) REVERT: D 320 MET cc_start: 0.1688 (mtm) cc_final: -0.0162 (ppp) REVERT: D 371 MET cc_start: 0.0199 (tmm) cc_final: -0.0641 (tpp) REVERT: D 456 ILE cc_start: 0.1876 (OUTLIER) cc_final: 0.1572 (tp) REVERT: E 327 GLN cc_start: 0.0976 (OUTLIER) cc_final: 0.0355 (pm20) REVERT: E 488 MET cc_start: -0.0719 (OUTLIER) cc_final: -0.1570 (tpt) outliers start: 135 outliers final: 107 residues processed: 298 average time/residue: 0.5666 time to fit residues: 212.7508 Evaluate side-chains 299 residues out of total 3832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 175 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 894 GLN Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER 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 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 714 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 59 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 422 optimal weight: 0.0770 chunk 152 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 384 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN B 545 HIS ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 598 ASN ** C 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.216573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150400 restraints weight = 51544.925| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.87 r_work: 0.3336 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.295 35926 Z= 0.201 Angle : 0.737 59.196 49118 Z= 0.414 Chirality : 0.047 0.812 5704 Planarity : 0.005 0.147 6140 Dihedral : 7.744 91.468 6686 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.60 % Allowed : 21.61 % Favored : 74.79 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 4304 helix: 1.35 (0.20), residues: 790 sheet: -0.59 (0.16), residues: 967 loop : -1.95 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1064 TYR 0.020 0.001 TYR B 90 PHE 0.017 0.001 PHE C 473 TRP 0.016 0.001 TRP A 174 HIS 0.192 0.002 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00444 (35749) covalent geometry : angle 0.71644 (48671) SS BOND : bond 0.00207 ( 84) SS BOND : angle 0.66749 ( 168) hydrogen bonds : bond 0.04285 ( 1083) hydrogen bonds : angle 4.82625 ( 2991) link_ALPHA1-3 : bond 0.00527 ( 6) link_ALPHA1-3 : angle 1.67742 ( 18) link_ALPHA1-4 : bond 0.01658 ( 3) link_ALPHA1-4 : angle 3.48446 ( 9) link_ALPHA1-6 : bond 0.00527 ( 3) link_ALPHA1-6 : angle 1.44504 ( 9) link_BETA1-4 : bond 0.00409 ( 15) link_BETA1-4 : angle 1.25377 ( 45) link_NAG-ASN : bond 0.00477 ( 66) link_NAG-ASN : angle 2.64539 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20183.21 seconds wall clock time: 342 minutes 33.59 seconds (20553.59 seconds total)